build.gradle

@@ -1,12 +1,10 @@
-
 plugins {
-    id 'maven-publish'
-    id 'signing'
-    id "io.github.gradle-nexus.publish-plugin" version "2.0.0-rc-1"
+    id "de.marcphilipp.nexus-publish" version "0.4.0"
+    id "io.codearte.nexus-staging" version "0.21.1"
 }
 
 wrapper {
-    gradleVersion = libs.versions.gradle.get()
+    gradleVersion = "${project.property('gradle.wrapper.version')}"
     distributionType = Wrapper.DistributionType.ALL
 }
 
@@ -27,9 +25,9 @@ ext {
 
 subprojects {
     apply plugin: 'java-library'
+    apply from: rootProject.file('gradle/ide/idea.gradle')
     apply from: rootProject.file('gradle/compile/java.gradle')
     apply from: rootProject.file('gradle/test/junit5.gradle')
-    apply from: rootProject.file('gradle/publish/maven.gradle')
+    apply from: rootProject.file('gradle/publishing/publication.gradle')
 }
-apply from: rootProject.file('gradle/publish/sonatype.gradle')
-apply from: rootProject.file('gradle/publish/forgejo.gradle')
+apply from: rootProject.file('gradle/publishing/sonatype.gradle')

gradle.properties

@@ -1,3 +1,5 @@
 group = org.xbib
 name = archive
-version = 4.0.0
+version = 1.0.0
+
+gradle.wrapper.version = 6.4.1

gradle/compile/java.gradle

@@ -2,12 +2,17 @@
 apply plugin: 'java-library'
 
 java {
-    toolchain {
-        languageVersion = JavaLanguageVersion.of(21)
-    }
     modularity.inferModulePath.set(true)
-    withSourcesJar()
-    withJavadocJar()
+}
+
+compileJava {
+    sourceCompatibility = JavaVersion.VERSION_11
+    targetCompatibility = JavaVersion.VERSION_11
+}
+
+compileTestJava {
+    sourceCompatibility = JavaVersion.VERSION_11
+    targetCompatibility = JavaVersion.VERSION_11
 }
 
 jar {
@@ -16,14 +21,15 @@ jar {
     }
 }
 
-tasks.withType(JavaCompile) {
-    options.fork = true
-    options.forkOptions.jvmArgs += ['-Duser.language=en','-Duser.country=US']
-    options.compilerArgs << '-Xlint:all,-fallthrough'
-    options.encoding = 'UTF-8'
+task sourcesJar(type: Jar, dependsOn: classes) {
+    classifier 'sources'
+    from sourceSets.main.allSource
 }
 
-javadoc {
-    options.addStringOption('Xdoclint:none', '-quiet')
-    options.encoding = 'UTF-8'
+task javadocJar(type: Jar, dependsOn: javadoc) {
+    classifier 'javadoc'
+}
+
+artifacts {
+    archives sourcesJar, javadocJar
 }

gradle/publish/forgejo.gradle

@@ -1,16 +0,0 @@
-if (project.hasProperty('forgeJoToken')) {
-    publishing {
-        repositories {
-            maven {
-                url 'https://xbib.org/api/packages/joerg/maven'
-                credentials(HttpHeaderCredentials) {
-                    name = "Authorization"
-                    value = "token ${project.property('forgeJoToken')}"
-                }
-                authentication {
-                    header(HttpHeaderAuthentication)
-                }
-            }
-        }
-    }
-}

gradle/publish/ivy.gradle

@@ -1,27 +0,0 @@
-apply plugin: 'ivy-publish'
-
-publishing {
-    repositories {
-        ivy {
-            url = "https://xbib.org/repo"
-        }
-    }
-    publications {
-        ivy(IvyPublication) {
-            from components.java
-            descriptor {
-                license {
-                    name = 'The Apache License, Version 2.0'
-                    url = 'http://www.apache.org/licenses/LICENSE-2.0.txt'
-                }
-                author {
-                    name = 'Jörg Prante'
-                    url = 'http://example.com/users/jane'
-                }
-                descriptor.description {
-                    text = rootProject.ext.description
-                }
-            }
-        }
-    }
-}

gradle/publish/sonatype.gradle

@@ -1,11 +0,0 @@
-if (project.hasProperty('ossrhUsername') && project.hasProperty('ossrhPassword')) {
-    nexusPublishing {
-        repositories {
-            sonatype {
-                username = project.property('ossrhUsername')
-                password = project.property('ossrhPassword')
-                packageGroup = "org.xbib"
-            }
-        }
-    }
-}

gradle/publishing/publication.gradle

@@ -1,10 +1,13 @@
 
+apply plugin: "de.marcphilipp.nexus-publish"
+
 publishing {
     publications {
-        "${project.name}"(MavenPublication) {
+        mavenJava(MavenPublication) {
             from components.java
+            artifact sourcesJar
+            artifact javadocJar
             pom {
-                artifactId = project.name
                 name = project.name
                 description = rootProject.ext.description
                 url = rootProject.ext.url
@@ -46,6 +49,16 @@ publishing {
 if (project.hasProperty("signing.keyId")) {
     apply plugin: 'signing'
     signing {
-        sign publishing.publications."${project.name}"
+        sign publishing.publications.mavenJava
+    }
+}
+
+nexusPublishing {
+    repositories {
+        sonatype {
+            username = project.property('ossrhUsername')
+            password = project.property('ossrhPassword')
+            packageGroup = "org.xbib"
+        }
     }
 }

gradle/publishing/sonatype.gradle

@@ -0,0 +1,11 @@
+
+if (project.hasProperty('ossrhUsername') && project.hasProperty('ossrhPassword')) {
+
+    apply plugin: 'io.codearte.nexus-staging'
+
+    nexusStaging {
+        username = project.property('ossrhUsername')
+        password = project.property('ossrhPassword')
+        packageGroup = "org.xbib"
+    }
+}

gradle/test/junit5.gradle

@@ -1,10 +1,12 @@
 
+def junitVersion = project.hasProperty('junit.version')?project.property('junit.version'):'5.6.2'
+def hamcrestVersion = project.hasProperty('hamcrest.version')?project.property('hamcrest.version'):'2.2'
+
 dependencies {
-    testImplementation testLibs.junit.jupiter.api
-    testImplementation testLibs.junit.jupiter.params
-    testImplementation testLibs.hamcrest
-    testRuntimeOnly testLibs.junit.jupiter.engine
-    testRuntimeOnly testLibs.junit.jupiter.platform.launcher
+    testImplementation "org.junit.jupiter:junit-jupiter-api:${junitVersion}"
+    testImplementation "org.junit.jupiter:junit-jupiter-params:${junitVersion}"
+    testImplementation "org.hamcrest:hamcrest-library:${hamcrestVersion}"
+    testRuntimeOnly "org.junit.jupiter:junit-jupiter-engine:${junitVersion}"
 }
 
 test {

gradle/wrapper/gradle-wrapper.properties

@@ -1,7 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-all.zip
-networkTimeout=10000
-validateDistributionUrl=true
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.4.1-all.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -1,7 +1,7 @@
-#!/bin/sh
+#!/usr/bin/env sh
 
 #
-# Copyright © 2015-2021 the original authors.
+# Copyright 2015 the original author or authors.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -17,99 +17,67 @@
 #
 
 ##############################################################################
-#
-#   Gradle start up script for POSIX generated by Gradle.
-#
-#   Important for running:
-#
-#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
-#       noncompliant, but you have some other compliant shell such as ksh or
-#       bash, then to run this script, type that shell name before the whole
-#       command line, like:
-#
-#           ksh Gradle
-#
-#       Busybox and similar reduced shells will NOT work, because this script
-#       requires all of these POSIX shell features:
-#         * functions;
-#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
-#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
-#         * compound commands having a testable exit status, especially «case»;
-#         * various built-in commands including «command», «set», and «ulimit».
-#
-#   Important for patching:
-#
-#   (2) This script targets any POSIX shell, so it avoids extensions provided
-#       by Bash, Ksh, etc; in particular arrays are avoided.
-#
-#       The "traditional" practice of packing multiple parameters into a
-#       space-separated string is a well documented source of bugs and security
-#       problems, so this is (mostly) avoided, by progressively accumulating
-#       options in "$@", and eventually passing that to Java.
-#
-#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
-#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
-#       see the in-line comments for details.
-#
-#       There are tweaks for specific operating systems such as AIX, CygWin,
-#       Darwin, MinGW, and NonStop.
-#
-#   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
-#       within the Gradle project.
-#
-#       You can find Gradle at https://github.com/gradle/gradle/.
-#
+##
+##  Gradle start up script for UN*X
+##
 ##############################################################################
 
 # Attempt to set APP_HOME
-
 # Resolve links: $0 may be a link
-app_path=$0
-
-# Need this for daisy-chained symlinks.
-while
-    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
-    [ -h "$app_path" ]
-do
-    ls=$( ls -ld "$app_path" )
-    link=${ls#*' -> '}
-    case $link in             #(
-      /*)   app_path=$link ;; #(
-      *)    app_path=$APP_HOME$link ;;
-    esac
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
 done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
 
-# This is normally unused
-# shellcheck disable=SC2034
-APP_BASE_NAME=${0##*/}
-# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
-APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD=maximum
+MAX_FD="maximum"
 
 warn () {
     echo "$*"
-} >&2
+}
 
 die () {
     echo
     echo "$*"
     echo
     exit 1
-} >&2
+}
 
 # OS specific support (must be 'true' or 'false').
 cygwin=false
 msys=false
 darwin=false
 nonstop=false
-case "$( uname )" in                #(
-  CYGWIN* )         cygwin=true  ;; #(
-  Darwin* )         darwin=true  ;; #(
-  MSYS* | MINGW* )  msys=true    ;; #(
-  NONSTOP* )        nonstop=true ;;
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
 esac
 
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
@@ -119,9 +87,9 @@ CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 if [ -n "$JAVA_HOME" ] ; then
     if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
         # IBM's JDK on AIX uses strange locations for the executables
-        JAVACMD=$JAVA_HOME/jre/sh/java
+        JAVACMD="$JAVA_HOME/jre/sh/java"
     else
-        JAVACMD=$JAVA_HOME/bin/java
+        JAVACMD="$JAVA_HOME/bin/java"
     fi
     if [ ! -x "$JAVACMD" ] ; then
         die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
@@ -130,120 +98,88 @@ Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
     fi
 else
-    JAVACMD=java
-    if ! command -v java >/dev/null 2>&1
-    then
-        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
 fi
-fi
 
 # Increase the maximum file descriptors if we can.
-if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
-    case $MAX_FD in #(
-      max*)
-        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC2039,SC3045
-        MAX_FD=$( ulimit -H -n ) ||
-            warn "Could not query maximum file descriptor limit"
-    esac
-    case $MAX_FD in  #(
-      '' | soft) :;; #(
-      *)
-        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC2039,SC3045
-        ulimit -n "$MAX_FD" ||
-            warn "Could not set maximum file descriptor limit to $MAX_FD"
-    esac
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
 fi
 
-# Collect all arguments for the java command, stacking in reverse order:
-#   * args from the command line
-#   * the main class name
-#   * -classpath
-#   * -D...appname settings
-#   * --module-path (only if needed)
-#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
 
 # For Cygwin or MSYS, switch paths to Windows format before running java
-if "$cygwin" || "$msys" ; then
-    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
-    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
     
-    JAVACMD=$( cygpath --unix "$JAVACMD" )
+    JAVACMD=`cygpath --unix "$JAVACMD"`
 
-    # Now convert the arguments - kludge to limit ourselves to /bin/sh
-    for arg do
-        if
-            case $arg in                                #(
-              -*)   false ;;                            # don't mess with options #(
-              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
-                    [ -e "$t" ] ;;                      #(
-              *)    false ;;
-            esac
-        then
-            arg=$( cygpath --path --ignore --mixed "$arg" )
-        fi
-        # Roll the args list around exactly as many times as the number of
-        # args, so each arg winds up back in the position where it started, but
-        # possibly modified.
-        #
-        # NB: a `for` loop captures its iteration list before it begins, so
-        # changing the positional parameters here affects neither the number of
-        # iterations, nor the values presented in `arg`.
-        shift                   # remove old arg
-        set -- "$@" "$arg"      # push replacement arg
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
     done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=`expr $i + 1`
+    done
+    case $i in
+        0) set -- ;;
+        1) set -- "$args0" ;;
+        2) set -- "$args0" "$args1" ;;
+        3) set -- "$args0" "$args1" "$args2" ;;
+        4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
 fi
 
+# Escape application args
+save () {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
+}
+APP_ARGS=`save "$@"`
 
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
-
-# Collect all arguments for the java command:
-#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
-#     and any embedded shellness will be escaped.
-#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
-#     treated as '${Hostname}' itself on the command line.
-
-set -- \
-        "-Dorg.gradle.appname=$APP_BASE_NAME" \
-        -classpath "$CLASSPATH" \
-        org.gradle.wrapper.GradleWrapperMain \
-        "$@"
-
-# Stop when "xargs" is not available.
-if ! command -v xargs >/dev/null 2>&1
-then
-    die "xargs is not available"
-fi
-
-# Use "xargs" to parse quoted args.
-#
-# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
-#
-# In Bash we could simply go:
-#
-#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
-#   set -- "${ARGS[@]}" "$@"
-#
-# but POSIX shell has neither arrays nor command substitution, so instead we
-# post-process each arg (as a line of input to sed) to backslash-escape any
-# character that might be a shell metacharacter, then use eval to reverse
-# that process (while maintaining the separation between arguments), and wrap
-# the whole thing up as a single "set" statement.
-#
-# This will of course break if any of these variables contains a newline or
-# an unmatched quote.
-#
-
-eval "set -- $(
-        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
-        xargs -n1 |
-        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
-        tr '\n' ' '
-    )" '"$@"'
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
 
 exec "$JAVACMD" "$@"

gradlew.bat

@@ -26,7 +26,6 @@ if "%OS%"=="Windows_NT" setlocal
 
 set DIRNAME=%~dp0
 if "%DIRNAME%" == "" set DIRNAME=.
-@rem This is normally unused
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
@@ -41,7 +40,7 @@ if defined JAVA_HOME goto findJavaFromJavaHome
 
 set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
-if %ERRORLEVEL% equ 0 goto execute
+if "%ERRORLEVEL%" == "0" goto init
 
 echo.
 echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -55,7 +54,7 @@ goto fail
 set JAVA_HOME=%JAVA_HOME:"=%
 set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
-if exist "%JAVA_EXE%" goto execute
+if exist "%JAVA_EXE%" goto init
 
 echo.
 echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
@@ -65,6 +64,21 @@ echo location of your Java installation.
 
 goto fail
 
+:init
+@rem Get command-line arguments, handling Windows variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+
 :execute
 @rem Setup the command line
 
@@ -72,19 +86,17 @@ set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
 
 
 @rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
 
 :end
 @rem End local scope for the variables with windows NT shell
-if %ERRORLEVEL% equ 0 goto mainEnd
+if "%ERRORLEVEL%"=="0" goto mainEnd
 
 :fail
 rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
 rem the _cmd.exe /c_ return code!
-set EXIT_CODE=%ERRORLEVEL%
-if %EXIT_CODE% equ 0 set EXIT_CODE=1
-if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
-exit /b %EXIT_CODE%
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
 
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal

io-archive-ar/src/main/java/module-info.java

@@ -1,4 +1,4 @@
 module org.xbib.io.archive.ar {
     exports org.xbib.io.archive.ar;
-    requires transitive org.xbib.io.archive;
+    requires org.xbib.io.archive;
 }

io-archive-ar/src/main/java/org/xbib/io/archive/ar/ArArchiveEntry.java

@@ -24,6 +24,7 @@ import java.util.Date;
  * can read but not write the GNU variant and doesn't support
  * the BSD variant at all.
  *
+ * <a href="http://www.freebsd.org/cgi/man.cgi?query=ar&sektion=5">ar man page</a>
  */
 public class ArArchiveEntry implements ArchiveEntry {
 

io-archive-cpio/src/main/java/module-info.java

@@ -1,4 +1,4 @@
 module org.xbib.io.archive.cpio {
     exports org.xbib.io.archive.cpio;
-    requires transitive org.xbib.io.archive;
+    requires org.xbib.io.archive;
 }

io-archive-cpio/src/main/java/org/xbib/io/archive/cpio/CpioArchiveInputStream.java

@@ -1,5 +1,6 @@
 package org.xbib.io.archive.cpio;
 
+import org.xbib.io.archive.entry.ArchiveEntry;
 import org.xbib.io.archive.stream.ArchiveInputStream;
 import org.xbib.io.archive.util.ArchiveUtils;
 
@@ -32,7 +33,7 @@ import java.io.InputStream;
  * Note: This implementation should be compatible to cpio 2.5
  */
 
-public class CpioArchiveInputStream extends ArchiveInputStream<CpioArchiveEntry> implements CpioConstants {
+public class CpioArchiveInputStream extends ArchiveInputStream implements CpioConstants {
 
     private boolean closed = false;
 
@@ -379,7 +380,7 @@ public class CpioArchiveInputStream extends ArchiveInputStream<CpioArchiveEntry>
     }
 
     @Override
-    public CpioArchiveEntry getNextEntry() throws IOException {
+    public ArchiveEntry getNextEntry() throws IOException {
         return getNextCPIOEntry();
     }
 

io-archive-dump/src/main/java/module-info.java

@@ -1,4 +1,4 @@
 module org.xbib.io.archive.dump {
     exports org.xbib.io.archive.dump;
-    requires transitive org.xbib.io.archive;
+    requires org.xbib.io.archive;
 }

io-archive-dump/src/main/java/org/xbib/io/archive/dump/DumpArchiveException.java

@@ -2,10 +2,10 @@ package org.xbib.io.archive.dump;
 
 import java.io.IOException;
 
+
 /**
  * Dump Archive Exception
  */
-@SuppressWarnings("serial")
 public class DumpArchiveException extends IOException {
 
     public DumpArchiveException(String msg) {

io-archive-dump/src/main/java/org/xbib/io/archive/dump/DumpArchiveInputStream.java

@@ -19,9 +19,9 @@ import java.util.Stack;
  * the archive, and the read each entry as a normal input stream
  * using read().
  */
-public class DumpArchiveInputStream extends ArchiveInputStream<DumpArchiveEntry> {
+public class DumpArchiveInputStream extends ArchiveInputStream {
 
-    private final DumpArchiveSummary summary;
+    private DumpArchiveSummary summary;
 
     private DumpArchiveEntry active;
 
@@ -35,7 +35,7 @@ public class DumpArchiveInputStream extends ArchiveInputStream<DumpArchiveEntry>
 
     private int readIdx;
 
-    private final byte[] readBuf = new byte[DumpArchiveConstants.TP_SIZE];
+    private byte[] readBuf = new byte[DumpArchiveConstants.TP_SIZE];
 
     private byte[] blockBuffer;
 
@@ -46,13 +46,13 @@ public class DumpArchiveInputStream extends ArchiveInputStream<DumpArchiveEntry>
     protected TapeInputStream raw;
 
     // map of ino -> dirent entry. We can use this to reconstruct full paths.
-    private final Map<Integer, Dirent> names = new HashMap<Integer, Dirent>();
+    private Map<Integer, Dirent> names = new HashMap<Integer, Dirent>();
 
     // map of ino -> (directory) entry when we're missing one or more elements in the path.
-    private final Map<Integer, DumpArchiveEntry> pending = new HashMap<Integer, DumpArchiveEntry>();
+    private Map<Integer, DumpArchiveEntry> pending = new HashMap<Integer, DumpArchiveEntry>();
 
     // queue of (directory) entries where we now have the full path.
-    private final Queue<DumpArchiveEntry> queue;
+    private Queue<DumpArchiveEntry> queue;
 
     /**
      * Constructor.

io-archive-dump/src/main/java/org/xbib/io/archive/dump/InvalidFormatException.java

@@ -1,10 +1,11 @@
+
 package org.xbib.io.archive.dump;
 
+
 /**
  * Invalid Format Exception. There was an error decoding a
  * tape segment header.
  */
-@SuppressWarnings("serial")
 public class InvalidFormatException extends DumpArchiveException {
 
     protected long offset;

io-archive-dump/src/main/java/org/xbib/io/archive/dump/TapeInputStream.java

@@ -8,24 +8,18 @@ import java.util.Arrays;
 import java.util.zip.DataFormatException;
 import java.util.zip.Inflater;
 
+
 /**
  * Filter stream that mimics a physical tape drive capable of compressing
  * the data stream
  */
-public class TapeInputStream extends FilterInputStream {
-
+class TapeInputStream extends FilterInputStream {
     private byte[] blockBuffer = new byte[DumpArchiveConstants.TP_SIZE];
-
     private int currBlkIdx = -1;
-
     private int blockSize = DumpArchiveConstants.TP_SIZE;
-
     private int recordSize = DumpArchiveConstants.TP_SIZE;
-
     private int readOffset = DumpArchiveConstants.TP_SIZE;
-
     private boolean isCompressed = false;
-
     private long bytesRead = 0;
 
     /**

io-archive-jar/src/main/java/module-info.java

@@ -1,4 +1,5 @@
 module org.xbib.io.archive.jar {
     exports org.xbib.io.archive.jar;
-    requires transitive org.xbib.io.archive.zip;
+    requires org.xbib.io.archive;
+    requires org.xbib.io.archive.zip;
 }

io-archive-jar/src/main/java/org/xbib/io/archive/jar/JarArchiveInputStream.java

@@ -1,6 +1,7 @@
 
 package org.xbib.io.archive.jar;
 
+import org.xbib.io.archive.entry.ArchiveEntry;
 import org.xbib.io.archive.zip.ZipArchiveEntry;
 import org.xbib.io.archive.zip.ZipArchiveInputStream;
 
@@ -10,7 +11,7 @@ import java.io.InputStream;
 /**
  * Implements an input stream that can read entries from jar files.
  */
-public class JarArchiveInputStream extends ZipArchiveInputStream<JarArchiveEntry> {
+public class JarArchiveInputStream extends ZipArchiveInputStream {
 
     public JarArchiveInputStream(final InputStream inputStream) {
         super(inputStream);
@@ -22,7 +23,7 @@ public class JarArchiveInputStream extends ZipArchiveInputStream<JarArchiveEntry
     }
 
     @Override
-    public JarArchiveEntry getNextEntry() throws IOException {
+    public ArchiveEntry getNextEntry() throws IOException {
         return getNextJarEntry();
     }
 

io-archive-tar/src/main/java/module-info.java

@@ -1,4 +1,4 @@
 module org.xbib.io.archive.tar {
     exports org.xbib.io.archive.tar;
-    requires transitive org.xbib.io.archive;
+    requires org.xbib.io.archive;
 }

io-archive-tar/src/main/java/org/xbib/io/archive/tar/TarArchiveEntry.java

@@ -546,207 +546,6 @@ public class TarArchiveEntry implements TarConstants, ArchiveEntry {
         parseTarHeader(header, encoding, false);
     }
 
-
-    /**
-     * Write an entry's header information to a header buffer.
-     *
-     * @param outbuf   The tar entry header buffer to fill in.
-     * @param encoding encoding to use when writing the file name.
-     * @param starMode whether to use the star/GNU tar/BSD tar
-     *                 extension for numeric fields if their value doesn't fit in the
-     *                 maximum size of standard tar archives
-     */
-    public void writeEntryHeader(byte[] outbuf, ArchiveEntryEncoding encoding, boolean starMode) throws IOException {
-        int offset = 0;
-        offset = ArchiveUtils.formatNameBytes(name, outbuf, offset, NAMELEN, encoding);
-        offset = writeEntryHeaderField(mode, outbuf, offset, MODELEN, starMode);
-        offset = writeEntryHeaderField(userId, outbuf, offset, UIDLEN, starMode);
-        offset = writeEntryHeaderField(groupId, outbuf, offset, GIDLEN, starMode);
-        offset = writeEntryHeaderField(size, outbuf, offset, SIZELEN, starMode);
-        offset = writeEntryHeaderField(modTime, outbuf, offset, MODTIMELEN, starMode);
-        int csOffset = offset;
-        for (int c = 0; c < CHKSUMLEN; ++c) {
-            outbuf[offset++] = (byte) ' ';
-        }
-        outbuf[offset++] = linkFlag;
-        offset = ArchiveUtils.formatNameBytes(linkName, outbuf, offset, NAMELEN, encoding);
-        offset = ArchiveUtils.formatNameBytes(MAGIC_POSIX, outbuf, offset, MAGICLEN);
-        offset = ArchiveUtils.formatNameBytes(version, outbuf, offset, VERSIONLEN);
-        offset = ArchiveUtils.formatNameBytes(userName, outbuf, offset, UNAMELEN, encoding);
-        offset = ArchiveUtils.formatNameBytes(groupName, outbuf, offset, GNAMELEN, encoding);
-        offset = writeEntryHeaderField(devMajor, outbuf, offset, DEVLEN, starMode);
-        offset = writeEntryHeaderField(devMinor, outbuf, offset, DEVLEN, starMode);
-        while (offset < outbuf.length) {
-            outbuf[offset++] = 0;
-        }
-        long chk = computeCheckSum(outbuf);
-        formatCheckSumOctalBytes(chk, outbuf, csOffset, CHKSUMLEN);
-    }
-
-    private int writeEntryHeaderField(long value, byte[] outbuf, int offset, int length, boolean starMode) {
-        if (!starMode && (value < 0
-                || value >= (1l << (3 * (length - 1))))) {
-            // value doesn't fit into field when written as octal
-            // number, will be written to PAX header or causes an
-            // error
-            return formatLongOctalBytes(0, outbuf, offset, length);
-        }
-        return formatLongOctalOrBinaryBytes(value, outbuf, offset, length);
-    }
-
-
-    /**
-     * Write an long integer into a buffer as an octal string if this
-     * will fit, or as a binary number otherwise.
-     * <p/>
-     * Uses {@link #formatUnsignedOctalString} to format
-     * the value as an octal string with leading zeros.
-     * The converted number is followed by a space.
-     *
-     * @param value  The value to write into the buffer.
-     * @param buf    The destination buffer.
-     * @param offset The starting offset into the buffer.
-     * @param length The length of the buffer.
-     * @return The updated offset.
-     * @throws IllegalArgumentException if the value (and trailer)
-     *                                  will not fit in the buffer.
-     */
-    private int formatLongOctalOrBinaryBytes(final long value, byte[] buf, final int offset, final int length) {
-        // Check whether we are dealing with UID/GID or SIZE field
-        final long maxAsOctalChar = length == UIDLEN ? MAXID : MAXSIZE;
-        final boolean negative = value < 0;
-        if (!negative && value <= maxAsOctalChar) { // OK to store as octal chars
-            return formatLongOctalBytes(value, buf, offset, length);
-        }
-        if (length < 9) {
-            formatLongBinary(value, buf, offset, length, negative);
-        }
-        formatBigIntegerBinary(value, buf, offset, length, negative);
-        buf[offset] = (byte) (negative ? 0xff : 0x80);
-        return offset + length;
-    }
-
-    private void formatLongBinary(final long value, byte[] buf, final int offset, final int length, final boolean negative) {
-        final int bits = (length - 1) * 8;
-        final long max = 1l << bits;
-        long val = Math.abs(value);
-        if (val >= max) {
-            throw new IllegalArgumentException("Value " + value +
-                    " is too large for " + length + " byte field.");
-        }
-        if (negative) {
-            val ^= max - 1;
-            val |= 0xff << bits;
-            val++;
-        }
-        for (int i = offset + length - 1; i >= offset; i--) {
-            buf[i] = (byte) val;
-            val >>= 8;
-        }
-    }
-
-    private void formatBigIntegerBinary(final long value, byte[] buf,
-                                        final int offset,
-                                        final int length,
-                                        final boolean negative) {
-        BigInteger val = BigInteger.valueOf(value);
-        final byte[] b = val.toByteArray();
-        final int len = b.length;
-        final int off = offset + length - len;
-        System.arraycopy(b, 0, buf, off, len);
-        final byte fill = (byte) (negative ? 0xff : 0);
-        for (int i = offset + 1; i < off; i++) {
-            buf[i] = fill;
-        }
-    }
-
-    /**
-     * Writes an octal value into a buffer.
-     * <p/>
-     * Uses {@link #formatUnsignedOctalString} to format
-     * the value as an octal string with leading zeros.
-     * The converted number is followed by NUL and then space.
-     *
-     * @param value  The value to convert
-     * @param buf    The destination buffer
-     * @param offset The starting offset into the buffer.
-     * @param length The size of the buffer.
-     * @return The updated value of offset, i.e. offset+length
-     * @throws IllegalArgumentException if the value (and trailer) will not fit in the buffer
-     */
-    private int formatCheckSumOctalBytes(final long value, byte[] buf, final int offset, final int length) {
-        int idx = length - 2;
-        formatUnsignedOctalString(value, buf, offset, idx);
-        buf[offset + idx++] = 0;
-        buf[offset + idx] = (byte) ' ';
-        return offset + length;
-    }
-
-    /**
-     * Write an octal long integer into a buffer.
-     * <p/>
-     * Uses {@link #formatUnsignedOctalString} to format
-     * the value as an octal string with leading zeros.
-     * The converted number is followed by a space.
-     *
-     * @param value  The value to write as octal
-     * @param buf    The destinationbuffer.
-     * @param offset The starting offset into the buffer.
-     * @param length The length of the buffer
-     * @return The updated offset
-     * @throws IllegalArgumentException if the value (and trailer) will not fit in the buffer
-     */
-    private int formatLongOctalBytes(final long value, byte[] buf, final int offset, final int length) {
-        int idx = length - 1; // For space
-        formatUnsignedOctalString(value, buf, offset, idx);
-        buf[offset + idx] = (byte) ' '; // Trailing space
-        return offset + length;
-    }
-
-    /**
-     * Fill buffer with unsigned octal number, padded with leading zeroes.
-     *
-     * @param value  number to convert to octal - treated as unsigned
-     * @param buffer destination buffer
-     * @param offset starting offset in buffer
-     * @param length length of buffer to fill
-     * @throws IllegalArgumentException if the value will not fit in the buffer
-     */
-    private void formatUnsignedOctalString(final long value, byte[] buffer, final int offset, final int length) {
-        int remaining = length;
-        remaining--;
-        if (value == 0) {
-            buffer[offset + remaining--] = (byte) '0';
-        } else {
-            long val = value;
-            for (; remaining >= 0 && val != 0; --remaining) {
-                buffer[offset + remaining] = (byte) ((byte) '0' + (byte) (val & 7));
-                val = val >>> 3;
-            }
-            if (val != 0) {
-                throw new IllegalArgumentException(value + "=" + Long.toOctalString(value) + " will not fit in octal number buffer of length " + length);
-            }
-        }
-
-        for (; remaining >= 0; --remaining) { // leading zeros
-            buffer[offset + remaining] = (byte) '0';
-        }
-    }
-
-    /**
-     * Compute the checksum of a tar entry header.
-     *
-     * @param buf The tar entry's header buffer.
-     * @return The computed checksum.
-     */
-    private long computeCheckSum(final byte[] buf) {
-        long sum = 0;
-        for (byte aBuf : buf) {
-            sum += 255 & aBuf;
-        }
-        return sum;
-    }
-
     private void parseTarHeader(byte[] header, ArchiveEntryEncoding encoding, final boolean oldStyle)
             throws IOException {
         int offset = 0;

io-archive-tar/src/main/java/org/xbib/io/archive/tar/TarArchiveOutputEntry.java

@@ -10,7 +10,7 @@ import java.math.BigInteger;
 import java.util.Date;
 
 /**
- * This class represents an entry in a Tar archive for output.
+ * This class represents an entry in a Tar archive for output
  */
 public class TarArchiveOutputEntry implements TarConstants, ArchiveEntry {
 

io-archive-tar/src/main/java/org/xbib/io/archive/tar/TarArchiveOutputStream.java

@@ -7,7 +7,7 @@ import org.xbib.io.archive.entry.ArchiveEntryEncodingHelper;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.io.StringWriter;
-import java.nio.charset.StandardCharsets;
+import java.nio.charset.Charset;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Map;
@@ -15,7 +15,7 @@ import java.util.Map;
 /**
  * The TarOutputStream writes a UNIX tar archive as an output stream
  */
-public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveEntry> implements TarConstants {
+public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveOutputEntry> implements TarConstants {
 
     private static final ArchiveEntryEncoding ASCII = ArchiveEntryEncodingHelper.getEncoding("ASCII");
 
@@ -239,8 +239,8 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveEntry>
     }
 
     @Override
-    public TarArchiveEntry newArchiveEntry() {
-        return new TarArchiveEntry();
+    public TarArchiveOutputEntry newArchiveEntry() {
+        return new TarArchiveOutputEntry();
     }
 
     /**
@@ -257,7 +257,7 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveEntry>
      * @throws ClassCastException  if archiveEntry is not an instance of TarArchiveEntry
      */
     @Override
-    public void putArchiveEntry(TarArchiveEntry archiveEntry) throws IOException {
+    public void putArchiveEntry(TarArchiveOutputEntry archiveEntry) throws IOException {
         if (finished) {
             throw new IOException("Stream has already been finished");
         }
@@ -272,7 +272,7 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveEntry>
             } else if (longFileMode == LONGFILE_GNU) {
                 // create a TarEntry for the LongLink, the contents
                 // of which are the entry's name
-                TarArchiveEntry longLinkEntry = new TarArchiveEntry(GNU_LONGLINK, LF_GNUTYPE_LONGNAME);
+                TarArchiveOutputEntry longLinkEntry = new TarArchiveOutputEntry(GNU_LONGLINK, LF_GNUTYPE_LONGNAME);
                 longLinkEntry.setEntrySize(nameBytes.length + 1); // +1 for NUL
                 putArchiveEntry(longLinkEntry);
                 write(nameBytes);
@@ -440,7 +440,7 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveEntry>
         if (name.length() >= NAMELEN) {
             name = name.substring(0, NAMELEN - 1);
         }
-        TarArchiveEntry pex = new TarArchiveEntry(name, LF_PAX_EXTENDED_HEADER_LC);
+        TarArchiveOutputEntry pex = new TarArchiveOutputEntry(name, LF_PAX_EXTENDED_HEADER_LC);
         StringWriter w = new StringWriter();
         for (Map.Entry<String, String> h : headers.entrySet()) {
             String key = h.getKey();
@@ -449,7 +449,7 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveEntry>
                     + 3 /* blank, equals and newline */
                     + 2 /* guess 9 < actual length < 100 */;
             String line = len + " " + key + "=" + value + "\n";
-            int actualLength = line.getBytes(StandardCharsets.UTF_8).length;
+            int actualLength = line.getBytes(Charset.forName("UTF-8")).length;
             while (len != actualLength) {
                 // Adjust for cases where length < 10 or > 100
                 // or where UTF-8 encoding isn't a single octet
@@ -458,11 +458,11 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveEntry>
                 // first pass so we'd need a second.
                 len = actualLength;
                 line = len + " " + key + "=" + value + "\n";
-                actualLength = line.getBytes(StandardCharsets.UTF_8).length;
+                actualLength = line.getBytes(Charset.forName("UTF-8")).length;
             }
             w.write(line);
         }
-        byte[] data = w.toString().getBytes(StandardCharsets.UTF_8);
+        byte[] data = w.toString().getBytes(Charset.forName("UTF-8"));
         pex.setEntrySize(data.length);
         putArchiveEntry(pex);
         write(data);
@@ -499,7 +499,7 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveEntry>
     }
 
     private void addPaxHeadersForBigNumbers(Map<String, String> paxHeaders,
-                                            TarArchiveEntry entry) {
+                                            TarArchiveOutputEntry entry) {
         addPaxHeaderForBigNumber(paxHeaders, "size", entry.getEntrySize(), MAXSIZE);
         addPaxHeaderForBigNumber(paxHeaders, "gid", entry.getGroupId(), MAXID);
         addPaxHeaderForBigNumber(paxHeaders, "mtime", entry.getLastModified().getTime() / 1000, MAXSIZE);
@@ -519,7 +519,7 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveEntry>
         }
     }
 
-    private void failForBigNumbers(TarArchiveEntry entry) {
+    private void failForBigNumbers(TarArchiveOutputEntry entry) {
         failForBigNumber("entry size", entry.getEntrySize(), MAXSIZE);
         failForBigNumber("group id", entry.getGroupId(), MAXID);
         failForBigNumber("last modification time", entry.getLastModified().getTime() / 1000, MAXSIZE);

io-archive-tar/src/test/java/org/xbib/io/archive/tar/TarTest.java

@@ -9,7 +9,7 @@ import org.junit.jupiter.api.Test;
 public class TarTest {
 
     @Test
-    public void testReadTar() throws IOException {
+    public void testTar() throws IOException {
         InputStream in = getClass().getResourceAsStream("test.tar");
         TarArchiveInputStream tarArchiveInputStream = new TarArchiveInputStream(in);
         byte[] buffer = new byte[1024];

io-archive-zip/src/main/java/module-info.java

@@ -1,4 +1,4 @@
 module org.xbib.io.archive.zip {
     exports org.xbib.io.archive.zip;
-    requires transitive org.xbib.io.archive;
+    requires org.xbib.io.archive;
 }

io-archive-zip/src/main/java/org/xbib/io/archive/zip/ExtraFieldUtils.java

@@ -1,3 +1,4 @@
+
 package org.xbib.io.archive.zip;
 
 import java.util.ArrayList;
@@ -19,7 +20,7 @@ public class ExtraFieldUtils {
     private static final Map<ZipShort, Class<?>> implementations;
 
     static {
-        implementations = new HashMap<>();
+        implementations = new HashMap<ZipShort, Class<?>>();
         register(AsiExtraField.class);
         register(JarMarker.class);
         register(UnicodePathExtraField.class);
@@ -36,10 +37,14 @@ public class ExtraFieldUtils {
      */
     public static void register(Class<?> c) {
         try {
-            ZipExtraField ze = (ZipExtraField) c.getDeclaredConstructor().newInstance();
+            ZipExtraField ze = (ZipExtraField) c.newInstance();
             implementations.put(ze.getHeaderId(), c);
-        } catch (Exception e) {
-            throw new RuntimeException(e);
+        } catch (ClassCastException cc) {
+            throw new RuntimeException(c + " doesn\'t implement ZipExtraField");
+        } catch (InstantiationException ie) {
+            throw new RuntimeException(c + " is not a concrete class");
+        } catch (IllegalAccessException ie) {
+            throw new RuntimeException(c + "\'s no-arg constructor is not public");
         }
     }
 
@@ -49,13 +54,14 @@ public class ExtraFieldUtils {
      *
      * @param headerId the header identifier
      * @return an instance of the appropiate ExtraField
-     * @throws Exception if unable to instantiate the class
+     * @throws InstantiationException if unable to instantiate the class
+     * @throws IllegalAccessException if not allowed to instatiate the class
      */
     public static ZipExtraField createExtraField(ZipShort headerId)
-            throws Exception {
+            throws InstantiationException, IllegalAccessException {
         Class<?> c = implementations.get(headerId);
         if (c != null) {
-            return (ZipExtraField) c.getDeclaredConstructor().newInstance();
+            return (ZipExtraField) c.newInstance();
         }
         UnrecognizedExtraField u = new UnrecognizedExtraField();
         u.setHeaderId(headerId);
@@ -151,7 +157,7 @@ public class ExtraFieldUtils {
                             length);
                 }
                 v.add(ze);
-            } catch (Exception ie) {
+            } catch (InstantiationException | IllegalAccessException ie) {
                 throw new ZipException(ie.getMessage());
             }
             start += (length + WORD);

io-archive-zip/src/main/java/org/xbib/io/archive/zip/UnsupportedZipFeatureException.java

@@ -7,7 +7,6 @@ import java.util.zip.ZipException;
  * Exception thrown when attempting to read or write data for a zip
  * entry that uses ZIP features not supported by this library.
  */
-@SuppressWarnings("serial")
 public class UnsupportedZipFeatureException extends ZipException {
 
     private final Feature reason;

io-archive-zip/src/main/java/org/xbib/io/archive/zip/Zip64RequiredException.java

@@ -8,7 +8,6 @@ import java.util.zip.ZipException;
  * support to an archive and {@link ZipArchiveOutputStream#setUseZip64
  * UseZip64} has been set to {@link Zip64Mode#Never Never}.
  */
-@SuppressWarnings("serial")
 public class Zip64RequiredException extends ZipException {
 
     /**

io-archive-zip/src/main/java/org/xbib/io/archive/zip/ZipArchiveInputStream.java

@@ -1,5 +1,6 @@
 package org.xbib.io.archive.zip;
 
+import org.xbib.io.archive.entry.ArchiveEntry;
 import org.xbib.io.archive.stream.ArchiveInputStream;
 import org.xbib.io.archive.entry.ArchiveEntryEncoding;
 import org.xbib.io.archive.entry.ArchiveEntryEncodingHelper;
@@ -33,7 +34,7 @@ import static org.xbib.io.archive.zip.ZipConstants.ZIP64_MAGIC;
  *
  * @see ZipFile
  */
-public class ZipArchiveInputStream<E extends ZipArchiveEntry> extends ArchiveInputStream<E> {
+public class ZipArchiveInputStream extends ArchiveInputStream {
 
     /**
      * The zip encoding to use for filenames and the file comment.
@@ -251,10 +252,9 @@ public class ZipArchiveInputStream<E extends ZipArchiveEntry> extends ArchiveInp
         }
     }
 
-    @SuppressWarnings("unchecked")
     @Override
-    public E getNextEntry() throws IOException {
-        return (E) getNextZipEntry();
+    public ArchiveEntry getNextEntry() throws IOException {
+        return getNextZipEntry();
     }
 
     @Override

io-archive-zip/src/main/java/org/xbib/io/archive/zip/ZipArchiveOutputStream.java

@@ -562,7 +562,6 @@ public class ZipArchiveOutputStream<E extends ZipArchiveEntry> extends ArchiveOu
         raf.seek(save);
     }
 
-    @SuppressWarnings("unchecked")
     @Override
     public E newArchiveEntry() {
         return (E)new ZipArchiveEntry();

io-archive-zip/src/main/java/org/xbib/io/archive/zip/ZipFile.java

@@ -316,6 +316,23 @@ public class ZipFile {
         }
     }
 
+    /**
+     * Ensures that the close method of this zipfile is called when
+     * there are no more references to it.
+     *
+     * @see #close()
+     */
+    @Override
+    protected void finalize() throws Throwable {
+        try {
+            if (!closed) {
+                close();
+            }
+        } finally {
+            super.finalize();
+        }
+    }
+
     /**
      * Length of a "central directory" entry structure without file
      * name, extra fields or comment.
@@ -353,7 +370,8 @@ public class ZipFile {
      */
     private Map<ZipArchiveEntry, NameAndComment> populateFromCentralDirectory()
             throws IOException {
-        HashMap<ZipArchiveEntry, NameAndComment> noUTF8Flag = new HashMap<>();
+        HashMap<ZipArchiveEntry, NameAndComment> noUTF8Flag =
+                new HashMap<ZipArchiveEntry, NameAndComment>();
 
         positionAtCentralDirectory();
 

io-archive-zip/src/test/java/org/xbib/io/archive/zip/ZipTest.java

@@ -9,7 +9,7 @@ public class ZipTest {
     @Test
     public void testZip() throws Exception {
         InputStream in = getClass().getResourceAsStream("test.zip");
-        ZipArchiveInputStream<ZipArchiveEntry> z = new ZipArchiveInputStream<>(in);
+        ZipArchiveInputStream z = new ZipArchiveInputStream(in);
         byte[] buffer = new byte[1024];
         long total = 0L;
         while ((z.getNextEntry()) != null) {

io-codec/build.gradle

@@ -1,6 +1,5 @@
 dependencies {
     api project(':io-archive')
-    implementation project(':io-compress-bgzf')
     implementation project(':io-compress-bzip2')
     implementation project(':io-compress-lzf')
     implementation project(':io-compress-xz')

io-codec/src/main/java/module-info.java

@@ -1,22 +1,20 @@
 module org.xbib.io.codec {
-    uses org.xbib.io.codec.StreamCodec;
     exports org.xbib.io.codec;
     exports org.xbib.io.codec.ar;
-    exports org.xbib.io.codec.bgzf;
     exports org.xbib.io.codec.cpio;
     exports org.xbib.io.codec.file;
     exports org.xbib.io.codec.jar;
     exports org.xbib.io.codec.tar;
     exports org.xbib.io.codec.zip;
-    requires transitive org.xbib.io.compress.bgzf;
     requires org.xbib.io.compress.bzip;
     requires org.xbib.io.compress.lzf;
     requires org.xbib.io.compress.xz;
     requires org.xbib.io.compress.zlib;
-    requires transitive org.xbib.io.archive.ar;
-    requires transitive org.xbib.io.archive.cpio;
-    requires transitive org.xbib.io.archive.dump;
-    requires transitive org.xbib.io.archive.jar;
-    requires transitive org.xbib.io.archive.tar;
-    requires transitive org.xbib.io.archive.zip;
+    requires org.xbib.io.archive;
+    requires org.xbib.io.archive.ar;
+    requires org.xbib.io.archive.cpio;
+    requires org.xbib.io.archive.dump;
+    requires org.xbib.io.archive.jar;
+    requires org.xbib.io.archive.tar;
+    requires org.xbib.io.archive.zip;
 }

io-codec/src/main/java/org/xbib/io/codec/ArchiveCodec.java

@@ -1,6 +1,5 @@
 package org.xbib.io.codec;
 
-import org.xbib.io.archive.entry.ArchiveEntry;
 import org.xbib.io.archive.stream.ArchiveInputStream;
 import org.xbib.io.archive.stream.ArchiveOutputStream;
 import java.io.IOException;
@@ -15,7 +14,7 @@ import java.io.OutputStream;
  * @param <I> the archive input stream type
  * @param <O> the archive output type
  */
-public interface ArchiveCodec<E extends ArchiveEntry, I extends ArchiveInputStream<E>, O extends ArchiveOutputStream<E>, S extends ArchiveSession<E, I, O>> {
+public interface ArchiveCodec<S extends ArchiveSession, I extends ArchiveInputStream, O extends ArchiveOutputStream> {
 
     /**
      * Returns the name of this archive codec ("cpio", "tar", "zip")
@@ -24,6 +23,14 @@ public interface ArchiveCodec<E extends ArchiveEntry, I extends ArchiveInputStre
      */
     String getName();
 
+    /**
+     * Creates a new archive session with a progress watcher.
+     *
+     * @param watcher the progress watcher
+     * @return the new archive session
+     */
+    S newSession(BytesProgressWatcher watcher);
+
     /**
      * Creates a new archive input stream
      *
@@ -42,11 +49,4 @@ public interface ArchiveCodec<E extends ArchiveEntry, I extends ArchiveInputStre
      */
     O createArchiveOutputStream(OutputStream out) throws IOException;
 
-    /**
-     * Creates a new archive session with a progress watcher.
-     *
-     * @param watcher the progress watcher
-     * @return the new archive session
-     */
-    S newSession(BytesProgressWatcher watcher);
 }

io-codec/src/main/java/org/xbib/io/codec/ArchiveSession.java

@@ -1,3 +1,34 @@
+/*
+ * Licensed to Jörg Prante and xbib under one or more contributor
+ * license agreements. See the NOTICE.txt file distributed with this work
+ * for additional information regarding copyright ownership.
+ *
+ * Copyright (C) 2012 Jörg Prante and xbib
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published
+ * by the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program; if not, see http://www.gnu.org/licenses
+ * or write to the Free Software Foundation, Inc., 51 Franklin Street,
+ * Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * The interactive user interfaces in modified source and object code
+ * versions of this program must display Appropriate Legal Notices,
+ * as required under Section 5 of the GNU Affero General Public License.
+ *
+ * In accordance with Section 7(b) of the GNU Affero General Public
+ * License, these Appropriate Legal Notices must retain the display of the
+ * "Powered by xbib" logo. If the display of the logo is not reasonably
+ * feasible for technical reasons, the Appropriate Legal Notices must display
+ * the words "Powered by xbib".
+ */
 package org.xbib.io.codec;
 
 import org.xbib.io.archive.entry.ArchiveEntry;
@@ -14,11 +45,13 @@ import java.util.Date;
 import java.util.Set;
 
 /**
- * Archive session.
+ * Archive session
  */
-public abstract class ArchiveSession<E extends ArchiveEntry, I extends ArchiveInputStream<E>, O extends ArchiveOutputStream<E>>
+public abstract class ArchiveSession<I extends ArchiveInputStream, O extends ArchiveOutputStream>
         implements Session<StringPacket> {
 
+    private final static StreamCodecService codecFactory = StreamCodecService.getInstance();
+
     private final static int DEFAULT_INPUT_BUFSIZE = 65536;
 
     protected int bufferSize = DEFAULT_INPUT_BUFSIZE;
@@ -32,13 +65,15 @@ public abstract class ArchiveSession<E extends ArchiveEntry, I extends ArchiveIn
     protected ArchiveSession() {
     }
 
-    public void setPath(Path path, OpenOption option) {
+    public ArchiveSession setPath(Path path, OpenOption option) {
         this.path = path;
         this.option = option;
+        return this;
     }
 
-    public void setBufferSize(int bufferSize) {
+    public ArchiveSession setBufferSize(int bufferSize) {
         this.bufferSize = bufferSize;
+        return this;
     }
 
     @Override
@@ -103,7 +138,7 @@ public abstract class ArchiveSession<E extends ArchiveEntry, I extends ArchiveIn
         byte[] buf = packet.toString().getBytes();
         if (buf.length > 0) {
             String name = packet.name();
-            E entry = getOutputStream().newArchiveEntry();
+            ArchiveEntry entry = getOutputStream().newArchiveEntry();
             entry.setName(name);
             entry.setLastModified(new Date());
             entry.setEntrySize(buf.length);

io-codec/src/main/java/org/xbib/io/codec/Session.java

@@ -7,7 +7,7 @@ import java.io.IOException;
  * operations, and being closed. Sessions must be opened before the first
  * operation and closed after the last operation.
  */
-public interface Session<P extends StringPacket> {
+public interface Session<P extends Packet> {
 
     enum Mode {
 

io-codec/src/main/java/org/xbib/io/codec/StreamCodecService.java

@@ -1,7 +1,5 @@
 package org.xbib.io.codec;
 
-import java.io.InputStream;
-import java.io.OutputStream;
 import java.util.Map;
 import java.util.ServiceLoader;
 import java.util.Set;
@@ -12,14 +10,13 @@ import java.util.WeakHashMap;
  */
 public class StreamCodecService {
 
-    private final static Map<String, StreamCodec<InputStream, OutputStream>> codecs = new WeakHashMap<>();
+    private final static Map<String, StreamCodec> codecs = new WeakHashMap<>();
 
     private final static StreamCodecService instance = new StreamCodecService();
 
-    @SuppressWarnings({"rawtypes","unchecked"})
     private StreamCodecService() {
         ServiceLoader<StreamCodec> loader = ServiceLoader.load(StreamCodec.class);
-        for (StreamCodec<InputStream, OutputStream> codec : loader) {
+        for (StreamCodec codec : loader) {
             if (!codecs.containsKey(codec.getName())) {
                 codecs.put(codec.getName(), codec);
             }
@@ -30,7 +27,7 @@ public class StreamCodecService {
         return instance;
     }
 
-    public StreamCodec<InputStream, OutputStream> getCodec(String suffix) {
+    public StreamCodec getCodec(String suffix) {
         if (codecs.containsKey(suffix)) {
             return codecs.get(suffix);
         }

io-codec/src/main/java/org/xbib/io/codec/ar/ArConnection.java

@@ -27,7 +27,6 @@ public class ArConnection extends URLConnection implements Connection<ArSession>
      * the object referenced by the URL is not created.
      *
      * @param url the specified URL.
-     * @throws URISyntaxException if URI is invalid
      */
     public ArConnection(URL url) throws URISyntaxException {
         super(url);

io-codec/src/main/java/org/xbib/io/codec/ar/ArSession.java

@@ -1,9 +1,9 @@
 package org.xbib.io.codec.ar;
 
-import org.xbib.io.archive.ar.ArArchiveEntry;
 import org.xbib.io.codec.ArchiveSession;
 import org.xbib.io.archive.ar.ArArchiveInputStream;
 import org.xbib.io.archive.ar.ArArchiveOutputStream;
+import org.xbib.io.codec.Packet;
 import org.xbib.io.codec.Session;
 import org.xbib.io.codec.StringPacket;
 import java.io.InputStream;
@@ -12,7 +12,7 @@ import java.io.OutputStream;
 /**
  * Ar Session
  */
-public class ArSession extends ArchiveSession<ArArchiveEntry, ArArchiveInputStream, ArArchiveOutputStream>
+public class ArSession extends ArchiveSession<ArArchiveInputStream, ArArchiveOutputStream>
         implements Session<StringPacket> {
 
     private final static String SUFFIX = "ar";

io-codec/src/main/java/org/xbib/io/codec/bgzf/BzgfStreamCodec.java

@@ -1,37 +0,0 @@
-package org.xbib.io.codec.bgzf;
-
-import org.xbib.io.codec.StreamCodec;
-import org.xbib.io.compress.bgzf.BlockCompressedInputStream;
-import org.xbib.io.compress.bgzf.BlockCompressedOutputStream;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-
-public class BzgfStreamCodec implements StreamCodec<BlockCompressedInputStream, BlockCompressedOutputStream> {
-
-    @Override
-    public String getName() {
-        return "bgzf";
-    }
-
-    @Override
-    public BlockCompressedInputStream decode(InputStream in) throws IOException {
-        return new BlockCompressedInputStream(in);
-    }
-
-    @Override
-    public BlockCompressedInputStream decode(InputStream in, int bufsize) throws IOException {
-        return new BlockCompressedInputStream(in);
-    }
-
-    @Override
-    public BlockCompressedOutputStream encode(OutputStream out) throws IOException {
-        return new BlockCompressedOutputStream(out);
-    }
-
-    @Override
-    public BlockCompressedOutputStream encode(OutputStream out, int bufsize) throws IOException {
-        return new BlockCompressedOutputStream(out);
-    }
-}

io-codec/src/main/java/org/xbib/io/codec/cpio/CpioSession.java

@@ -1,6 +1,5 @@
 package org.xbib.io.codec.cpio;
 
-import org.xbib.io.archive.cpio.CpioArchiveEntry;
 import org.xbib.io.codec.ArchiveSession;
 import org.xbib.io.archive.cpio.CpioArchiveInputStream;
 import org.xbib.io.archive.cpio.CpioArchiveOutputStream;
@@ -10,7 +9,7 @@ import java.io.OutputStream;
 /**
  * Cpio Session
  */
-public class CpioSession extends ArchiveSession<CpioArchiveEntry, CpioArchiveInputStream, CpioArchiveOutputStream> {
+public class CpioSession extends ArchiveSession<CpioArchiveInputStream, CpioArchiveOutputStream> {
 
     private final static String SUFFIX = "cpio";
 

io-codec/src/main/java/org/xbib/io/codec/jar/JarSession.java

@@ -1,13 +1,12 @@
 package org.xbib.io.codec.jar;
 
-import org.xbib.io.archive.jar.JarArchiveEntry;
 import org.xbib.io.codec.ArchiveSession;
 import org.xbib.io.archive.jar.JarArchiveInputStream;
 import org.xbib.io.archive.jar.JarArchiveOutputStream;
 import java.io.InputStream;
 import java.io.OutputStream;
 
-public class JarSession extends ArchiveSession<JarArchiveEntry, JarArchiveInputStream, JarArchiveOutputStream> {
+public class JarSession extends ArchiveSession<JarArchiveInputStream, JarArchiveOutputStream> {
 
     private final static String SUFFIX = "jar";
 

io-codec/src/main/java/org/xbib/io/codec/tar/TarSession.java

@@ -31,7 +31,6 @@
  */
 package org.xbib.io.codec.tar;
 
-import org.xbib.io.archive.tar.TarArchiveEntry;
 import org.xbib.io.codec.ArchiveSession;
 import org.xbib.io.archive.tar.TarArchiveInputStream;
 import org.xbib.io.archive.tar.TarArchiveOutputStream;
@@ -39,7 +38,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 
-public class TarSession extends ArchiveSession<TarArchiveEntry, TarArchiveInputStream, TarArchiveOutputStream> {
+public class TarSession extends ArchiveSession<TarArchiveInputStream, TarArchiveOutputStream> {
 
     private final static String SUFFIX = "tar";
 

io-codec/src/main/java/org/xbib/io/codec/zip/ZipSession.java

@@ -1,37 +1,37 @@
 package org.xbib.io.codec.zip;
 
-import org.xbib.io.archive.zip.ZipArchiveEntry;
 import org.xbib.io.codec.ArchiveSession;
 import org.xbib.io.archive.zip.ZipArchiveInputStream;
 import org.xbib.io.archive.zip.ZipArchiveOutputStream;
 import java.io.InputStream;
 import java.io.OutputStream;
 
-public class ZipSession extends ArchiveSession<ZipArchiveEntry, ZipArchiveInputStream<ZipArchiveEntry>, ZipArchiveOutputStream<ZipArchiveEntry>> {
+public class ZipSession extends ArchiveSession<ZipArchiveInputStream, ZipArchiveOutputStream> {
 
     private final static String SUFFIX = "zip";
 
-    private ZipArchiveInputStream<ZipArchiveEntry> in;
+    private ZipArchiveInputStream in;
 
-    private ZipArchiveOutputStream<ZipArchiveEntry> out;
+    private ZipArchiveOutputStream out;
 
     protected String getSuffix() {
         return SUFFIX;
     }
 
     protected void open(InputStream in) {
-        this.in = new ZipArchiveInputStream<>(in);
+        this.in = new ZipArchiveInputStream(in);
     }
 
     protected void open(OutputStream out) {
-        this.out = new ZipArchiveOutputStream<>(out);
+        this.out = new ZipArchiveOutputStream(out);
     }
 
-    public ZipArchiveInputStream<ZipArchiveEntry> getInputStream() {
+    public ZipArchiveInputStream getInputStream() {
         return in;
     }
 
-    public ZipArchiveOutputStream<ZipArchiveEntry> getOutputStream() {
+    public ZipArchiveOutputStream getOutputStream() {
         return out;
     }
+
 }

io-compress-bgzf/LICENSE.txt

@@ -1,21 +0,0 @@
-/*
- * The MIT License
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */

io-compress-bgzf/src/main/java/module-info.java

@@ -1,3 +0,0 @@
-module org.xbib.io.compress.bgzf {
-    exports org.xbib.io.compress.bgzf;
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BGZFException.java

@@ -1,19 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-@SuppressWarnings("serial")
-public class BGZFException extends RuntimeException {
-
-    public BGZFException() {}
-
-    public BGZFException(final String s) {
-        super(s);
-    }
-
-    public BGZFException(final String s, final Throwable throwable) {
-        super(s, throwable);
-    }
-
-    public BGZFException(final Throwable throwable) {
-        super(throwable);
-    }
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BGZFFilePointerUtil.java

@@ -1,67 +0,0 @@
-
-package org.xbib.io.compress.bgzf;
-
-public class BGZFFilePointerUtil {
-
-    private static final int SHIFT_AMOUNT = 16;
-    private static final int OFFSET_MASK = 0xffff;
-    private static final long ADDRESS_MASK = 0xFFFFFFFFFFFFL;
-
-    public static final long MAX_BLOCK_ADDRESS = ADDRESS_MASK;
-    public static final int MAX_OFFSET = OFFSET_MASK;
-
-    public static int compare(final long vfp1, final long vfp2) {
-        if (vfp1 == vfp2) return 0;
-        // When treating as unsigned, negative number is > positive.
-        if (vfp1 < 0 && vfp2 >= 0) return 1;
-        if (vfp1 >= 0 && vfp2 < 0) return -1;
-        // Either both negative or both non-negative, so regular comparison works.
-        if (vfp1 < vfp2) return -1;
-        return 1; // vfp1 > vfp2
-    }
-
-    /**
-     * @return true if vfp2 points to somewhere in the same BGZF block, or the one immediately
-     *         following vfp1's BGZF block.
-     */
-    public static boolean areInSameOrAdjacentBlocks(final long vfp1, final long vfp2) {
-        final long block1 = getBlockAddress(vfp1);
-        final long block2 = getBlockAddress(vfp2);
-        return (block1 == block2 || block1 + 1 == block2);
-    }
-
-    /**
-     * @param blockAddress File offset of start of BGZF block.
-     * @param blockOffset Offset into uncompressed block.
-     * @return Virtual file pointer that embodies the input parameters.
-     */
-    static long makeFilePointer(final long blockAddress, final int blockOffset) {
-        if (blockOffset < 0) {
-            throw new IllegalArgumentException("Negative blockOffset " + blockOffset
-                + " not allowed.");
-        }
-        if (blockAddress < 0) {
-            throw new IllegalArgumentException("Negative blockAddress " + blockAddress
-                + " not allowed.");
-        }
-        if (blockOffset > MAX_OFFSET) {
-            throw new IllegalArgumentException("blockOffset " + blockOffset + " too large.");
-        }
-        if (blockAddress > MAX_BLOCK_ADDRESS) {
-            throw new IllegalArgumentException("blockAddress " + blockAddress + " too large.");
-        }
-        return blockAddress << SHIFT_AMOUNT | blockOffset;
-    }
-
-    public static long getBlockAddress(final long virtualFilePointer) {
-        return (virtualFilePointer >> SHIFT_AMOUNT) & ADDRESS_MASK;
-    }
-
-    public static int getBlockOffset(final long virtualFilePointer) {
-        return (int)(virtualFilePointer & OFFSET_MASK);
-    }
-
-    public static String asString(final long vfp) {
-        return String.format("%d(0x%x): (block address: %d, offset: %d)", vfp, vfp, getBlockAddress(vfp), getBlockOffset(vfp));
-    }
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BGZFFormatException.java

@@ -1,19 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-@SuppressWarnings("serial")
-public class BGZFFormatException extends BGZFException {
-
-    public BGZFFormatException() {}
-
-    public BGZFFormatException(final String s) {
-        super(s);
-    }
-
-    public BGZFFormatException(final String s, final Throwable throwable) {
-        super(s, throwable);
-    }
-
-    public BGZFFormatException(final Throwable throwable) {
-        super(throwable);
-    }
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BGZFStreamConstants.java

@@ -1,95 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-/**
- * Constants shared by BlockCompressed{Input,Output}Stream classes
- */
-public class BGZFStreamConstants {
-
-    // Number of bytes in the gzip block before the deflated data.
-    // This is not the standard header size, because we include one optional subfield,
-    // but it is the standard for us.
-    public static final int BLOCK_HEADER_LENGTH = 18;
-
-    // Location in the gzip block of the total block size (actually total block size - 1)
-    public static final int BLOCK_LENGTH_OFFSET = 16;
-
-    // Number of bytes that follow the deflated data
-    public static final int BLOCK_FOOTER_LENGTH = 8;
-
-    // We require that a compressed block (including header and footer, be <= this)
-    public static final int MAX_COMPRESSED_BLOCK_SIZE = 64 * 1024;
-
-    // Gzip overhead is the header, the footer, and the block size (encoded as a short).
-    public static final int GZIP_OVERHEAD = BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH + 2;
-
-    // If Deflater has compression level == NO_COMPRESSION, 10 bytes of overhead (determined experimentally).
-    public static final int NO_COMPRESSION_OVERHEAD = 10;
-
-    // Push out a gzip block when this many uncompressed bytes have been accumulated.
-    // This size is selected so that if data is not compressible,  if Deflater is given
-    // compression level == NO_COMPRESSION, compressed size is guaranteed to be <= MAX_COMPRESSED_BLOCK_SIZE.
-    public static final int DEFAULT_UNCOMPRESSED_BLOCK_SIZE = 64 * 1024 - (GZIP_OVERHEAD + NO_COMPRESSION_OVERHEAD);
-
-    // Magic numbers
-    public static final byte GZIP_ID1 = 31;
-    public static final int GZIP_ID2 = 139;
-
-    // FEXTRA flag means there are optional fields
-    public static final int GZIP_FLG = 4;
-
-    // extra flags
-    public static final int GZIP_XFL = 0;
-
-    // length of extra subfield
-    public static final short GZIP_XLEN = 6;
-
-    // The deflate compression, which is customarily used by gzip
-    public static final byte GZIP_CM_DEFLATE = 8;
-
-    public static final int DEFAULT_COMPRESSION_LEVEL = 5;
-
-    // We don't care about OS because we're not doing line terminator translation
-    public static final int GZIP_OS_UNKNOWN = 255;
-
-    // The subfield ID
-    public static final byte BGZF_ID1 = 66;
-    public static final byte BGZF_ID2 = 67;
-
-    // subfield length in bytes
-    public static final byte BGZF_LEN = 2;
-
-    public static final byte[] EMPTY_GZIP_BLOCK = {
-            BGZFStreamConstants.GZIP_ID1,
-            (byte)BGZFStreamConstants.GZIP_ID2,
-            BGZFStreamConstants.GZIP_CM_DEFLATE,
-            BGZFStreamConstants.GZIP_FLG,
-            0, 0, 0, 0, // Modification time
-            BGZFStreamConstants.GZIP_XFL,
-            (byte)BGZFStreamConstants.GZIP_OS_UNKNOWN,
-            BGZFStreamConstants.GZIP_XLEN, 0, // Little-endian short
-            BGZFStreamConstants.BGZF_ID1,
-            BGZFStreamConstants.BGZF_ID2,
-            BGZFStreamConstants.BGZF_LEN, 0, // Little-endian short
-            // Total block size - 1
-            BGZFStreamConstants.BLOCK_HEADER_LENGTH +
-                    BGZFStreamConstants.BLOCK_FOOTER_LENGTH - 1 + 2, 0, // Little-endian short
-            // Dummy payload?
-            3, 0,
-            0, 0, 0, 0, // crc
-            0, 0, 0, 0, // uncompressedSize
-    };
-
-    public static final byte[] GZIP_BLOCK_PREAMBLE = {
-            BGZFStreamConstants.GZIP_ID1,
-            (byte)BGZFStreamConstants.GZIP_ID2,
-            BGZFStreamConstants.GZIP_CM_DEFLATE,
-            BGZFStreamConstants.GZIP_FLG,
-            0, 0, 0, 0, // Modification time
-            BGZFStreamConstants.GZIP_XFL,
-            (byte)BGZFStreamConstants.GZIP_OS_UNKNOWN,
-            BGZFStreamConstants.GZIP_XLEN, 0, // Little-endian short
-            BGZFStreamConstants.BGZF_ID1,
-            BGZFStreamConstants.BGZF_ID2,
-            BGZFStreamConstants.BGZF_LEN, 0, // Little-endian short
-    };
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BinaryCodec.java

@@ -1,666 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-import java.io.ByteArrayInputStream;
-import java.io.EOFException;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.io.SyncFailedException;
-import java.nio.ByteBuffer;
-import java.nio.ByteOrder;
-
-/**
- * Encapsulates file representation of various primitive data types. Forces little-endian disk
- * representation. Note that this class is currently not very efficient. There are plans to increase
- * the size of the ByteBuffer, and move data between the ByteBuffer and the underlying input or
- * output stream in larger chunks.
- *
- * All the read methods throw EOFException if the input stream is exhausted before the
- * required number of bytes are read.
- */
-public class BinaryCodec {
-
-    // Outstream to write to
-    private OutputStream outputStream;
-    // If a file or filename was given it will be stored here. Used for error reporting.
-    private String outputFileName;
-
-    // Input stream to read from
-    private InputStream inputStream;
-    // If a file or filename was give to read from it will be stored here. Used for error reporting.
-    private String inputFileName;
-
-    /*
-     * Mode that the BinaryCodec is in. It is either writing to a binary file or reading from. This
-     * is set to true if it is writing to a binary file Right now we don't support reading and
-     * writing to the same file with the same BinaryCodec instance
-     */
-    private boolean isWriting;
-
-    /**
-     * For byte swapping.
-     */
-    private ByteBuffer byteBuffer;
-
-    /**
-     * For reading Strings of known length, this can reduce object creation
-     */
-    private final byte[] scratchBuffer = new byte[16];
-
-    // Byte order used in BAM files.
-    private static final ByteOrder LITTLE_ENDIAN = ByteOrder.LITTLE_ENDIAN;
-    private static final byte[] NULL_BYTE = {0};
-
-    private static final long MAX_UBYTE = (Byte.MAX_VALUE * 2) + 1;
-    private static final long MAX_USHORT = (Short.MAX_VALUE * 2) + 1;
-    private static final long MAX_UINT = ((long)Integer.MAX_VALUE * 2) + 1;
-
-    // We never serialize more than this much at a time (except for Strings)
-    private static final int MAX_BYTE_BUFFER = 8;
-    /**
-     * Constructs BinaryCodec from a file and set it's mode to writing or not
-     *
-     * @param file file to be written to or read from
-     * @param writing whether the file is being written to
-     * @throws FileNotFoundException
-     */
-    public BinaryCodec(final File file, final boolean writing) throws FileNotFoundException {
-        this();
-
-        this.isWriting = writing;
-        if (this.isWriting) {
-            this.outputStream = new FileOutputStream(file);
-            this.outputFileName = file.getName();
-        } else {
-            this.inputStream = new FileInputStream(file);
-            this.inputFileName = file.getName();
-        }
-    }
-
-    /**
-     * Constructs BinaryCodec from a file name and set it's mode to writing or not
-     *
-     * @param fileName name of the file to be written to or read from
-     * @param writing writing whether the file is being written to
-     * @throws FileNotFoundException
-     */
-    public BinaryCodec(final String fileName, final boolean writing) throws FileNotFoundException {
-        this(new File(fileName), writing);
-    }
-
-    /**
-     * Constructs BinaryCodec from an output stream
-     *
-     * @param outputStream Stream to write to, since it's an output stream we know that isWriting
-     *        should be set to true
-     */
-    public BinaryCodec(final OutputStream outputStream) {
-        this();
-        setOutputStream(outputStream);
-    }
-
-    /**
-     * Constructs BinaryCodec from an input stream
-     *
-     * @param inputStream Stream to read from, since we are reading isWriting is set to false
-     */
-    public BinaryCodec(final InputStream inputStream) {
-        this();
-        setInputStream(inputStream);
-    }
-
-    /**
-     * Ambiguous whether reading or writing until set{In,Out}putStream is called
-     */
-    public BinaryCodec() {
-        initByteBuffer();
-    }
-
-    /**
-     * Shared among ctors. Note that if endianness is changed, all the unsigned methods must also be
-     * changed.
-     */
-    private void initByteBuffer() {
-        byteBuffer = ByteBuffer.allocate(MAX_BYTE_BUFFER);
-        byteBuffer.order(LITTLE_ENDIAN);
-    }
-
-
-    /**
-     * Write whatever has been put into the byte buffer
-     *
-     * @param numBytes -- how much to write. Note that in case of writing an unsigned value, more
-     *        bytes were put into the ByteBuffer than will get written out.
-     * @throws IOException
-     */
-    private void writeByteBuffer(final int numBytes) throws IOException {
-        assert (numBytes <= byteBuffer.limit());
-        writeBytes(byteBuffer.array(), 0, numBytes);
-    }
-
-    /**
-     * Writes a byte to the output buffer
-     *
-     * @param bite byte array to write
-     * @throws IOException
-     */
-    public void writeByte(final byte bite) throws IOException {
-        byteBuffer.clear();
-        byteBuffer.put(bite);
-        writeByteBuffer(1);
-    }
-
-    public void writeByte(final int b) throws IOException {
-        writeByte((byte)b);
-    }
-
-    /**
-     * Writes a byte array to the output buffer
-     *
-     * @param bytes value to write
-     * @throws IOException
-     */
-    public void writeBytes(final byte[] bytes) throws IOException {
-        writeBytes(bytes, 0, bytes.length);
-    }
-
-    public void writeBytes(final byte[] bytes, final int startOffset, final int numBytes) throws IOException {
-        if (!isWriting) {
-            throw new IllegalStateException("Calling write method on BinaryCodec open for read.");
-        }
-
-        outputStream.write(bytes, startOffset, numBytes);
-    }
-
-    /**
-     * Write a 32-bit int to the output stream
-     *
-     * @param value int to write
-     * @throws IOException
-     */
-    public void writeInt(final int value) throws IOException {
-        byteBuffer.clear();
-        byteBuffer.putInt(value);
-        writeByteBuffer(4);
-    }
-
-    /**
-     * Write a double (8 bytes) to the output stream
-     *
-     * @param value double to write
-     * @throws IOException
-     */
-    public void writeDouble(final double value) throws IOException {
-        byteBuffer.clear();
-        byteBuffer.putDouble(value);
-        writeByteBuffer(8);
-    }
-
-    /**
-     * Write a 64-bit long to the output stream
-     *
-     * @param value long to write
-     * @throws IOException
-     */
-    public void writeLong(final long value) throws IOException {
-        byteBuffer.clear();
-        byteBuffer.putLong(value);
-        writeByteBuffer(8);
-    }
-
-
-    /**
-     * Write a 16-bit short to output stream
-     *
-     * @throws IOException
-     */
-    public void writeShort(final short value) throws IOException {
-        byteBuffer.clear();
-        byteBuffer.putShort(value);
-        writeByteBuffer(2);
-    }
-
-    /**
-     * Write a float (4 bytes) to the output stream
-     *
-     * @param value float to write
-     * @throws IOException
-     */
-    public void writeFloat(final float value) throws IOException {
-        byteBuffer.clear();
-        byteBuffer.putFloat(value);
-        writeByteBuffer(4);
-    }
-
-    /**
-     * Writes a boolean (1 byte) to the output buffer
-     *
-     * @param value boolean to write
-     * @throws IOException
-     */
-    public void writeBoolean(final boolean value) throws IOException {
-        byteBuffer.clear();
-        byteBuffer.put(value ? (byte)1 : (byte)0);
-        writeByteBuffer(1);
-    }
-
-    /**
-     * Writes a string to the buffer as ASCII bytes
-     *
-     * @param value string to write to buffer
-     * @param writeLength prefix the string with the length as a 32-bit int
-     * @param appendNull add a null byte to the end of the string
-     * @throws IOException
-     */
-    public void writeString(final String value, final boolean writeLength, final boolean appendNull) throws IOException {
-        if (writeLength) {
-            int lengthToWrite = value.length();
-            if (appendNull) lengthToWrite++;
-            writeInt(lengthToWrite);
-        }
-
-        // Actually writes the string to a buffer
-        writeString(value);
-
-        if (appendNull) writeBytes(NULL_BYTE);
-
-    }
-
-
-    /**
-     * Write a string to the buffer as ASCII bytes
-     *
-     * @param value string to write
-     * @throws IOException
-     */
-    private void writeString(final String value) throws IOException {
-        final byte[] byteBuffer = new byte[value.length()];
-        final char[] charBuffer = value.toCharArray();
-        for (int i = 0; i < charBuffer.length; ++i) {
-            byteBuffer[i] = (byte)(charBuffer[i] & 0xff);
-        }
-        writeBytes(byteBuffer);
-    }
-
-    /**
-     * Write an 8-bit unsigned byte. NOTE: This method will break if we change to big-endian.
-     *
-     * @throws IOException
-     */
-    public void writeUByte(final short val) throws IOException {
-        if (val < 0) {
-            throw new IllegalArgumentException("Negative value (" + val
-                + ") passed to unsigned writing method.");
-        }
-        if (val > MAX_UBYTE) {
-            throw new IllegalArgumentException("Value (" + val
-                + ") to large to be written as ubyte.");
-        }
-        byteBuffer.clear();
-        byteBuffer.putShort(val);
-        writeByteBuffer(1);
-    }
-
-    /**
-     * Write a 16-bit unsigned short. NOTE: This method will break if we change to big-endian.
-     *
-     * @throws IOException
-     */
-    public void writeUShort(final int val) throws IOException {
-        if (val < 0) {
-            throw new IllegalArgumentException("Negative value (" + val
-                + ") passed to unsigned writing method.");
-        }
-        if (val > MAX_USHORT) {
-            throw new IllegalArgumentException("Value (" + val
-                + ") to large to be written as ushort.");
-        }
-        byteBuffer.clear();
-        byteBuffer.putInt(val);
-        writeByteBuffer(2);
-    }
-
-    /**
-     * Write a 32-bit unsigned int. NOTE: This method will break if we change to big-endian.
-     *
-     * @throws IOException
-     */
-    public void writeUInt(final long val) throws IOException {
-        if (val < 0) {
-            throw new IllegalArgumentException("Negative value (" + val
-                + ") passed to unsigned writing method.");
-        }
-        if (val > MAX_UINT) {
-            throw new IllegalArgumentException("Value (" + val
-                + ") to large to be written as uint.");
-        }
-        byteBuffer.clear();
-        byteBuffer.putLong(val);
-        writeByteBuffer(4);
-    }
-
-    /**
-     * Read a byte array from the input stream.
-     *
-     * @throws IOException
-     */
-    public void readBytes(final byte[] buffer) throws IOException {
-        readBytes(buffer, 0, buffer.length);
-    }
-
-    /**
-     * Read a byte array from the input stream
-     *
-     * @param buffer where to put bytes read
-     * @param offset offset to start putting bytes into buffer
-     * @param length number of bytes to read
-     * @throws IOException
-     */
-    public void readBytes(final byte[] buffer, final int offset, final int length) throws IOException {
-        int totalNumRead = 0;
-        do {
-            final int numRead =
-                readBytesOrFewer(buffer, offset + totalNumRead, length - totalNumRead);
-            if (numRead < 0) {
-                throw new EOFException(constructErrorMessage("Premature EOF"));
-            } else {
-                totalNumRead += numRead;
-            }
-        } while (totalNumRead < length);
-    }
-
-    /**
-     * Reads a byte array from the input stream.
-     *
-     * @param buffer where to put bytes read
-     * @param offset offset to start putting bytes into buffer
-     * @param length number of bytes to read. Fewer bytes may be read if EOF is reached before
-     *        length bytes have been read.
-     * @return the total number of bytes read into the buffer, or -1 if there is no more data
-     *         because the end of the stream has been reached.
-     * @throws IOException
-     */
-    public int readBytesOrFewer(final byte[] buffer, final int offset, final int length) throws IOException {
-        if (isWriting) {
-            throw new IllegalStateException("Calling read method on BinaryCodec open for write.");
-        }
-
-        return inputStream.read(buffer, offset, length);
-    }
-
-    /**
-     * @return a single byte read from the input stream.
-     * @throws IOException
-     */
-    public byte readByte() throws IOException {
-        if (isWriting) {
-            throw new IllegalStateException("Calling read method on BinaryCodec open for write.");
-        }
-
-        final int ret = inputStream.read();
-        if (ret == -1) {
-            throw new EOFException(constructErrorMessage("Premature EOF"));
-        }
-        return (byte)ret;
-    }
-
-    /**
-     * @return true if it is possible to know for sure if at EOF, and it is known for sure. If the
-     *         input stream is a ByteArrayInputStream, this is faster than causing a
-     *         RuntimeEOFException to be thrown.
-     * @throws IOException
-     */
-    public boolean knownAtEof() throws IOException {
-        if (isWriting) {
-            throw new IllegalStateException(
-                "Calling knownAtEof method on BinaryCodec open for write.");
-        }
-
-        return inputStream instanceof ByteArrayInputStream && inputStream.available() == 0;
-    }
-
-    /**
-     * Read a string off the input stream, as ASCII bytes
-     *
-     * @param length length of string to read
-     * @return String read from stream
-     * @throws IOException
-     */
-    public String readString(final int length) throws IOException {
-        final byte[] buffer;
-        // Recycle single buffer if possible
-        if (length <= scratchBuffer.length) {
-            buffer = scratchBuffer;
-        } else {
-            buffer = new byte[length];
-
-        }
-        readBytes(buffer, 0, length);
-
-        final char[] charBuffer = new char[length];
-        for (int i = 0; i < length; ++i) {
-            charBuffer[i] = (char)buffer[i];
-        }
-        return new String(charBuffer);
-    }
-
-    /**
-     * Read ASCII bytes from the input stream until a null byte is read
-     *
-     * @return String constructed from the ASCII bytes read
-     * @throws IOException
-     */
-    public String readNullTerminatedString() throws IOException {
-        final StringBuilder ret = new StringBuilder();
-        for (byte b = this.readByte(); b != 0; b = this.readByte()) {
-            ret.append((char)(b & 0xff));
-        }
-        return ret.toString();
-    }
-
-    /**
-     * Read an int length, and then a String of that length
-     *
-     * @param devourNull if true, the length include a null terminator, which is read and discarded
-     * @throws IOException
-     */
-    public String readLengthAndString(final boolean devourNull) throws IOException {
-        int length = readInt();
-        if (devourNull) {
-            --length;
-        }
-        final String ret = readString(length);
-        if (devourNull) {
-            readByte();
-        }
-        return ret;
-    }
-
-    private void readByteBuffer(final int numBytes) throws IOException {
-        assert (numBytes <= byteBuffer.capacity());
-        readBytes(byteBuffer.array(), 0, numBytes);
-        byteBuffer.limit(byteBuffer.capacity());
-        byteBuffer.position(numBytes);
-    }
-
-    /**
-     * Read an int off the input stream
-     *
-     * @return int from input stream
-     * @throws IOException
-     */
-    public int readInt() throws IOException {
-        readByteBuffer(4);
-        byteBuffer.flip();
-        return byteBuffer.getInt();
-    }
-
-    /**
-     * Reads a double off the input stream
-     *
-     * @return double
-     * @throws IOException
-     */
-    public double readDouble() throws IOException {
-        readByteBuffer(8);
-        byteBuffer.flip();
-        return byteBuffer.getDouble();
-    }
-
-    /**
-     * Reads a long off the input stream
-     *
-     * @return long
-     * @throws IOException
-     */
-    public long readLong() throws IOException {
-        readByteBuffer(8);
-        byteBuffer.flip();
-        return byteBuffer.getLong();
-    }
-
-    public short readShort() throws IOException {
-        readByteBuffer(2);
-        byteBuffer.flip();
-        return byteBuffer.getShort();
-    }
-
-    /**
-     * Reads a float off the input stream
-     *
-     * @return float
-     * @throws IOException
-     */
-    public float readFloat() throws IOException {
-        readByteBuffer(4);
-        byteBuffer.flip();
-        return byteBuffer.getFloat();
-    }
-
-    /**
-     * Reads a boolean off the input stream, represented as a byte with value 1 or 0
-     *
-     * @return boolean
-     * @throws IOException
-     */
-    public boolean readBoolean() throws IOException {
-        return ((readByte()) == 1);
-    }
-
-    /**
-     * Reads an 8-bit unsigned byte from the input stream. This method assumes little-endianness.
-     *
-     * @throws IOException
-     */
-    public short readUByte() throws IOException {
-        readByteBuffer(1);
-        byteBuffer.put((byte)0);
-        byteBuffer.flip();
-        return byteBuffer.getShort();
-    }
-
-    /**
-     * Reads a 16-bit unsigned short from the input stream. This method assumes little-endianness.
-     *
-     * @throws IOException
-     */
-    public int readUShort() throws IOException {
-        readByteBuffer(2);
-        byteBuffer.putShort((short)0);
-        byteBuffer.flip();
-        return byteBuffer.getInt();
-    }
-
-    /**
-     * Reads a 32-bit unsigned int from the input stream. This method assumes little-endianness.
-     *
-     * @throws IOException
-     */
-    public long readUInt() throws IOException {
-        readByteBuffer(4);
-        byteBuffer.putInt(0);
-        byteBuffer.flip();
-        return byteBuffer.getLong();
-    }
-
-    /**
-     * Close the appropriate stream
-     *
-     * @throws IOException
-     */
-    public void close() throws IOException {
-        if (this.isWriting) {
-            // To the degree possible, make sure the bytes get forced to the file system,
-            // or else cause an exception to be thrown.
-            if (this.outputStream instanceof FileOutputStream) {
-                this.outputStream.flush();
-                FileOutputStream fos = (FileOutputStream)this.outputStream;
-                try {
-                    fos.getFD().sync();
-                } catch (SyncFailedException e) {
-                    // ignore
-                }
-            }
-            this.outputStream.close();
-        } else {
-            this.inputStream.close();
-        }
-    }
-
-    private String constructErrorMessage(final String msg) {
-        final StringBuilder sb = new StringBuilder(msg);
-        sb.append("; BinaryCodec in ");
-        sb.append(isWriting ? "write" : "read");
-        sb.append("mode; ");
-        final String filename = isWriting ? outputFileName : inputFileName;
-        if (filename != null) {
-            sb.append("file: ");
-            sb.append(filename);
-        } else {
-            sb.append("streamed file (filename not available)");
-        }
-        return sb.toString();
-    }
-
-    public String getInputFileName() {
-        return inputFileName;
-    }
-
-    public String getOutputFileName() {
-        return outputFileName;
-    }
-
-    public void setOutputFileName(final String outputFileName) {
-        this.outputFileName = outputFileName;
-    }
-
-    public void setInputFileName(final String inputFileName) {
-        this.inputFileName = inputFileName;
-    }
-
-    public boolean isWriting() {
-        return isWriting;
-    }
-
-    public OutputStream getOutputStream() {
-        return outputStream;
-    }
-
-    public InputStream getInputStream() {
-        return inputStream;
-    }
-
-    public void setInputStream(final InputStream is) {
-        isWriting = false;
-        this.inputStream = is;
-    }
-
-    public void setOutputStream(final OutputStream os) {
-        isWriting = true;
-        this.outputStream = os;
-    }
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BlockCompressedInputStream.java

@@ -1,709 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-import java.io.BufferedInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.EOFException;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.nio.ByteBuffer;
-import java.nio.ByteOrder;
-import java.nio.channels.SeekableByteChannel;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.StandardOpenOption;
-import java.util.Arrays;
-
-/**
- * Stream class for reading BGZF block compressed files.  The caller can treat this file like any other InputStream.
- * It probably is not necessary to wrap this stream in a buffering stream, because there is internal buffering.
- * The advantage of BGZF over conventional GZip format is that BGZF allows for seeking without having to read the
- * entire file up to the location being sought.  Note that seeking is only possible if the input stream is seekable.
- * 
- * Note that this implementation is not synchronized. If multiple threads access an instance concurrently, it must be synchronized externally. 
- *
- * @see <a href="http://samtools.sourceforge.net/SAM1.pdf">http://samtools.sourceforge.net/SAM1.pdf</a> for details of BGZF file format.
- */
-public class BlockCompressedInputStream extends InputStream {
-
-    public final static String INCORRECT_HEADER_SIZE_MSG = "Incorrect header size for file: ";
-    public final static String UNEXPECTED_BLOCK_LENGTH_MSG = "Unexpected compressed block length: ";
-    public final static String PREMATURE_END_MSG = "Premature end of file: ";
-    public final static String CANNOT_SEEK_STREAM_MSG = "Cannot seek a position for a non-file stream";
-    public final static String CANNOT_SEEK_CLOSED_STREAM_MSG = "Cannot seek a position for a closed stream";
-    public final static String INVALID_FILE_PTR_MSG = "Invalid file pointer: ";
-
-    private InputStream mStream;
-    private boolean mIsClosed = false;
-    private SeekableStream mFile;
-    private byte[] mFileBuffer = null;
-    private DecompressedBlock mCurrentBlock = null;
-    private int mCurrentOffset = 0;
-    private long mStreamOffset = 0;
-    private final BlockGunzipper blockGunzipper;
-
-    private volatile ByteArrayOutputStream buf = null;
-    private static final byte eol = '\n';
-    private static final byte eolCr = '\r';
-
-    /**
-     * Note that seek() is not supported if this ctor is used.
-     * @param stream source of bytes
-     */
-    public BlockCompressedInputStream(final InputStream stream) {
-        this(stream, true, BlockGunzipper.getDefaultInflaterFactory());
-    }
-
-    /**
-     * Note that seek() is not supported if this ctor is used.
-     * @param stream source of bytes
-     * @param inflaterFactory {@link InflaterFactory} used by {@link BlockGunzipper}
-     */
-    public BlockCompressedInputStream(final InputStream stream, final InflaterFactory inflaterFactory) {
-        this(stream, true, inflaterFactory);
-    }
-
-    /**
-     * Note that seek() is not supported if this ctor is used.
-     * @param stream source of bytes
-     * @param allowBuffering if true, allow buffering
-     */
-    public BlockCompressedInputStream(final InputStream stream, final boolean allowBuffering) {
-        this(stream, allowBuffering, BlockGunzipper.getDefaultInflaterFactory());
-    }
-
-    /**
-     * Note that seek() is not supported if this ctor is used.
-     * @param stream source of bytes
-     * @param allowBuffering if true, allow buffering
-     * @param inflaterFactory {@link InflaterFactory} used by {@link BlockGunzipper}
-     */
-    public BlockCompressedInputStream(final InputStream stream, final boolean allowBuffering, final InflaterFactory inflaterFactory) {
-        if (allowBuffering) {
-            mStream = new BufferedInputStream(stream);
-        }
-        else {
-            mStream = stream;
-        }
-
-        mFile = null;
-        blockGunzipper = new BlockGunzipper(inflaterFactory);
-    }
-
-    /**
-     * Use this ctor if you wish to call seek()
-     * @param file source of bytes
-     * @throws IOException
-     */
-    public BlockCompressedInputStream(final File file) throws IOException {
-        this(file, BlockGunzipper.getDefaultInflaterFactory());
-    }
-
-    /**
-     * Use this ctor if you wish to call seek()
-     * @param file source of bytes
-     * @param inflaterFactory {@link InflaterFactory} used by {@link BlockGunzipper}
-     * @throws IOException
-     */
-    public BlockCompressedInputStream(final File file, final InflaterFactory inflaterFactory) throws IOException {
-        mFile = new SeekableFileStream(file);
-        mStream = null;
-        blockGunzipper = new BlockGunzipper(inflaterFactory);
-    }
-
-    /**
-     * For providing some arbitrary data source.  No additional buffering is
-     * provided, so if the underlying source is not buffered, wrap it in a
-     * SeekableBufferedStream before passing to this ctor.
-     * @param strm source of bytes
-     */
-    public BlockCompressedInputStream(final SeekableStream strm) {
-        this(strm, BlockGunzipper.getDefaultInflaterFactory());
-    }
-
-    /**
-     * For providing some arbitrary data source.  No additional buffering is
-     * provided, so if the underlying source is not buffered, wrap it in a
-     * SeekableBufferedStream before passing to this ctor.
-     * @param strm source of bytes
-     * @param inflaterFactory {@link InflaterFactory} used by {@link BlockGunzipper}
-     */
-    public BlockCompressedInputStream(final SeekableStream strm, final InflaterFactory inflaterFactory) {
-        mFile = strm;
-        mStream = null;
-        blockGunzipper = new BlockGunzipper(inflaterFactory);
-    }
-
-    /**
-     * Determines whether or not the inflater will re-calculated the CRC on the decompressed data
-     * and check it against the value stored in the GZIP header.  CRC checking is an expensive
-     * operation and should be used accordingly.
-     */
-    public void setCheckCrcs(final boolean check) {
-        this.blockGunzipper.setCheckCrcs(check);
-    }
-
-    /**
-     * @return the number of bytes that can be read (or skipped over) from this input stream without blocking by the
-     * next caller of a method for this input stream. The next caller might be the same thread or another thread.
-     * Note that although the next caller can read this many bytes without blocking, the available() method call itself
-     * may block in order to fill an internal buffer if it has been exhausted.
-     */
-    @Override
-    public int available() throws IOException {
-        if (mCurrentBlock == null || mCurrentOffset == mCurrentBlock.mBlock.length) {
-            readBlock();
-        }
-        if (mCurrentBlock == null) {
-            return 0;
-        }
-        return mCurrentBlock.mBlock.length - mCurrentOffset;
-    }
-
-    /**
-     * @return <code>true</code> if the stream is at the end of a BGZF block,
-     * <code>false</code> otherwise.
-     */
-    public boolean endOfBlock() {
-        return (mCurrentBlock != null && mCurrentOffset == mCurrentBlock.mBlock.length);
-    }
-
-    /**
-     * Closes the underlying InputStream or RandomAccessFile
-     */
-    @Override
-    public void close() throws IOException {
-        if (mFile != null) {
-            mFile.close();
-            mFile = null;
-        } else if (mStream != null) {
-            mStream.close();
-            mStream = null;
-        }
-        // Encourage garbage collection
-        mFileBuffer = null;
-        mCurrentBlock = null;
-
-        // Mark as closed
-        mIsClosed = true;
-    }
-
-    /**
-     * Reads the next byte of data from the input stream. The value byte is returned as an int in the range 0 to 255.
-     * If no byte is available because the end of the stream has been reached, the value -1 is returned.
-     * This method blocks until input data is available, the end of the stream is detected, or an exception is thrown.
-
-     * @return the next byte of data, or -1 if the end of the stream is reached.
-     */
-    @Override
-    public int read() throws IOException {
-        return (available() > 0) ? (mCurrentBlock.mBlock[mCurrentOffset++] & 0xFF) : -1;
-    }
-
-    /**
-     * Reads some number of bytes from the input stream and stores them into the buffer array b. The number of bytes
-     * actually read is returned as an integer. This method blocks until input data is available, end of file is detected,
-     * or an exception is thrown.
-     *
-     * read(buf) has the same effect as read(buf, 0, buf.length).
-     *
-     * @param buffer the buffer into which the data is read.
-     * @return the total number of bytes read into the buffer, or -1 is there is no more data because the end of
-     * the stream has been reached.
-     */
-    @Override
-    public int read(final byte[] buffer) throws IOException {
-        return read(buffer, 0, buffer.length);
-    }
-
-    /**
-     * Reads a whole line. A line is considered to be terminated by either a line feed ('\n'), 
-     * carriage return ('\r') or carriage return followed by a line feed ("\r\n").
-     *
-     * @return  A String containing the contents of the line, excluding the line terminating
-     *          character, or null if the end of the stream has been reached
-     *
-     * @exception  IOException  If an I/O error occurs
-     */
-    public String readLine() throws IOException {
-        int available = available();
-        if (available == 0) {
-            return null;
-        }
-        if(null == buf){ // lazy initialisation 
-            buf = new ByteArrayOutputStream(8192);
-        }
-        buf.reset();
-        boolean done = false;
-        boolean foundCr = false; // \r found flag
-        while (!done) {
-            int linetmpPos = mCurrentOffset;
-            int bCnt = 0;
-            while((available-- > 0)){
-                final byte c = mCurrentBlock.mBlock[linetmpPos++];
-                if(c == eol){ // found \n
-                    done = true;
-                    break;
-                } else if(foundCr){  // previous char was \r
-                    --linetmpPos; // current char is not \n so put it back
-                    done = true;
-                    break;
-                } else if(c == eolCr){ // found \r
-                    foundCr = true;
-                    continue; // no ++bCnt
-                }
-                ++bCnt;
-            }
-            if(mCurrentOffset < linetmpPos) {
-                buf.write(mCurrentBlock.mBlock, mCurrentOffset, bCnt);
-                mCurrentOffset = linetmpPos;
-            }
-            available = available();
-            if(available == 0) {
-                // EOF
-                done = true;
-            }
-        }
-        return buf.toString();
-    }
-
-    /**
-     * Reads up to len bytes of data from the input stream into an array of bytes. An attempt is made to read
-     * as many as len bytes, but a smaller number may be read. The number of bytes actually read is returned as an integer.
-     *
-     * This method blocks until input data is available, end of file is detected, or an exception is thrown.
-     *
-     * @param buffer buffer into which data is read.
-     * @param offset the start offset in array b  at which the data is written.
-     * @param length the maximum number of bytes to read.
-     * @return the total number of bytes read into the buffer, or -1 if there is no more data because the end of
-     * the stream has been reached.
-     */
-    @Override
-    public int read(final byte[] buffer, int offset, int length) throws IOException {
-        final int originalLength = length;
-        while (length > 0) {
-            final int available = available();
-            if (available == 0) {
-                // Signal EOF to caller
-                if (originalLength == length) {
-                    return -1;
-                }
-                break;
-            }
-            final int copyLength = Math.min(length, available);
-            System.arraycopy(mCurrentBlock.mBlock, mCurrentOffset, buffer, offset, copyLength);
-            mCurrentOffset += copyLength;
-            offset += copyLength;
-            length -= copyLength;
-        }
-        return originalLength - length;
-    }
-
-    /**
-     * Seek to the given position in the file.  Note that pos is a special virtual file pointer,
-     * not an actual byte offset.
-     *
-     * @param pos virtual file pointer position
-     * @throws IOException if stream is closed or not a file based stream
-     */
-    public void seek(final long pos) throws IOException {
-        // Must be before the mFile == null check because mFile == null for closed files and streams
-        if (mIsClosed) {
-            throw new IOException(CANNOT_SEEK_CLOSED_STREAM_MSG);
-        }
-
-        // Cannot seek on streams that are not file based
-        if (mFile == null) {
-            throw new IOException(CANNOT_SEEK_STREAM_MSG);
-        }
-
-        // Decode virtual file pointer
-        // Upper 48 bits is the byte offset into the compressed stream of a
-        // block.
-        // Lower 16 bits is the byte offset into the uncompressed stream inside
-        // the block.
-        final long compressedOffset = BGZFFilePointerUtil.getBlockAddress(pos);
-        final int uncompressedOffset = BGZFFilePointerUtil.getBlockOffset(pos);
-        final int available;
-        if (mCurrentBlock != null && mCurrentBlock.mBlockAddress == compressedOffset) {
-            available = mCurrentBlock.mBlock.length;
-        } else {
-            prepareForSeek();
-            mFile.seek(compressedOffset);
-            mStreamOffset = compressedOffset;
-            mCurrentBlock = nextBlock(getBufferForReuse(mCurrentBlock));
-            mCurrentOffset = 0;
-            available = available();
-        }
-        if (uncompressedOffset > available || (uncompressedOffset == available && !eof())) {
-            throw new IOException(INVALID_FILE_PTR_MSG + pos + " for " + getSource());
-        }
-        mCurrentOffset = uncompressedOffset;
-    }
-    
-    /**
-     * Performs cleanup required before seek is called on the underlying stream 
-     */
-    protected void prepareForSeek() {
-    }
-
-    private boolean eof() throws IOException {
-        if (mFile.eof()) {
-            return true;
-        }
-        // If the last remaining block is the size of the EMPTY_GZIP_BLOCK, this is the same as being at EOF.
-        return (mFile.length() - (mCurrentBlock.mBlockAddress
-                + mCurrentBlock.mBlockCompressedSize) == BGZFStreamConstants.EMPTY_GZIP_BLOCK.length);
-    }
-
-    /**
-     * @return virtual file pointer that can be passed to seek() to return to the current position.  This is
-     * not an actual byte offset, so arithmetic on file pointers cannot be done to determine the distance between
-     * the two.
-     */
-    public long getFilePointer() {
-        if (mCurrentBlock == null) {
-            // Haven't read anything yet = at start of stream
-            return BGZFFilePointerUtil.makeFilePointer(0, 0);
-        }
-        if (mCurrentOffset > 0 && mCurrentOffset == mCurrentBlock.mBlock.length) {
-            // If current offset is at the end of the current block, file
-            // pointer should point
-            // to the beginning of the next block.
-            return BGZFFilePointerUtil.makeFilePointer(mCurrentBlock.mBlockAddress + mCurrentBlock.mBlockCompressedSize, 0);
-        }
-        return BGZFFilePointerUtil.makeFilePointer(mCurrentBlock.mBlockAddress, mCurrentOffset);
-    }
-
-    public long getPosition() {
-        return getFilePointer();
-    }
-
-    public static long getFileBlock(final long bgzfOffset) {
-        return BGZFFilePointerUtil.getBlockAddress(bgzfOffset);
-    }
-    
-    /**
-     * @param stream Must be at start of file.  Throws RuntimeException if !stream.markSupported().
-     * @return true if the given file looks like a valid BGZF file.
-     */
-    public static boolean isValidFile(final InputStream stream) throws IOException {
-        if (!stream.markSupported()) {
-            throw new RuntimeException("Cannot test non-buffered stream");
-        }
-        stream.mark(BGZFStreamConstants.BLOCK_HEADER_LENGTH);
-        final byte[] buffer = new byte[BGZFStreamConstants.BLOCK_HEADER_LENGTH];
-        final int count = readBytes(stream, buffer, 0, BGZFStreamConstants.BLOCK_HEADER_LENGTH);
-        stream.reset();
-        return count == BGZFStreamConstants.BLOCK_HEADER_LENGTH && isValidBlockHeader(buffer);
-    }
-
-    private static boolean isValidBlockHeader(final byte[] buffer) {
-        return (buffer[0] == BGZFStreamConstants.GZIP_ID1 &&
-                (buffer[1] & 0xFF) == BGZFStreamConstants.GZIP_ID2 &&
-                (buffer[3] & BGZFStreamConstants.GZIP_FLG) != 0 &&
-                buffer[10] == BGZFStreamConstants.GZIP_XLEN &&
-                buffer[12] == BGZFStreamConstants.BGZF_ID1 &&
-                buffer[13] == BGZFStreamConstants.BGZF_ID2);
-    }
-
-    private void readBlock() throws IOException {
-        mCurrentBlock = nextBlock(getBufferForReuse(mCurrentBlock));
-        mCurrentOffset = 0;
-        checkAndRethrowDecompressionException();
-    }
-    /**
-     * Reads and decompresses the next block
-     * @param bufferAvailableForReuse decompression buffer available for reuse
-     * @return next block in the decompressed stream
-     */
-    protected DecompressedBlock nextBlock(byte[] bufferAvailableForReuse) {
-        return processNextBlock(bufferAvailableForReuse);
-    }
-    /**
-     * Rethrows an exception encountered during decompression
-     * @throws IOException
-     */
-    private void checkAndRethrowDecompressionException() throws IOException {
-        if (mCurrentBlock.mException != null) {
-            if (mCurrentBlock.mException instanceof IOException) {
-                throw (IOException) mCurrentBlock.mException;
-            } else if (mCurrentBlock.mException instanceof RuntimeException) {
-                throw (RuntimeException) mCurrentBlock.mException;
-            } else {
-                throw new RuntimeException(mCurrentBlock.mException);
-            }
-        }
-    }
-    
-    /**
-     * Attempt to reuse the buffer of the given block 
-     * @param block owning block
-     * @return null decompressing buffer to reuse, null if no buffer is available
-     */
-    private byte[] getBufferForReuse(DecompressedBlock block) {
-        if (block == null) return null;
-        return block.mBlock;
-    }
-    
-    /**
-     * Decompress the next block from the input stream. When using asynchronous 
-     * IO, this will be called by the background thread.
-     * @param bufferAvailableForReuse buffer in which to place decompressed block. A null or
-     *  incorrectly sized buffer will result in the buffer being ignored and
-     *  a new buffer allocated for decompression.
-     * @return next block in input stream
-     */
-    protected DecompressedBlock processNextBlock(byte[] bufferAvailableForReuse) {
-        if (mFileBuffer == null) {
-            mFileBuffer = new byte[BGZFStreamConstants.MAX_COMPRESSED_BLOCK_SIZE];
-        }
-        long blockAddress = mStreamOffset;
-        try {
-            final int headerByteCount = readBytes(mFileBuffer, 0, BGZFStreamConstants.BLOCK_HEADER_LENGTH);
-            mStreamOffset += headerByteCount;
-            if (headerByteCount == 0) {
-                // Handle case where there is no empty gzip block at end.
-                return new DecompressedBlock(blockAddress, new byte[0], 0);
-            }
-            if (headerByteCount != BGZFStreamConstants.BLOCK_HEADER_LENGTH) {
-                return new DecompressedBlock(blockAddress, headerByteCount, new IOException(INCORRECT_HEADER_SIZE_MSG + getSource()));
-            }
-            final int blockLength = unpackInt16(mFileBuffer, BGZFStreamConstants.BLOCK_LENGTH_OFFSET) + 1;
-            if (blockLength < BGZFStreamConstants.BLOCK_HEADER_LENGTH || blockLength > mFileBuffer.length) {
-                return new DecompressedBlock(blockAddress, blockLength,
-                        new IOException(UNEXPECTED_BLOCK_LENGTH_MSG + blockLength + " for " + getSource()));
-            }
-            final int remaining = blockLength - BGZFStreamConstants.BLOCK_HEADER_LENGTH;
-            final int dataByteCount = readBytes(mFileBuffer, BGZFStreamConstants.BLOCK_HEADER_LENGTH,
-                    remaining);
-            mStreamOffset += dataByteCount;
-            if (dataByteCount != remaining) {
-                return new DecompressedBlock(blockAddress, blockLength,
-                        new BGZFException(PREMATURE_END_MSG + getSource()));
-            }
-            final byte[] decompressed = inflateBlock(mFileBuffer, blockLength, bufferAvailableForReuse);
-            return new DecompressedBlock(blockAddress, decompressed, blockLength);
-        } catch (IOException e) {
-            return new DecompressedBlock(blockAddress, 0, e);
-        }
-    }
-
-    private byte[] inflateBlock(final byte[] compressedBlock, final int compressedLength,
-            final byte[] bufferAvailableForReuse) throws IOException {
-        final int uncompressedLength = unpackInt32(compressedBlock, compressedLength - 4);
-        if (uncompressedLength < 0) {
-            throw new BGZFException(getSource() + " has invalid uncompressedLength: " + uncompressedLength);
-        }
-        byte[] buffer = bufferAvailableForReuse;
-        if (buffer == null || uncompressedLength != buffer.length) {
-        	// can't reuse the buffer since the size is incorrect
-            buffer = new byte[uncompressedLength];
-        }
-        blockGunzipper.unzipBlock(buffer, compressedBlock, compressedLength);
-        return buffer;
-    }
-
-    private String getSource() {
-        return mFile == null ? "data stream" : mFile.getSource();
-    }
-
-    private int readBytes(final byte[] buffer, final int offset, final int length) throws IOException {
-        if (mFile != null) {
-            return readBytes(mFile, buffer, offset, length);
-        } else if (mStream != null) {
-            return readBytes(mStream, buffer, offset, length);
-        } else {
-            return 0;
-        }
-    }
-
-    private static int readBytes(final SeekableStream file, final byte[] buffer, final int offset, final int length) throws IOException {
-        int bytesRead = 0;
-        while (bytesRead < length) {
-            final int count = file.read(buffer, offset + bytesRead, length - bytesRead);
-            if (count <= 0) {
-                break;
-            }
-            bytesRead += count;
-        }
-        return bytesRead;
-    }
-
-    private static int readBytes(final InputStream stream, final byte[] buffer, final int offset, final int length) throws IOException {
-        int bytesRead = 0;
-        while (bytesRead < length) {
-            final int count = stream.read(buffer, offset + bytesRead, length - bytesRead);
-            if (count <= 0) {
-                break;
-            }
-            bytesRead += count;
-        }
-        return bytesRead;
-    }
-
-    private int unpackInt16(final byte[] buffer, final int offset) {
-        return ((buffer[offset] & 0xFF) |
-                ((buffer[offset+1] & 0xFF) << 8));
-    }
-
-    private int unpackInt32(final byte[] buffer, final int offset) {
-        return ((buffer[offset] & 0xFF) |
-                ((buffer[offset+1] & 0xFF) << 8) |
-                ((buffer[offset+2] & 0xFF) << 16) |
-                ((buffer[offset+3] & 0xFF) << 24));
-    }
-
-    public enum FileTermination {HAS_TERMINATOR_BLOCK, HAS_HEALTHY_LAST_BLOCK, DEFECTIVE}
-
-    /**
-     *
-     * @param file the file to check
-     * @return status of the last compressed block
-     * @throws IOException
-     */
-    public static FileTermination checkTermination(final File file) throws IOException {
-        return checkTermination(file.toPath());
-    }
-
-    /**
-     *
-     * @param path to the file to check
-     * @return status of the last compressed block
-     * @throws IOException
-     */
-    public static FileTermination checkTermination(final Path path) throws IOException {
-        try( final SeekableByteChannel channel = Files.newByteChannel(path, StandardOpenOption.READ) ){
-            return checkTermination(channel);
-        }
-    }
-
-    /**
-     * check the status of the final bzgipped block for the given bgzipped resource
-     *
-     * @param channel an open channel to read from,
-     * the channel will remain open and the initial position will be restored when the operation completes
-     * this makes no guarantee about the state of the channel if an exception is thrown during reading
-     *
-     * @return the status of the last compressed black
-     * @throws IOException
-     */
-    public static FileTermination checkTermination(SeekableByteChannel channel) throws IOException {
-        final long fileSize = channel.size();
-        if (fileSize < BGZFStreamConstants.EMPTY_GZIP_BLOCK.length) {
-            return FileTermination.DEFECTIVE;
-        }
-        final long initialPosition = channel.position();
-        boolean exceptionThrown = false;
-        try {
-            channel.position(fileSize - BGZFStreamConstants.EMPTY_GZIP_BLOCK.length);
-
-            //Check if the end of the file is an empty gzip block which is used as the terminator for a bgzipped file
-            final ByteBuffer lastBlockBuffer = ByteBuffer.allocate(BGZFStreamConstants.EMPTY_GZIP_BLOCK.length);
-            readFully(channel, lastBlockBuffer);
-            if (Arrays.equals(lastBlockBuffer.array(), BGZFStreamConstants.EMPTY_GZIP_BLOCK)) {
-                return FileTermination.HAS_TERMINATOR_BLOCK;
-            }
-
-            //if the last block isn't an empty gzip block, check to see if it is a healthy compressed block or if it's corrupted
-            final int bufsize = (int) Math.min(fileSize, BGZFStreamConstants.MAX_COMPRESSED_BLOCK_SIZE);
-            final byte[] bufferArray = new byte[bufsize];
-            channel.position(fileSize - bufsize);
-            readFully(channel, ByteBuffer.wrap(bufferArray));
-            for (int i = bufferArray.length - BGZFStreamConstants.EMPTY_GZIP_BLOCK.length;
-                 i >= 0; --i) {
-                if (!preambleEqual(BGZFStreamConstants.GZIP_BLOCK_PREAMBLE,
-                                   bufferArray, i, BGZFStreamConstants.GZIP_BLOCK_PREAMBLE.length)) {
-                    continue;
-                }
-                final ByteBuffer byteBuffer = ByteBuffer.wrap(bufferArray,
-                                                              i + BGZFStreamConstants.GZIP_BLOCK_PREAMBLE.length,
-                                                              4);
-                byteBuffer.order(ByteOrder.LITTLE_ENDIAN);
-                final int totalBlockSizeMinusOne = byteBuffer.getShort() & 0xFFFF;
-                if (bufferArray.length - i == totalBlockSizeMinusOne + 1) {
-                    return FileTermination.HAS_HEALTHY_LAST_BLOCK;
-                } else {
-                    return FileTermination.DEFECTIVE;
-                }
-            }
-            return FileTermination.DEFECTIVE;
-        } catch (final Throwable e) {
-            exceptionThrown = true;
-            throw e;
-        } finally {
-            //if an exception was thrown we don't want to reset the position because that would be likely to throw again
-            //and suppress the initial exception
-            if(!exceptionThrown) {
-                channel.position(initialPosition);
-            }
-        }
-    }
-
-    /**
-     * read as many bytes as dst's capacity into dst or throw if that's not possible
-     *
-     * @throws EOFException if channel has fewer bytes available than dst's capacity
-     */
-    static void readFully(SeekableByteChannel channel, ByteBuffer dst) throws IOException {
-        int totalBytesRead = 0;
-        final int capacity = dst.capacity();
-        while (totalBytesRead < capacity) {
-            final int bytesRead = channel.read(dst);
-            if (bytesRead == -1) {
-                throw new EOFException();
-            }
-            totalBytesRead += bytesRead;
-        }
-    }
-
-    public static void assertNonDefectiveFile(final File file) throws IOException {
-        if (checkTermination(file) == FileTermination.DEFECTIVE) {
-            throw new BGZFException(file.getAbsolutePath() + " does not have a valid GZIP block at the end of the file.");
-        }
-    }
-
-    private static boolean preambleEqual(final byte[] preamble, final byte[] buf, final int startOffset, final int length) {
-        for (int i = 0; i < length; ++i) {
-            if (preamble[i] != buf[i + startOffset]) {
-                return false;
-            }
-        }
-        return true;
-    }
-
-    protected static class DecompressedBlock {
-        /**
-         * Decompressed block
-         */
-        private final byte[] mBlock;
-        /**
-         * Compressed size of block (the uncompressed size can be found using
-         * mBlock.length)
-         */
-        private final int mBlockCompressedSize;
-        /**
-         * Stream offset of start of block
-         */
-        private final long mBlockAddress;
-        /**
-         * Exception thrown (if any) when attempting to decompress block
-         */
-        private final Exception mException;
-
-        public DecompressedBlock(long blockAddress, byte[] block, int compressedSize) {
-            mBlock = block;
-            mBlockAddress = blockAddress;
-            mBlockCompressedSize = compressedSize;
-            mException = null;
-        }
-
-        public DecompressedBlock(long blockAddress, int compressedSize, Exception exception) {
-            mBlock = new byte[0];
-            mBlockAddress = blockAddress;
-            mBlockCompressedSize = compressedSize;
-            mException = exception;
-        }
-    }
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BlockCompressedOutputStream.java

@@ -1,358 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.zip.CRC32;
-import java.util.zip.Deflater;
-
-/**
- * Stream class for a file that is a series of gzip blocks (BGZF format). The caller just treats it as an
- * OutputStream, and under the covers a gzip block is written when the amount of uncompressed as-yet-unwritten
- * bytes reaches a threshold.
- *
- * The advantage of BGZF over conventional gzip is that BGZF allows for seeking without having to scan through
- * the entire file up to the position being sought.
- *
- * Note that the flush() method should not be called by client
- * unless you know what you're doing, because it forces a gzip block to be written even if the
- * number of buffered bytes has not reached threshold.  close(), on the other hand, must be called
- * when done writing in order to force the last gzip block to be written.
- *
- * @see <a href="http://samtools.sourceforge.net/SAM1.pdf">http://samtools.sourceforge.net/SAM1.pdf</a> for details of BGZF file format.
- */
-public class BlockCompressedOutputStream extends OutputStream {
-
-    private static int defaultCompressionLevel = BGZFStreamConstants.DEFAULT_COMPRESSION_LEVEL;
-    private static DeflaterFactory defaultDeflaterFactory = new DeflaterFactory();
-
-    public static void setDefaultCompressionLevel(final int compressionLevel) {
-        if (compressionLevel < Deflater.NO_COMPRESSION || compressionLevel > Deflater.BEST_COMPRESSION) {
-            throw new IllegalArgumentException("Invalid compression level: " + compressionLevel);
-        }
-        defaultCompressionLevel = compressionLevel;
-    }
-
-    public static int getDefaultCompressionLevel() {
-        return defaultCompressionLevel;
-    }
-
-    /**
-     * Sets the default {@link DeflaterFactory} that will be used for all instances unless specified otherwise in the constructor.
-     * If this method is not called the default is a factory that will create the JDK {@link Deflater}.
-     * @param deflaterFactory non-null default factory.
-     */
-    public static void setDefaultDeflaterFactory(final DeflaterFactory deflaterFactory) {
-        if (deflaterFactory == null) {
-            throw new IllegalArgumentException("null deflaterFactory");
-        }
-        defaultDeflaterFactory = deflaterFactory;
-    }
-
-    public static DeflaterFactory getDefaultDeflaterFactory() {
-        return defaultDeflaterFactory;
-    }
-
-    private final BinaryCodec codec;
-    private final byte[] uncompressedBuffer = new byte[BGZFStreamConstants.DEFAULT_UNCOMPRESSED_BLOCK_SIZE];
-    private int numUncompressedBytes = 0;
-    private final byte[] compressedBuffer =
-            new byte[BGZFStreamConstants.MAX_COMPRESSED_BLOCK_SIZE -
-                    BGZFStreamConstants.BLOCK_HEADER_LENGTH];
-    private final Deflater deflater;
-
-    // A second deflater is created for the very unlikely case where the regular deflation actually makes
-    // things bigger, and the compressed block is too big.  It should be possible to downshift the
-    // primary deflater to NO_COMPRESSION level, recompress, and then restore it to its original setting,
-    // but in practice that doesn't work.
-    // The motivation for deflating at NO_COMPRESSION level is that it will predictably produce compressed
-    // output that is 10 bytes larger than the input, and the threshold at which a block is generated is such that
-    // the size of tbe final gzip block will always be <= 64K.  This is preferred over the previous method,
-    // which would attempt to compress up to 64K bytes, and if the resulting compressed block was too large,
-    // try compressing fewer input bytes (aka "downshifting').  The problem with downshifting is that
-    // getFilePointer might return an inaccurate value.
-    // I assume (AW 29-Oct-2013) that there is no value in using hardware-assisted deflater for no-compression mode,
-    // so just use JDK standard.
-    private final Deflater noCompressionDeflater = new Deflater(Deflater.NO_COMPRESSION, true);
-    private final CRC32 crc32 = new CRC32();
-    private Path file = null;
-    private long mBlockAddress = 0;
-
-    /**
-     * Uses default compression level, which is 5 unless changed by setCompressionLevel
-     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
-     * Use {@link #BlockCompressedOutputStream(File, int, DeflaterFactory)} to specify a custom factory.
-     */
-    public BlockCompressedOutputStream(final String filename) throws FileNotFoundException {
-        this(filename, defaultCompressionLevel);
-    }
-
-    /**
-     * Uses default compression level, which is 5 unless changed by setCompressionLevel
-     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
-     * Use {@link #BlockCompressedOutputStream(File, int, DeflaterFactory)} to specify a custom factory.
-     */
-    public BlockCompressedOutputStream(final File file) throws FileNotFoundException {
-        this(file, defaultCompressionLevel);
-    }
-
-    public BlockCompressedOutputStream(final String filename, final int compressionLevel) throws FileNotFoundException {
-        this(new File(filename), compressionLevel);
-    }
-
-    public BlockCompressedOutputStream(final File file, final int compressionLevel) throws FileNotFoundException {
-        this(file, compressionLevel, defaultDeflaterFactory);
-    }
-
-    public BlockCompressedOutputStream(final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) throws FileNotFoundException {
-        this.file = file.toPath();
-        codec = new BinaryCodec(file, true);
-        deflater = deflaterFactory.makeDeflater(compressionLevel, true);
-    }
-
-    /**
-     * Uses default compression level, which is 5 unless changed by setCompressionLevel
-     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
-     * Use {@link #BlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory)} to specify a custom factory.
-     */
-    public BlockCompressedOutputStream(final OutputStream os) {
-        this(os, (File)null, defaultCompressionLevel);
-    }
-
-    /**
-     * Uses default compression level, which is 5 unless changed by setCompressionLevel
-     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
-     * Use {@link #BlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory)} to specify a custom factory.
-     *
-     * @param file may be null
-     */
-    public BlockCompressedOutputStream(final OutputStream os, final Path file) {
-        this(os, file, defaultCompressionLevel);
-    }
-
-    /**
-     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
-     * Use {@link #BlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory)} to specify a custom factory.
-     */
-    public BlockCompressedOutputStream(final OutputStream os, final File file, final int compressionLevel) {
-        this(os, file, compressionLevel, defaultDeflaterFactory);
-    }
-
-    /**
-     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
-     * Use {@link #BlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory)} to specify a custom factory.
-     */
-    public BlockCompressedOutputStream(final OutputStream os, final Path file, final int compressionLevel) {
-        this(os, file, compressionLevel, defaultDeflaterFactory);
-    }
-
-    /**
-     * Creates the output stream.
-     * @param os output stream to create a BlockCompressedOutputStream from
-     * @param file file to which to write the output or null if not available
-     * @param compressionLevel the compression level (0-9)
-     * @param deflaterFactory custom factory to create deflaters (overrides the default)
-     */
-    public BlockCompressedOutputStream(final OutputStream os, final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) {
-        this(os, file != null ? file.toPath() : null, compressionLevel, deflaterFactory);
-    }
-
-    /**
-     * Creates the output stream.
-     * @param os output stream to create a BlockCompressedOutputStream from
-     * @param file file to which to write the output or null if not available
-     * @param compressionLevel the compression level (0-9)
-     * @param deflaterFactory custom factory to create deflaters (overrides the default)
-     */
-    public BlockCompressedOutputStream(final OutputStream os, final Path file, final int compressionLevel, final DeflaterFactory deflaterFactory) {
-        this.file = file;
-        codec = new BinaryCodec(os);
-        if (file != null) {
-            codec.setOutputFileName(file.toAbsolutePath().toUri().toString());
-        }
-        deflater = deflaterFactory.makeDeflater(compressionLevel, true);
-    }
-
-    /**
-     * @param output May or not already be a BlockCompressedOutputStream.
-     * @return A BlockCompressedOutputStream, either by wrapping the given OutputStream, or by casting if it already
-     *         is a BCOS.
-     */
-    public static BlockCompressedOutputStream maybeBgzfWrapOutputStream(OutputStream output) {
-        if (!(output instanceof BlockCompressedOutputStream)) {
-           return new BlockCompressedOutputStream(output);
-        } else {
-           return (BlockCompressedOutputStream)output;
-        }
-    }
-
-    /**
-     * Writes b.length bytes from the specified byte array to this output stream. The general contract for write(b)
-     * is that it should have exactly the same effect as the call write(b, 0, b.length).
-     * @param bytes the data
-     */
-    @Override
-    public void write(final byte[] bytes) throws IOException {
-        write(bytes, 0, bytes.length);
-    }
-
-    /**
-     * Writes len bytes from the specified byte array starting at offset off to this output stream. The general
-     * contract for write(b, off, len) is that some of the bytes in the array b are written to the output stream in order;
-     * element b[off] is the first byte written and b[off+len-1] is the last byte written by this operation.
-     *
-     * @param bytes the data
-     * @param startIndex the start offset in the data
-     * @param numBytes the number of bytes to write
-     */
-    @Override
-    public void write(final byte[] bytes, int startIndex, int numBytes) throws IOException {
-        while (numBytes > 0) {
-            final int bytesToWrite = Math.min(uncompressedBuffer.length - numUncompressedBytes, numBytes);
-            System.arraycopy(bytes, startIndex, uncompressedBuffer, numUncompressedBytes, bytesToWrite);
-            numUncompressedBytes += bytesToWrite;
-            startIndex += bytesToWrite;
-            numBytes -= bytesToWrite;
-            if (numUncompressedBytes == uncompressedBuffer.length) {
-                deflateBlock();
-            }
-        }
-    }
-
-    @Override
-    public void write(final int b) throws IOException {
-        uncompressedBuffer[numUncompressedBytes++] = (byte) b;
-        if (numUncompressedBytes == uncompressedBuffer.length) deflateBlock();
-    }
-
-    /**
-     * WARNING: flush() affects the output format, because it causes the current contents of uncompressedBuffer
-     * to be compressed and written, even if it isn't full.  Unless you know what you're doing, don't call flush().
-     * Instead, call close(), which will flush any unwritten data before closing the underlying stream.
-     *
-     */
-    @Override
-    public void flush() throws IOException {
-        while (numUncompressedBytes > 0) {
-            deflateBlock();
-        }
-        codec.getOutputStream().flush();
-    }
-
-    /**
-     * close() must be called in order to flush any remaining buffered bytes.  An unclosed file will likely be
-     * defective.
-     *
-     */
-    @Override
-    public void close() throws IOException {
-        close(true);
-    }
-
-    public void close(final boolean writeTerminatorBlock) throws IOException {
-        flush();
-        // For debugging...
-        // if (numberOfThrottleBacks > 0) {
-        //     System.err.println("In BlockCompressedOutputStream, had to throttle back " + numberOfThrottleBacks +
-        //                        " times for file " + codec.getOutputFileName());
-        // }
-        if (writeTerminatorBlock) {
-            codec.writeBytes(BGZFStreamConstants.EMPTY_GZIP_BLOCK);
-        }
-        codec.close();
-
-        // If a terminator block was written, ensure that it's there and valid
-        if (writeTerminatorBlock) {
-            // Can't re-open something that is not a regular file, e.g. a named pipe or an output stream
-            if (this.file == null || !Files.isRegularFile(this.file)) return;
-            if (BlockCompressedInputStream.checkTermination(this.file) !=
-                    BlockCompressedInputStream.FileTermination.HAS_TERMINATOR_BLOCK) {
-                throw new IOException("Terminator block not found after closing BGZF file " + this.file);
-            }
-        }
-    }
-
-    /** Encode virtual file pointer
-     * Upper 48 bits is the byte offset into the compressed stream of a block.
-     * Lower 16 bits is the byte offset into the uncompressed stream inside the block.
-     */
-    public long getFilePointer(){
-        return BGZFFilePointerUtil.makeFilePointer(mBlockAddress, numUncompressedBytes);
-    }
-
-    public long getPosition() {
-        return getFilePointer();
-    }
-
-    /**
-     * Attempt to write the data in uncompressedBuffer to the underlying file in a gzip block.
-     * If the entire uncompressedBuffer does not fit in the maximum allowed size, reduce the amount
-     * of data to be compressed, and slide the excess down in uncompressedBuffer so it can be picked
-     * up in the next deflate event.
-     * @return size of gzip block that was written.
-     */
-    private int deflateBlock() throws IOException {
-        if (numUncompressedBytes == 0) {
-            return 0;
-        }
-        final int bytesToCompress = numUncompressedBytes;
-        // Compress the input
-        deflater.reset();
-        deflater.setInput(uncompressedBuffer, 0, bytesToCompress);
-        deflater.finish();
-        int compressedSize = deflater.deflate(compressedBuffer, 0, compressedBuffer.length);
-
-        // If it didn't all fit in compressedBuffer.length, set compression level to NO_COMPRESSION
-        // and try again.  This should always fit.
-        if (!deflater.finished()) {
-            noCompressionDeflater.reset();
-            noCompressionDeflater.setInput(uncompressedBuffer, 0, bytesToCompress);
-            noCompressionDeflater.finish();
-            compressedSize = noCompressionDeflater.deflate(compressedBuffer, 0, compressedBuffer.length);
-            if (!noCompressionDeflater.finished()) {
-                throw new IllegalStateException("unpossible");
-            }
-        }
-        // Data compressed small enough, so write it out.
-        crc32.reset();
-        crc32.update(uncompressedBuffer, 0, bytesToCompress);
-
-        final int totalBlockSize = writeGzipBlock(compressedSize, bytesToCompress, crc32.getValue());
-
-        // Clear out from uncompressedBuffer the data that was written
-        numUncompressedBytes = 0;
-        mBlockAddress += totalBlockSize;
-        return totalBlockSize;
-    }
-
-    /**
-     * Writes the entire gzip block, assuming the compressed data is stored in compressedBuffer
-     * @return  size of gzip block that was written.
-     */
-    private int writeGzipBlock(final int compressedSize, final int uncompressedSize, final long crc) throws IOException {
-        // Init gzip header
-        codec.writeByte(BGZFStreamConstants.GZIP_ID1);
-        codec.writeByte(BGZFStreamConstants.GZIP_ID2);
-        codec.writeByte(BGZFStreamConstants.GZIP_CM_DEFLATE);
-        codec.writeByte(BGZFStreamConstants.GZIP_FLG);
-        codec.writeInt(0); // Modification time
-        codec.writeByte(BGZFStreamConstants.GZIP_XFL);
-        codec.writeByte(BGZFStreamConstants.GZIP_OS_UNKNOWN);
-        codec.writeShort(BGZFStreamConstants.GZIP_XLEN);
-        codec.writeByte(BGZFStreamConstants.BGZF_ID1);
-        codec.writeByte(BGZFStreamConstants.BGZF_ID2);
-        codec.writeShort(BGZFStreamConstants.BGZF_LEN);
-        final int totalBlockSize = compressedSize + BGZFStreamConstants.BLOCK_HEADER_LENGTH +
-                BGZFStreamConstants.BLOCK_FOOTER_LENGTH;
-
-        // I don't know why we store block size - 1, but that is what the spec says
-        codec.writeShort((short)(totalBlockSize - 1));
-        codec.writeBytes(compressedBuffer, 0, compressedSize);
-        codec.writeInt((int)crc);
-        codec.writeInt(uncompressedSize);
-        return totalBlockSize;
-    }
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BlockGunzipper.java

@@ -1,114 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-import java.nio.ByteBuffer;
-import java.nio.ByteOrder;
-import java.util.zip.CRC32;
-import java.util.zip.DataFormatException;
-import java.util.zip.Inflater;
-
-/**
- * For decompressing GZIP blocks that are already loaded into a byte[].
- * The main advantage is that this object can be used over and over again to decompress many blocks,
- * whereas a new GZIPInputStream and ByteArrayInputStream would otherwise need to be created for each
- * block to be decompressed.
- *
- * This code requires that the GZIP header conform to the GZIP blocks written to BAM files, with
- * a specific subfield and no other optional stuff.
- */
-public class BlockGunzipper {
-    private static InflaterFactory defaultInflaterFactory = new InflaterFactory();
-    private final Inflater inflater;
-    private final CRC32 crc32 = new CRC32();
-    private boolean checkCrcs = false;
-    BlockGunzipper() {
-        inflater = defaultInflaterFactory.makeInflater(true); // GZIP mode
-    }
-
-    /**
-     * Create a BlockGunzipper using the provided inflaterFactory
-     * @param inflaterFactory
-     */
-    BlockGunzipper(InflaterFactory inflaterFactory) {
-        inflater = inflaterFactory.makeInflater(true); // GZIP mode
-    }
-
-    /**
-     * Sets the default {@link InflaterFactory} that will be used for all instances unless specified otherwise in the constructor.
-     * If this method is not called the default is a factory that will create the JDK {@link Inflater}.
-     * @param inflaterFactory non-null default factory.
-     */
-    public static void setDefaultInflaterFactory(final InflaterFactory inflaterFactory) {
-        if (inflaterFactory == null) {
-            throw new IllegalArgumentException("null inflaterFactory");
-        }
-        defaultInflaterFactory = inflaterFactory;
-    }
-
-    public static InflaterFactory getDefaultInflaterFactory() {
-        return defaultInflaterFactory;
-    }
-    /** Allows the caller to decide whether or not to check CRCs on when uncompressing blocks. */
-    public void setCheckCrcs(final boolean check) {
-        this.checkCrcs = check;
-    }
-
-    /**
-     * Decompress GZIP-compressed data
-     * @param uncompressedBlock must be big enough to hold decompressed output.
-     * @param compressedBlock compressed data starting at offset 0
-     * @param compressedLength size of compressed data, possibly less than the size of the buffer.
-     */
-    void unzipBlock(byte[] uncompressedBlock, byte[] compressedBlock, int compressedLength) {
-        try {
-            ByteBuffer byteBuffer = ByteBuffer.wrap(compressedBlock, 0, compressedLength);
-            byteBuffer.order(ByteOrder.LITTLE_ENDIAN);
-
-            // Validate GZIP header
-            if (byteBuffer.get() != BGZFStreamConstants.GZIP_ID1 ||
-                    byteBuffer.get() != (byte)BGZFStreamConstants.GZIP_ID2 ||
-                    byteBuffer.get() != BGZFStreamConstants.GZIP_CM_DEFLATE ||
-                    byteBuffer.get() != BGZFStreamConstants.GZIP_FLG
-                    ) {
-                throw new BGZFFormatException("Invalid GZIP header");
-            }
-            // Skip MTIME, XFL, OS fields
-            byteBuffer.position(byteBuffer.position() + 6);
-            if (byteBuffer.getShort() != BGZFStreamConstants.GZIP_XLEN) {
-                throw new BGZFFormatException("Invalid GZIP header");
-            }
-            // Skip blocksize subfield intro
-            byteBuffer.position(byteBuffer.position() + 4);
-            // Read ushort
-            final int totalBlockSize = (byteBuffer.getShort() & 0xffff) + 1;
-            if (totalBlockSize != compressedLength) {
-                throw new BGZFFormatException("GZIP blocksize disagreement");
-            }
-
-            // Read expected size and CRD from end of GZIP block
-            final int deflatedSize = compressedLength - BGZFStreamConstants.BLOCK_HEADER_LENGTH - BGZFStreamConstants.BLOCK_FOOTER_LENGTH;
-            byteBuffer.position(byteBuffer.position() + deflatedSize);
-            int expectedCrc = byteBuffer.getInt();
-            int uncompressedSize = byteBuffer.getInt();
-            inflater.reset();
-
-            // Decompress
-            inflater.setInput(compressedBlock, BGZFStreamConstants.BLOCK_HEADER_LENGTH, deflatedSize);
-            final int inflatedBytes = inflater.inflate(uncompressedBlock, 0, uncompressedSize);
-            if (inflatedBytes != uncompressedSize) {
-                throw new BGZFFormatException("Did not inflate expected amount");
-            }
-
-            // Validate CRC if so desired
-            if (this.checkCrcs) {
-                crc32.reset();
-                crc32.update(uncompressedBlock, 0, uncompressedSize);
-                final long crc = crc32.getValue();
-                if ((int)crc != expectedCrc) {
-                    throw new BGZFFormatException("CRC mismatch");
-                }
-            }
-        } catch (DataFormatException e) {
-            throw new BGZFException(e);
-        }
-    }
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/DeflaterFactory.java

@@ -1,24 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-import java.util.zip.Deflater;
-
-/**
- * Factory for {@link Deflater} objects used by {@link BlockCompressedOutputStream}.
- * This class may be extended to provide alternative deflaters (e.g., for improved performance).
- */
-public class DeflaterFactory {
-
-    public DeflaterFactory() {
-        //Note: made explicit constructor to make searching for references easier
-    }
-
-    /**
-     * Returns a deflater object that will be used when writing BAM files.
-     * Subclasses may override to provide their own deflater implementation.
-     * @param compressionLevel the compression level (0-9)
-     * @param gzipCompatible if true then use GZIP compatible compression
-     */
-    public Deflater makeDeflater(final int compressionLevel, final boolean gzipCompatible) {
-        return new Deflater(compressionLevel, gzipCompatible);
-    }
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/InflaterFactory.java

@@ -1,20 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-import java.util.zip.Inflater;
-
-/**
- * Factory for {@link Inflater} objects used by {@link BlockGunzipper}.
- * This class may be extended to provide alternative inflaters (e.g., for improved performance).
- * The default implementation returns a JDK {@link Inflater}
- */
-public class InflaterFactory {
-    /**
-     * Returns an inflater object that will be used when reading DEFLATE compressed files.
-     * Subclasses may override to provide their own inflater implementation.
-     * The default implementation returns a JDK {@link Inflater}
-     * @param gzipCompatible if true then use GZIP compatible compression
-     */
-    public Inflater makeInflater(final boolean gzipCompatible) {
-        return new Inflater(gzipCompatible);
-    }
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/SeekableBufferedStream.java

@@ -1,105 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-import java.io.BufferedInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-
-/**
- * A wrapper class to provide buffered read access to a SeekableStream.  Just wrapping such a stream with
- * a BufferedInputStream will not work as it does not support seeking.  In this implementation a
- * seek call is delegated to the wrapped stream, and the buffer reset.
- */
-public class SeekableBufferedStream extends SeekableStream {
-
-    /** Little extension to buffered input stream to give access to the available bytes in the buffer. */
-    private static class ExtBufferedInputStream extends BufferedInputStream {
-        private ExtBufferedInputStream(final InputStream inputStream, final int i) {
-            super(inputStream, i);
-        }
-
-        /** Returns the number of bytes that can be read from the buffer without reading more into the buffer. */
-        int getBytesInBufferAvailable() {
-            if (this.count == this.pos) return 0; // documented test for "is buffer empty"
-            else return this.buf.length - this.pos;
-        }
-    }
-
-    public static final int DEFAULT_BUFFER_SIZE = 512000;
-
-    final private int bufferSize;
-    final SeekableStream wrappedStream;
-    ExtBufferedInputStream bufferedStream;
-    long position;
-
-    public SeekableBufferedStream(final SeekableStream stream, final int bufferSize) {
-        this.bufferSize = bufferSize;
-        this.wrappedStream = stream;
-        this.position = 0;
-        bufferedStream = new ExtBufferedInputStream(wrappedStream, bufferSize);
-    }
-
-    public SeekableBufferedStream(final SeekableStream stream) {
-        this(stream, DEFAULT_BUFFER_SIZE);
-    }
-
-    @Override
-    public long length() {
-        return wrappedStream.length();
-    }
-
-    @Override
-    public long skip(final long skipLength) throws IOException {
-        if (skipLength < this.bufferedStream.getBytesInBufferAvailable()) {
-            final long retval = this.bufferedStream.skip(skipLength);
-            this.position += retval;
-            return retval;
-        } else {
-            final long position = this.position + skipLength;
-            seek(position);
-            return skipLength;
-        }
-    }
-
-    @Override
-    public void seek(final long position) throws IOException {
-        this.position = position;
-        wrappedStream.seek(position);
-        bufferedStream = new ExtBufferedInputStream(wrappedStream, bufferSize);
-    }
-
-    @Override
-    public int read() throws IOException {
-        int b = bufferedStream.read();
-        position++;
-        return b;
-    }
-
-    @Override
-    public int read(final byte[] buffer, final int offset, final int length) throws IOException {
-        final int nBytesRead = bufferedStream.read(buffer, offset, length);
-        if (nBytesRead > 0) {
-            position += nBytesRead;
-        }
-        return nBytesRead;
-    }
-
-    @Override
-    public void close() throws IOException {
-        wrappedStream.close();
-    }
-
-    @Override
-    public boolean eof() throws IOException {
-        return position >= wrappedStream.length();
-    }
-
-    @Override
-    public String getSource() {
-        return wrappedStream.getSource();
-    }
-
-    @Override
-    public long position() throws IOException {
-        return position;
-    }
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/SeekableFileStream.java

@@ -1,110 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.RandomAccessFile;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-
-public class SeekableFileStream extends SeekableStream {
-
-    /**
-     * Collection of all open instances.  SeekableFileStream objects are usually open and kept open for the
-     * duration of a session.  This collection supports a method to close them all.
-     */
-    private static final Collection<SeekableFileStream> allInstances = Collections.synchronizedCollection(new HashSet<>());
-
-    File file;
-    RandomAccessFile fis;
-
-    public SeekableFileStream(final File file) throws FileNotFoundException {
-        this.file = file;
-        fis = new RandomAccessFile(file, "r");
-        allInstances.add(this);
-    }
-
-    @Override
-    public long length() {
-        return file.length();
-    }
-
-    @Override
-    public boolean eof() throws IOException {
-        return fis.length() == fis.getFilePointer();
-    }
-
-    @Override
-    public void seek(final long position) throws IOException {
-        fis.seek(position);
-    }
-
-    @Override
-    public long position() throws IOException {
-        return fis.getChannel().position();
-    }
-
-    @Override
-    public long skip(long n) throws IOException {
-        long initPos = position();
-        fis.getChannel().position(initPos + n);
-        return position() - initPos;
-    }
-
-    @Override
-    public int read(final byte[] buffer, final int offset, final int length) throws IOException {
-        if (length < 0) {
-            throw new IndexOutOfBoundsException();
-        }
-        int n = 0;
-        while (n < length) {
-            final int count = fis.read(buffer, offset + n, length - n);
-            if (count < 0) {
-              if (n > 0) {
-                return n;
-              } else {
-                return count;
-              }
-            }
-            n += count;
-        }
-        return n;
-
-    }
-
-    @Override
-    public int read() throws IOException {
-        return fis.read();
-    }
-
-    @Override
-    public int read(byte[] b) throws IOException {
-        return fis.read(b);
-    }
-
-    @Override
-    public String getSource() {
-        return file.getAbsolutePath();
-    }
-
-
-    @Override
-    public void close() throws IOException {
-        allInstances.remove(this);
-        fis.close();
-
-    }
-
-    public static synchronized void closeAllInstances() {
-        Collection<SeekableFileStream> clonedInstances = new HashSet<>(allInstances);
-        for (SeekableFileStream sfs : clonedInstances) {
-            try {
-                sfs.close();
-            } catch (IOException e) {
-                //
-            }
-        }
-        allInstances.clear();
-    }
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/SeekableStream.java

@@ -1,44 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-import java.io.EOFException;
-import java.io.IOException;
-import java.io.InputStream;
-
-public abstract class SeekableStream extends InputStream {
-
-    public abstract long length();
-
-    public abstract long position() throws IOException;
-
-    public abstract void seek(long position) throws IOException;
-
-    @Override
-    public abstract int read(byte[] buffer, int offset, int length) throws IOException;
-
-    @Override
-    public abstract void close() throws IOException;
-
-    public abstract boolean eof() throws IOException;
-
-    /**
-     * @return String representation of source (e.g. URL, file path, etc.), or null if not available.
-     */
-    public abstract String getSource();
-
-    /**
-     * Read enough bytes to fill the input buffer.
-     * @param b byte array
-     * @throws EOFException If EOF is reached before buffer is filled
-     */
-    public void readFully(byte[] b) throws IOException {
-        int len = b.length;
-        int n = 0;
-        while (n < len) {
-            int count = read(b, n, len - n);
-            if (count < 0){
-                throw new EOFException();
-            }
-            n += count;
-        }
-    }
-}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/SeekableStreamFactory.java

@@ -1,11 +0,0 @@
-package org.xbib.io.compress.bgzf;
-
-import java.io.File;
-import java.io.IOException;
-
-public class SeekableStreamFactory {
-
-    public static SeekableStream getStreamFor(String path) throws IOException {
-        return new SeekableFileStream(new File(path));
-    }
-}

io-compress-lzf/src/main/java/org/xbib/io/compress/lzf/ChunkDecoderFactory.java

@@ -30,7 +30,7 @@ public class ChunkDecoderFactory {
      */
     public static ChunkDecoder optimalInstance() {
         try {
-            return INSTANCE.implClass.getDeclaredConstructor().newInstance();
+            return INSTANCE.implClass.newInstance();
         } catch (Exception e) {
             throw new IllegalStateException("Failed to load a ChunkDecoder instance (" + e.getClass().getName() + "): "
                     + e.getMessage(), e);

io-compress-xz/src/main/java/org/xbib/io/compress/xz/IndexIndicatorException.java

@@ -1,5 +1,5 @@
+
 package org.xbib.io.compress.xz;
 
-@SuppressWarnings("serial")
 class IndexIndicatorException extends Exception {
 }

io-compress-xz/src/main/java/org/xbib/io/compress/xz/index/IndexEncoder.java

@@ -1,3 +1,4 @@
+
 package org.xbib.io.compress.xz.index;
 
 import org.xbib.io.compress.xz.XZIOException;
@@ -6,12 +7,11 @@ import org.xbib.io.compress.xz.common.EncoderUtil;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.util.ArrayList;
-import java.util.List;
+import java.util.Iterator;
 import java.util.zip.CheckedOutputStream;
 
 public class IndexEncoder extends IndexBase {
-
-    private final List<IndexRecord> records = new ArrayList<>();
+    private final ArrayList records = new ArrayList();
 
     public IndexEncoder() {
         super(new XZIOException("XZ Stream or its Index has grown too big"));
@@ -34,7 +34,8 @@ public class IndexEncoder extends IndexBase {
         EncoderUtil.encodeVLI(outChecked, recordCount);
 
         // List of Records
-        for (IndexRecord record : records) {
+        for (Iterator i = records.iterator(); i.hasNext(); ) {
+            IndexRecord record = (IndexRecord) i.next();
             EncoderUtil.encodeVLI(outChecked, record.unpadded);
             EncoderUtil.encodeVLI(outChecked, record.uncompressed);
         }

settings.gradle

@@ -1,21 +1,3 @@
-dependencyResolutionManagement {
-    versionCatalogs {
-        libs {
-            version('gradle', '8.5')
-        }
-        testLibs {
-            version('junit', '5.10.1')
-            library('junit-jupiter-api', 'org.junit.jupiter', 'junit-jupiter-api').versionRef('junit')
-            library('junit-jupiter-params', 'org.junit.jupiter', 'junit-jupiter-params').versionRef('junit')
-            library('junit-jupiter-engine', 'org.junit.jupiter', 'junit-jupiter-engine').versionRef('junit')
-            library('junit-jupiter-platform-launcher', 'org.junit.platform', 'junit-platform-launcher').version('1.10.1')
-            library('junit4', 'junit', 'junit').version('4.13.2')
-            library('hamcrest', 'org.hamcrest', 'hamcrest-library').version('2.2')
-        }
-    }
-}
-
-include 'io-compress-bgzf'
 include 'io-compress-bzip2'
 include 'io-compress-lzf'
 include 'io-compress-xz'