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milaboratory/milib | src/main/java/com/milaboratory/primitivio/PrimitivIO.java | PrimitivIO.dummySerializer | public static <T> Serializer<T> dummySerializer() {
return new Serializer<T>() {
@Override
public void write(PrimitivO output, T object) {
throw new RuntimeException("Dummy serializer.");
}
@Override
public T read(PrimitivI input) {
... | java | public static <T> Serializer<T> dummySerializer() {
return new Serializer<T>() {
@Override
public void write(PrimitivO output, T object) {
throw new RuntimeException("Dummy serializer.");
}
@Override
public T read(PrimitivI input) {
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/AffineGapAlignmentScoring.java | AffineGapAlignmentScoring.getNucleotideBLASTScoring | public static AffineGapAlignmentScoring<NucleotideSequence> getNucleotideBLASTScoring(int gapOpenPenalty, int gapExtensionPenalty) {
return new AffineGapAlignmentScoring<>(NucleotideSequence.ALPHABET, 5, -4, gapOpenPenalty, gapExtensionPenalty);
} | java | public static AffineGapAlignmentScoring<NucleotideSequence> getNucleotideBLASTScoring(int gapOpenPenalty, int gapExtensionPenalty) {
return new AffineGapAlignmentScoring<>(NucleotideSequence.ALPHABET, 5, -4, gapOpenPenalty, gapExtensionPenalty);
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/AffineGapAlignmentScoring.java | AffineGapAlignmentScoring.getAminoAcidBLASTScoring | public static AffineGapAlignmentScoring<AminoAcidSequence> getAminoAcidBLASTScoring(BLASTMatrix matrix, int gapOpenPenalty, int gapExtensionPenalty) {
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return new AffineGapAlignmentScoring<>(AminoAcidSequence.ALPHABET,
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequencesUtils.java | SequencesUtils.belongsToAlphabet | public static boolean belongsToAlphabet(Alphabet<?> alphabet, String string) {
for (int i = 0; i < string.length(); ++i)
if (alphabet.symbolToCode(string.charAt(i)) == -1)
return false;
return true;
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for (int i = 0; i < string.length(); ++i)
if (alphabet.symbolToCode(string.charAt(i)) == -1)
return false;
return true;
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequencesUtils.java | SequencesUtils.possibleAlphabets | public static Set<Alphabet<?>> possibleAlphabets(String string) {
HashSet<Alphabet<?>> alphabets = new HashSet<>();
for (Alphabet alphabet : Alphabets.getAll()) {
if (belongsToAlphabet(alphabet, string))
alphabets.add(alphabet);
}
return alphabets;
} | java | public static Set<Alphabet<?>> possibleAlphabets(String string) {
HashSet<Alphabet<?>> alphabets = new HashSet<>();
for (Alphabet alphabet : Alphabets.getAll()) {
if (belongsToAlphabet(alphabet, string))
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return alphabets;
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequencesUtils.java | SequencesUtils.concatenate | public static <S extends Seq<S>> S concatenate(S... sequences) {
if (sequences.length == 0)
throw new IllegalArgumentException("Zero arguments");
if (sequences.length == 1)
return sequences[0];
int size = 0;
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int size = 0;
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequencesUtils.java | SequencesUtils.convertNSequenceToBit2Array | public static Bit2Array convertNSequenceToBit2Array(NucleotideSequence seq) {
if (seq.containWildcards())
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bar... | java | public static Bit2Array convertNSequenceToBit2Array(NucleotideSequence seq) {
if (seq.containWildcards())
throw new IllegalArgumentException("Sequences with wildcards are not supported.");
Bit2Array bar = new Bit2Array(seq.size());
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequencesUtils.java | SequencesUtils.convertBit2ArrayToNSequence | public static NucleotideSequence convertBit2ArrayToNSequence(Bit2Array bar) {
SequenceBuilder<NucleotideSequence> seq = NucleotideSequence.ALPHABET.createBuilder().ensureCapacity(bar.size());
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return seq.createAndDest... | java | public static NucleotideSequence convertBit2ArrayToNSequence(Bit2Array bar) {
SequenceBuilder<NucleotideSequence> seq = NucleotideSequence.ALPHABET.createBuilder().ensureCapacity(bar.size());
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milaboratory/milib | src/main/java/com/milaboratory/core/io/util/FileIndexBuilder.java | FileIndexBuilder.setStartingRecordNumber | public FileIndexBuilder setStartingRecordNumber(long recordNumber) {
checkIfDestroyed();
if (index.size() != 1)
throw new IllegalStateException("Initial record is already initialised to " + index.get(0));
startingRecordNumber = recordNumber;
return this;
} | java | public FileIndexBuilder setStartingRecordNumber(long recordNumber) {
checkIfDestroyed();
if (index.size() != 1)
throw new IllegalStateException("Initial record is already initialised to " + index.get(0));
startingRecordNumber = recordNumber;
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milaboratory/milib | src/main/java/com/milaboratory/core/io/util/FileIndexBuilder.java | FileIndexBuilder.putMetadata | public FileIndexBuilder putMetadata(String key, String value) {
checkIfDestroyed();
metadata.put(key, value);
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} | java | public FileIndexBuilder putMetadata(String key, String value) {
checkIfDestroyed();
metadata.put(key, value);
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@param value metadata value
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milaboratory/milib | src/main/java/com/milaboratory/core/io/util/FileIndexBuilder.java | FileIndexBuilder.appendNextRecord | public FileIndexBuilder appendNextRecord(long recordSize) {
checkIfDestroyed();
if (recordSize < 0)
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index.add(startingByte + currentByte);
currentRecord = 0;
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checkIfDestroyed();
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milaboratory/milib | src/main/java/com/milaboratory/core/io/util/IOUtil.java | IOUtil.computeRawVarint64Size | public static int computeRawVarint64Size(final long value) {
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if ((value & (0xffffffffffffffffL << 14)) == 0) return 2;
if ((value & (0xffffffffffffffffL << 21)) == 0) return 3;
if ((value & (0xffffffffffffffffL << 28)) == 0) return... | java | public static int computeRawVarint64Size(final long value) {
if ((value & (0xffffffffffffffffL << 7)) == 0) return 1;
if ((value & (0xffffffffffffffffL << 14)) == 0) return 2;
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milaboratory/milib | src/main/java/com/milaboratory/util/LightFileDescriptor.java | LightFileDescriptor.checkModified | public boolean checkModified(LightFileDescriptor other) {
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if (!name.equals(other.name))
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if (isAlwaysModified() || other.isAlwaysModified())
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if (!name.equals(other.name))
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if (!(hasChecksum() && other.hasChecksum()) && !(hasModificationDate() && other.hasModificationDate()))
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milaboratory/milib | src/main/java/com/milaboratory/util/LightFileDescriptor.java | LightFileDescriptor.toBase64 | public String toBase64() {
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} | java | public String toBase64() {
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequenceQuality.java | SequenceQuality.minValue | public byte minValue() {
if (data.length == 0)
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byte min = Byte.MAX_VALUE;
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return min;
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if (data.length == 0)
return 0;
byte min = Byte.MAX_VALUE;
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min = b;
return min;
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequenceQuality.java | SequenceQuality.meanValue | public byte meanValue() {
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return (byte) (sum / data.length);
} | java | public byte meanValue() {
if (data.length == 0)
return 0;
int sum = 0;
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequenceQuality.java | SequenceQuality.getRange | @Override
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byte[] data = new byte[length];
Arrays.fill(data, qualityValue);
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/BandedLinearAligner.java | BandedLinearAligner.alignLeftAdded | public static Alignment<NucleotideSequence> alignLeftAdded(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2,
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/kaligner2/KAligner2.java | KAligner2.addReference | public int addReference(NucleotideSequence sequence) {
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int id = mapper.addReference(sequence);
assert sequences.size() == id;
sequences.add(sequence);
... | java | public int addReference(NucleotideSequence sequence) {
if (sequence.containWildcards())
throw new IllegalArgumentException("Reference sequences with wildcards not supported.");
int id = mapper.addReference(sequence);
assert sequences.size() == id;
sequences.add(sequence);
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milaboratory/milib | src/main/java/com/milaboratory/core/motif/Motif.java | Motif.or | public Motif<S> or(Motif<S> other) {
if (other.size != size)
throw new IllegalArgumentException("Supports only motifs with the same size as this.");
BitArray result = data.clone();
result.or(other.data);
return new Motif<>(alphabet, size, result);
} | java | public Motif<S> or(Motif<S> other) {
if (other.size != size)
throw new IllegalArgumentException("Supports only motifs with the same size as this.");
BitArray result = data.clone();
result.or(other.data);
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/BandedAligner.java | BandedAligner.alignGlobal | public static Alignment<NucleotideSequence> alignGlobal(final AlignmentScoring<NucleotideSequence> scoring,
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final int offset1, final int l... | java | public static Alignment<NucleotideSequence> alignGlobal(final AlignmentScoring<NucleotideSequence> scoring,
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/Aligner.java | Aligner.alignGlobal | public static <S extends Sequence<S>> Alignment<S> alignGlobal(AlignmentScoring<S> alignmentScoring,
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S seq1, S seq2) {
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/Aligner.java | Aligner.alignLocal | public static <S extends Sequence<S>> Alignment<S> alignLocal(AlignmentScoring<S> alignmentScoring,
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milaboratory/milib | src/main/java/com/milaboratory/core/clustering/Cluster.java | Cluster.processAllChildren | public void processAllChildren(TObjectProcedure<Cluster<T>> procedure) {
if (children == null)
return;
for (Cluster<T> child : children) {
procedure.execute(child);
child.processAllChildren(procedure);
}
} | java | public void processAllChildren(TObjectProcedure<Cluster<T>> procedure) {
if (children == null)
return;
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procedure.execute(child);
child.processAllChildren(procedure);
}
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/Alphabet.java | Alphabet.getEmptySequence | public S getEmptySequence() {
if (empty == null)
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if (empty == null)
empty = createBuilder().createAndDestroy();
}
return empty;
} | java | public S getEmptySequence() {
if (empty == null)
synchronized (this) {
if (empty == null)
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/Alphabet.java | Alphabet.parse | public final S parse(String string) {
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byte code = symbolToCode(string.charAt(i));
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SequenceBuilder<S> builder = createBuilder().ensureCapacity(string.length());
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milaboratory/milib | src/main/java/com/milaboratory/cli/PipelineConfiguration.java | PipelineConfiguration.compatibleWith | public boolean compatibleWith(PipelineConfiguration oth) {
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if (pipelineSteps.length != oth.pipelineSteps.length)
return false;
for (int i = 0; i < pipelineSteps.length; ++i)
if (!pipelineSteps[i].compatibleWith(oth.pipelineSteps[... | java | public boolean compatibleWith(PipelineConfiguration oth) {
if (oth == null)
return false;
if (pipelineSteps.length != oth.pipelineSteps.length)
return false;
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milaboratory/milib | src/main/java/com/milaboratory/cli/PipelineConfiguration.java | PipelineConfiguration.appendStep | public static PipelineConfiguration
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List<String> inputFiles,
ActionConfiguration configuration,
AppVersionInfo versionInfo) {
LightFileDescriptor[] inputDescriptors = inputFiles
.stream()
... | java | public static PipelineConfiguration
appendStep(PipelineConfiguration history,
List<String> inputFiles,
ActionConfiguration configuration,
AppVersionInfo versionInfo) {
LightFileDescriptor[] inputDescriptors = inputFiles
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milaboratory/milib | src/main/java/com/milaboratory/cli/PipelineConfiguration.java | PipelineConfiguration.mkInitial | public static PipelineConfiguration
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/AlignmentUtils.java | AlignmentUtils.shiftIndelsAtHomopolymers | public static <S extends Sequence<S>> Alignment<S> shiftIndelsAtHomopolymers(Alignment<S> alignment) {
return new Alignment<>(alignment.sequence1,
MutationsUtil.shiftIndelsAtHomopolymers(alignment.sequence1, alignment.sequence1Range.getFrom(), alignment.mutations),
alignment.sequ... | java | public static <S extends Sequence<S>> Alignment<S> shiftIndelsAtHomopolymers(Alignment<S> alignment) {
return new Alignment<>(alignment.sequence1,
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milaboratory/milib | src/main/java/com/milaboratory/core/mutations/MutationsUtil.java | MutationsUtil.btopDecode | public static int[] btopDecode(String alignment, Alphabet alphabet) {
Matcher matcher = btopPattern.matcher(alignment);
IntArrayList mutations = new IntArrayList();
int sPosition = 0;
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String g = matcher.group();
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Matcher matcher = btopPattern.matcher(alignment);
IntArrayList mutations = new IntArrayList();
int sPosition = 0;
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String g = matcher.group();
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milaboratory/milib | src/main/java/com/milaboratory/core/mutations/MutationsUtil.java | MutationsUtil.nt2aaDetailed | public static MutationNt2AADescriptor[] nt2aaDetailed(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations,
TranslationParameters translationParameters,
int maxShiftedTriplets) {
Mutat... | java | public static MutationNt2AADescriptor[] nt2aaDetailed(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations,
TranslationParameters translationParameters,
int maxShiftedTriplets) {
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milaboratory/milib | src/main/java/com/milaboratory/core/Range.java | Range.convertPointToRelativePosition | public int convertPointToRelativePosition(int absolutePosition) {
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throw new IllegalArgumentException("Position outside this range (" + absolutePosition + ").");
if (reversed)
return upper - 1 - absolutePosition;
... | java | public int convertPointToRelativePosition(int absolutePosition) {
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milaboratory/milib | src/main/java/com/milaboratory/core/Range.java | Range.convertBoundaryToRelativePosition | public int convertBoundaryToRelativePosition(int absolutePosition) {
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milaboratory/milib | src/main/java/com/milaboratory/core/Range.java | Range.without | @SuppressWarnings("unchecked")
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milaboratory/milib | src/main/java/com/milaboratory/core/Range.java | Range.convertPointToAbsolutePosition | public int convertPointToAbsolutePosition(int relativePosition) {
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milaboratory/milib | src/main/java/com/milaboratory/core/Range.java | Range.convertBoundaryToAbsolutePosition | public int convertBoundaryToAbsolutePosition(int relativePosition) {
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aeshell/aesh-readline | terminal-telnet/src/main/java/org/aesh/terminal/telnet/TelnetConnection.java | TelnetConnection.write | public final void write(byte[] data) {
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send(new byte[]{-1, -1});
prev = i + 1;
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}
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int prev = 0;
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rawWrite(data, prev, i - prev);
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/history/FileHistory.java | FileHistory.readFile | private void readFile() {
if(historyFile.exists()) {
try (BufferedReader reader = new BufferedReader(new FileReader(historyFile))) {
String line;
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push(Parser.toCodePoints(line));
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if(historyFile.exists()) {
try (BufferedReader reader = new BufferedReader(new FileReader(historyFile))) {
String line;
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push(Parser.toCodePoints(line));
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/history/FileHistory.java | FileHistory.writeFile | private void writeFile() throws IOException {
historyFile.delete();
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}
if (historyFilePermission != null) {
... | java | private void writeFile() throws IOException {
historyFile.delete();
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/terminal/impl/WinSysTerminal.java | WinSysTerminal.setVTMode | private static boolean setVTMode() {
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/util/Parser.java | Parser.formatDisplayCompactListTerminalString | public static String formatDisplayCompactListTerminalString(List<TerminalString> displayList, int termWidth) {
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/util/Parser.java | Parser.canDisplayColumns | private static boolean canDisplayColumns(List<TerminalString> displayList, int numRows, int terminalWidth) {
int numColumns = displayList.size() / numRows;
if (displayList.size() % numRows > 0) {
numColumns++;
}
int[] columnSizes = calculateColumnSizes(displayList, numColum... | java | private static boolean canDisplayColumns(List<TerminalString> displayList, int numRows, int terminalWidth) {
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if (displayList.size() % numRows > 0) {
numColumns++;
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/util/Parser.java | Parser.trimOptionName | public static String trimOptionName(String word) {
if (word.startsWith("--"))
return word.substring(2);
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else
return word;
} | java | public static String trimOptionName(String word) {
if (word.startsWith("--"))
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/util/Parser.java | Parser.findStartsWithOperation | public static String findStartsWithOperation(List<? extends CompleteOperation> coList) {
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String s = findStartsWith(co.getFormattedCompletionCandidates());
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tmpList.a... | java | public static String findStartsWithOperation(List<? extends CompleteOperation> coList) {
List<String> tmpList = new ArrayList<>();
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/util/Parser.java | Parser.findCurrentWordFromCursor | public static String findCurrentWordFromCursor(String text, int cursor) {
if (text.length() <= cursor + 1) {
// return last word
if (text.contains(SPACE)) {
if (doWordContainEscapedSpace(text)) {
if (doWordContainOnlyEscapedSpace(text))
... | java | public static String findCurrentWordFromCursor(String text, int cursor) {
if (text.length() <= cursor + 1) {
// return last word
if (text.contains(SPACE)) {
if (doWordContainEscapedSpace(text)) {
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/util/Parser.java | Parser.findEscapedSpaceWordCloseToEnd | public static String findEscapedSpaceWordCloseToEnd(String text) {
int index;
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}
... | java | public static String findEscapedSpaceWordCloseToEnd(String text) {
int index;
String originalText = text;
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/util/Parser.java | Parser.doesStringContainOpenQuote | public static boolean doesStringContainOpenQuote(String text) {
boolean doubleQuote = false;
boolean singleQuote = false;
boolean escapedByBackSlash = false;
// do not parse comment
if (commentPattern.matcher(text).find())
return false;
for (int i = 0; i < te... | java | public static boolean doesStringContainOpenQuote(String text) {
boolean doubleQuote = false;
boolean singleQuote = false;
boolean escapedByBackSlash = false;
// do not parse comment
if (commentPattern.matcher(text).find())
return false;
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/util/Parser.java | Parser.findNumberOfSpacesInWord | public static int findNumberOfSpacesInWord(String word) {
int count = 0;
for (int i = 0; i < word.length(); i++)
if (word.charAt(i) == SPACE_CHAR && (i == 0 || word.charAt(i - 1) != BACK_SLASH))
count++;
return count;
} | java | public static int findNumberOfSpacesInWord(String word) {
int count = 0;
for (int i = 0; i < word.length(); i++)
if (word.charAt(i) == SPACE_CHAR && (i == 0 || word.charAt(i - 1) != BACK_SLASH))
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/util/Parser.java | Parser.trimInFront | public static String trimInFront(String buffer) {
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int count = 0;
for (int i = 0; i < buffer.length(); i++) {
if (buffer.charAt(i) == SPACE_CHAR)
count++;
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break;
}
if (count > 0)
ret... | java | public static String trimInFront(String buffer) {
// remove spaces in front
int count = 0;
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if (buffer.charAt(i) == SPACE_CHAR)
count++;
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/editing/InputrcParser.java | InputrcParser.mapQuoteKeys | public static int[] mapQuoteKeys(String keys) {
if(keys != null && keys.length() > 1)
return mapKeys(keys.substring(1));
else
return null;
} | java | public static int[] mapQuoteKeys(String keys) {
if(keys != null && keys.length() > 1)
return mapKeys(keys.substring(1));
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return null;
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aeshell/aesh-readline | terminal-api/src/main/java/org/aesh/utils/ANSI.java | ANSI.printAnsi | public static int[] printAnsi(char... out) {
int[] ansi = new int[out.length+2];
ansi[0] = 27;
ansi[1] = '[';
int counter = 0;
for (char anOut : out) {
if (anOut == '\t') {
Arrays.fill(ansi, counter + 2, counter + 2 + TAB, ' ');
counter... | java | public static int[] printAnsi(char... out) {
int[] ansi = new int[out.length+2];
ansi[0] = 27;
ansi[1] = '[';
int counter = 0;
for (char anOut : out) {
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osglworks/java-di | src/main/java/org/osgl/inject/util/AnnotationUtil.java | AnnotationUtil.createAnnotation | @SuppressWarnings("unchecked")
public static <T extends Annotation> T createAnnotation(final Class<T> clazz) {
return (T) Proxy.newProxyInstance(clazz.getClassLoader(), new Class[]{clazz, Annotation.class}, new SimpleAnnoInvocationHandler(clazz));
} | java | @SuppressWarnings("unchecked")
public static <T extends Annotation> T createAnnotation(final Class<T> clazz) {
return (T) Proxy.newProxyInstance(clazz.getClassLoader(), new Class[]{clazz, Annotation.class}, new SimpleAnnoInvocationHandler(clazz));
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osglworks/java-di | src/main/java/org/osgl/inject/util/AnnotationUtil.java | AnnotationUtil.hashMember | static int hashMember(String name, Object value) {
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}
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if (value.getClass().isArray()) {
return part1 ^ arrayMemberHash(value.getClass().getComponentType(), value);
}
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osglworks/java-di | src/main/java/org/osgl/inject/BeanSpec.java | BeanSpec.beanSpecOf | private BeanSpec beanSpecOf(Field field, Type genericType) {
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// int len = typeArgs.size();
// for (int i = 0; i < len; ++i) {
// if (genericType.equals(typeArgs.get(i))) {
// return of(field, typeImpls.get(i), injector());
// ... | java | private BeanSpec beanSpecOf(Field field, Type genericType) {
return of(field, genericType, injector);
// int len = typeArgs.size();
// for (int i = 0; i < len; ++i) {
// if (genericType.equals(typeArgs.get(i))) {
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osglworks/java-di | src/main/java/org/osgl/inject/BeanSpec.java | BeanSpec.storeTagAnnotation | private void storeTagAnnotation(Annotation anno) {
Class<? extends Annotation> annoType = anno.annotationType();
Annotation[] tags = annoType.getAnnotations();
for (Annotation tag : tags) {
Class<? extends Annotation> tagType = tag.annotationType();
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Class<? extends Annotation> annoType = anno.annotationType();
Annotation[] tags = annoType.getAnnotations();
for (Annotation tag : tags) {
Class<? extends Annotation> tagType = tag.annotationType();
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att/openstacksdk | openstack-java-sdk/openstack-client/src/main/java/com/woorea/openstack/base/client/OpenStackRequest.java | OpenStackRequest.queryString | public OpenStackRequest<R> queryString(String queryString) {
if (queryString != null) {
String[] params = queryString.split("&");
for (String param : params) {
String[] s = param.split("=");
if (s[0] != null && s[1] != null) {
queryPara... | java | public OpenStackRequest<R> queryString(String queryString) {
if (queryString != null) {
String[] params = queryString.split("&");
for (String param : params) {
String[] s = param.split("=");
if (s[0] != null && s[1] != null) {
queryPara... | [
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att/openstacksdk | openstack-java-sdk/nova-client/src/main/java/com/woorea/openstack/nova/api/ServersResource.java | ServersResource.evacuate | public EvacuateAction evacuate(String serverId, String host) {
return evacuate(serverId, host, null, null);
} | java | public EvacuateAction evacuate(String serverId, String host) {
return evacuate(serverId, host, null, null);
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att/openstacksdk | openstack-java-sdk/openstack-client-connectors/jersey-connector/src/main/java/com/woorea/openstack/connector/JerseyConnector.java | JerseyConnector.getSSLContext | private SSLContext getSSLContext() throws NoSuchAlgorithmException, KeyManagementException {
SSLContext sslContext = SSLContext.getInstance("SSL");
sslContext.init(null, new TrustManager[] {
new X509TrustManager() {
@Override
public void checkClientTrusted(X50... | java | private SSLContext getSSLContext() throws NoSuchAlgorithmException, KeyManagementException {
SSLContext sslContext = SSLContext.getInstance("SSL");
sslContext.init(null, new TrustManager[] {
new X509TrustManager() {
@Override
public void checkClientTrusted(X50... | [
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/DockerSlaveTemplate.java | DockerSlaveTemplate.getRetentionStrategyCopy | public RetentionStrategy getRetentionStrategyCopy() {
if (retentionStrategy instanceof DockerOnceRetentionStrategy) {
DockerOnceRetentionStrategy onceRetention = (DockerOnceRetentionStrategy) retentionStrategy;
return new DockerOnceRetentionStrategy(onceRetention.getIdleMinutes());
... | java | public RetentionStrategy getRetentionStrategyCopy() {
if (retentionStrategy instanceof DockerOnceRetentionStrategy) {
DockerOnceRetentionStrategy onceRetention = (DockerOnceRetentionStrategy) retentionStrategy;
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/DockerSlaveTemplate.java | DockerSlaveTemplate.readResolve | @SuppressWarnings("unused")
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/launcher/DockerComputerJNLPLauncher.java | DockerComputerJNLPLauncher.getPreparedLauncher | @Override
public DockerComputerLauncher getPreparedLauncher(String cloudId, DockerSlaveTemplate template,
InspectContainerResponse containerInspectResponse) {
final DockerComputerJNLPLauncher cloneJNLPlauncher = new DockerComputerJNLPLauncher();
clone... | java | @Override
public DockerComputerLauncher getPreparedLauncher(String cloudId, DockerSlaveTemplate template,
InspectContainerResponse containerInspectResponse) {
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/DockerCloud.java | DockerCloud.runContainer | public String runContainer(DockerSlaveTemplate slaveTemplate) throws DockerException, IOException {
final DockerCreateContainer dockerCreateContainer = slaveTemplate.getDockerContainerLifecycle().getCreateContainer();
final String image = slaveTemplate.getDockerContainerLifecycle().getImage();
... | java | public String runContainer(DockerSlaveTemplate slaveTemplate) throws DockerException, IOException {
final DockerCreateContainer dockerCreateContainer = slaveTemplate.getDockerContainerLifecycle().getCreateContainer();
final String image = slaveTemplate.getDockerContainerLifecycle().getImage();
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/DockerCloud.java | DockerCloud.appendContainerConfig | private void appendContainerConfig(DockerSlaveTemplate slaveTemplate, CreateContainerCmd containerConfig) {
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Map<String, String> labels = containerConfig.getLabels();
if (labels == null) labels = new HashMap<>();
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/DockerCloud.java | DockerCloud.determineOsType | private OsType determineOsType(String imageId) {
InspectImageResponse ir = getClient().inspectImageCmd(imageId).exec();
if ("linux".equalsIgnoreCase(ir.getOs())) {
LOG.trace("Detected LINUX operating system for image: {}", imageId);
return OsType.LINUX;
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InspectImageResponse ir = getClient().inspectImageCmd(imageId).exec();
if ("linux".equalsIgnoreCase(ir.getOs())) {
LOG.trace("Detected LINUX operating system for image: {}", imageId);
return OsType.LINUX;
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/DockerCloud.java | DockerCloud.countCurrentDockerSlaves | public int countCurrentDockerSlaves(final DockerSlaveTemplate template) throws Exception {
int count = 0;
List<Container> containers = getClient().listContainersCmd().exec();
for (Container container : containers) {
final Map<String, String> labels = container.getLabels();
... | java | public int countCurrentDockerSlaves(final DockerSlaveTemplate template) throws Exception {
int count = 0;
List<Container> containers = getClient().listContainersCmd().exec();
for (Container container : containers) {
final Map<String, String> labels = container.getLabels();
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/DockerCloud.java | DockerCloud.addProvisionedSlave | private synchronized boolean addProvisionedSlave(DockerSlaveTemplate template) throws Exception {
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/utils/DockerFunctions.java | DockerFunctions.getDockerComputerLauncherDescriptors | public static List<Descriptor<ComputerLauncher>> getDockerComputerLauncherDescriptors() {
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launchers.add(getInstance().getDescriptor(DockerComputerSSHLauncher.class));
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/utils/DockerFunctions.java | DockerFunctions.getDockerRetentionStrategyDescriptors | public static List<Descriptor<RetentionStrategy<?>>> getDockerRetentionStrategyDescriptors() {
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strategies.add(getInstance().getDescriptor(DockerOnceRetentionStrategy.class));
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List<Descriptor<RetentionStrategy<?>>> strategies = new ArrayList<>();
strategies.add(getInstance().getDescriptor(DockerOnceRetentionStrategy.class));
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/utils/DockerFunctions.java | DockerFunctions.getAllDockerClouds | @Nonnull
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} | java | @Nonnull
public static List<DockerCloud> getAllDockerClouds() {
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/commons/DockerContainerRestartPolicy.java | DockerContainerRestartPolicy.getRestartPolicy | @CheckForNull
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if (isNull(policyName)) return null;
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public RestartPolicy getRestartPolicy() {
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/utils/VariableUtils.java | VariableUtils.resolveVar | public static String resolveVar(String var, Run run, TaskListener taskListener) {
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KostyaSha/yet-another-docker-plugin | yet-another-docker-its/src/main/java/hudson/cli/DockerCLI.java | DockerCLI.getCliTcpPort | protected CliPort getCliTcpPort(String jenkinsAddr) throws IOException {
URL jenkinsUrl = new URL(jenkinsAddr);
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URL jenkinsUrl = new URL(jenkinsAddr);
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KostyaSha/yet-another-docker-plugin | yet-another-docker-its/src/main/java/hudson/cli/DockerCLI.java | DockerCLI.close | public void close() throws IOException, InterruptedException {
channel.close();
channel.join();
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c.close();
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channel.close();
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] | 40b12e39ff94c3834cff7e028c3dd01c88e87d77 | https://github.com/KostyaSha/yet-another-docker-plugin/blob/40b12e39ff94c3834cff7e028c3dd01c88e87d77/yet-another-docker-its/src/main/java/hudson/cli/DockerCLI.java#L232-L239 | train |
KostyaSha/yet-another-docker-plugin | yet-another-docker-its/src/main/java/hudson/cli/DockerCLI.java | DockerCLI.upgrade | public void upgrade() {
ByteArrayOutputStream out = new ByteArrayOutputStream();
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.getBytes(defaultCharset()... | java | public void upgrade() {
ByteArrayOutputStream out = new ByteArrayOutputStream();
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/steps/DockerShellStep.java | DockerShellStep.getEnvVars | protected static EnvVars getEnvVars(Run run, TaskListener listener) throws IOException, InterruptedException {
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/steps/DockerShellStep.java | DockerShellStep.insertLabels | protected static void insertLabels(CreateContainerCmd containerConfig, Run run) {
// add tags
Map<String, String> labels = containerConfig.getLabels();
if (labels == null) labels = new HashMap<>();
labels.put("YAD_PLUGIN", DockerShellStep.class.getName());
labels.put("JENKINS_JO... | java | protected static void insertLabels(CreateContainerCmd containerConfig, Run run) {
// add tags
Map<String, String> labels = containerConfig.getLabels();
if (labels == null) labels = new HashMap<>();
labels.put("YAD_PLUGIN", DockerShellStep.class.getName());
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KostyaSha/yet-another-docker-plugin | yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/DockerProvisioningStrategy.java | DockerProvisioningStrategy.setEnabled | public void setEnabled(boolean enabled) {
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DockerProvisioningStrategy strategy = strategies.get(DockerProvisioningStrategy.class);
if (isNull(strategy)) {
LOG.debug("YAD strategy was nu... | java | public void setEnabled(boolean enabled) {
final ExtensionList<NodeProvisioner.Strategy> strategies = lookup(NodeProvisioner.Strategy.class);
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/dht/Range.java | Range.isWrapAround | public static <T extends RingPosition<T>> boolean isWrapAround(T left, T right)
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/dht/Range.java | Range.subtractContained | private ArrayList<Range<T>> subtractContained(Range<T> contained)
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dif... | java | private ArrayList<Range<T>> subtractContained(Range<T> contained)
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ArrayList<Range<T>> difference = new ArrayList<Range<T>>(2);
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/dht/Range.java | Range.deoverlap | private static <T extends RingPosition<T>> List<Range<T>> deoverlap(List<Range<T>> ranges)
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/dht/Range.java | Range.makeRowRange | public static Range<RowPosition> makeRowRange(Token left, Token right, IPartitioner partitioner)
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return new Range<RowPosition>(left.maxKeyBound(partitioner), right.maxKeyBound(partitioner), partitioner);
} | java | public static Range<RowPosition> makeRowRange(Token left, Token right, IPartitioner partitioner)
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/db/AbstractNativeCell.java | AbstractNativeCell.compareTo | @Inline
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/db/CounterMutation.java | CounterMutation.processModifications | private ColumnFamily processModifications(ColumnFamily changesCF)
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/db/CounterMutation.java | CounterMutation.getCurrentValuesFromCache | private int getCurrentValuesFromCache(List<CounterUpdateCell> counterUpdateCells,
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int cacheMisses = 0;
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... | java | private int getCurrentValuesFromCache(List<CounterUpdateCell> counterUpdateCells,
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/db/CounterMutation.java | CounterMutation.getCurrentValuesFromCFS | private void getCurrentValuesFromCFS(List<CounterUpdateCell> counterUpdateCells,
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/cql3/functions/BytesConversionFcts.java | BytesConversionFcts.makeToBlobFunction | public static Function makeToBlobFunction(AbstractType<?> fromType)
{
String name = fromType.asCQL3Type() + "asblob";
return new AbstractFunction(name, BytesType.instance, fromType)
{
public ByteBuffer execute(List<ByteBuffer> parameters)
{
return para... | java | public static Function makeToBlobFunction(AbstractType<?> fromType)
{
String name = fromType.asCQL3Type() + "asblob";
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/hadoop/cql3/CqlRecordWriter.java | RangeClient.run | public void run()
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bindVariables = queue.take();
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catch (InterruptedException e)
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/hadoop/cql3/CqlRecordWriter.java | RangeClient.preparedStatement | private int preparedStatement(Cassandra.Client client)
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Integer itemId = preparedStatements.get(client);
if (itemId == null)
{
CqlPreparedResult result;
try
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result = client.prepare_cql3_query(ByteBufferUti... | java | private int preparedStatement(Cassandra.Client client)
{
Integer itemId = preparedStatements.get(client);
if (itemId == null)
{
CqlPreparedResult result;
try
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] | f6416b43ad5309083349ad56266450fa8c6a2106 | https://github.com/Stratio/stratio-cassandra/blob/f6416b43ad5309083349ad56266450fa8c6a2106/src/java/org/apache/cassandra/hadoop/cql3/CqlRecordWriter.java#L292-L315 | train |
Stratio/stratio-cassandra | src/java/org/apache/cassandra/repair/Validator.java | Validator.complete | public void complete()
{
completeTree();
StageManager.getStage(Stage.ANTI_ENTROPY).execute(this);
if (logger.isDebugEnabled())
{
// log distribution of rows in tree
logger.debug("Validated {} partitions for {}. Partitions per leaf are:", validated, desc.ses... | java | public void complete()
{
completeTree();
StageManager.getStage(Stage.ANTI_ENTROPY).execute(this);
if (logger.isDebugEnabled())
{
// log distribution of rows in tree
logger.debug("Validated {} partitions for {}. Partitions per leaf are:", validated, desc.ses... | [
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/repair/Validator.java | Validator.fail | public void fail()
{
logger.error("Failed creating a merkle tree for {}, {} (see log for details)", desc, initiator);
// send fail message only to nodes >= version 2.0
MessagingService.instance().sendOneWay(new ValidationComplete(desc).createMessage(), initiator);
} | java | public void fail()
{
logger.error("Failed creating a merkle tree for {}, {} (see log for details)", desc, initiator);
// send fail message only to nodes >= version 2.0
MessagingService.instance().sendOneWay(new ValidationComplete(desc).createMessage(), initiator);
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/repair/Validator.java | Validator.run | public void run()
{
// respond to the request that triggered this validation
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logger.info(String.format("[repair #%s] Sending completed merkle tree to %s for %s/%s", desc.sessionId, initiator, desc.keyspace, desc.columnFamily));
... | java | public void run()
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// respond to the request that triggered this validation
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/concurrent/SEPExecutor.java | SEPExecutor.maybeSchedule | boolean maybeSchedule()
{
if (pool.spinningCount.get() > 0 || !takeWorkPermit(true))
return false;
pool.schedule(new Work(this));
return true;
} | java | boolean maybeSchedule()
{
if (pool.spinningCount.get() > 0 || !takeWorkPermit(true))
return false;
pool.schedule(new Work(this));
return true;
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/concurrent/SEPExecutor.java | SEPExecutor.returnWorkPermit | void returnWorkPermit()
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while (true)
{
long current = permits.get();
int workPermits = workPermits(current);
if (permits.compareAndSet(current, updateWorkPermits(current, workPermits + 1)))
return;
}
} | java | void returnWorkPermit()
{
while (true)
{
long current = permits.get();
int workPermits = workPermits(current);
if (permits.compareAndSet(current, updateWorkPermits(current, workPermits + 1)))
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/cql3/ErrorCollector.java | ErrorCollector.areTokensValid | private static boolean areTokensValid(Token... tokens)
{
for (Token token : tokens)
{
if (!isTokenValid(token))
return false;
}
return true;
} | java | private static boolean areTokensValid(Token... tokens)
{
for (Token token : tokens)
{
if (!isTokenValid(token))
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return true;
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/cql3/ErrorCollector.java | ErrorCollector.highlightToken | private static String highlightToken(String line, Token token)
{
String newLine = insertChar(line, getLastCharPositionInLine(token), ']');
return insertChar(newLine, token.getCharPositionInLine(), '[');
} | java | private static String highlightToken(String line, Token token)
{
String newLine = insertChar(line, getLastCharPositionInLine(token), ']');
return insertChar(newLine, token.getCharPositionInLine(), '[');
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/repair/Differencer.java | Differencer.run | public void run()
{
// compare trees, and collect differences
differences.addAll(MerkleTree.difference(r1.tree, r2.tree));
// choose a repair method based on the significance of the difference
String format = String.format("[repair #%s] Endpoints %s and %s %%s for %s", desc.sessionI... | java | public void run()
{
// compare trees, and collect differences
differences.addAll(MerkleTree.difference(r1.tree, r2.tree));
// choose a repair method based on the significance of the difference
String format = String.format("[repair #%s] Endpoints %s and %s %%s for %s", desc.sessionI... | [
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/repair/Differencer.java | Differencer.minEndpoint | private InetAddress minEndpoint()
{
return FBUtilities.compareUnsigned(r1.endpoint.getAddress(), r2.endpoint.getAddress()) < 0
? r1.endpoint
: r2.endpoint;
} | java | private InetAddress minEndpoint()
{
return FBUtilities.compareUnsigned(r1.endpoint.getAddress(), r2.endpoint.getAddress()) < 0
? r1.endpoint
: r2.endpoint;
} | [
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