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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) {
throw new RuntimeException("Dummy serializer.");
}
@Override
public boolean isReference() {
return true;
}
@Override
public boolean handlesReference() {
return false;
}
};
} | 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) {
throw new RuntimeException("Dummy serializer.");
}
@Override
public boolean isReference() {
return true;
}
@Override
public boolean handlesReference() {
return false;
}
};
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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) {
return new AffineGapAlignmentScoring<>(AminoAcidSequence.ALPHABET,
matrix.getMatrix(),
gapOpenPenalty, gapExtensionPenalty);
} | java | public static AffineGapAlignmentScoring<AminoAcidSequence> getAminoAcidBLASTScoring(BLASTMatrix matrix, int gapOpenPenalty, int gapExtensionPenalty) {
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;
} | java | 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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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;
for (S s : sequences)
size += s.size();
SeqBuilder<S> builder = sequences[0].getBuilder().ensureCapacity(size);
for (S s : sequences)
builder.append(s);
return builder.createAndDestroy();
} | java | 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;
for (S s : sequences)
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SeqBuilder<S> builder = sequences[0].getBuilder().ensureCapacity(size);
for (S s : sequences)
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return builder.createAndDestroy();
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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())
throw new IllegalArgumentException("Sequences with wildcards are not supported.");
Bit2Array bar = new Bit2Array(seq.size());
for (int i = 0; i < seq.size(); i++)
bar.set(i, seq.codeAt(i));
return 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());
for (int i = 0; i < seq.size(); i++)
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return bar;
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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());
for (int i = 0; i < bar.size(); i++)
seq.append((byte) bar.get(i));
return seq.createAndDestroy();
} | java | public static NucleotideSequence convertBit2ArrayToNSequence(Bit2Array bar) {
SequenceBuilder<NucleotideSequence> seq = NucleotideSequence.ALPHABET.createBuilder().ensureCapacity(bar.size());
for (int i = 0; i < bar.size(); i++)
seq.append((byte) bar.get(i));
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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) {
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currentRecord = 0;
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currentByte += recordSize;
++currentRecord;
return this;
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return this;
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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) {
if ((value & (0xffffffffffffffffL << 7)) == 0) return 1;
if ((value & (0xffffffffffffffffL << 14)) == 0) return 2;
if ((value & (0xffffffffffffffffL << 21)) == 0) return 3;
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if ((value & (0xffffffffffffffffL << 63)) == 0) return 9;
return 10;
} | java | public static int computeRawVarint64Size(final long value) {
if ((value & (0xffffffffffffffffL << 7)) == 0) return 1;
if ((value & (0xffffffffffffffffL << 14)) == 0) return 2;
if ((value & (0xffffffffffffffffL << 21)) == 0) return 3;
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if ((value & (0xffffffffffffffffL << 56)) == 0) return 8;
if ((value & (0xffffffffffffffffL << 63)) == 0) return 9;
return 10;
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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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return false;
} | java | public boolean checkModified(LightFileDescriptor other) {
if (isAlwaysModified() || other.isAlwaysModified())
return true;
if (!name.equals(other.name))
return true;
if (!(hasChecksum() && other.hasChecksum()) && !(hasModificationDate() && other.hasModificationDate()))
// No intersecting characteristics, cant compare => file is modified
return true;
if (hasChecksum() && other.hasChecksum() && !Arrays.equals(checksum, other.checksum))
return true;
if (hasModificationDate() && other.hasModificationDate() && !lastModified.equals(other.lastModified))
return true;
return false;
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milaboratory/milib | src/main/java/com/milaboratory/util/LightFileDescriptor.java | LightFileDescriptor.toBase64 | public String toBase64() {
return name
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} | java | public String toBase64() {
return name
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] | 2349b3dccdd3c7948643760e570238d6e30d5a34 | https://github.com/milaboratory/milib/blob/2349b3dccdd3c7948643760e570238d6e30d5a34/src/main/java/com/milaboratory/util/LightFileDescriptor.java#L200-L204 | train |
milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequenceQuality.java | SequenceQuality.minValue | public byte minValue() {
if (data.length == 0)
return 0;
byte min = Byte.MAX_VALUE;
for (byte b : data)
if (b < min)
min = b;
return min;
} | java | public byte minValue() {
if (data.length == 0)
return 0;
byte min = Byte.MAX_VALUE;
for (byte b : data)
if (b < min)
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 0;
int sum = 0;
for (byte b : data)
sum += b;
return (byte) (sum / data.length);
} | java | public byte meanValue() {
if (data.length == 0)
return 0;
int sum = 0;
for (byte b : data)
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequenceQuality.java | SequenceQuality.getRange | @Override
public SequenceQuality getRange(Range range) {
byte[] rdata = Arrays.copyOfRange(data, range.getLower(), range.getUpper());
if (range.isReverse())
ArraysUtils.reverse(rdata);
return new SequenceQuality(rdata, true);
} | java | @Override
public SequenceQuality getRange(Range range) {
byte[] rdata = Arrays.copyOfRange(data, range.getLower(), range.getUpper());
if (range.isReverse())
ArraysUtils.reverse(rdata);
return new SequenceQuality(rdata, true);
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequenceQuality.java | SequenceQuality.encodeTo | public void encodeTo(QualityFormat format, byte[] buffer, int offset) {
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byte[] copy = new byte[data.length];
for (int i = copy.length - 1; i >= 0; --i)
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return copy;
} | java | public void encodeTo(QualityFormat format, byte[] buffer, int offset) {
byte vo = format.getOffset();
for (int i = 0; i < data.length; ++i)
buffer[offset++] = (byte) (data[i] + vo);
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/**
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*
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/SequenceQuality.java | SequenceQuality.getUniformQuality | public static SequenceQuality getUniformQuality(byte qualityValue, int length) {
byte[] data = new byte[length];
Arrays.fill(data, qualityValue);
return new SequenceQuality(data, true);
} | java | public static SequenceQuality getUniformQuality(byte qualityValue, int length) {
byte[] data = new byte[length];
Arrays.fill(data, qualityValue);
return new SequenceQuality(data, true);
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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,
int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2,
int width) {
try {
MutationsBuilder<NucleotideSequence> mutations = new MutationsBuilder<>(NucleotideSequence.ALPHABET);
BandedSemiLocalResult result = alignLeftAdded0(scoring, seq1, seq2,
offset1, length1, addedNucleotides1, offset2, length2, addedNucleotides2,
width, mutations, AlignmentCache.get());
return new Alignment<>(seq1, mutations.createAndDestroy(),
new Range(result.sequence1Stop, offset1 + length1), new Range(result.sequence2Stop, offset2 + length2),
result.score);
} finally {
AlignmentCache.release();
}
} | java | public static Alignment<NucleotideSequence> alignLeftAdded(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2,
int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2,
int width) {
try {
MutationsBuilder<NucleotideSequence> mutations = new MutationsBuilder<>(NucleotideSequence.ALPHABET);
BandedSemiLocalResult result = alignLeftAdded0(scoring, seq1, seq2,
offset1, length1, addedNucleotides1, offset2, length2, addedNucleotides2,
width, mutations, AlignmentCache.get());
return new Alignment<>(seq1, mutations.createAndDestroy(),
new Range(result.sequence1Stop, offset1 + length1), new Range(result.sequence2Stop, offset2 + length2),
result.score);
} finally {
AlignmentCache.release();
}
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milaboratory/milib | src/main/java/com/milaboratory/core/alignment/kaligner2/KAligner2.java | KAligner2.addReference | 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);
return id;
} | 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);
return id;
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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,
final NucleotideSequence seq1, final NucleotideSequence seq2,
final int offset1, final int length1,
final int offset2, final int length2,
final int width) {
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else
return BandedLinearAligner.align((LinearGapAlignmentScoring<NucleotideSequence>) scoring, seq1, seq2, offset1, length1, offset2, length2, width);
} | java | public static Alignment<NucleotideSequence> alignGlobal(final AlignmentScoring<NucleotideSequence> scoring,
final NucleotideSequence seq1, final NucleotideSequence seq2,
final int offset1, final int length1,
final int offset2, final int length2,
final int width) {
if (scoring instanceof AffineGapAlignmentScoring)
return BandedAffineAligner.align((AffineGapAlignmentScoring<NucleotideSequence>) scoring, seq1, seq2, offset1, length1, offset2, length2, width);
else
return BandedLinearAligner.align((LinearGapAlignmentScoring<NucleotideSequence>) scoring, seq1, seq2, offset1, length1, offset2, length2, width);
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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,
S seq1, S seq2) {
if (alignmentScoring instanceof AffineGapAlignmentScoring)
return alignGlobalAffine((AffineGapAlignmentScoring<S>) alignmentScoring, seq1, seq2);
if (alignmentScoring instanceof LinearGapAlignmentScoring)
return alignGlobalLinear((LinearGapAlignmentScoring<S>) alignmentScoring, seq1, seq2);
throw new RuntimeException("Unknown scoring type.");
} | java | public static <S extends Sequence<S>> Alignment<S> alignGlobal(AlignmentScoring<S> alignmentScoring,
S seq1, S seq2) {
if (alignmentScoring instanceof AffineGapAlignmentScoring)
return alignGlobalAffine((AffineGapAlignmentScoring<S>) alignmentScoring, seq1, seq2);
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throw new RuntimeException("Unknown scoring type.");
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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,
S seq1, S seq2) {
if (alignmentScoring instanceof AffineGapAlignmentScoring)
return alignLocalAffine((AffineGapAlignmentScoring<S>) alignmentScoring, seq1, seq2);
if (alignmentScoring instanceof LinearGapAlignmentScoring)
return alignLocalLinear((LinearGapAlignmentScoring<S>) alignmentScoring, seq1, seq2);
throw new RuntimeException("Unknown scoring type.");
} | java | public static <S extends Sequence<S>> Alignment<S> alignLocal(AlignmentScoring<S> alignmentScoring,
S seq1, S seq2) {
if (alignmentScoring instanceof AffineGapAlignmentScoring)
return alignLocalAffine((AffineGapAlignmentScoring<S>) alignmentScoring, seq1, seq2);
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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;
for (Cluster<T> child : children) {
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)
synchronized (this) {
if (empty == null)
empty = createBuilder().createAndDestroy();
}
return empty;
} | java | public S getEmptySequence() {
if (empty == null)
synchronized (this) {
if (empty == null)
empty = createBuilder().createAndDestroy();
}
return empty;
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milaboratory/milib | src/main/java/com/milaboratory/core/sequence/Alphabet.java | Alphabet.parse | public final S parse(String string) {
SequenceBuilder<S> builder = createBuilder().ensureCapacity(string.length());
for (int i = 0; i < string.length(); ++i) {
byte code = symbolToCode(string.charAt(i));
if (code == -1)
throw new IllegalArgumentException("Letter \'" + string.charAt(i) + "\' is not defined in \'" + toString() + "\'.");
builder.append(code);
}
return builder.createAndDestroy();
} | java | public final S parse(String string) {
SequenceBuilder<S> builder = createBuilder().ensureCapacity(string.length());
for (int i = 0; i < string.length(); ++i) {
byte code = symbolToCode(string.charAt(i));
if (code == -1)
throw new IllegalArgumentException("Letter \'" + string.charAt(i) + "\' is not defined in \'" + toString() + "\'.");
builder.append(code);
}
return builder.createAndDestroy();
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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)
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return false;
return true;
} | java | public boolean compatibleWith(PipelineConfiguration oth) {
if (oth == null)
return false;
if (pipelineSteps.length != oth.pipelineSteps.length)
return false;
for (int i = 0; i < pipelineSteps.length; ++i)
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return true;
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milaboratory/milib | src/main/java/com/milaboratory/cli/PipelineConfiguration.java | PipelineConfiguration.appendStep | public static PipelineConfiguration
appendStep(PipelineConfiguration history,
List<String> inputFiles,
ActionConfiguration configuration,
AppVersionInfo versionInfo) {
LightFileDescriptor[] inputDescriptors = inputFiles
.stream()
.map(f -> LightFileDescriptor.calculate(Paths.get(f)))
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return new PipelineConfiguration(
Stream.concat(
Stream.of(history.pipelineSteps),
Stream.of(new PipelineStep(versionInfo, inputDescriptors, configuration))
).toArray(PipelineStep[]::new));
} | java | public static PipelineConfiguration
appendStep(PipelineConfiguration history,
List<String> inputFiles,
ActionConfiguration configuration,
AppVersionInfo versionInfo) {
LightFileDescriptor[] inputDescriptors = inputFiles
.stream()
.map(f -> LightFileDescriptor.calculate(Paths.get(f)))
.toArray(LightFileDescriptor[]::new);
return new PipelineConfiguration(
Stream.concat(
Stream.of(history.pipelineSteps),
Stream.of(new PipelineStep(versionInfo, inputDescriptors, configuration))
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milaboratory/milib | src/main/java/com/milaboratory/cli/PipelineConfiguration.java | PipelineConfiguration.mkInitial | public static PipelineConfiguration
mkInitial(List<String> inputFiles,
ActionConfiguration configuration,
AppVersionInfo versionInfo) {
LightFileDescriptor[] inputDescriptors = inputFiles.stream()
.map(f -> LightFileDescriptor.calculate(Paths.get(f))).toArray(LightFileDescriptor[]::new);
return new PipelineConfiguration(
new PipelineStep[] { new PipelineStep(versionInfo, inputDescriptors, configuration) });
} | java | public static PipelineConfiguration
mkInitial(List<String> inputFiles,
ActionConfiguration configuration,
AppVersionInfo versionInfo) {
LightFileDescriptor[] inputDescriptors = inputFiles.stream()
.map(f -> LightFileDescriptor.calculate(Paths.get(f))).toArray(LightFileDescriptor[]::new);
return new PipelineConfiguration(
new PipelineStep[] { new PipelineStep(versionInfo, inputDescriptors, configuration) });
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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.sequence1Range, alignment.sequence2Range, alignment.score);
} | java | 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.sequence1Range, alignment.sequence2Range, alignment.score);
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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;
while (matcher.find()) {
String g = matcher.group();
if (isPositiveInteger(g))
sPosition += Integer.parseInt(g);
else if (g.charAt(0) == '-') {
mutations.add(createDeletion(sPosition, alphabet.symbolToCodeWithException(g.charAt(1))));
++sPosition;
} else if (g.charAt(1) == '-')
mutations.add(createInsertion(sPosition, alphabet.symbolToCodeWithException(g.charAt(0))));
else {
mutations.add(createSubstitution(sPosition, alphabet.symbolToCodeWithException(g.charAt(1)), alphabet.symbolToCodeWithException(g.charAt(0))));
++sPosition;
}
}
return mutations.toArray();
} | java | public static int[] btopDecode(String alignment, Alphabet alphabet) {
Matcher matcher = btopPattern.matcher(alignment);
IntArrayList mutations = new IntArrayList();
int sPosition = 0;
while (matcher.find()) {
String g = matcher.group();
if (isPositiveInteger(g))
sPosition += Integer.parseInt(g);
else if (g.charAt(0) == '-') {
mutations.add(createDeletion(sPosition, alphabet.symbolToCodeWithException(g.charAt(1))));
++sPosition;
} else if (g.charAt(1) == '-')
mutations.add(createInsertion(sPosition, alphabet.symbolToCodeWithException(g.charAt(0))));
else {
mutations.add(createSubstitution(sPosition, alphabet.symbolToCodeWithException(g.charAt(1)), alphabet.symbolToCodeWithException(g.charAt(0))));
++sPosition;
}
}
return mutations.toArray();
} | [
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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) {
MutationsWitMapping mutationsWitMapping = nt2aaWithMapping(seq1, mutations, translationParameters, maxShiftedTriplets);
int[] individualMutations = nt2IndividualAA(seq1, mutations, translationParameters);
MutationNt2AADescriptor[] result = new MutationNt2AADescriptor[mutations.size()];
for (int i = 0; i < mutations.size(); i++) {
result[i] = new MutationNt2AADescriptor(mutations.getMutation(i), individualMutations[i],
mutationsWitMapping.mapping[i] == -1 ? NON_MUTATION :
mutationsWitMapping.mutations.getMutation(mutationsWitMapping.mapping[i]));
}
return result;
} | java | public static MutationNt2AADescriptor[] nt2aaDetailed(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations,
TranslationParameters translationParameters,
int maxShiftedTriplets) {
MutationsWitMapping mutationsWitMapping = nt2aaWithMapping(seq1, mutations, translationParameters, maxShiftedTriplets);
int[] individualMutations = nt2IndividualAA(seq1, mutations, translationParameters);
MutationNt2AADescriptor[] result = new MutationNt2AADescriptor[mutations.size()];
for (int i = 0; i < mutations.size(); i++) {
result[i] = new MutationNt2AADescriptor(mutations.getMutation(i), individualMutations[i],
mutationsWitMapping.mapping[i] == -1 ? NON_MUTATION :
mutationsWitMapping.mutations.getMutation(mutationsWitMapping.mapping[i]));
}
return result;
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@param seq1 the reference nucleotide sequence
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milaboratory/milib | src/main/java/com/milaboratory/core/Range.java | Range.convertPointToRelativePosition | public int convertPointToRelativePosition(int absolutePosition) {
if (absolutePosition < lower || absolutePosition >= upper)
throw new IllegalArgumentException("Position outside this range (" + absolutePosition + ").");
if (reversed)
return upper - 1 - absolutePosition;
else
return absolutePosition - lower;
} | java | public int convertPointToRelativePosition(int absolutePosition) {
if (absolutePosition < lower || absolutePosition >= upper)
throw new IllegalArgumentException("Position outside this range (" + absolutePosition + ").");
if (reversed)
return upper - 1 - absolutePosition;
else
return absolutePosition - lower;
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milaboratory/milib | src/main/java/com/milaboratory/core/Range.java | Range.convertBoundaryToRelativePosition | public int convertBoundaryToRelativePosition(int absolutePosition) {
if (absolutePosition < lower || absolutePosition > upper)
throw new IllegalArgumentException("Position outside this range (" + absolutePosition + ") this=" + this + ".");
if (reversed)
return upper - absolutePosition;
else
return absolutePosition - lower;
} | java | public int convertBoundaryToRelativePosition(int absolutePosition) {
if (absolutePosition < lower || absolutePosition > upper)
throw new IllegalArgumentException("Position outside this range (" + absolutePosition + ") this=" + this + ".");
if (reversed)
return upper - absolutePosition;
else
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milaboratory/milib | src/main/java/com/milaboratory/core/Range.java | Range.without | @SuppressWarnings("unchecked")
public List<Range> without(Range range) {
if (!intersectsWith(range))
return Collections.singletonList(this);
if (upper <= range.upper)
return range.lower <= lower ? Collections.EMPTY_LIST : Collections.singletonList(new Range(lower, range.lower, reversed));
if (range.lower <= lower)
return Collections.singletonList(new Range(range.upper, upper, reversed));
return Arrays.asList(new Range(lower, range.lower, reversed), new Range(range.upper, upper, reversed));
} | java | @SuppressWarnings("unchecked")
public List<Range> without(Range range) {
if (!intersectsWith(range))
return Collections.singletonList(this);
if (upper <= range.upper)
return range.lower <= lower ? Collections.EMPTY_LIST : Collections.singletonList(new Range(lower, range.lower, reversed));
if (range.lower <= lower)
return Collections.singletonList(new Range(range.upper, upper, reversed));
return Arrays.asList(new Range(lower, range.lower, reversed), new Range(range.upper, upper, reversed));
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milaboratory/milib | src/main/java/com/milaboratory/core/Range.java | Range.convertPointToAbsolutePosition | public int convertPointToAbsolutePosition(int relativePosition) {
if (relativePosition < 0 || relativePosition >= length())
throw new IllegalArgumentException("Relative position outside this range (" + relativePosition + ").");
if (reversed)
return upper - 1 - relativePosition;
else
return relativePosition + lower;
} | java | public int convertPointToAbsolutePosition(int relativePosition) {
if (relativePosition < 0 || relativePosition >= length())
throw new IllegalArgumentException("Relative position outside this range (" + relativePosition + ").");
if (reversed)
return upper - 1 - relativePosition;
else
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milaboratory/milib | src/main/java/com/milaboratory/core/Range.java | Range.convertBoundaryToAbsolutePosition | public int convertBoundaryToAbsolutePosition(int relativePosition) {
if (relativePosition < 0 || relativePosition > length())
throw new IllegalArgumentException("Relative position outside this range (" + relativePosition + ").");
if (reversed)
return upper - relativePosition;
else
return relativePosition + lower;
} | java | public int convertBoundaryToAbsolutePosition(int relativePosition) {
if (relativePosition < 0 || relativePosition > length())
throw new IllegalArgumentException("Relative position outside this range (" + relativePosition + ").");
if (reversed)
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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) {
if (sendBinary) {
int prev = 0;
for (int i = 0;i < data.length;i++) {
if (data[i] == -1) {
rawWrite(data, prev, i - prev);
send(new byte[]{-1, -1});
prev = i + 1;
}
}
rawWrite(data, prev, data.length - prev);
} else {
for (int i = 0;i < data.length;i++) {
data[i] = (byte)(data[i] & 0x7F);
}
send(data);
}
} | java | public final void write(byte[] data) {
if (sendBinary) {
int prev = 0;
for (int i = 0;i < data.length;i++) {
if (data[i] == -1) {
rawWrite(data, prev, i - prev);
send(new byte[]{-1, -1});
prev = i + 1;
}
}
rawWrite(data, prev, data.length - prev);
} else {
for (int i = 0;i < data.length;i++) {
data[i] = (byte)(data[i] & 0x7F);
}
send(data);
}
} | [
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] | 3d7258f6490a422658ec85c8457514390c03232d | https://github.com/aeshell/aesh-readline/blob/3d7258f6490a422658ec85c8457514390c03232d/terminal-telnet/src/main/java/org/aesh/terminal/telnet/TelnetConnection.java#L122-L139 | train |
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;
while((line = reader.readLine()) != null)
push(Parser.toCodePoints(line));
} catch(FileNotFoundException ignored) {
//AESH-205
} catch (IOException e) {
if(logging)
LOGGER.log(Level.WARNING, "Failed to read from history file, ", e);
}
}
} | java | private void readFile() {
if(historyFile.exists()) {
try (BufferedReader reader = new BufferedReader(new FileReader(historyFile))) {
String line;
while((line = reader.readLine()) != null)
push(Parser.toCodePoints(line));
} catch(FileNotFoundException ignored) {
//AESH-205
} catch (IOException e) {
if(logging)
LOGGER.log(Level.WARNING, "Failed to read from history file, ", e);
}
}
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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();
try (FileWriter fw = new FileWriter(historyFile)) {
for(int i=0; i < size();i++)
fw.write(Parser.fromCodePoints(get(i)) + (Config.getLineSeparator()));
}
if (historyFilePermission != null) {
historyFile.setReadable(false, false);
historyFile.setReadable(historyFilePermission.isReadable(), historyFilePermission.isReadableOwnerOnly());
historyFile.setWritable(false, false);
historyFile.setWritable(historyFilePermission.isWritable(), historyFilePermission.isWritableOwnerOnly());
historyFile.setExecutable(false, false);
historyFile.setExecutable(historyFilePermission.isExecutable(),
historyFilePermission.isExecutableOwnerOnly());
}
} | java | private void writeFile() throws IOException {
historyFile.delete();
try (FileWriter fw = new FileWriter(historyFile)) {
for(int i=0; i < size();i++)
fw.write(Parser.fromCodePoints(get(i)) + (Config.getLineSeparator()));
}
if (historyFilePermission != null) {
historyFile.setReadable(false, false);
historyFile.setReadable(historyFilePermission.isReadable(), historyFilePermission.isReadableOwnerOnly());
historyFile.setWritable(false, false);
historyFile.setWritable(historyFilePermission.isWritable(), historyFilePermission.isWritableOwnerOnly());
historyFile.setExecutable(false, false);
historyFile.setExecutable(historyFilePermission.isExecutable(),
historyFilePermission.isExecutableOwnerOnly());
}
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aeshell/aesh-readline | readline/src/main/java/org/aesh/readline/terminal/impl/WinSysTerminal.java | WinSysTerminal.setVTMode | private static boolean setVTMode() {
long console = GetStdHandle(STD_OUTPUT_HANDLE);
int[] mode = new int[1];
if (Kernel32.GetConsoleMode(console, mode) == 0) {
// No need to go further, not supported.
return false;
}
if (Kernel32.SetConsoleMode(console, mode[0] | VIRTUAL_TERMINAL_PROCESSING) == 0) {
// No need to go further, not supported.
return false;
}
return true;
} | java | private static boolean setVTMode() {
long console = GetStdHandle(STD_OUTPUT_HANDLE);
int[] mode = new int[1];
if (Kernel32.GetConsoleMode(console, mode) == 0) {
// No need to go further, not supported.
return false;
}
if (Kernel32.SetConsoleMode(console, mode[0] | VIRTUAL_TERMINAL_PROCESSING) == 0) {
// No need to go further, not supported.
return false;
}
return true;
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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) {
if (displayList == null || displayList.size() < 1)
return "";
// make sure that termWidth is > 0
if (termWidth < 1)
termWidth = 80; // setting it to default
int numRows = 1;
// increase numRows and check in loop if it's possible to format strings to columns
while (!canDisplayColumns(displayList, numRows, termWidth) && numRows < displayList.size()) {
numRows++;
}
int numColumns = displayList.size() / numRows;
if (displayList.size() % numRows > 0) {
numColumns++;
}
int[] columnsSizes = calculateColumnSizes(displayList, numColumns, numRows, termWidth);
StringBuilder stringOutput = new StringBuilder();
for (int i = 0; i < numRows; i++) {
for (int c = 0; c < numColumns; c++) {
int fetch = i + (c * numRows);
int nextFetch = i + ((c + 1) * numRows);
if (fetch < displayList.size()) {
// don't need to format last column of row = nextFetch doesn't exit
if (nextFetch < displayList.size()) {
stringOutput.append(padRight(columnsSizes[c] + displayList.get(i + (c * numRows)).getANSILength(),
displayList.get(i + (c * numRows)).toString()));
}
else {
stringOutput.append(displayList.get(i + (c * numRows)).toString());
}
}
else {
break;
}
}
stringOutput.append(Config.getLineSeparator());
}
return stringOutput.toString();
} | java | public static String formatDisplayCompactListTerminalString(List<TerminalString> displayList, int termWidth) {
if (displayList == null || displayList.size() < 1)
return "";
// make sure that termWidth is > 0
if (termWidth < 1)
termWidth = 80; // setting it to default
int numRows = 1;
// increase numRows and check in loop if it's possible to format strings to columns
while (!canDisplayColumns(displayList, numRows, termWidth) && numRows < displayList.size()) {
numRows++;
}
int numColumns = displayList.size() / numRows;
if (displayList.size() % numRows > 0) {
numColumns++;
}
int[] columnsSizes = calculateColumnSizes(displayList, numColumns, numRows, termWidth);
StringBuilder stringOutput = new StringBuilder();
for (int i = 0; i < numRows; i++) {
for (int c = 0; c < numColumns; c++) {
int fetch = i + (c * numRows);
int nextFetch = i + ((c + 1) * numRows);
if (fetch < displayList.size()) {
// don't need to format last column of row = nextFetch doesn't exit
if (nextFetch < displayList.size()) {
stringOutput.append(padRight(columnsSizes[c] + displayList.get(i + (c * numRows)).getANSILength(),
displayList.get(i + (c * numRows)).toString()));
}
else {
stringOutput.append(displayList.get(i + (c * numRows)).toString());
}
}
else {
break;
}
}
stringOutput.append(Config.getLineSeparator());
}
return stringOutput.toString();
} | [
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@param displayList to format
@param termWidth max width
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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, numColumns, numRows, terminalWidth);
int totalSize = 0;
for (int columnSize : columnSizes) {
totalSize += columnSize;
}
return totalSize <= terminalWidth;
} | java | 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, numColumns, numRows, terminalWidth);
int totalSize = 0;
for (int columnSize : columnSizes) {
totalSize += columnSize;
}
return totalSize <= terminalWidth;
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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);
else if (word.startsWith("-"))
return word.substring(1);
else
return word;
} | java | public static String trimOptionName(String word) {
if (word.startsWith("--"))
return word.substring(2);
else if (word.startsWith("-"))
return word.substring(1);
else
return word;
} | [
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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) {
List<String> tmpList = new ArrayList<>();
for (CompleteOperation co : coList) {
String s = findStartsWith(co.getFormattedCompletionCandidates());
if (s.length() > 0)
tmpList.add(s);
else
return "";
}
return findStartsWith(tmpList);
} | java | public static String findStartsWithOperation(List<? extends CompleteOperation> coList) {
List<String> tmpList = new ArrayList<>();
for (CompleteOperation co : coList) {
String s = findStartsWith(co.getFormattedCompletionCandidates());
if (s.length() > 0)
tmpList.add(s);
else
return "";
}
return findStartsWith(tmpList);
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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))
return switchEscapedSpacesToSpacesInWord(text);
else {
return switchEscapedSpacesToSpacesInWord(findEscapedSpaceWordCloseToEnd(text));
}
}
else {
if (text.lastIndexOf(SPACE) >= cursor) // cant use lastIndexOf
return text.substring(text.substring(0, cursor).lastIndexOf(SPACE)).trim();
else
return text.substring(text.lastIndexOf(SPACE)).trim();
}
}
else
return text.trim();
}
else {
String rest;
if (text.length() > cursor + 1)
rest = text.substring(0, cursor + 1);
else
rest = text;
if (doWordContainOnlyEscapedSpace(rest)) {
if (cursor > 1 &&
text.charAt(cursor) == SPACE_CHAR && text.charAt(cursor - 1) == SPACE_CHAR)
return "";
else
return switchEscapedSpacesToSpacesInWord(rest);
}
else {
if (cursor > 1 &&
text.charAt(cursor) == SPACE_CHAR && text.charAt(cursor - 1) == SPACE_CHAR)
return "";
// only if it contains a ' ' and its not at the end of the string
if (rest.trim().contains(SPACE))
return rest.substring(rest.trim().lastIndexOf(" ")).trim();
else
return rest.trim();
}
}
} | java | 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))
return switchEscapedSpacesToSpacesInWord(text);
else {
return switchEscapedSpacesToSpacesInWord(findEscapedSpaceWordCloseToEnd(text));
}
}
else {
if (text.lastIndexOf(SPACE) >= cursor) // cant use lastIndexOf
return text.substring(text.substring(0, cursor).lastIndexOf(SPACE)).trim();
else
return text.substring(text.lastIndexOf(SPACE)).trim();
}
}
else
return text.trim();
}
else {
String rest;
if (text.length() > cursor + 1)
rest = text.substring(0, cursor + 1);
else
rest = text;
if (doWordContainOnlyEscapedSpace(rest)) {
if (cursor > 1 &&
text.charAt(cursor) == SPACE_CHAR && text.charAt(cursor - 1) == SPACE_CHAR)
return "";
else
return switchEscapedSpacesToSpacesInWord(rest);
}
else {
if (cursor > 1 &&
text.charAt(cursor) == SPACE_CHAR && text.charAt(cursor - 1) == SPACE_CHAR)
return "";
// only if it contains a ' ' and its not at the end of the string
if (rest.trim().contains(SPACE))
return rest.substring(rest.trim().lastIndexOf(" ")).trim();
else
return rest.trim();
}
}
} | [
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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;
String originalText = text;
while ((index = text.lastIndexOf(SPACE)) > -1) {
if (index > 0 && text.charAt(index - 1) == BACK_SLASH) {
text = text.substring(0, index - 1);
}
else
return originalText.substring(index + 1);
}
return originalText;
} | java | public static String findEscapedSpaceWordCloseToEnd(String text) {
int index;
String originalText = text;
while ((index = text.lastIndexOf(SPACE)) > -1) {
if (index > 0 && text.charAt(index - 1) == BACK_SLASH) {
text = text.substring(0, index - 1);
}
else
return originalText.substring(index + 1);
}
return originalText;
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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 < text.length(); i++) {
if (text.charAt(i) == BACK_SLASH || escapedByBackSlash) {
escapedByBackSlash = !escapedByBackSlash;
continue;
}
if (text.charAt(i) == SINGLE_QUOTE) {
if (!doubleQuote)
singleQuote = !singleQuote;
}
else if (text.charAt(i) == DOUBLE_QUOTE) {
if (!singleQuote)
doubleQuote = !doubleQuote;
}
}
return doubleQuote || singleQuote;
} | 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;
for (int i = 0; i < text.length(); i++) {
if (text.charAt(i) == BACK_SLASH || escapedByBackSlash) {
escapedByBackSlash = !escapedByBackSlash;
continue;
}
if (text.charAt(i) == SINGLE_QUOTE) {
if (!doubleQuote)
singleQuote = !singleQuote;
}
else if (text.charAt(i) == DOUBLE_QUOTE) {
if (!singleQuote)
doubleQuote = !doubleQuote;
}
}
return doubleQuote || singleQuote;
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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))
count++;
return count;
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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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count++;
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break;
}
if (count > 0)
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else
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} | java | public static String trimInFront(String buffer) {
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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));
else
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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;
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counter += TAB - 1;
}
else
ansi[counter + 2] = anOut;
counter++;
}
return ansi;
} | 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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return ansi;
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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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}
if (value instanceof Annotation) {
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}
return part1 ^ value.hashCode();
} | java | static int hashMember(String name, Object value) {
int part1 = name.hashCode() * 127;
if (value.getClass().isArray()) {
return part1 ^ arrayMemberHash(value.getClass().getComponentType(), value);
}
if (value instanceof Annotation) {
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return part1 ^ value.hashCode();
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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());
// }
// }
// return of(field, 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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continue;
}
Set<Annotation> tagged = tagAnnotations.get(tagType);
if (null == tagged) {
tagged = new HashSet<>();
tagAnnotations.put(tagType, tagged);
}
tagged.add(anno);
}
} | java | 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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continue;
}
Set<Annotation> tagged = tagAnnotations.get(tagType);
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tagged = new HashSet<>();
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tagged.add(anno);
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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) {
queryParam(s[0], s[1]);
}
}
}
return this;
} | 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) {
queryParam(s[0], s[1]);
}
}
}
return this;
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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(X509Certificate[] certs, String authType) {
// nop
}
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public void checkServerTrusted(X509Certificate[] certs, String authType) {
// nop
}
@Override
public java.security.cert.X509Certificate[] getAcceptedIssuers() {
return null;
}
}
}, new java.security.SecureRandom());
return sslContext;
} | java | private SSLContext getSSLContext() throws NoSuchAlgorithmException, KeyManagementException {
SSLContext sslContext = SSLContext.getInstance("SSL");
sslContext.init(null, new TrustManager[] {
new X509TrustManager() {
@Override
public void checkClientTrusted(X509Certificate[] certs, String authType) {
// nop
}
@Override
public void checkServerTrusted(X509Certificate[] certs, String authType) {
// nop
}
@Override
public java.security.cert.X509Certificate[] getAcceptedIssuers() {
return null;
}
}
}, new java.security.SecureRandom());
return sslContext;
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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());
}
return retentionStrategy;
} | java | public RetentionStrategy getRetentionStrategyCopy() {
if (retentionStrategy instanceof DockerOnceRetentionStrategy) {
DockerOnceRetentionStrategy onceRetention = (DockerOnceRetentionStrategy) retentionStrategy;
return new DockerOnceRetentionStrategy(onceRetention.getIdleMinutes());
}
return 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")
public Object readResolve() {
if (configVersion < 1) {
if (isNull(nodeProperties)) nodeProperties = new ArrayList<>();
nodeProperties.add(new DockerNodeProperty("DOCKER_CONTAINER_ID", "JENKINS_CLOUD_ID", "DOCKER_HOST"));
configVersion = 1;
}
// real @Nonnull
if (mode == null) {
mode = Node.Mode.NORMAL;
}
if (retentionStrategy == null) {
retentionStrategy = new DockerOnceRetentionStrategy(10);
}
try {
labelSet = Label.parse(getLabelString()); // fails sometimes under debugger
} catch (Throwable t) {
LOG.error("Can't parse labels: {}", t);
}
return this;
} | java | @SuppressWarnings("unused")
public Object readResolve() {
if (configVersion < 1) {
if (isNull(nodeProperties)) nodeProperties = new ArrayList<>();
nodeProperties.add(new DockerNodeProperty("DOCKER_CONTAINER_ID", "JENKINS_CLOUD_ID", "DOCKER_HOST"));
configVersion = 1;
}
// real @Nonnull
if (mode == null) {
mode = Node.Mode.NORMAL;
}
if (retentionStrategy == null) {
retentionStrategy = new DockerOnceRetentionStrategy(10);
}
try {
labelSet = Label.parse(getLabelString()); // fails sometimes under debugger
} catch (Throwable t) {
LOG.error("Can't parse labels: {}", t);
}
return this;
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] | 40b12e39ff94c3834cff7e028c3dd01c88e87d77 | https://github.com/KostyaSha/yet-another-docker-plugin/blob/40b12e39ff94c3834cff7e028c3dd01c88e87d77/yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/DockerSlaveTemplate.java#L126-L150 | train |
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();
cloneJNLPlauncher.setLaunchTimeout(getLaunchTimeout());
cloneJNLPlauncher.setUser(getUser());
cloneJNLPlauncher.setJvmOpts(getJvmOpts());
cloneJNLPlauncher.setSlaveOpts(getSlaveOpts());
cloneJNLPlauncher.setJenkinsUrl(getJenkinsUrl());
cloneJNLPlauncher.setNoCertificateCheck(isNoCertificateCheck());
cloneJNLPlauncher.setNoReconnect(isNoReconnect());
return cloneJNLPlauncher;
} | java | @Override
public DockerComputerLauncher getPreparedLauncher(String cloudId, DockerSlaveTemplate template,
InspectContainerResponse containerInspectResponse) {
final DockerComputerJNLPLauncher cloneJNLPlauncher = new DockerComputerJNLPLauncher();
cloneJNLPlauncher.setLaunchTimeout(getLaunchTimeout());
cloneJNLPlauncher.setUser(getUser());
cloneJNLPlauncher.setJvmOpts(getJvmOpts());
cloneJNLPlauncher.setSlaveOpts(getSlaveOpts());
cloneJNLPlauncher.setJenkinsUrl(getJenkinsUrl());
cloneJNLPlauncher.setNoCertificateCheck(isNoCertificateCheck());
cloneJNLPlauncher.setNoReconnect(isNoReconnect());
return cloneJNLPlauncher;
} | [
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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();
CreateContainerCmd containerConfig = getClient().createContainerCmd(image);
// template specific options
dockerCreateContainer.fillContainerConfig(containerConfig, null);
// launcher specific options
slaveTemplate.getLauncher().appendContainerConfig(slaveTemplate, containerConfig);
// cloud specific options
appendContainerConfig(slaveTemplate, containerConfig);
// create
CreateContainerResponse response = containerConfig.exec();
String containerId = response.getId();
LOG.debug("Created container {}, for {}", containerId, getDisplayName());
slaveTemplate.getLauncher().afterContainerCreate(getClient(), containerId);
// start
StartContainerCmd startCommand = getClient().startContainerCmd(containerId);
try {
startCommand.exec();
LOG.debug("Running container {}, for {}", containerId, getDisplayName());
} catch (Exception ex) {
try {
getClient().logContainerCmd(containerId)
.withStdErr(true)
.withStdOut(true)
.exec(new MyLogContainerResultCallback())
.awaitCompletion();
} catch (Throwable t) {
LOG.warn("Can't get logs for container start", t);
}
throw ex;
}
return containerId;
} | java | public String runContainer(DockerSlaveTemplate slaveTemplate) throws DockerException, IOException {
final DockerCreateContainer dockerCreateContainer = slaveTemplate.getDockerContainerLifecycle().getCreateContainer();
final String image = slaveTemplate.getDockerContainerLifecycle().getImage();
CreateContainerCmd containerConfig = getClient().createContainerCmd(image);
// template specific options
dockerCreateContainer.fillContainerConfig(containerConfig, null);
// launcher specific options
slaveTemplate.getLauncher().appendContainerConfig(slaveTemplate, containerConfig);
// cloud specific options
appendContainerConfig(slaveTemplate, containerConfig);
// create
CreateContainerResponse response = containerConfig.exec();
String containerId = response.getId();
LOG.debug("Created container {}, for {}", containerId, getDisplayName());
slaveTemplate.getLauncher().afterContainerCreate(getClient(), containerId);
// start
StartContainerCmd startCommand = getClient().startContainerCmd(containerId);
try {
startCommand.exec();
LOG.debug("Running container {}, for {}", containerId, getDisplayName());
} catch (Exception ex) {
try {
getClient().logContainerCmd(containerId)
.withStdErr(true)
.withStdOut(true)
.exec(new MyLogContainerResultCallback())
.awaitCompletion();
} catch (Throwable t) {
LOG.warn("Can't get logs for container start", t);
}
throw ex;
}
return containerId;
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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) {
Map<String, String> labels = containerConfig.getLabels();
if (labels == null) labels = new HashMap<>();
labels.put(DOCKER_CLOUD_LABEL, getDisplayName());
labels.put(DOCKER_TEMPLATE_LABEL, slaveTemplate.getId());
containerConfig.withLabels(labels);
} | java | private void appendContainerConfig(DockerSlaveTemplate slaveTemplate, CreateContainerCmd containerConfig) {
Map<String, String> labels = containerConfig.getLabels();
if (labels == null) labels = new HashMap<>();
labels.put(DOCKER_CLOUD_LABEL, getDisplayName());
labels.put(DOCKER_TEMPLATE_LABEL, slaveTemplate.getId());
containerConfig.withLabels(labels);
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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;
} else if ("windows".equalsIgnoreCase(ir.getOs())) {
LOG.trace("Detected WINDOWS operating system for image: {}", imageId);
return OsType.WINDOWS;
} else {
LOG.trace("Detected OTHER operating system ({}) for image: {}", ir.getOs(), imageId);
return OsType.OTHER;
}
} | java | 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;
} else if ("windows".equalsIgnoreCase(ir.getOs())) {
LOG.trace("Detected WINDOWS operating system for image: {}", imageId);
return OsType.WINDOWS;
} else {
LOG.trace("Detected OTHER operating system ({}) for image: {}", ir.getOs(), imageId);
return OsType.OTHER;
}
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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();
if (labels.containsKey(DOCKER_CLOUD_LABEL) && labels.get(DOCKER_CLOUD_LABEL).equals(getDisplayName())) {
if (template == null) {
// count only total cloud capacity
count++;
} else if (labels.containsKey(DOCKER_TEMPLATE_LABEL) &&
labels.get(DOCKER_TEMPLATE_LABEL).equals(template.getId())) {
count++;
}
}
}
return count;
} | 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();
if (labels.containsKey(DOCKER_CLOUD_LABEL) && labels.get(DOCKER_CLOUD_LABEL).equals(getDisplayName())) {
if (template == null) {
// count only total cloud capacity
count++;
} else if (labels.containsKey(DOCKER_TEMPLATE_LABEL) &&
labels.get(DOCKER_TEMPLATE_LABEL).equals(template.getId())) {
count++;
}
}
}
return count;
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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 {
final DockerContainerLifecycle dockerCreateContainer = template.getDockerContainerLifecycle();
String dockerImageName = dockerCreateContainer.getImage();
int templateCapacity = template.getMaxCapacity();
int estimatedTotalSlaves = countCurrentDockerSlaves(null);
int estimatedAmiSlaves = countCurrentDockerSlaves(template);
synchronized (provisionedImages) {
int currentProvisioning = 0;
if (provisionedImages.containsKey(template)) {
currentProvisioning = provisionedImages.get(template);
}
for (int amiCount : provisionedImages.values()) {
estimatedTotalSlaves += amiCount;
}
estimatedAmiSlaves += currentProvisioning;
if (estimatedTotalSlaves >= getContainerCap()) {
LOG.info("Not Provisioning '{}'; Server '{}' full with '{}' container(s)",
dockerImageName, name, getContainerCap());
return false; // maxed out
}
if (templateCapacity != 0 && estimatedAmiSlaves >= templateCapacity) {
LOG.info("Not Provisioning '{}'. Instance limit of '{}' reached on server '{}'",
dockerImageName, templateCapacity, name);
return false; // maxed out
}
LOG.info("Provisioning '{}' number '{}' on '{}'; Total containers: '{}'",
dockerImageName, estimatedAmiSlaves, name, estimatedTotalSlaves);
provisionedImages.put(template, currentProvisioning + 1);
return true;
}
} | java | private synchronized boolean addProvisionedSlave(DockerSlaveTemplate template) throws Exception {
final DockerContainerLifecycle dockerCreateContainer = template.getDockerContainerLifecycle();
String dockerImageName = dockerCreateContainer.getImage();
int templateCapacity = template.getMaxCapacity();
int estimatedTotalSlaves = countCurrentDockerSlaves(null);
int estimatedAmiSlaves = countCurrentDockerSlaves(template);
synchronized (provisionedImages) {
int currentProvisioning = 0;
if (provisionedImages.containsKey(template)) {
currentProvisioning = provisionedImages.get(template);
}
for (int amiCount : provisionedImages.values()) {
estimatedTotalSlaves += amiCount;
}
estimatedAmiSlaves += currentProvisioning;
if (estimatedTotalSlaves >= getContainerCap()) {
LOG.info("Not Provisioning '{}'; Server '{}' full with '{}' container(s)",
dockerImageName, name, getContainerCap());
return false; // maxed out
}
if (templateCapacity != 0 && estimatedAmiSlaves >= templateCapacity) {
LOG.info("Not Provisioning '{}'. Instance limit of '{}' reached on server '{}'",
dockerImageName, templateCapacity, name);
return false; // maxed out
}
LOG.info("Provisioning '{}' number '{}' on '{}'; Total containers: '{}'",
dockerImageName, estimatedAmiSlaves, name, estimatedTotalSlaves);
provisionedImages.put(template, currentProvisioning + 1);
return true;
}
} | [
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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() {
List<Descriptor<ComputerLauncher>> launchers = new ArrayList<>();
launchers.add(getInstance().getDescriptor(DockerComputerSSHLauncher.class));
launchers.add(getInstance().getDescriptor(DockerComputerJNLPLauncher.class));
launchers.add(getInstance().getDescriptor(DockerComputerIOLauncher.class));
return launchers;
} | java | public static List<Descriptor<ComputerLauncher>> getDockerComputerLauncherDescriptors() {
List<Descriptor<ComputerLauncher>> launchers = new ArrayList<>();
launchers.add(getInstance().getDescriptor(DockerComputerSSHLauncher.class));
launchers.add(getInstance().getDescriptor(DockerComputerJNLPLauncher.class));
launchers.add(getInstance().getDescriptor(DockerComputerIOLauncher.class));
return launchers;
} | [
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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() {
List<Descriptor<RetentionStrategy<?>>> strategies = new ArrayList<>();
strategies.add(getInstance().getDescriptor(DockerOnceRetentionStrategy.class));
strategies.add(getInstance().getDescriptor(DockerCloudRetentionStrategy.class));
strategies.add(getInstance().getDescriptor(DockerComputerIOLauncher.class));
return strategies;
} | java | public static List<Descriptor<RetentionStrategy<?>>> getDockerRetentionStrategyDescriptors() {
List<Descriptor<RetentionStrategy<?>>> strategies = new ArrayList<>();
strategies.add(getInstance().getDescriptor(DockerOnceRetentionStrategy.class));
strategies.add(getInstance().getDescriptor(DockerCloudRetentionStrategy.class));
strategies.add(getInstance().getDescriptor(DockerComputerIOLauncher.class));
return strategies;
} | [
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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
public static List<DockerCloud> getAllDockerClouds() {
return getInstance().clouds.stream()
.filter(Objects::nonNull)
.filter(DockerCloud.class::isInstance)
.map(cloud -> (DockerCloud) cloud)
.collect(Collectors.toList());
} | java | @Nonnull
public static List<DockerCloud> getAllDockerClouds() {
return getInstance().clouds.stream()
.filter(Objects::nonNull)
.filter(DockerCloud.class::isInstance)
.map(cloud -> (DockerCloud) cloud)
.collect(Collectors.toList());
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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
public RestartPolicy getRestartPolicy() {
if (isNull(policyName)) return null;
return RestartPolicy.parse(String.format("%s:%d",
policyName.toString().toLowerCase(Locale.ENGLISH).replace("_", "-"), getMaximumRetryCount()));
} | java | @CheckForNull
public RestartPolicy getRestartPolicy() {
if (isNull(policyName)) return null;
return RestartPolicy.parse(String.format("%s:%d",
policyName.toString().toLowerCase(Locale.ENGLISH).replace("_", "-"), getMaximumRetryCount()));
} | [
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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) {
String resolvedVar = var;
try {
final EnvVars envVars = run.getEnvironment(taskListener);
resolvedVar = envVars.expand(var);
} catch (IOException | InterruptedException e) {
LOG.warn("Can't resolve variable " + var + " for {}", run, e);
}
return resolvedVar;
} | java | public static String resolveVar(String var, Run run, TaskListener taskListener) {
String resolvedVar = var;
try {
final EnvVars envVars = run.getEnvironment(taskListener);
resolvedVar = envVars.expand(var);
} catch (IOException | InterruptedException e) {
LOG.warn("Can't resolve variable " + var + " for {}", run, e);
}
return resolvedVar;
} | [
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] | 40b12e39ff94c3834cff7e028c3dd01c88e87d77 | https://github.com/KostyaSha/yet-another-docker-plugin/blob/40b12e39ff94c3834cff7e028c3dd01c88e87d77/yet-another-docker-plugin/src/main/java/com/github/kostyasha/yad/utils/VariableUtils.java#L24-L33 | train |
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);
if (jenkinsUrl.getHost() == null || jenkinsUrl.getHost().length() == 0) {
throw new IOException("Invalid URL: " + jenkinsAddr);
}
URLConnection head = jenkinsUrl.openConnection();
try {
head.connect();
} catch (IOException e) {
throw (IOException) new IOException("Failed to connect to " + jenkinsAddr).initCause(e);
}
String h = head.getHeaderField("X-Jenkins-CLI-Host");
if (h == null) h = head.getURL().getHost();
String identity = head.getHeaderField("X-Instance-Identity");
flushURLConnection(head);
return new CliPort(new InetSocketAddress(h, exposedPort), identity, 2);
} | java | protected CliPort getCliTcpPort(String jenkinsAddr) throws IOException {
URL jenkinsUrl = new URL(jenkinsAddr);
if (jenkinsUrl.getHost() == null || jenkinsUrl.getHost().length() == 0) {
throw new IOException("Invalid URL: " + jenkinsAddr);
}
URLConnection head = jenkinsUrl.openConnection();
try {
head.connect();
} catch (IOException e) {
throw (IOException) new IOException("Failed to connect to " + jenkinsAddr).initCause(e);
}
String h = head.getHeaderField("X-Jenkins-CLI-Host");
if (h == null) h = head.getURL().getHost();
String identity = head.getHeaderField("X-Instance-Identity");
flushURLConnection(head);
return new CliPort(new InetSocketAddress(h, exposedPort), identity, 2);
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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();
if (ownsPool)
pool.shutdown();
for (Closeable c : closables)
c.close();
} | java | public void close() throws IOException, InterruptedException {
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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();
if (execute(Arrays.asList("groovy", "="),
new ByteArrayInputStream(
"hudson.remoting.Channel.current().setRestricted(false)"
.getBytes(defaultCharset())),
out, out) != 0) {
throw new SecurityException(out.toString()); // failed to upgrade
}
} | java | public void upgrade() {
ByteArrayOutputStream out = new ByteArrayOutputStream();
if (execute(Arrays.asList("groovy", "="),
new ByteArrayInputStream(
"hudson.remoting.Channel.current().setRestricted(false)"
.getBytes(defaultCharset())),
out, out) != 0) {
throw new SecurityException(out.toString()); // failed to upgrade
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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 {
final EnvVars envVars = run.getCharacteristicEnvVars();
// from run.getEnvironment(listener) but without computer vars
for (EnvironmentContributor ec : EnvironmentContributor.all().reverseView()) {
// job vars
ec.buildEnvironmentFor(run.getParent(), envVars, listener);
// build vars
if (ec instanceof CoreEnvironmentContributor) {
// exclude executor computer related vars
envVars.put("BUILD_DISPLAY_NAME", run.getDisplayName());
String rootUrl = Jenkins.getInstance().getRootUrl();
if (rootUrl != null) {
envVars.put("BUILD_URL", rootUrl + run.getUrl());
}
// and remove useless job var from CoreEnvironmentContributor
envVars.remove("JENKINS_HOME");
envVars.remove("HUDSON_HOME");
} else {
ec.buildEnvironmentFor(run, envVars, listener); // build vars
}
}
return envVars;
} | java | protected static EnvVars getEnvVars(Run run, TaskListener listener) throws IOException, InterruptedException {
final EnvVars envVars = run.getCharacteristicEnvVars();
// from run.getEnvironment(listener) but without computer vars
for (EnvironmentContributor ec : EnvironmentContributor.all().reverseView()) {
// job vars
ec.buildEnvironmentFor(run.getParent(), envVars, listener);
// build vars
if (ec instanceof CoreEnvironmentContributor) {
// exclude executor computer related vars
envVars.put("BUILD_DISPLAY_NAME", run.getDisplayName());
String rootUrl = Jenkins.getInstance().getRootUrl();
if (rootUrl != null) {
envVars.put("BUILD_URL", rootUrl + run.getUrl());
}
// and remove useless job var from CoreEnvironmentContributor
envVars.remove("JENKINS_HOME");
envVars.remove("HUDSON_HOME");
} else {
ec.buildEnvironmentFor(run, envVars, listener); // build vars
}
}
return envVars;
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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_JOB_BASE_NAME", run.getParent().getName());
labels.put("JENKINS_INSTANCE_IDENTITY",
new String(encodeBase64(InstanceIdentity.get().getPublic().getEncoded()), UTF_8));
containerConfig.withLabels(labels);
} | 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());
labels.put("JENKINS_JOB_BASE_NAME", run.getParent().getName());
labels.put("JENKINS_INSTANCE_IDENTITY",
new String(encodeBase64(InstanceIdentity.get().getPublic().getEncoded()), UTF_8));
containerConfig.withLabels(labels);
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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) {
final ExtensionList<NodeProvisioner.Strategy> strategies = lookup(NodeProvisioner.Strategy.class);
DockerProvisioningStrategy strategy = strategies.get(DockerProvisioningStrategy.class);
if (isNull(strategy)) {
LOG.debug("YAD strategy was null, creating new.");
strategy = new DockerProvisioningStrategy();
} else {
LOG.debug("Removing YAD strategy.");
strategies.remove(strategy);
}
LOG.debug("Inserting YAD strategy at position 0");
strategies.add(0, strategy);
} | java | public void setEnabled(boolean enabled) {
final ExtensionList<NodeProvisioner.Strategy> strategies = lookup(NodeProvisioner.Strategy.class);
DockerProvisioningStrategy strategy = strategies.get(DockerProvisioningStrategy.class);
if (isNull(strategy)) {
LOG.debug("YAD strategy was null, creating new.");
strategy = new DockerProvisioningStrategy();
} else {
LOG.debug("Removing YAD strategy.");
strategies.remove(strategy);
}
LOG.debug("Inserting YAD strategy at position 0");
strategies.add(0, strategy);
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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)
{
return left.compareTo(right) >= 0;
} | java | public static <T extends RingPosition<T>> boolean isWrapAround(T left, T right)
{
return left.compareTo(right) >= 0;
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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)
{
ArrayList<Range<T>> difference = new ArrayList<Range<T>>(2);
if (!left.equals(contained.left))
difference.add(new Range<T>(left, contained.left, partitioner));
if (!right.equals(contained.right))
difference.add(new Range<T>(contained.right, right, partitioner));
return difference;
} | java | private ArrayList<Range<T>> subtractContained(Range<T> contained)
{
ArrayList<Range<T>> difference = new ArrayList<Range<T>>(2);
if (!left.equals(contained.left))
difference.add(new Range<T>(left, contained.left, partitioner));
if (!right.equals(contained.right))
difference.add(new Range<T>(contained.right, right, partitioner));
return difference;
} | [
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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)
{
if (ranges.isEmpty())
return ranges;
List<Range<T>> output = new ArrayList<Range<T>>();
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T min = (T) current.partitioner.minValue(current.left.getClass());
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{
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if (current.right.equals(min))
{
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if (current.left.equals(min))
return Collections.<Range<T>>singletonList(current);
output.add(new Range<T>(current.left, min));
return output;
}
Range<T> next = iter.next();
// if next left is equal to current right, we do not intersect per se, but replacing (A, B] and (B, C] by (A, C] is
// legit, and since this avoid special casing and will result in more "optimal" ranges, we do the transformation
if (next.left.compareTo(current.right) <= 0)
{
// We do overlap
// (we've handled current.right.equals(min) already)
if (next.right.equals(min) || current.right.compareTo(next.right) < 0)
current = new Range<T>(current.left, next.right);
}
else
{
output.add(current);
current = next;
}
}
output.add(current);
return output;
} | java | private static <T extends RingPosition<T>> List<Range<T>> deoverlap(List<Range<T>> ranges)
{
if (ranges.isEmpty())
return ranges;
List<Range<T>> output = new ArrayList<Range<T>>();
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T min = (T) current.partitioner.minValue(current.left.getClass());
while (iter.hasNext())
{
// If current goes to the end of the ring, we're done
if (current.right.equals(min))
{
// If one range is the full range, we return only that
if (current.left.equals(min))
return Collections.<Range<T>>singletonList(current);
output.add(new Range<T>(current.left, min));
return output;
}
Range<T> next = iter.next();
// if next left is equal to current right, we do not intersect per se, but replacing (A, B] and (B, C] by (A, C] is
// legit, and since this avoid special casing and will result in more "optimal" ranges, we do the transformation
if (next.left.compareTo(current.right) <= 0)
{
// We do overlap
// (we've handled current.right.equals(min) already)
if (next.right.equals(min) || current.right.compareTo(next.right) < 0)
current = new Range<T>(current.left, next.right);
}
else
{
output.add(current);
current = next;
}
}
output.add(current);
return output;
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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)
{
return new Range<RowPosition>(left.maxKeyBound(partitioner), right.maxKeyBound(partitioner), partitioner);
} | java | public static Range<RowPosition> makeRowRange(Token left, Token right, IPartitioner partitioner)
{
return new Range<RowPosition>(left.maxKeyBound(partitioner), right.maxKeyBound(partitioner), partitioner);
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/db/AbstractNativeCell.java | AbstractNativeCell.compareTo | @Inline
public final int compareTo(final Composite that)
{
if (isStatic() != that.isStatic())
{
// Static sorts before non-static no matter what, except for empty which
// always sort first
if (isEmpty())
return that.isEmpty() ? 0 : -1;
if (that.isEmpty())
return 1;
return isStatic() ? -1 : 1;
}
int size = size();
int size2 = that.size();
int minSize = Math.min(size, size2);
int startDelta = 0;
int cellNamesOffset = nameDeltaOffset(size);
for (int i = 0 ; i < minSize ; i++)
{
int endDelta = i < size - 1 ? getShort(nameDeltaOffset(i + 1)) : valueStartOffset() - cellNamesOffset;
long offset = peer + cellNamesOffset + startDelta;
int length = endDelta - startDelta;
int cmp = FastByteOperations.UnsafeOperations.compareTo(null, offset, length, that.get(i));
if (cmp != 0)
return cmp;
startDelta = endDelta;
}
EOC eoc = that.eoc();
if (size == size2)
return this.eoc().compareTo(eoc);
return size < size2 ? this.eoc().prefixComparisonResult : -eoc.prefixComparisonResult;
} | java | @Inline
public final int compareTo(final Composite that)
{
if (isStatic() != that.isStatic())
{
// Static sorts before non-static no matter what, except for empty which
// always sort first
if (isEmpty())
return that.isEmpty() ? 0 : -1;
if (that.isEmpty())
return 1;
return isStatic() ? -1 : 1;
}
int size = size();
int size2 = that.size();
int minSize = Math.min(size, size2);
int startDelta = 0;
int cellNamesOffset = nameDeltaOffset(size);
for (int i = 0 ; i < minSize ; i++)
{
int endDelta = i < size - 1 ? getShort(nameDeltaOffset(i + 1)) : valueStartOffset() - cellNamesOffset;
long offset = peer + cellNamesOffset + startDelta;
int length = endDelta - startDelta;
int cmp = FastByteOperations.UnsafeOperations.compareTo(null, offset, length, that.get(i));
if (cmp != 0)
return cmp;
startDelta = endDelta;
}
EOC eoc = that.eoc();
if (size == size2)
return this.eoc().compareTo(eoc);
return size < size2 ? this.eoc().prefixComparisonResult : -eoc.prefixComparisonResult;
} | [
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/db/CounterMutation.java | CounterMutation.processModifications | private ColumnFamily processModifications(ColumnFamily changesCF)
{
ColumnFamilyStore cfs = Keyspace.open(getKeyspaceName()).getColumnFamilyStore(changesCF.id());
ColumnFamily resultCF = changesCF.cloneMeShallow();
List<CounterUpdateCell> counterUpdateCells = new ArrayList<>(changesCF.getColumnCount());
for (Cell cell : changesCF)
{
if (cell instanceof CounterUpdateCell)
counterUpdateCells.add((CounterUpdateCell)cell);
else
resultCF.addColumn(cell);
}
if (counterUpdateCells.isEmpty())
return resultCF; // only DELETEs
ClockAndCount[] currentValues = getCurrentValues(counterUpdateCells, cfs);
for (int i = 0; i < counterUpdateCells.size(); i++)
{
ClockAndCount currentValue = currentValues[i];
CounterUpdateCell update = counterUpdateCells.get(i);
long clock = currentValue.clock + 1L;
long count = currentValue.count + update.delta();
resultCF.addColumn(new BufferCounterCell(update.name(),
CounterContext.instance().createGlobal(CounterId.getLocalId(), clock, count),
update.timestamp()));
}
return resultCF;
} | java | private ColumnFamily processModifications(ColumnFamily changesCF)
{
ColumnFamilyStore cfs = Keyspace.open(getKeyspaceName()).getColumnFamilyStore(changesCF.id());
ColumnFamily resultCF = changesCF.cloneMeShallow();
List<CounterUpdateCell> counterUpdateCells = new ArrayList<>(changesCF.getColumnCount());
for (Cell cell : changesCF)
{
if (cell instanceof CounterUpdateCell)
counterUpdateCells.add((CounterUpdateCell)cell);
else
resultCF.addColumn(cell);
}
if (counterUpdateCells.isEmpty())
return resultCF; // only DELETEs
ClockAndCount[] currentValues = getCurrentValues(counterUpdateCells, cfs);
for (int i = 0; i < counterUpdateCells.size(); i++)
{
ClockAndCount currentValue = currentValues[i];
CounterUpdateCell update = counterUpdateCells.get(i);
long clock = currentValue.clock + 1L;
long count = currentValue.count + update.delta();
resultCF.addColumn(new BufferCounterCell(update.name(),
CounterContext.instance().createGlobal(CounterId.getLocalId(), clock, count),
update.timestamp()));
}
return resultCF;
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/db/CounterMutation.java | CounterMutation.getCurrentValuesFromCache | private int getCurrentValuesFromCache(List<CounterUpdateCell> counterUpdateCells,
ColumnFamilyStore cfs,
ClockAndCount[] currentValues)
{
int cacheMisses = 0;
for (int i = 0; i < counterUpdateCells.size(); i++)
{
ClockAndCount cached = cfs.getCachedCounter(key(), counterUpdateCells.get(i).name());
if (cached != null)
currentValues[i] = cached;
else
cacheMisses++;
}
return cacheMisses;
} | java | private int getCurrentValuesFromCache(List<CounterUpdateCell> counterUpdateCells,
ColumnFamilyStore cfs,
ClockAndCount[] currentValues)
{
int cacheMisses = 0;
for (int i = 0; i < counterUpdateCells.size(); i++)
{
ClockAndCount cached = cfs.getCachedCounter(key(), counterUpdateCells.get(i).name());
if (cached != null)
currentValues[i] = cached;
else
cacheMisses++;
}
return cacheMisses;
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/db/CounterMutation.java | CounterMutation.getCurrentValuesFromCFS | private void getCurrentValuesFromCFS(List<CounterUpdateCell> counterUpdateCells,
ColumnFamilyStore cfs,
ClockAndCount[] currentValues)
{
SortedSet<CellName> names = new TreeSet<>(cfs.metadata.comparator);
for (int i = 0; i < currentValues.length; i++)
if (currentValues[i] == null)
names.add(counterUpdateCells.get(i).name());
ReadCommand cmd = new SliceByNamesReadCommand(getKeyspaceName(), key(), cfs.metadata.cfName, Long.MIN_VALUE, new NamesQueryFilter(names));
Row row = cmd.getRow(cfs.keyspace);
ColumnFamily cf = row == null ? null : row.cf;
for (int i = 0; i < currentValues.length; i++)
{
if (currentValues[i] != null)
continue;
Cell cell = cf == null ? null : cf.getColumn(counterUpdateCells.get(i).name());
if (cell == null || !cell.isLive()) // absent or a tombstone.
currentValues[i] = ClockAndCount.BLANK;
else
currentValues[i] = CounterContext.instance().getLocalClockAndCount(cell.value());
}
} | java | private void getCurrentValuesFromCFS(List<CounterUpdateCell> counterUpdateCells,
ColumnFamilyStore cfs,
ClockAndCount[] currentValues)
{
SortedSet<CellName> names = new TreeSet<>(cfs.metadata.comparator);
for (int i = 0; i < currentValues.length; i++)
if (currentValues[i] == null)
names.add(counterUpdateCells.get(i).name());
ReadCommand cmd = new SliceByNamesReadCommand(getKeyspaceName(), key(), cfs.metadata.cfName, Long.MIN_VALUE, new NamesQueryFilter(names));
Row row = cmd.getRow(cfs.keyspace);
ColumnFamily cf = row == null ? null : row.cf;
for (int i = 0; i < currentValues.length; i++)
{
if (currentValues[i] != null)
continue;
Cell cell = cf == null ? null : cf.getColumn(counterUpdateCells.get(i).name());
if (cell == null || !cell.isLive()) // absent or a tombstone.
currentValues[i] = ClockAndCount.BLANK;
else
currentValues[i] = CounterContext.instance().getLocalClockAndCount(cell.value());
}
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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 parameters.get(0);
}
};
} | java | 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 parameters.get(0);
}
};
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/hadoop/cql3/CqlRecordWriter.java | RangeClient.run | public void run()
{
outer:
while (run || !queue.isEmpty())
{
List<ByteBuffer> bindVariables;
try
{
bindVariables = queue.take();
}
catch (InterruptedException e)
{
// re-check loop condition after interrupt
continue;
}
Iterator<InetAddress> iter = endpoints.iterator();
while (true)
{
// send the mutation to the last-used endpoint. first time through, this will NPE harmlessly.
try
{
int i = 0;
int itemId = preparedStatement(client);
while (bindVariables != null)
{
client.execute_prepared_cql3_query(itemId, bindVariables, ConsistencyLevel.ONE);
i++;
if (i >= batchThreshold)
break;
bindVariables = queue.poll();
}
break;
}
catch (Exception e)
{
closeInternal();
if (!iter.hasNext())
{
lastException = new IOException(e);
break outer;
}
}
// attempt to connect to a different endpoint
try
{
InetAddress address = iter.next();
String host = address.getHostName();
int port = ConfigHelper.getOutputRpcPort(conf);
client = CqlOutputFormat.createAuthenticatedClient(host, port, conf);
}
catch (Exception e)
{
closeInternal();
// TException means something unexpected went wrong to that endpoint, so
// we should try again to another. Other exceptions (auth or invalid request) are fatal.
if ((!(e instanceof TException)) || !iter.hasNext())
{
lastException = new IOException(e);
break outer;
}
}
}
}
// close all our connections once we are done.
closeInternal();
} | java | public void run()
{
outer:
while (run || !queue.isEmpty())
{
List<ByteBuffer> bindVariables;
try
{
bindVariables = queue.take();
}
catch (InterruptedException e)
{
// re-check loop condition after interrupt
continue;
}
Iterator<InetAddress> iter = endpoints.iterator();
while (true)
{
// send the mutation to the last-used endpoint. first time through, this will NPE harmlessly.
try
{
int i = 0;
int itemId = preparedStatement(client);
while (bindVariables != null)
{
client.execute_prepared_cql3_query(itemId, bindVariables, ConsistencyLevel.ONE);
i++;
if (i >= batchThreshold)
break;
bindVariables = queue.poll();
}
break;
}
catch (Exception e)
{
closeInternal();
if (!iter.hasNext())
{
lastException = new IOException(e);
break outer;
}
}
// attempt to connect to a different endpoint
try
{
InetAddress address = iter.next();
String host = address.getHostName();
int port = ConfigHelper.getOutputRpcPort(conf);
client = CqlOutputFormat.createAuthenticatedClient(host, port, conf);
}
catch (Exception e)
{
closeInternal();
// TException means something unexpected went wrong to that endpoint, so
// we should try again to another. Other exceptions (auth or invalid request) are fatal.
if ((!(e instanceof TException)) || !iter.hasNext())
{
lastException = new IOException(e);
break outer;
}
}
}
}
// close all our connections once we are done.
closeInternal();
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Stratio/stratio-cassandra | src/java/org/apache/cassandra/hadoop/cql3/CqlRecordWriter.java | RangeClient.preparedStatement | private int preparedStatement(Cassandra.Client client)
{
Integer itemId = preparedStatements.get(client);
if (itemId == null)
{
CqlPreparedResult result;
try
{
result = client.prepare_cql3_query(ByteBufferUtil.bytes(cql), Compression.NONE);
}
catch (InvalidRequestException e)
{
throw new RuntimeException("failed to prepare cql query " + cql, e);
}
catch (TException e)
{
throw new RuntimeException("failed to prepare cql query " + cql, e);
}
Integer previousId = preparedStatements.putIfAbsent(client, Integer.valueOf(result.itemId));
itemId = previousId == null ? result.itemId : previousId;
}
return itemId;
} | java | private int preparedStatement(Cassandra.Client client)
{
Integer itemId = preparedStatements.get(client);
if (itemId == null)
{
CqlPreparedResult result;
try
{
result = client.prepare_cql3_query(ByteBufferUtil.bytes(cql), Compression.NONE);
}
catch (InvalidRequestException e)
{
throw new RuntimeException("failed to prepare cql query " + cql, e);
}
catch (TException e)
{
throw new RuntimeException("failed to prepare cql query " + cql, e);
}
Integer previousId = preparedStatements.putIfAbsent(client, Integer.valueOf(result.itemId));
itemId = previousId == null ? result.itemId : previousId;
}
return itemId;
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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.sessionId);
tree.histogramOfRowCountPerLeaf().log(logger);
logger.debug("Validated {} partitions for {}. Partition sizes are:", validated, desc.sessionId);
tree.histogramOfRowSizePerLeaf().log(logger);
}
} | 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.sessionId);
tree.histogramOfRowCountPerLeaf().log(logger);
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tree.histogramOfRowSizePerLeaf().log(logger);
}
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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
if (!initiator.equals(FBUtilities.getBroadcastAddress()))
logger.info(String.format("[repair #%s] Sending completed merkle tree to %s for %s/%s", desc.sessionId, initiator, desc.keyspace, desc.columnFamily));
MessagingService.instance().sendOneWay(new ValidationComplete(desc, tree).createMessage(), initiator);
} | java | public void run()
{
// respond to the request that triggered this validation
if (!initiator.equals(FBUtilities.getBroadcastAddress()))
logger.info(String.format("[repair #%s] Sending completed merkle tree to %s for %s/%s", desc.sessionId, initiator, desc.keyspace, desc.columnFamily));
MessagingService.instance().sendOneWay(new ValidationComplete(desc, tree).createMessage(), initiator);
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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()
{
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)))
return;
}
} | [
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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))
return false;
}
return true;
} | [
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@param tokens the tokens to check
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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.sessionId, r1.endpoint, r2.endpoint, desc.columnFamily);
if (differences.isEmpty())
{
logger.info(String.format(format, "are consistent"));
// send back sync complete message
MessagingService.instance().sendOneWay(new SyncComplete(desc, r1.endpoint, r2.endpoint, true).createMessage(), FBUtilities.getLocalAddress());
return;
}
// non-0 difference: perform streaming repair
logger.info(String.format(format, "have " + differences.size() + " range(s) out of sync"));
performStreamingRepair();
} | 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.sessionId, r1.endpoint, r2.endpoint, desc.columnFamily);
if (differences.isEmpty())
{
logger.info(String.format(format, "are consistent"));
// send back sync complete message
MessagingService.instance().sendOneWay(new SyncComplete(desc, r1.endpoint, r2.endpoint, true).createMessage(), FBUtilities.getLocalAddress());
return;
}
// non-0 difference: perform streaming repair
logger.info(String.format(format, "have " + differences.size() + " range(s) out of sync"));
performStreamingRepair();
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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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