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Refactoring of VDJCAlignments on road:
- added SequenceHistory to each alignment - added original reads ! doesn't compiles
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src/main/java/com/milaboratory/mixcr/basictypes/SequenceHistory.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,185 @@ | ||
| package com.milaboratory.mixcr.basictypes; | ||
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| import com.milaboratory.util.ArraysUtils; | ||
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| import static java.lang.Math.abs; | ||
| import static java.lang.Math.max; | ||
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| public interface SequenceHistory { | ||
| /** | ||
| * Length of target | ||
| */ | ||
| int length(); | ||
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| /** | ||
| * Shift read index by specified value (used in .vdjca files merging) | ||
| */ | ||
| SequenceHistory shiftReadId(long shift); | ||
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| /** | ||
| * Return all raw read ids (sorted) occurring in the history | ||
| */ | ||
| long[] readIds(); | ||
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| /** | ||
| * Return minimal raw read id occurring in the history | ||
| */ | ||
| long minReadId(); | ||
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| /** | ||
| * Initial event, starting point of the history (single fastq record read from file) | ||
| */ | ||
| final class RawSequence implements SequenceHistory { | ||
| /** | ||
| * Read index in the initial .fastq file | ||
| */ | ||
| public final long readId; | ||
| /** | ||
| * Read index in pair | ||
| */ | ||
| public final byte mateIndex; | ||
| /** | ||
| * Read length | ||
| */ | ||
| public final int length; | ||
| /** | ||
| * Is reverse complement | ||
| */ | ||
| public final boolean isReverseComplement; | ||
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| public RawSequence(long readId, byte mateIndex, int length, boolean isReverseComplement) { | ||
| this.readId = readId; | ||
| this.mateIndex = mateIndex; | ||
| this.length = length; | ||
| this.isReverseComplement = isReverseComplement; | ||
| } | ||
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| @Override | ||
| public int length() { return length; } | ||
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| @Override | ||
| public SequenceHistory shiftReadId(long shift) { | ||
| return new RawSequence(readId + shift, mateIndex, length, isReverseComplement); | ||
| } | ||
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| @Override | ||
| public long[] readIds() { | ||
| return new long[]{readId}; | ||
| } | ||
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| @Override | ||
| public long minReadId() { | ||
| return readId; | ||
| } | ||
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| @Override | ||
| public boolean equals(Object o) { | ||
| if (this == o) return true; | ||
| if (o == null || getClass() != o.getClass()) return false; | ||
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| RawSequence that = (RawSequence) o; | ||
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| if (readId != that.readId) return false; | ||
| if (mateIndex != that.mateIndex) return false; | ||
| if (length != that.length) return false; | ||
| return isReverseComplement == that.isReverseComplement; | ||
| } | ||
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| @Override | ||
| public int hashCode() { | ||
| int result = (int) (readId ^ (readId >>> 32)); | ||
| result = 31 * result + (int) mateIndex; | ||
| result = 31 * result + length; | ||
| result = 31 * result + (isReverseComplement ? 1 : 0); | ||
| return result; | ||
| } | ||
| } | ||
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| /** | ||
| * Parent for all events when two alignments or reads are merged into a single one | ||
| */ | ||
| abstract class Merge implements SequenceHistory { | ||
| /** | ||
| * Histories of merged alignments | ||
| */ | ||
| public final SequenceHistory left, right; | ||
| /** | ||
| * Position of the first nucleotide of the right target in the left target | ||
| */ | ||
| public final int offset; | ||
| /** | ||
| * Number of mismatches | ||
| */ | ||
| public final int nMismatches; | ||
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| Merge(SequenceHistory left, SequenceHistory right, int offset, int nMismatches) { | ||
| this.left = left; | ||
| this.right = right; | ||
| this.offset = offset; | ||
| this.nMismatches = nMismatches; | ||
| } | ||
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| @Override | ||
| public int length() { | ||
| return abs(offset) + | ||
| (offset >= 0 ? | ||
| max(left.length() - offset, right.length()) : | ||
| max(left.length(), right.length() + offset) // offset is negative here | ||
| ); | ||
| } | ||
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| @Override | ||
| public long[] readIds() { | ||
| return ArraysUtils.getSortedDistinct(ArraysUtils.concatenate(left.readIds(), right.readIds())); | ||
| } | ||
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| @Override | ||
| public long minReadId() { | ||
| return Math.min(left.minReadId(), right.minReadId()); | ||
| } | ||
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| @Override | ||
| public boolean equals(Object o) { | ||
| if (this == o) return true; | ||
| if (o == null || getClass() != o.getClass()) return false; | ||
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| Merge merge = (Merge) o; | ||
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| if (offset != merge.offset) return false; | ||
| if (nMismatches != merge.nMismatches) return false; | ||
| if (!left.equals(merge.left)) return false; | ||
| return right.equals(merge.right); | ||
| } | ||
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| @Override | ||
| public int hashCode() { | ||
| int result = left.hashCode(); | ||
| result = 31 * result + right.hashCode(); | ||
| result = 31 * result + offset; | ||
| result = 31 * result + nMismatches; | ||
| return result; | ||
| } | ||
| } | ||
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| final class SequenceOverlap extends Merge { | ||
| public SequenceOverlap(SequenceHistory left, SequenceHistory right, int offset, int nMismatches) { | ||
| super(left, right, offset, nMismatches); | ||
| } | ||
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| @Override | ||
| public SequenceOverlap shiftReadId(long shift) { | ||
| return new SequenceOverlap(left.shiftReadId(shift), right.shiftReadId(shift), offset, nMismatches); | ||
| } | ||
| } | ||
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| final class AlignmentOverlap extends Merge { | ||
| public AlignmentOverlap(SequenceHistory left, SequenceHistory right, int offset, int nMismatches) { | ||
| super(left, right, offset, nMismatches); | ||
| } | ||
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| @Override | ||
| public AlignmentOverlap shiftReadId(long shift) { | ||
| return new AlignmentOverlap(left.shiftReadId(shift), right.shiftReadId(shift), offset, nMismatches); | ||
| } | ||
| } | ||
| } |
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