QSequenceCommonBlockFactory.java
package de.regnis.q.sequence
public abstract de.regnis.q.sequence.QSequenceCommonBlockFactory extends java.lang.Object {
	public abstract java.lang.Object createCommonBlock (int, int, int, int) 
	public abstract java.lang.Object createDistinctBlock (int, int, int, int) 
}

QSequenceCommonBlocks.java
package de.regnis.q.sequence
public de.regnis.q.sequence.QSequenceCommonBlocks extends java.lang.Object {
	public void <init> () 
	public static java.util.List createBlocks (boolean[], boolean[], de.regnis.q.sequence.QSequenceCommonBlockFactory) 
		Object block
		Object block
		int leftStart
		int rightStart
		boolean[] leftCommonPoints
		boolean[] rightCommonPoints
		de.regnis.q.sequence.QSequenceCommonBlockFactory factory
		java.util.List blocks
		int leftIndex
		int rightIndex
}

QSequenceDifference.java
package de.regnis.q.sequence
public de.regnis.q.sequence.QSequenceDifference extends java.lang.Object implements de.regnis.q.sequence.core.QSequenceSnakeRegister de.regnis.q.sequence.QSequenceCommonBlockFactory  {
	private final de.regnis.q.sequence.core.QSequenceMedia media
	private final de.regnis.q.sequence.media.QSequenceMediaIndexTransformer indexTransformer
	private final boolean[] leftCommonPoints
	private final boolean[] rightCommonPoints
	private final int maximumSearchDepth
	public void <init> (de.regnis.q.sequence.core.QSequenceMedia, de.regnis.q.sequence.media.QSequenceMediaIndexTransformer) 
		de.regnis.q.sequence.core.QSequenceMedia media
		de.regnis.q.sequence.media.QSequenceMediaIndexTransformer indexTransformer
	public void <init> (de.regnis.q.sequence.core.QSequenceMedia, de.regnis.q.sequence.media.QSequenceMediaIndexTransformer, int) 
		de.regnis.q.sequence.core.QSequenceMedia media
		de.regnis.q.sequence.media.QSequenceMediaIndexTransformer indexTransformer
		int maximumSearchDepth
	public void registerSnake (int, int, int, int)  throws de.regnis.q.sequence.core.QSequenceCancelledException 
		int leftIndex
		int rightIndex
		int leftFrom
		int leftTo
		int rightFrom
		int rightTo
	public java.lang.Object createCommonBlock (int, int, int, int) 
		int leftFrom
		int leftTo
		int rightFrom
		int rightTo
	public java.lang.Object createDistinctBlock (int, int, int, int) 
		int leftFrom
		int leftTo
		int rightFrom
		int rightTo
	public java.util.List getBlocks ()  throws de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.core.QSequenceAlgorithm algorithm
}

QSequenceDifferenceBlock.java
package de.regnis.q.sequence
public de.regnis.q.sequence.QSequenceDifferenceBlock extends java.lang.Object {
	private int leftFrom
	private int leftTo
	private int rightFrom
	private int rightTo
	public void <init> (int, int, int, int) 
		int leftFrom
		int leftTo
		int rightFrom
		int rightTo
	public int getLeftFrom () 
	public int getLeftTo () 
	public int getLeftSize () 
	public int getRightFrom () 
	public int getRightTo () 
	public int getRightSize () 
	void setLeftFrom (int) 
		int leftFrom
	void setLeftTo (int) 
		int leftTo
	void setRightFrom (int) 
		int rightFrom
	void setRightTo (int) 
		int rightTo
	public java.lang.String toString () 
}

QSequenceDifferenceBlockShifter.java
package de.regnis.q.sequence
public de.regnis.q.sequence.QSequenceDifferenceBlockShifter extends java.lang.Object {
	private final de.regnis.q.sequence.core.QSequenceMedia media
	private final de.regnis.q.sequence.media.QSequenceMediaComparer comparer
	public static void joinBlocks (java.util.List) 
		de.regnis.q.sequence.QSequenceDifferenceBlock block
		int index
		java.util.List blocks
		de.regnis.q.sequence.QSequenceDifferenceBlock lastBlock
	public void <init> (de.regnis.q.sequence.core.QSequenceMedia, de.regnis.q.sequence.media.QSequenceMediaComparer) 
		de.regnis.q.sequence.core.QSequenceMedia media
		de.regnis.q.sequence.media.QSequenceMediaComparer comparer
	public void shiftBlocks (java.util.List)  throws de.regnis.q.sequence.core.QSequenceException 
		int index
		int index
		java.util.List blocks
	public boolean tryShiftUp (java.util.List, int, boolean)  throws de.regnis.q.sequence.core.QSequenceException 
		java.util.List blocks
		int blockIndex
		boolean requireMerge
		de.regnis.q.sequence.QSequenceDifferenceBlock prevBlock
		de.regnis.q.sequence.QSequenceDifferenceBlock block
		int prevLeftTo
		int prevRightTo
		int leftFrom
		int leftTo
		int rightFrom
		int rightTo
	public boolean tryShiftDown (java.util.List, int)  throws de.regnis.q.sequence.core.QSequenceException 
		java.util.List blocks
		int blockIndex
		de.regnis.q.sequence.QSequenceDifferenceBlock nextBlock
		de.regnis.q.sequence.QSequenceDifferenceBlock block
		int nextLeftFrom
		int nextRightFrom
		int leftFrom
		int leftTo
		int rightFrom
		int rightTo
}

QSequenceDifferenceBlockUtils.java
package de.regnis.q.sequence
public de.regnis.q.sequence.QSequenceDifferenceBlockUtils extends java.lang.Object {
	public void <init> () 
	public static java.util.List createCopy (java.util.List) 
		de.regnis.q.sequence.QSequenceDifferenceBlock block
		java.util.Iterator it
		java.util.List blocks
		java.util.List copy
	public static de.regnis.q.sequence.QSequenceDifferenceBlock createCopy (de.regnis.q.sequence.QSequenceDifferenceBlock) 
		de.regnis.q.sequence.QSequenceDifferenceBlock block
}

QSequenceSimpleLCS.java
package de.regnis.q.sequence
public de.regnis.q.sequence.QSequenceSimpleLCS extends java.lang.Object implements de.regnis.q.sequence.core.QSequenceSnakeRegister  {
	private final de.regnis.q.sequence.core.QSequenceMedia media
	private final java.util.List commands
	public void <init> (de.regnis.q.sequence.core.QSequenceMedia) 
		de.regnis.q.sequence.core.QSequenceMedia media
	public void registerSnake (int, int, int, int) 
		int leftFrom
		int leftTo
		int rightFrom
		int rightTo
	public java.util.List getCommands ()  throws de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.core.QSequenceAlgorithm algorithm
}

QSequenceSimpleLCSCommand.java
package de.regnis.q.sequence
public de.regnis.q.sequence.QSequenceSimpleLCSCommand extends java.lang.Object {
	private final boolean left
	private final int from
	private final int to
	public void <init> (boolean, int, int) 
		boolean left
		int from
		int to
	public boolean isLeft () 
	public int getFrom () 
	public int getTo () 
}

QSequenceAlgorithm.java
package de.regnis.q.sequence.core
public de.regnis.q.sequence.core.QSequenceAlgorithm extends java.lang.Object {
	public static final boolean ASSERTIONS
	private final de.regnis.q.sequence.core.QSequenceMedia mainMedia
	private final de.regnis.q.sequence.core.QSequenceSnakeRegister snakeRegister
	private final de.regnis.q.sequence.core.QSequenceMiddleSnakeFinder finder
	public void <init> (de.regnis.q.sequence.core.QSequenceMedia, de.regnis.q.sequence.core.QSequenceSnakeRegister, int) 
		de.regnis.q.sequence.core.QSequenceMedia media
		de.regnis.q.sequence.core.QSequenceSnakeRegister snakeRegister
		int maximumSearchDepth
	public void produceSnakesInOrder ()  throws de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.core.QSequenceRestrictedMedia media
	private void produceSnakesInOrder (de.regnis.q.sequence.core.QSequenceRestrictedMedia)  throws de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.core.QSequenceRestrictedMedia media
		int leftLength
		int rightLength
		int dee
		int leftFrom
		int rightFrom
		int leftTo
		int rightTo
		int leftMin
		int rightMin
		int leftMax
		int rightMax
	private void registerSnake (de.regnis.q.sequence.core.QSequenceRestrictedMedia, int, int, int, int)  throws de.regnis.q.sequence.core.QSequenceException 
		int index
		de.regnis.q.sequence.core.QSequenceRestrictedMedia media
		int leftFrom
		int leftTo
		int rightFrom
		int rightTo
}

QSequenceAssert.java
package de.regnis.q.sequence.core
public final de.regnis.q.sequence.core.QSequenceAssert extends java.lang.Object {
	public static void assertNotNull (java.lang.Object) 
		Object obj
	public static void assertNotNull (java.lang.Object, java.lang.String) 
		Object obj
		String text
	public static void assertEquals (int, int) 
		int i1
		int i2
	public static void assertEquals (long, long) 
		long l1
		long l2
	public static void assertTrue (boolean) 
		boolean forceTrueCondition
	public static void assertTrue (boolean, java.lang.String) 
		boolean forceTrueCondition
		String text
	public static void error (java.lang.String) 
		String text
	public static void fatal (java.lang.String) 
		String text
	private void <init> () 
}

QSequenceCancelledException.java
package de.regnis.q.sequence.core
public de.regnis.q.sequence.core.QSequenceCancelledException extends de.regnis.q.sequence.core.QSequenceException {
	public void <init> () 
}

QSequenceCanceller.java
package de.regnis.q.sequence.core
public abstract de.regnis.q.sequence.core.QSequenceCanceller extends java.lang.Object {
	public abstract void checkCancelled ()  throws de.regnis.q.sequence.core.QSequenceCancelledException 
}

QSequenceDeePathBackwardExtender.java
package de.regnis.q.sequence.core
final de.regnis.q.sequence.core.QSequenceDeePathBackwardExtender extends de.regnis.q.sequence.core.QSequenceDeePathExtender {
	private int delta
	private int mediaLeftLength
	private int mediaRightLength
	public void <init> (int, int) 
		int maximumMediaLeftLength
		int maximumMediaRightLength
	protected int getNextX (de.regnis.q.sequence.core.QSequenceDeePathExtenderArray, int, int) 
		de.regnis.q.sequence.core.QSequenceDeePathExtenderArray xs
		int diagonal
		int dee
	protected int getSnakeX (de.regnis.q.sequence.core.QSequenceMedia, int, int)  throws de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.core.QSequenceMedia media
		int x
		int y
	protected final void reset (de.regnis.q.sequence.core.QSequenceMedia, de.regnis.q.sequence.core.QSequenceDeePathExtenderArray) 
		de.regnis.q.sequence.core.QSequenceMedia media
		de.regnis.q.sequence.core.QSequenceDeePathExtenderArray xs
	public int getProgress (int) 
		int diagonal
}

QSequenceDeePathExtender.java
package de.regnis.q.sequence.core
abstract de.regnis.q.sequence.core.QSequenceDeePathExtender extends java.lang.Object {
	private final de.regnis.q.sequence.core.QSequenceDeePathExtenderArray xs
	private int snakeStartLeft
	private int snakeStartRight
	protected abstract int getNextX (de.regnis.q.sequence.core.QSequenceDeePathExtenderArray, int, int) 
	protected abstract int getSnakeX (de.regnis.q.sequence.core.QSequenceMedia, int, int)  throws de.regnis.q.sequence.core.QSequenceException 
	protected abstract void reset (de.regnis.q.sequence.core.QSequenceMedia, de.regnis.q.sequence.core.QSequenceDeePathExtenderArray) 
	public abstract int getProgress (int) 
	protected void <init> (de.regnis.q.sequence.core.QSequenceDeePathExtenderArray) 
		de.regnis.q.sequence.core.QSequenceDeePathExtenderArray xs
	public final int getLeft (int) 
		int diagonal
	public final int getRight (int) 
		int diagonal
	public final int getSnakeStartLeft () 
	public final int getSnakeStartRight () 
	public final void extendDeePath (de.regnis.q.sequence.core.QSequenceMedia, int, int)  throws de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.core.QSequenceMedia media
		int dee
		int diagonal
		int x
		int y
	public final void reset (de.regnis.q.sequence.core.QSequenceMedia) 
		de.regnis.q.sequence.core.QSequenceMedia media
	public final void print (de.regnis.q.sequence.core.QSequenceMedia, int, int) 
		int ch
		int line
		int left
		int right
		int diagonal
		de.regnis.q.sequence.core.QSequenceMedia media
		int fromDiagonal
		int toDiagonal
		StringBuffer[] lines
}

QSequenceDeePathExtenderArray.java
package de.regnis.q.sequence.core
 de.regnis.q.sequence.core.QSequenceDeePathExtenderArray extends java.lang.Object {
	private final int[] xs
	private final int offset
	private int delta
	public void <init> (int) 
		int maximumMediaLeftRightLength
	public void set (int, int) 
		int diagonal
		int maxLeft
	public int get (int) 
		int diagonal
		int left
	public void setDelta (int) 
		int delta
}

QSequenceDeePathForwardExtender.java
package de.regnis.q.sequence.core
 de.regnis.q.sequence.core.QSequenceDeePathForwardExtender extends de.regnis.q.sequence.core.QSequenceDeePathExtender {
	public void <init> (int, int) 
		int maximumMediaLeftLength
		int maximumMediaRightLength
	protected int getNextX (de.regnis.q.sequence.core.QSequenceDeePathExtenderArray, int, int) 
		de.regnis.q.sequence.core.QSequenceDeePathExtenderArray xs
		int diagonal
		int dee
	protected int getSnakeX (de.regnis.q.sequence.core.QSequenceMedia, int, int)  throws de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.core.QSequenceMedia media
		int x
		int y
	protected final void reset (de.regnis.q.sequence.core.QSequenceMedia, de.regnis.q.sequence.core.QSequenceDeePathExtenderArray) 
		de.regnis.q.sequence.core.QSequenceMedia media
		de.regnis.q.sequence.core.QSequenceDeePathExtenderArray xs
	public int getProgress (int) 
		int diagonal
}

QSequenceDummyCanceller.java
package de.regnis.q.sequence.core
public de.regnis.q.sequence.core.QSequenceDummyCanceller extends java.lang.Object implements de.regnis.q.sequence.core.QSequenceCanceller  {
	public void <init> () 
	public void checkCancelled () 
}

QSequenceException.java
package de.regnis.q.sequence.core
public de.regnis.q.sequence.core.QSequenceException extends java.lang.Exception {
	public void <init> () 
	public void <init> (java.lang.Throwable) 
		Throwable cause
}

QSequenceMedia.java
package de.regnis.q.sequence.core
public abstract de.regnis.q.sequence.core.QSequenceMedia extends java.lang.Object {
	public abstract int getLeftLength () 
	public abstract int getRightLength () 
	public abstract boolean equals (int, int)  throws de.regnis.q.sequence.core.QSequenceException 
}

QSequenceMiddleSnakeFinder.java
package de.regnis.q.sequence.core
 de.regnis.q.sequence.core.QSequenceMiddleSnakeFinder extends java.lang.Object {
	private final de.regnis.q.sequence.core.QSequenceDeePathForwardExtender forwardDeePathExtender
	private final de.regnis.q.sequence.core.QSequenceDeePathBackwardExtender backwardDeePathExtender
	private final de.regnis.q.sequence.core.QSequenceMiddleSnakeFinderResult result
	private final int maximumSearchDepth
	public void <init> (int, int, int) 
		int maximumMediaLeftLength
		int maximumMediaRightLength
		int maximumSearchDepth
	public de.regnis.q.sequence.core.QSequenceMiddleSnakeFinderResult getResult () 
	public int determineMiddleSnake (de.regnis.q.sequence.core.QSequenceMedia)  throws de.regnis.q.sequence.core.QSequenceException 
		int diagonal
		int deltadDiagonal
		int diagonal
		int dee
		de.regnis.q.sequence.core.QSequenceMedia media
		int delta
		int deeMax
	private boolean isForwardAndBackwardOverlapping (int) 
		int diagonal
		int forwardLeft
		int backwardLeft
	private int determineBestSnake (de.regnis.q.sequence.core.QSequenceMedia, int, int) 
		int left
		int right
		de.regnis.q.sequence.core.QSequenceMedia media
		int dee
		int delta
		int bestForwardDiagonal
		int bestBackwardDiagonal
		int left
		int right
	private int getBestForwardDiagonal (int, int) 
		int progress
		int diagonal
		int dee
		int delta
		int bestDiagonal
		int bestProgress
	private int getBestBackwardDiagonal (int, int) 
		int deltadDiagonal
		int progress
		int diagonal
		int dee
		int delta
		int bestDiagonal
		int bestProgress
	public static void setMiddleSnake (de.regnis.q.sequence.core.QSequenceMiddleSnakeFinderResult, de.regnis.q.sequence.core.QSequenceDeePathExtender, int) 
		de.regnis.q.sequence.core.QSequenceMiddleSnakeFinderResult result
		de.regnis.q.sequence.core.QSequenceDeePathExtender extender
		int diagonal
	private static boolean checkForwardOverlapping (int, int, int) 
		int delta
		int diagonal
		int dee
	private static boolean checkBackwardOverlapping (int, int, int) 
		int delta
		int diagonal
		int dee
}

QSequenceMiddleSnakeFinderResult.java
package de.regnis.q.sequence.core
 de.regnis.q.sequence.core.QSequenceMiddleSnakeFinderResult extends java.lang.Object {
	private int leftFrom
	private int rightFrom
	private int leftTo
	private int rightTo
	void <init> () 
	public int getLeftFrom () 
	public int getRightFrom () 
	public int getLeftTo () 
	public int getRightTo () 
	public void reset () 
	public void setMiddleSnake (int, int, int, int) 
		int leftFrom
		int rightFrom
		int leftTo
		int rightTo
}

QSequenceRestrictedMedia.java
package de.regnis.q.sequence.core
 de.regnis.q.sequence.core.QSequenceRestrictedMedia extends java.lang.Object implements de.regnis.q.sequence.core.QSequenceMedia  {
	private final de.regnis.q.sequence.core.QSequenceMedia media
	private int leftMin
	private int rightMin
	private int leftMax
	private int rightMax
	public void <init> (de.regnis.q.sequence.core.QSequenceMedia) 
		de.regnis.q.sequence.core.QSequenceMedia media
	public void restrictTo (int, int, int, int) 
		int leftMin
		int leftMax
		int rightMin
		int rightMax
	public int getLeftLength () 
	public int getRightLength () 
	public boolean equals (int, int)  throws de.regnis.q.sequence.core.QSequenceException 
		int leftIndex
		int rightIndex
	public int getLeftMin () 
	public int getLeftMax () 
	public int getRightMin () 
	public int getRightMax () 
}

QSequenceSnakeRegister.java
package de.regnis.q.sequence.core
public abstract de.regnis.q.sequence.core.QSequenceSnakeRegister extends java.lang.Object {
	public abstract void registerSnake (int, int, int, int)  throws de.regnis.q.sequence.core.QSequenceCancelledException 
}

QSequenceLine.java
package de.regnis.q.sequence.line
public final de.regnis.q.sequence.line.QSequenceLine extends java.lang.Object {
	private final long from
	private final byte[] contentBytes
	private final byte[] compareBytes
	public void <init> (long, byte[], de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier) 
		long from
		byte[] contentBytes
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier simplifier
	public long getFrom () 
	public long getTo () 
	public int getContentLength () 
	public byte[] getContentBytes () 
	public byte[] getBytes () 
	public int getCompareHash () 
	public boolean equals (java.lang.Object) 
		int index
		Object obj
		byte[] otherBytes
	public int hashCode () 
		int index
		int hashCode
	public java.lang.String toString () 
}

QSequenceLineCache.java
package de.regnis.q.sequence.line
public abstract de.regnis.q.sequence.line.QSequenceLineCache extends java.lang.Object {
	public abstract int getLineCount () 
	public abstract void addLine (de.regnis.q.sequence.line.QSequenceLine)  throws java.io.IOException 
	public abstract de.regnis.q.sequence.line.QSequenceLine getLine (int)  throws java.io.IOException 
	public abstract int getLineHash (int)  throws java.io.IOException 
	public abstract void close ()  throws java.io.IOException 
}

QSequenceLineFileSystemCache.java
package de.regnis.q.sequence.line
final de.regnis.q.sequence.line.QSequenceLineFileSystemCache extends java.lang.Object implements de.regnis.q.sequence.line.QSequenceLineCache  {
	private final de.regnis.q.sequence.line.QSequenceLineRAData data
	private final de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier simplifier
	private final de.regnis.q.sequence.line.QSequenceLineFileSystemCacheSegments segments
	private int lineCount
	public static de.regnis.q.sequence.line.QSequenceLineFileSystemCache create (de.regnis.q.sequence.line.QSequenceLineRAData, de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory, int, int, de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier)  throws java.io.IOException 
		de.regnis.q.sequence.line.QSequenceLineRAData data
		de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory tempDirectoryFactory
		int maximumBytesInMemory
		int maximumSegmentSize
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier simplifier
		de.regnis.q.sequence.line.QSequenceLineFileSystemCache cache
		de.regnis.q.sequence.line.QSequenceLineReader reader
		java.io.InputStream stream
	private void <init> (de.regnis.q.sequence.line.QSequenceLineRAData, de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory, int, int, de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier) 
		de.regnis.q.sequence.line.QSequenceLineRAData data
		de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory tempDirectoryFactory
		int maximumBytesInMemory
		int maximumSegmentSize
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier simplifier
	public void close ()  throws java.io.IOException 
	public void addLine (de.regnis.q.sequence.line.QSequenceLine)  throws java.io.IOException 
		de.regnis.q.sequence.line.QSequenceLine line
	public int getLineCount () 
	public de.regnis.q.sequence.line.QSequenceLine getLine (int)  throws java.io.IOException 
		int index
		long from
		int length
		byte[] bytes
	public int getLineHash (int)  throws java.io.IOException 
		int index
}

QSequenceLineFileSystemCacheSegment.java
package de.regnis.q.sequence.line
 de.regnis.q.sequence.line.QSequenceLineFileSystemCacheSegment extends java.lang.Object {
	private final long segmentIndex
	private final int maximumEntryCount
	private long[] froms
	private int[] lengths
	private int[] hashes
	public void <init> (long, int) 
		long segmentIndex
		int maximumEntryCount
	public boolean isLoaded () 
	public long getFrom (int) 
		int index
	public int getLength (int) 
		int index
	public int getHash (int) 
		int index
	public void setFromLengthHash (int, long, int, int) 
		int index
		long from
		int length
		int hash
	public void load (java.io.RandomAccessFile)  throws java.io.IOException 
		int index
		java.io.RandomAccessFile file
		byte[] bytes
		java.io.ByteArrayInputStream bis
		java.io.DataInputStream is
	public void unload (java.io.RandomAccessFile)  throws java.io.IOException 
		int index
		java.io.RandomAccessFile file
		java.io.ByteArrayOutputStream bos
		java.io.DataOutputStream os
		byte[] bytes
		long offset
}

QSequenceLineFileSystemCacheSegments.java
package de.regnis.q.sequence.line
 de.regnis.q.sequence.line.QSequenceLineFileSystemCacheSegments extends java.lang.Object {
	private final de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory tempDirectoryFactory
	private final int maximumEntriesPerSegment
	private final int maximumSegmentsInMemory
	private final java.util.List segments
	private final java.util.List memorySegments
	private java.io.File filePath
	private java.io.RandomAccessFile file
	public void <init> (de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory, int, int) 
		de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory tempDirectoryFactory
		int maximumBytesInMemory
		int segmentBytesSize
		de.regnis.q.sequence.line.QSequenceLineFileSystemCacheSegment segment
	public long getFrom (int)  throws java.io.IOException 
		int index
		int segmentIndex
		int relativeIndex
	public int getLength (int)  throws java.io.IOException 
		int index
		int segmentIndex
		int relativeIndex
	public int getHash (int)  throws java.io.IOException 
		int index
		int segmentIndex
		int relativeIndex
	public void setFromLengthHash (int, long, int, int)  throws java.io.IOException 
		int index
		long from
		int length
		int hash
		int segmentIndex
		int relativeIndex
		de.regnis.q.sequence.line.QSequenceLineFileSystemCacheSegment segment
	public void close ()  throws java.io.IOException 
	private de.regnis.q.sequence.line.QSequenceLineFileSystemCacheSegment getSegment (int)  throws java.io.IOException 
		de.regnis.q.sequence.line.QSequenceLineFileSystemCacheSegment segment
		int segmentIndex
		de.regnis.q.sequence.line.QSequenceLineFileSystemCacheSegment segment
	private void maybeUnloadSegments ()  throws java.io.IOException 
		de.regnis.q.sequence.line.QSequenceLineFileSystemCacheSegment segment
	private java.io.RandomAccessFile getFile ()  throws java.io.IOException 
		java.io.File tempDirectory
}

QSequenceLineFixedTempDirectoryFactory.java
package de.regnis.q.sequence.line
public de.regnis.q.sequence.line.QSequenceLineFixedTempDirectoryFactory extends java.lang.Object implements de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory  {
	private final java.io.File tempDirectory
	public void <init> (java.io.File) 
		java.io.File tempDirectory
	public java.io.File getTempDirectory ()  throws java.io.IOException 
	public void close () 
}

QSequenceLineMedia.java
package de.regnis.q.sequence.line
public final de.regnis.q.sequence.line.QSequenceLineMedia extends java.lang.Object implements de.regnis.q.sequence.media.QSequenceCachableMedia de.regnis.q.sequence.media.QSequenceMediaComparer  {
	public static final int FILE_SEGMENT_SIZE
	public static final int SEGMENT_ENTRY_SIZE
	public static final int MEMORY_THRESHOLD
	public static final double SEARCH_DEPTH_EXPONENT
	private final de.regnis.q.sequence.line.QSequenceLineCache leftCache
	private final de.regnis.q.sequence.line.QSequenceLineCache rightCache
	public static de.regnis.q.sequence.line.QSequenceLineCache readLines (de.regnis.q.sequence.line.QSequenceLineRAData)  throws java.io.IOException 
		java.io.InputStream stream
		de.regnis.q.sequence.line.QSequenceLineRAData data
	public static de.regnis.q.sequence.line.QSequenceLineResult createBlocks (de.regnis.q.sequence.line.QSequenceLineRAData, de.regnis.q.sequence.line.QSequenceLineRAData)  throws java.io.IOException de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.line.QSequenceLineRAData leftData
		de.regnis.q.sequence.line.QSequenceLineRAData rightData
	public static de.regnis.q.sequence.line.QSequenceLineResult createBlocks (de.regnis.q.sequence.line.QSequenceLineRAData, de.regnis.q.sequence.line.QSequenceLineRAData, de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier)  throws java.io.IOException de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.line.QSequenceLineRAData leftData
		de.regnis.q.sequence.line.QSequenceLineRAData rightData
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier simplifier
	public static de.regnis.q.sequence.line.QSequenceLineResult createBlocks (de.regnis.q.sequence.line.QSequenceLineRAData, de.regnis.q.sequence.line.QSequenceLineRAData, int, int, double, de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory, de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier)  throws java.io.IOException de.regnis.q.sequence.core.QSequenceException 
		java.io.InputStream leftStream
		java.io.InputStream rightStream
		de.regnis.q.sequence.line.QSequenceLineRAData leftData
		de.regnis.q.sequence.line.QSequenceLineRAData rightData
		int memoryThreshold
		int fileSegmentSize
		double searchDepthExponent
		de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory tempDirectoryFactory
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier simplifier
	static de.regnis.q.sequence.line.QSequenceLineResult createBlocksInMemory (java.io.InputStream, java.io.InputStream, double, de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier)  throws java.io.IOException de.regnis.q.sequence.core.QSequenceException 
		java.io.InputStream leftStream
		java.io.InputStream rightStream
		double searchDepthExponent
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier simplifier
		de.regnis.q.sequence.line.QSequenceLineMemoryCache leftCache
		de.regnis.q.sequence.line.QSequenceLineMemoryCache rightCache
		de.regnis.q.sequence.line.QSequenceLineMedia lineMedia
		de.regnis.q.sequence.media.QSequenceCachingMedia cachingMedia
		de.regnis.q.sequence.media.QSequenceDiscardingMedia discardingMedia
		java.util.List blocks
	static de.regnis.q.sequence.line.QSequenceLineResult createBlocksInFilesystem (de.regnis.q.sequence.line.QSequenceLineRAData, de.regnis.q.sequence.line.QSequenceLineRAData, de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory, double, int, int, de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier)  throws java.io.IOException de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.line.QSequenceLineRAData leftData
		de.regnis.q.sequence.line.QSequenceLineRAData rightData
		de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory tempDirectoryFactory
		double searchDepthExponent
		int memoryThreshold
		int fileSegmentSize
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier simplifier
		de.regnis.q.sequence.line.QSequenceLineFileSystemCache leftCache
		de.regnis.q.sequence.line.QSequenceLineFileSystemCache rightCache
		de.regnis.q.sequence.line.QSequenceLineMedia lineMedia
		java.util.List blocks
	public void <init> (de.regnis.q.sequence.line.QSequenceLineCache, de.regnis.q.sequence.line.QSequenceLineCache) 
		de.regnis.q.sequence.line.QSequenceLineCache leftCache
		de.regnis.q.sequence.line.QSequenceLineCache rightCache
	public int getLeftLength () 
	public int getRightLength () 
	public java.lang.Object getMediaLeftObject (int)  throws de.regnis.q.sequence.core.QSequenceException 
		java.io.IOException ex
		int index
	public java.lang.Object getMediaRightObject (int)  throws de.regnis.q.sequence.core.QSequenceException 
		java.io.IOException ex
		int index
	public boolean equals (int, int)  throws de.regnis.q.sequence.core.QSequenceException 
		int leftHash
		int rightHash
		java.io.IOException ex
		int leftIndex
		int rightIndex
	public boolean equalsLeft (int, int)  throws de.regnis.q.sequence.core.QSequenceException 
		java.io.IOException ex
		int left1
		int left2
	public boolean equalsRight (int, int)  throws de.regnis.q.sequence.core.QSequenceException 
		java.io.IOException ex
		int right1
		int right2
	private static int getSearchDepth (de.regnis.q.sequence.line.QSequenceLineMedia, double) 
		de.regnis.q.sequence.line.QSequenceLineMedia lineMedia
		double searchDepthExponent
	private static int parseMemoryTreshold (java.lang.String) 
		int amount
		NumberFormatException e
		String value
		int factor
	static void <clinit> () 
}

QSequenceLineMemoryCache.java
package de.regnis.q.sequence.line
final de.regnis.q.sequence.line.QSequenceLineMemoryCache extends java.lang.Object implements de.regnis.q.sequence.line.QSequenceLineCache  {
	private final java.util.List lines
	public static de.regnis.q.sequence.line.QSequenceLineMemoryCache read (java.io.InputStream, de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier)  throws java.io.IOException 
		java.io.InputStream is
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier simplifier
		de.regnis.q.sequence.line.QSequenceLineMemoryCache cache
		de.regnis.q.sequence.line.QSequenceLineReader reader
	public void <init> () 
	public void addLine (de.regnis.q.sequence.line.QSequenceLine) 
		de.regnis.q.sequence.line.QSequenceLine line
	public int getLineCount () 
	public int getLineHash (int) 
		int index
	public de.regnis.q.sequence.line.QSequenceLine getLine (int) 
		int index
	public void close () 
}

QSequenceLineRAByteData.java
package de.regnis.q.sequence.line
public final de.regnis.q.sequence.line.QSequenceLineRAByteData extends java.lang.Object implements de.regnis.q.sequence.line.QSequenceLineRAData  {
	private final byte[] bytes
	public static de.regnis.q.sequence.line.QSequenceLineRAByteData create (java.io.InputStream)  throws java.io.IOException 
		int b
		java.io.InputStream is
		java.io.ByteArrayOutputStream os
	public void <init> (byte[]) 
		byte[] bytes
	public long length () 
	public void get (byte[], long, long) 
		byte[] bytes
		long offset
		long length
	public java.io.InputStream read (long, long) 
		long offset
		long length
}

QSequenceLineRAData.java
package de.regnis.q.sequence.line
public abstract de.regnis.q.sequence.line.QSequenceLineRAData extends java.lang.Object {
	public abstract long length ()  throws java.io.IOException 
	public abstract void get (byte[], long, long)  throws java.io.IOException 
	public abstract java.io.InputStream read (long, long)  throws java.io.IOException 
}

QSequenceLineRAFileData.java
package de.regnis.q.sequence.line
public final de.regnis.q.sequence.line.QSequenceLineRAFileData extends java.lang.Object implements de.regnis.q.sequence.line.QSequenceLineRAData  {
	private final java.io.RandomAccessFile randomAccessFile
	private de.regnis.q.sequence.line.QSequenceLineRAFileDataStream stream
	public void <init> (java.io.RandomAccessFile) 
		java.io.RandomAccessFile randomAccessFile
	public long length ()  throws java.io.IOException 
	public void get (byte[], long, long)  throws java.io.IOException 
		byte[] bytes
		long offset
		long length
	public java.io.InputStream read (long, long) 
		long offset
		long length
}

QSequenceLineRAFileDataStream.java
package de.regnis.q.sequence.line
final de.regnis.q.sequence.line.QSequenceLineRAFileDataStream extends java.io.InputStream {
	private final java.io.RandomAccessFile myFile
	private long offset
	private int length
	public void <init> (java.io.RandomAccessFile, long, int) 
		java.io.RandomAccessFile myFile
		long offset
		int length
	public int read ()  throws java.io.IOException 
		byte[] buffer
	public int read (byte[], int, int)  throws java.io.IOException 
		byte[] buffer
		int userOffset
		int userLength
		int available
		int toRead
		long pos
		int result
	public void reset (long, int) 
		long offset
		int length
}

QSequenceLineRandomAccessFileFactory.java
package de.regnis.q.sequence.line
final de.regnis.q.sequence.line.QSequenceLineRandomAccessFileFactory$1 extends java.lang.Thread {
	void <init> () 
	public void run () 
		java.io.IOException ex
		java.io.File file
		java.io.RandomAccessFile raFile
		java.util.Iterator it
}

QSequenceLineRandomAccessFileFactory.java
package de.regnis.q.sequence.line
public de.regnis.q.sequence.line.QSequenceLineRandomAccessFileFactory extends java.lang.Object {
	private static final java.util.Map fileToRaFile
	public void <init> () 
	public static java.io.RandomAccessFile createRandomAccessFile (java.io.File, java.lang.String)  throws java.io.FileNotFoundException 
		java.io.File file
		String mode
		java.io.RandomAccessFile raFile
	static java.util.Map access$000 () 
	static void <clinit> () 
}

QSequenceLineReader.java
package de.regnis.q.sequence.line
final de.regnis.q.sequence.line.QSequenceLineReader extends java.lang.Object {
	private byte[] buffer
	public void <init> () 
	public void <init> (int) 
		int initialBufferSize
	public void read (java.io.InputStream, de.regnis.q.sequence.line.QSequenceLineCache, de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier)  throws java.io.IOException 
		byte[] bytes
		int ch
		int pushBack
		int from
		int length
		java.io.InputStream rawStream
		de.regnis.q.sequence.line.QSequenceLineCache cache
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier simplifier
		java.io.BufferedInputStream stream
	private void append (int, byte) 
		byte[] newArray
		int position
		byte ch
}

QSequenceLineResult.java
package de.regnis.q.sequence.line
public final de.regnis.q.sequence.line.QSequenceLineResult extends java.lang.Object {
	private final java.util.List blocks
	private final de.regnis.q.sequence.line.QSequenceLineCache leftCache
	private final de.regnis.q.sequence.line.QSequenceLineCache rightCache
	public void <init> (java.util.List, de.regnis.q.sequence.line.QSequenceLineCache, de.regnis.q.sequence.line.QSequenceLineCache) 
		java.util.List blocks
		de.regnis.q.sequence.line.QSequenceLineCache leftCache
		de.regnis.q.sequence.line.QSequenceLineCache rightCache
	public java.util.List getBlocks () 
	public de.regnis.q.sequence.line.QSequenceLineCache getLeftCache () 
	public de.regnis.q.sequence.line.QSequenceLineCache getRightCache () 
	public void close ()  throws java.io.IOException 
}

QSequenceLineSystemTempDirectoryFactory.java
package de.regnis.q.sequence.line
public de.regnis.q.sequence.line.QSequenceLineSystemTempDirectoryFactory extends java.lang.Object implements de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory  {
	private java.io.File tempDirectory
	public void <init> () 
	public java.io.File getTempDirectory ()  throws java.io.IOException 
		java.io.IOException ex
		int tries
	public void close () 
}

QSequenceLineTempDirectoryFactory.java
package de.regnis.q.sequence.line
public abstract de.regnis.q.sequence.line.QSequenceLineTempDirectoryFactory extends java.lang.Object {
	public abstract java.io.File getTempDirectory ()  throws java.io.IOException 
	public abstract void close () 
}

QDiffGenerator.java
package de.regnis.q.sequence.line.diff
public abstract de.regnis.q.sequence.line.diff.QDiffGenerator extends java.lang.Object {
	public abstract void generateDiffHeader (java.lang.String, java.lang.String, java.lang.String, java.io.Writer)  throws java.io.IOException 
	public abstract void generateTextDiff (java.io.InputStream, java.io.InputStream, java.lang.String, java.io.Writer)  throws java.io.IOException 
	public abstract void generateTextDiff (java.io.RandomAccessFile, java.io.RandomAccessFile, java.lang.String, java.io.Writer)  throws java.io.IOException 
	public abstract void generateTextDiff (de.regnis.q.sequence.line.QSequenceLineRAData, de.regnis.q.sequence.line.QSequenceLineRAData, java.lang.String, java.io.Writer)  throws java.io.IOException 
	public abstract void generateBinaryDiff (java.io.InputStream, java.io.InputStream, java.lang.String, java.io.Writer)  throws java.io.IOException 
}

QDiffGeneratorFactory.java
package de.regnis.q.sequence.line.diff
public abstract de.regnis.q.sequence.line.diff.QDiffGeneratorFactory extends java.lang.Object {
	public static final String GUTTER_PROPERTY
	public static final String EOL_PROPERTY
	public static final String WHITESPACE_PROPERTY
	public static final String IGNORE_EOL_PROPERTY
	public static final String IGNORE_SPACE_PROPERTY
	public static final String IGNORE_SPACE_CHANGE
	public static final String IGNORE_ALL_SPACE
	public static final String HUNK_DELIMITER
	public abstract de.regnis.q.sequence.line.diff.QDiffGenerator createGenerator (java.util.Map) 
}

QDiffManager.java
package de.regnis.q.sequence.line.diff
public final de.regnis.q.sequence.line.diff.QDiffManager extends java.lang.Object {
	public static final String DEFAULT_TYPE
	private static java.util.Map ourDiffGeneratorFactories
	public static void setup () 
	public static de.regnis.q.sequence.line.diff.QDiffGenerator getDiffGenerator (java.lang.String, java.util.Map) 
		String type
		java.util.Map properties
	public static void generateDiffHeader (java.lang.String, java.lang.String, java.lang.String, java.io.Writer, de.regnis.q.sequence.line.diff.QDiffGenerator)  throws java.io.IOException 
		String path
		String leftInfo
		String rightInfo
		java.io.Writer output
		de.regnis.q.sequence.line.diff.QDiffGenerator generator
	public static void generateTextDiff (java.io.InputStream, java.io.InputStream, java.lang.String, java.io.Writer, de.regnis.q.sequence.line.diff.QDiffGenerator)  throws java.io.IOException 
		java.io.InputStream left
		java.io.InputStream right
		String encoding
		java.io.Writer output
		de.regnis.q.sequence.line.diff.QDiffGenerator generator
	public static void generateTextDiff (java.io.RandomAccessFile, java.io.RandomAccessFile, java.lang.String, java.io.Writer, de.regnis.q.sequence.line.diff.QDiffGenerator)  throws java.io.IOException 
		java.io.RandomAccessFile left
		java.io.RandomAccessFile right
		String encoding
		java.io.Writer output
		de.regnis.q.sequence.line.diff.QDiffGenerator generator
	public static void generateBinaryDiff (java.io.InputStream, java.io.InputStream, java.lang.String, java.io.Writer, de.regnis.q.sequence.line.diff.QDiffGenerator)  throws java.io.IOException 
		java.io.InputStream left
		java.io.InputStream right
		String encoding
		java.io.Writer output
		de.regnis.q.sequence.line.diff.QDiffGenerator generator
	public static void registerDiffGeneratorFactory (de.regnis.q.sequence.line.diff.QDiffGeneratorFactory, java.lang.String) 
		de.regnis.q.sequence.line.diff.QDiffGeneratorFactory factory
		String type
	private void <init> () 
}

QDiffNormalGenerator.java
package de.regnis.q.sequence.line.diff
public final de.regnis.q.sequence.line.diff.QDiffNormalGenerator extends de.regnis.q.sequence.line.diff.QDiffSequenceGenerator implements de.regnis.q.sequence.line.diff.QDiffGeneratorFactory  {
	public static final String TYPE
	private java.util.Map myGeneratorsCache
	public static void setup () 
	private void <init> (java.util.Map) 
		java.util.Map properties
	private void <init> () 
	public void generateDiffHeader (java.lang.String, java.lang.String, java.lang.String, java.io.Writer)  throws java.io.IOException 
		String item
		String leftInfo
		String rightInfo
		java.io.Writer output
	protected void processBlock (de.regnis.q.sequence.QSequenceDifferenceBlock[], de.regnis.q.sequence.line.QSequenceLineCache, de.regnis.q.sequence.line.QSequenceLineCache, java.lang.String, java.io.Writer)  throws java.io.IOException 
		de.regnis.q.sequence.QSequenceDifferenceBlock block
		int i
		de.regnis.q.sequence.QSequenceDifferenceBlock[] segment
		de.regnis.q.sequence.line.QSequenceLineCache sourceLines
		de.regnis.q.sequence.line.QSequenceLineCache targetLines
		String encoding
		java.io.Writer output
	public de.regnis.q.sequence.line.diff.QDiffGenerator createGenerator (java.util.Map) 
		java.util.Map properties
		de.regnis.q.sequence.line.diff.QDiffGenerator generator
	protected void processBlock (int, int, de.regnis.q.sequence.line.QSequenceLineCache, int, int, de.regnis.q.sequence.line.QSequenceLineCache, java.lang.String, java.io.Writer)  throws java.io.IOException 
		int sourceStartLine
		int sourceEndLine
		de.regnis.q.sequence.line.QSequenceLineCache sourceLines
		int targetStartLine
		int targetEndLine
		de.regnis.q.sequence.line.QSequenceLineCache targetLines
		String encoding
		java.io.Writer output
	protected java.lang.String displayWhiteSpace (java.lang.String) 
		String s
	protected void delete (int, int, int, de.regnis.q.sequence.line.QSequenceLineCache, java.lang.String, java.io.Writer)  throws java.io.IOException 
		int deleteAt
		int deleteStart
		int deleteEnd
		de.regnis.q.sequence.line.QSequenceLineCache deleteLines
		String encoding
		java.io.Writer output
		int displayStart
		int displayEnd
		int displayAt
		int delLine
	protected void add (int, int, int, de.regnis.q.sequence.line.QSequenceLineCache, java.lang.String, java.io.Writer)  throws java.io.IOException 
		int addAt
		int addStart
		int addEnd
		de.regnis.q.sequence.line.QSequenceLineCache addLines
		String encoding
		java.io.Writer output
		int displayStart
		int displayEnd
		int displayAt
		int addLine
	protected void change (int, int, de.regnis.q.sequence.line.QSequenceLineCache, int, int, de.regnis.q.sequence.line.QSequenceLineCache, java.lang.String, java.io.Writer)  throws java.io.IOException 
		int replaceStart
		int replaceEnd
		de.regnis.q.sequence.line.QSequenceLineCache replaceLines
		int replaceWithStart
		int replaceWithEnd
		de.regnis.q.sequence.line.QSequenceLineCache replaceWithLines
		String encoding
		java.io.Writer output
		int displayStart
		int displayEnd
		int displayWithStart
		int displayWithEnd
		int replaceLine
		int replaceWithLine
}

QDiffSequenceGenerator.java
package de.regnis.q.sequence.line.diff
public abstract de.regnis.q.sequence.line.diff.QDiffSequenceGenerator extends java.lang.Object implements de.regnis.q.sequence.line.diff.QDiffGenerator  {
	private final String header
	private java.util.Map myProperties
	protected abstract void processBlock (de.regnis.q.sequence.QSequenceDifferenceBlock[], de.regnis.q.sequence.line.QSequenceLineCache, de.regnis.q.sequence.line.QSequenceLineCache, java.lang.String, java.io.Writer)  throws java.io.IOException 
	protected void <init> (java.util.Map, java.lang.String) 
		java.util.Map properties
		String header
	public void generateBinaryDiff (java.io.InputStream, java.io.InputStream, java.lang.String, java.io.Writer)  throws java.io.IOException 
		java.io.InputStream left
		java.io.InputStream right
		String encoding
		java.io.Writer output
	public void generateTextDiff (java.io.InputStream, java.io.InputStream, java.lang.String, java.io.Writer)  throws java.io.IOException 
		java.io.InputStream left
		java.io.InputStream right
		String encoding
		java.io.Writer output
	public void generateTextDiff (de.regnis.q.sequence.line.QSequenceLineRAData, de.regnis.q.sequence.line.QSequenceLineRAData, java.lang.String, java.io.Writer)  throws java.io.IOException 
		de.regnis.q.sequence.core.QSequenceException ex
		java.util.List segment
		de.regnis.q.sequence.QSequenceDifferenceBlock[] segmentBlocks
		java.util.Iterator it
		java.util.List combinedBlocks
		boolean headerWritten
		de.regnis.q.sequence.line.QSequenceLineRAData left
		de.regnis.q.sequence.line.QSequenceLineRAData right
		String encoding
		java.io.Writer output
		de.regnis.q.sequence.line.QSequenceLineResult result
	public void generateTextDiff (java.io.RandomAccessFile, java.io.RandomAccessFile, java.lang.String, java.io.Writer)  throws java.io.IOException 
		java.io.RandomAccessFile left
		java.io.RandomAccessFile right
		String encoding
		java.io.Writer output
		de.regnis.q.sequence.line.QSequenceLineRAData leftData
		de.regnis.q.sequence.line.QSequenceLineRAData rightData
	protected java.util.Map getProperties () 
	protected java.lang.String getHunkDelimiter () 
		Object hunkDelimiter
	protected java.lang.String getEOL () 
	protected de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier getSimplifier () 
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier baseSimplifier
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier baseSimplifier
		Object ignore
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier baseSimplifier
	protected int getGutter () 
		NumberFormatException e
		Object gutterStr
	protected java.lang.String printLine (de.regnis.q.sequence.line.QSequenceLine, java.lang.String)  throws java.io.IOException 
		de.regnis.q.sequence.line.QSequenceLine line
		String encoding
		String str
	protected void println (java.io.Writer)  throws java.io.IOException 
		java.io.Writer output
	protected void println (java.lang.String, java.io.Writer)  throws java.io.IOException 
		String str
		java.io.Writer output
	protected void print (java.lang.String, java.io.Writer)  throws java.io.IOException 
		String str
		java.io.Writer output
	private static java.util.List combineBlocks (java.util.List, int) 
		int leftDifference
		int rightDifference
		de.regnis.q.sequence.QSequenceDifferenceBlock currentBlock
		java.util.Iterator blocks
		java.util.List blocksList
		int gutter
		java.util.List combinedBlocks
		java.util.List currentList
		de.regnis.q.sequence.QSequenceDifferenceBlock lastBlock
}

QDiffUniGenerator.java
package de.regnis.q.sequence.line.diff
public final de.regnis.q.sequence.line.diff.QDiffUniGenerator extends de.regnis.q.sequence.line.diff.QDiffSequenceGenerator implements de.regnis.q.sequence.line.diff.QDiffGeneratorFactory  {
	public static final String TYPE
	private java.util.Map myGeneratorsCache
	public static void setup () 
	public void <init> (java.util.Map, java.lang.String) 
		java.util.Map properties
		String header
	private void <init> () 
	public void generateDiffHeader (java.lang.String, java.lang.String, java.lang.String, java.io.Writer)  throws java.io.IOException 
		String item
		String leftInfo
		String rightInfo
		java.io.Writer output
	protected void processBlock (de.regnis.q.sequence.QSequenceDifferenceBlock[], de.regnis.q.sequence.line.QSequenceLineCache, de.regnis.q.sequence.line.QSequenceLineCache, java.lang.String, java.io.Writer)  throws java.io.IOException 
		int i
		String line
		int j
		String line
		int j
		int plannedEnd
		String line
		int j
		de.regnis.q.sequence.QSequenceDifferenceBlock block
		int plannedEnd
		int end
		int i
		de.regnis.q.sequence.QSequenceDifferenceBlock[] segment
		de.regnis.q.sequence.line.QSequenceLineCache sourceLines
		de.regnis.q.sequence.line.QSequenceLineCache targetLines
		String encoding
		java.io.Writer output
		int gutter
		StringBuffer header
		int sourceStartLine
		int sourceEndLine
		int targetStartLine
		int targetEndLine
		int leftStart
		int rightStart
		int leftEnd
		int rightEnd
	public de.regnis.q.sequence.line.diff.QDiffGenerator createGenerator (java.util.Map) 
		java.util.Map properties
		de.regnis.q.sequence.line.diff.QDiffGenerator generator
	private void printNoNewLine (java.io.Writer, java.lang.String)  throws java.io.IOException 
		java.io.Writer output
		String line
	private static java.util.Map initProperties (java.util.Map) 
		java.util.Map properties
}

QSequenceLineDummySimplifier.java
package de.regnis.q.sequence.line.simplifier
public de.regnis.q.sequence.line.simplifier.QSequenceLineDummySimplifier extends java.lang.Object implements de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier  {
	public void <init> () 
	public byte[] simplify (byte[]) 
		byte[] bytes
}

QSequenceLineEOLUnifyingSimplifier.java
package de.regnis.q.sequence.line.simplifier
public de.regnis.q.sequence.line.simplifier.QSequenceLineEOLUnifyingSimplifier extends java.lang.Object implements de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier  {
	public void <init> () 
	public byte[] simplify (byte[]) 
		byte[] bytes
		String line
		boolean trimmed
}

QSequenceLineSimplifier.java
package de.regnis.q.sequence.line.simplifier
public abstract de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier extends java.lang.Object {
	public abstract byte[] simplify (byte[]) 
}

QSequenceLineTeeSimplifier.java
package de.regnis.q.sequence.line.simplifier
public de.regnis.q.sequence.line.simplifier.QSequenceLineTeeSimplifier extends java.lang.Object implements de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier  {
	private final de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier first
	private final de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier second
	public void <init> (de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier, de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier) 
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier first
		de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier second
	public byte[] simplify (byte[]) 
		byte[] bytes
}

QSequenceLineWhiteSpaceReducingSimplifier.java
package de.regnis.q.sequence.line.simplifier
public de.regnis.q.sequence.line.simplifier.QSequenceLineWhiteSpaceReducingSimplifier extends java.lang.Object implements de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier  {
	public void <init> () 
	public static java.lang.String reduceWhiteSpaces (java.lang.String) 
		char ch
		int index
		String text
		StringBuffer buffer
		boolean lastWasWhiteSpace
	public byte[] simplify (byte[]) 
		byte[] bytes
}

QSequenceLineWhiteSpaceSkippingSimplifier.java
package de.regnis.q.sequence.line.simplifier
public de.regnis.q.sequence.line.simplifier.QSequenceLineWhiteSpaceSkippingSimplifier extends java.lang.Object implements de.regnis.q.sequence.line.simplifier.QSequenceLineSimplifier  {
	public void <init> () 
	public static java.lang.String removeWhiteSpaces (java.lang.String) 
		char ch
		int index
		String text
		StringBuffer buffer
	public byte[] simplify (byte[]) 
		byte[] bytes
}

QSequenceCachableMedia.java
package de.regnis.q.sequence.media
public abstract de.regnis.q.sequence.media.QSequenceCachableMedia extends java.lang.Object implements de.regnis.q.sequence.core.QSequenceMedia  {
	public abstract java.lang.Object getMediaLeftObject (int)  throws de.regnis.q.sequence.core.QSequenceException 
	public abstract java.lang.Object getMediaRightObject (int)  throws de.regnis.q.sequence.core.QSequenceException 
}

QSequenceCachableMediaGetter.java
package de.regnis.q.sequence.media
public abstract de.regnis.q.sequence.media.QSequenceCachableMediaGetter extends java.lang.Object {
	public abstract int getMediaLength (de.regnis.q.sequence.media.QSequenceCachableMedia) 
	public abstract java.lang.Object getMediaObject (de.regnis.q.sequence.media.QSequenceCachableMedia, int)  throws de.regnis.q.sequence.core.QSequenceException 
}

QSequenceCachableMediaLeftGetter.java
package de.regnis.q.sequence.media
public de.regnis.q.sequence.media.QSequenceCachableMediaLeftGetter extends java.lang.Object implements de.regnis.q.sequence.media.QSequenceCachableMediaGetter  {
	public void <init> () 
	public int getMediaLength (de.regnis.q.sequence.media.QSequenceCachableMedia) 
		de.regnis.q.sequence.media.QSequenceCachableMedia media
	public java.lang.Object getMediaObject (de.regnis.q.sequence.media.QSequenceCachableMedia, int)  throws de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.media.QSequenceCachableMedia media
		int index
}

QSequenceCachableMediaRightGetter.java
package de.regnis.q.sequence.media
public de.regnis.q.sequence.media.QSequenceCachableMediaRightGetter extends java.lang.Object implements de.regnis.q.sequence.media.QSequenceCachableMediaGetter  {
	public void <init> () 
	public int getMediaLength (de.regnis.q.sequence.media.QSequenceCachableMedia) 
		de.regnis.q.sequence.media.QSequenceCachableMedia media
	public java.lang.Object getMediaObject (de.regnis.q.sequence.media.QSequenceCachableMedia, int)  throws de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.media.QSequenceCachableMedia media
		int index
}

QSequenceCachingMedia.java
package de.regnis.q.sequence.media
public de.regnis.q.sequence.media.QSequenceCachingMedia extends de.regnis.q.sequence.media.QSequenceIntMedia {
	private final de.regnis.q.sequence.media.QSequenceCachingMediaSymbolMap symbolMap
	private final int[] leftSymbols
	private final int[] rightSymbols
	public void <init> (de.regnis.q.sequence.media.QSequenceCachableMedia, de.regnis.q.sequence.core.QSequenceCanceller)  throws de.regnis.q.sequence.core.QSequenceException 
		de.regnis.q.sequence.media.QSequenceCachableMedia media
		de.regnis.q.sequence.core.QSequenceCanceller canceller
	public int getLeftLength () 
	public int getRightLength () 
	public boolean equals (int, int)  throws de.regnis.q.sequence.core.QSequenceCancelledException 
		int leftIndex
		int rightIndex
	public int getSymbolCount () 
	public int[] getLeftSymbols () 
	public int[] getRightSymbols () 
}

QSequenceCachingMediaSymbolMap.java
package de.regnis.q.sequence.media
public de.regnis.q.sequence.media.QSequenceCachingMediaSymbolMap extends java.lang.Object {
	private final java.util.Map map
	private int symbolCount
	public void <init> (int) 
		int maximumSize
	public int getSymbolCount () 
	public int[] createSymbols (de.regnis.q.sequence.media.QSequenceCachableMedia, de.regnis.q.sequence.media.QSequenceCachableMediaGetter)  throws de.regnis.q.sequence.core.QSequenceException 
		Object object
		int index
		de.regnis.q.sequence.media.QSequenceCachableMedia media
		de.regnis.q.sequence.media.QSequenceCachableMediaGetter mediaGetter
		int length
		int[] symbols
	private int getSymbol (java.lang.Object) 
		Object obj
		Integer symbol
}

QSequenceDiscardingMedia.java
package de.regnis.q.sequence.media
public de.regnis.q.sequence.media.QSequenceDiscardingMedia extends java.lang.Object implements de.regnis.q.sequence.core.QSequenceMedia de.regnis.q.sequence.media.QSequenceMediaIndexTransformer  {
	private final de.regnis.q.sequence.media.QSequenceIntMedia media
	private final de.regnis.q.sequence.core.QSequenceCanceller canceller
	private final de.regnis.q.sequence.media.QSequenceDiscardingMediaBlock leftBlock
	private final de.regnis.q.sequence.media.QSequenceDiscardingMediaBlock rightBlock
	private final int[] undiscardedLeftSymbols
	private final int[] undiscardedRightSymbols
	private final int undiscardedLeftSymbolCount
	private final int undiscardedRightSymbolCount
	public void <init> (de.regnis.q.sequence.media.QSequenceIntMedia, de.regnis.q.sequence.media.QSequenceDiscardingMediaConfusionDetector, de.regnis.q.sequence.core.QSequenceCanceller) 
		de.regnis.q.sequence.media.QSequenceIntMedia media
		de.regnis.q.sequence.media.QSequenceDiscardingMediaConfusionDetector confusionDetector
		de.regnis.q.sequence.core.QSequenceCanceller canceller
	public int getLeftLength () 
	public int getRightLength () 
	public boolean equals (int, int)  throws de.regnis.q.sequence.core.QSequenceCancelledException 
		int leftIndex
		int rightIndex
	public int getMediaLeftIndex (int) 
		int index
	public int getMediaRightIndex (int) 
		int index
	public int getMediaLeftLength () 
	public int getMediaRightLength () 
}

QSequenceDiscardingMediaBlock.java
package de.regnis.q.sequence.media
public abstract de.regnis.q.sequence.media.QSequenceDiscardingMediaBlock extends java.lang.Object {
	private final de.regnis.q.sequence.media.QSequenceIntMedia media
	private final int[] undiscardedSymbols
	private final int[] undiscardedIndices
	private int undiscardedSymbolCount
	protected abstract int[] getAllSymbols (de.regnis.q.sequence.media.QSequenceIntMedia) 
	protected void <init> (de.regnis.q.sequence.media.QSequenceIntMedia) 
		de.regnis.q.sequence.media.QSequenceIntMedia media
	public int getUndiscardedSymbolCount () 
	public int[] getUndiscardedSymbols () 
	public int getMediaIndex (int) 
		int index
	public void init (de.regnis.q.sequence.media.QSequenceDiscardingMediaBlock, de.regnis.q.sequence.media.QSequenceDiscardingMediaConfusionDetector) 
		int index
		de.regnis.q.sequence.media.QSequenceDiscardingMediaBlock thatBlock
		de.regnis.q.sequence.media.QSequenceDiscardingMediaConfusionDetector confusionDetector
		int[] thisAllSymbols
		int[] thatAllSymbols
		int[] otherEquivalences
		byte[] discardableMarkers
	private static int[] createEquivalences (int[], de.regnis.q.sequence.media.QSequenceIntMedia) 
		int index
		int[] symbols
		de.regnis.q.sequence.media.QSequenceIntMedia media
		int[] equivalences
	private static byte[] createDiscardableMarkers (int[], int[], de.regnis.q.sequence.media.QSequenceDiscardingMediaConfusionDetector) 
		int occurences
		int index
		int[] symbols
		int[] otherEquivalences
		de.regnis.q.sequence.media.QSequenceDiscardingMediaConfusionDetector confusionDetector
		byte[] discardableMarkers
}

QSequenceDiscardingMediaConfusionDetector.java
package de.regnis.q.sequence.media
public abstract de.regnis.q.sequence.media.QSequenceDiscardingMediaConfusionDetector extends java.lang.Object {
	public abstract void init (int) 
	public abstract boolean isAbsolute (int) 
	public abstract boolean isProvisional (int) 
}

QSequenceDiscardingMediaLeftBlock.java
package de.regnis.q.sequence.media
public de.regnis.q.sequence.media.QSequenceDiscardingMediaLeftBlock extends de.regnis.q.sequence.media.QSequenceDiscardingMediaBlock {
	public void <init> (de.regnis.q.sequence.media.QSequenceIntMedia) 
		de.regnis.q.sequence.media.QSequenceIntMedia media
	protected int[] getAllSymbols (de.regnis.q.sequence.media.QSequenceIntMedia) 
		de.regnis.q.sequence.media.QSequenceIntMedia media
}

QSequenceDiscardingMediaNoConfusionDectector.java
package de.regnis.q.sequence.media
public de.regnis.q.sequence.media.QSequenceDiscardingMediaNoConfusionDectector extends java.lang.Object implements de.regnis.q.sequence.media.QSequenceDiscardingMediaConfusionDetector  {
	private final boolean discardAbsolutes
	public void <init> (boolean) 
		boolean discardAbsolutes
	public void init (int) 
		int symbolCount
	public boolean isAbsolute (int) 
		int occurences
	public boolean isProvisional (int) 
		int occurences
}

QSequenceDiscardingMediaRightBlock.java
package de.regnis.q.sequence.media
public de.regnis.q.sequence.media.QSequenceDiscardingMediaRightBlock extends de.regnis.q.sequence.media.QSequenceDiscardingMediaBlock {
	public void <init> (de.regnis.q.sequence.media.QSequenceIntMedia) 
		de.regnis.q.sequence.media.QSequenceIntMedia media
	protected int[] getAllSymbols (de.regnis.q.sequence.media.QSequenceIntMedia) 
		de.regnis.q.sequence.media.QSequenceIntMedia media
}

QSequenceIntMedia.java
package de.regnis.q.sequence.media
public abstract de.regnis.q.sequence.media.QSequenceIntMedia extends java.lang.Object implements de.regnis.q.sequence.core.QSequenceMedia de.regnis.q.sequence.media.QSequenceMediaComparer  {
	private final de.regnis.q.sequence.core.QSequenceCanceller canceller
	public abstract int getSymbolCount () 
	public abstract int[] getLeftSymbols () 
	public abstract int[] getRightSymbols () 
	protected void <init> (de.regnis.q.sequence.core.QSequenceCanceller) 
		de.regnis.q.sequence.core.QSequenceCanceller canceller
	public final boolean equalsLeft (int, int)  throws de.regnis.q.sequence.core.QSequenceCancelledException 
		int left1
		int left2
	public final boolean equalsRight (int, int)  throws de.regnis.q.sequence.core.QSequenceCancelledException 
		int right1
		int right2
	public final void checkCancelled ()  throws de.regnis.q.sequence.core.QSequenceCancelledException 
}

QSequenceMediaComparer.java
package de.regnis.q.sequence.media
public abstract de.regnis.q.sequence.media.QSequenceMediaComparer extends java.lang.Object {
	public abstract boolean equalsLeft (int, int)  throws de.regnis.q.sequence.core.QSequenceException 
	public abstract boolean equalsRight (int, int)  throws de.regnis.q.sequence.core.QSequenceException 
}

QSequenceMediaDummyIndexTransformer.java
package de.regnis.q.sequence.media
public de.regnis.q.sequence.media.QSequenceMediaDummyIndexTransformer extends java.lang.Object implements de.regnis.q.sequence.media.QSequenceMediaIndexTransformer  {
	private final int mediaLeftLength
	private final int mediaRightLength
	public void <init> (de.regnis.q.sequence.core.QSequenceMedia) 
		de.regnis.q.sequence.core.QSequenceMedia media
	public void <init> (int, int) 
		int mediaLeftLength
		int mediaRightLength
	public int getMediaLeftIndex (int) 
		int index
	public int getMediaRightIndex (int) 
		int index
	public int getMediaLeftLength () 
	public int getMediaRightLength () 
}

QSequenceMediaIndexTransformer.java
package de.regnis.q.sequence.media
public abstract de.regnis.q.sequence.media.QSequenceMediaIndexTransformer extends java.lang.Object {
	public abstract int getMediaLeftIndex (int) 
	public abstract int getMediaRightIndex (int) 
	public abstract int getMediaLeftLength () 
	public abstract int getMediaRightLength () 
}

Indexes created Tue Jul 24 14:28:13 CEST 2018