META-INF/
META-INF/MANIFEST.MF
META-INF/LICENSE.txt
de/
de/regnis/
de/regnis/q/
de/regnis/q/sequence/
de/regnis/q/sequence/QSequenceCommonBlockFactory.class
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) }
de/regnis/q/sequence/QSequenceCommonBlocks.class
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 }
de/regnis/q/sequence/QSequenceDifference.class
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 }
de/regnis/q/sequence/QSequenceDifferenceBlock.class
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 () }
de/regnis/q/sequence/QSequenceDifferenceBlockShifter.class
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 }
de/regnis/q/sequence/QSequenceDifferenceBlockUtils.class
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 }
de/regnis/q/sequence/QSequenceSimpleLCS.class
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 }
de/regnis/q/sequence/QSequenceSimpleLCSCommand.class
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 () }
de/regnis/q/sequence/core/
de/regnis/q/sequence/core/QSequenceAlgorithm.class
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 }
de/regnis/q/sequence/core/QSequenceAssert.class
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> () }
de/regnis/q/sequence/core/QSequenceCancelledException.class
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> () }
de/regnis/q/sequence/core/QSequenceCanceller.class
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 }
de/regnis/q/sequence/core/QSequenceDeePathBackwardExtender.class
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 }
de/regnis/q/sequence/core/QSequenceDeePathExtender.class
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 }
de/regnis/q/sequence/core/QSequenceDeePathExtenderArray.class
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 }
de/regnis/q/sequence/core/QSequenceDeePathForwardExtender.class
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 }
de/regnis/q/sequence/core/QSequenceDummyCanceller.class
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 () }
de/regnis/q/sequence/core/QSequenceException.class
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 }
de/regnis/q/sequence/core/QSequenceMedia.class
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 }
de/regnis/q/sequence/core/QSequenceMiddleSnakeFinder.class
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 }
de/regnis/q/sequence/core/QSequenceMiddleSnakeFinderResult.class
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 }
de/regnis/q/sequence/core/QSequenceRestrictedMedia.class
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 () }
de/regnis/q/sequence/core/QSequenceSnakeRegister.class
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 }
de/regnis/q/sequence/line/
de/regnis/q/sequence/line/QSequenceLine.class
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 () }
de/regnis/q/sequence/line/QSequenceLineCache.class
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 }
de/regnis/q/sequence/line/QSequenceLineFileSystemCache.class
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 }
de/regnis/q/sequence/line/QSequenceLineFileSystemCacheSegment.class
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 }
de/regnis/q/sequence/line/QSequenceLineFileSystemCacheSegments.class
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 }
de/regnis/q/sequence/line/QSequenceLineFixedTempDirectoryFactory.class
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 () }
de/regnis/q/sequence/line/QSequenceLineMedia.class
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> () }
de/regnis/q/sequence/line/QSequenceLineMemoryCache.class
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 () }
de/regnis/q/sequence/line/QSequenceLineRAByteData.class
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 }
de/regnis/q/sequence/line/QSequenceLineRAData.class
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 }
de/regnis/q/sequence/line/QSequenceLineRAFileData.class
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 }
de/regnis/q/sequence/line/QSequenceLineRAFileDataStream.class
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 }
de/regnis/q/sequence/line/QSequenceLineRandomAccessFileFactory$1.class
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 }
de/regnis/q/sequence/line/QSequenceLineRandomAccessFileFactory.class
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> () }
de/regnis/q/sequence/line/QSequenceLineReader.class
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 }
de/regnis/q/sequence/line/QSequenceLineResult.class
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 }
de/regnis/q/sequence/line/QSequenceLineSystemTempDirectoryFactory.class
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 () }
de/regnis/q/sequence/line/QSequenceLineTempDirectoryFactory.class
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 () }
de/regnis/q/sequence/line/diff/
de/regnis/q/sequence/line/diff/QDiffGenerator.class
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 }
de/regnis/q/sequence/line/diff/QDiffGeneratorFactory.class
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) }
de/regnis/q/sequence/line/diff/QDiffManager.class
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> () }
de/regnis/q/sequence/line/diff/QDiffNormalGenerator.class
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 }
de/regnis/q/sequence/line/diff/QDiffSequenceGenerator.class
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 }
de/regnis/q/sequence/line/diff/QDiffUniGenerator.class
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 }
de/regnis/q/sequence/line/simplifier/
de/regnis/q/sequence/line/simplifier/QSequenceLineDummySimplifier.class
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 }
de/regnis/q/sequence/line/simplifier/QSequenceLineEOLUnifyingSimplifier.class
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 }
de/regnis/q/sequence/line/simplifier/QSequenceLineSimplifier.class
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[]) }
de/regnis/q/sequence/line/simplifier/QSequenceLineTeeSimplifier.class
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 }
de/regnis/q/sequence/line/simplifier/QSequenceLineWhiteSpaceReducingSimplifier.class
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 }
de/regnis/q/sequence/line/simplifier/QSequenceLineWhiteSpaceSkippingSimplifier.class
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 }
de/regnis/q/sequence/media/
de/regnis/q/sequence/media/QSequenceCachableMedia.class
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 }
de/regnis/q/sequence/media/QSequenceCachableMediaGetter.class
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 }
de/regnis/q/sequence/media/QSequenceCachableMediaLeftGetter.class
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 }
de/regnis/q/sequence/media/QSequenceCachableMediaRightGetter.class
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 }
de/regnis/q/sequence/media/QSequenceCachingMedia.class
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 () }
de/regnis/q/sequence/media/QSequenceCachingMediaSymbolMap.class
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 }
de/regnis/q/sequence/media/QSequenceDiscardingMedia.class
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 () }
de/regnis/q/sequence/media/QSequenceDiscardingMediaBlock.class
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 }
de/regnis/q/sequence/media/QSequenceDiscardingMediaConfusionDetector.class
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) }
de/regnis/q/sequence/media/QSequenceDiscardingMediaLeftBlock.class
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 }
de/regnis/q/sequence/media/QSequenceDiscardingMediaNoConfusionDectector.class
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 }
de/regnis/q/sequence/media/QSequenceDiscardingMediaRightBlock.class
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 }
de/regnis/q/sequence/media/QSequenceIntMedia.class
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 }
de/regnis/q/sequence/media/QSequenceMediaComparer.class
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 }
de/regnis/q/sequence/media/QSequenceMediaDummyIndexTransformer.class
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 () }
de/regnis/q/sequence/media/QSequenceMediaIndexTransformer.class
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 () }