Deleting / archiving no longer classes
-- AminoAcidTable and AminoAcid goes to the archive -- Removing two unused SAMRecord classes
This commit is contained in:
Mark DePristo
parent
38cc496de8
commit
5558a6b8f7
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@ -1,60 +0,0 @@
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/*
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* The MIT License
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*
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* Copyright (c) 2009 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in
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* all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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* THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.indels;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMRecordCoordinateComparator;
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/**
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* Extends Picard's Comparator for sorting SAMRecords by coordinate. This one actually deals with unmapped reads
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* (among other things) sitting at the same position as their mates (so that they both can be put into the same set).
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*/
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public class SAMRecordCoordinateComparatorWithUnmappedReads extends SAMRecordCoordinateComparator {
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public int compare(final SAMRecord samRecord1, final SAMRecord samRecord2) {
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int cmp = fileOrderCompare(samRecord1, samRecord2);
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if ( cmp != 0 )
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return cmp;
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// deal with unmapped reads
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if ( samRecord1.getReadUnmappedFlag() != samRecord2.getReadUnmappedFlag() )
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return (samRecord1.getReadUnmappedFlag()? 1: -1);
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if ( samRecord1.getReadNegativeStrandFlag() != samRecord2.getReadNegativeStrandFlag() )
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return (samRecord1.getReadNegativeStrandFlag()? 1: -1);
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// even the names can be the same
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cmp = samRecord1.getReadName().compareTo(samRecord2.getReadName());
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if ( cmp != 0 )
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return cmp;
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if ( samRecord1.getDuplicateReadFlag() != samRecord2.getDuplicateReadFlag() )
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return (samRecord1.getDuplicateReadFlag()? -1: 1);
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if ( samRecord1.getReadPairedFlag() && samRecord2.getReadPairedFlag() && samRecord1.getFirstOfPairFlag() != samRecord2.getFirstOfPairFlag() )
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return (samRecord1.getFirstOfPairFlag()? -1: 1);
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// such a case was actually observed
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return samRecord1.getMappingQuality() - samRecord2.getMappingQuality();
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}
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}
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@ -1,93 +0,0 @@
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils;
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/**
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* Represents a single amino acid.
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*/
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public class AminoAcid {
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private String name;
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private String threeLetterCode;
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private String letter;
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/**
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* Constructor.
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*
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* @param letter The 1 letter code. (eg. I). This is '*' for the stop codon.
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* @param name The full name of the AA (eg. Isoleucine).
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* @param code The 3 letter code. (eg. Ile).
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*/
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public AminoAcid( String letter, String name, String code) {
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this.name = name;
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this.threeLetterCode = code;
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this.letter = letter;
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}
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/** Equality based on the amino acid code. */
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public boolean equals(Object o) {
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if (this == o) { return true; }
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if (o == null || !(o instanceof AminoAcid)) { return false; }
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final AminoAcid aminoAcid = (AminoAcid) o;
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return !(getCode() != null ? !getCode().equals(aminoAcid.getCode()) : aminoAcid.getCode() != null);
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}
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/** Hashes the three letter code. */
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public int hashCode() {
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return (getCode() != null ? getCode().hashCode() : 0);
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}
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/**
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* Returns the full name of this AA.
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*/
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public String getName() { return name; }
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/**
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* Returns the 1 letter code for this AA.
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*/
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public String getLetter() { return letter; }
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/**
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* Returns the 3 letter code.
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*/
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public String getCode() { return threeLetterCode; }
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/** Returns true if the amino acid is really just a stop codon. */
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public boolean isStop() {
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return "*".equals(getLetter());
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}
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/** Returns true if the amino acid is really just a stop codon. */
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public boolean isUnknown() {
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return "X".equals(getLetter());
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}
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public String toString() {
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return name;
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}
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}
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@ -1,214 +0,0 @@
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils;
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import java.util.HashMap;
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/**
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* A simple {codon -> amino acid name} lookup table.
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* Handles differences between mitochondrial and nuclear genes.
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*/
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public class AminoAcidTable {
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protected static final AminoAcid UNKNOWN = new AminoAcid("X" , "Unknown", "Unk");
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protected static final AminoAcid ISOLEUCINE = new AminoAcid("I" , "Isoleucine", "Ile");
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protected static final AminoAcid LEUCINE = new AminoAcid("L" , "Leucine", "Leu");
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protected static final AminoAcid VALINE = new AminoAcid("V" , "Valine", "Val");
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protected static final AminoAcid PHENYLALANINE = new AminoAcid("F" , "Phenylalanine", "Phe");
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protected static final AminoAcid METHIONINE = new AminoAcid("M" , "Methionine", "Met");
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protected static final AminoAcid CYSTEINE = new AminoAcid("C" , "Cysteine", "Cys");
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protected static final AminoAcid ALANINE = new AminoAcid("A" , "Alanine", "Ala");
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protected static final AminoAcid STOP_CODON = new AminoAcid("*" , "Stop Codon", "Stop");
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protected static final AminoAcid GLYCINE = new AminoAcid("G" , "Glycine", "Gly");
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protected static final AminoAcid PROLINE = new AminoAcid("P" , "Proline", "Pro");
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protected static final AminoAcid THEONINE = new AminoAcid("T" , "Threonine", "Thr");
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protected static final AminoAcid SERINE = new AminoAcid("S" , "Serine", "Ser");
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protected static final AminoAcid TYROSINE = new AminoAcid("Y" , "Tyrosine", "Tyr");
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protected static final AminoAcid TRYPTOPHAN = new AminoAcid("W" , "Tryptophan", "Trp");
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protected static final AminoAcid GLUTAMINE = new AminoAcid("Q" , "Glutamine", "Gln");
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protected static final AminoAcid ASPARAGINE = new AminoAcid("N" , "Asparagine", "Asn");
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protected static final AminoAcid HISTIDINE = new AminoAcid("H" , "Histidine", "His");
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protected static final AminoAcid GLUTAMIC_ACID = new AminoAcid("E" , "Glutamic acid", "Glu");
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protected static final AminoAcid ASPARTIC_ACID = new AminoAcid("D" , "Aspartic acid", "Asp");
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protected static final AminoAcid LYSINE = new AminoAcid("K" , "Lysine", "Lys");
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protected static final AminoAcid ARGININE = new AminoAcid("R" , "Arginine", "Arg");
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protected static HashMap<String, AminoAcid> aminoAcidTable = new HashMap<String, AminoAcid>();
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protected static HashMap<String, AminoAcid> mitochondrialAminoAcidTable = new HashMap<String, AminoAcid>();
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static {
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//populate the tables
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aminoAcidTable.put("ATT", ISOLEUCINE);
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aminoAcidTable.put("ATC", ISOLEUCINE);
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aminoAcidTable.put("ATA", ISOLEUCINE);
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aminoAcidTable.put("CTT", LEUCINE);
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aminoAcidTable.put("CTC", LEUCINE);
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aminoAcidTable.put("CTA", LEUCINE);
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aminoAcidTable.put("CTG", LEUCINE);
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aminoAcidTable.put("TTA", LEUCINE);
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aminoAcidTable.put("TTG", LEUCINE);
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aminoAcidTable.put("GTT", VALINE);
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aminoAcidTable.put("GTC", VALINE);
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aminoAcidTable.put("GTA", VALINE);
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aminoAcidTable.put("GTG", VALINE);
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aminoAcidTable.put("TTT", PHENYLALANINE);
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aminoAcidTable.put("TTC", PHENYLALANINE);
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aminoAcidTable.put("ATG", METHIONINE);
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aminoAcidTable.put("TGT", CYSTEINE);
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aminoAcidTable.put("TGC", CYSTEINE);
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aminoAcidTable.put("GCT", ALANINE);
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aminoAcidTable.put("GCC", ALANINE);
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aminoAcidTable.put("GCA", ALANINE);
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aminoAcidTable.put("GCG", ALANINE);
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aminoAcidTable.put("GGT", GLYCINE);
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aminoAcidTable.put("GGC", GLYCINE);
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aminoAcidTable.put("GGA", GLYCINE);
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aminoAcidTable.put("GGG", GLYCINE);
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aminoAcidTable.put("CCT", PROLINE);
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aminoAcidTable.put("CCC", PROLINE);
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aminoAcidTable.put("CCA", PROLINE);
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aminoAcidTable.put("CCG", PROLINE);
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aminoAcidTable.put("ACT", THEONINE);
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aminoAcidTable.put("ACC", THEONINE);
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aminoAcidTable.put("ACA", THEONINE);
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aminoAcidTable.put("ACG", THEONINE);
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aminoAcidTable.put("TCT", SERINE);
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aminoAcidTable.put("TCC", SERINE);
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aminoAcidTable.put("TCA", SERINE);
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aminoAcidTable.put("TCG", SERINE);
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aminoAcidTable.put("AGT", SERINE);
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aminoAcidTable.put("AGC", SERINE);
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aminoAcidTable.put("TAT", TYROSINE);
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aminoAcidTable.put("TAC", TYROSINE);
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aminoAcidTable.put("TGG", TRYPTOPHAN);
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aminoAcidTable.put("CAA", GLUTAMINE);
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aminoAcidTable.put("CAG", GLUTAMINE);
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aminoAcidTable.put("AAT", ASPARAGINE);
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aminoAcidTable.put("AAC", ASPARAGINE);
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aminoAcidTable.put("CAT", HISTIDINE);
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aminoAcidTable.put("CAC", HISTIDINE);
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aminoAcidTable.put("GAA", GLUTAMIC_ACID);
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aminoAcidTable.put("GAG", GLUTAMIC_ACID);
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aminoAcidTable.put("GAT", ASPARTIC_ACID);
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aminoAcidTable.put("GAC", ASPARTIC_ACID);
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aminoAcidTable.put("AAA", LYSINE);
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aminoAcidTable.put("AAG", LYSINE);
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aminoAcidTable.put("CGT", ARGININE);
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aminoAcidTable.put("CGC", ARGININE);
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aminoAcidTable.put("CGA", ARGININE);
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aminoAcidTable.put("CGG", ARGININE);
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aminoAcidTable.put("AGA", ARGININE);
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aminoAcidTable.put("AGG", ARGININE);
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aminoAcidTable.put("TAA", STOP_CODON );
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aminoAcidTable.put("TAG", STOP_CODON);
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aminoAcidTable.put("TGA", STOP_CODON);
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//populate the mitochondrial AA table
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mitochondrialAminoAcidTable.putAll(aminoAcidTable);
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mitochondrialAminoAcidTable.put("AGA", STOP_CODON);
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mitochondrialAminoAcidTable.put("AGG", STOP_CODON);
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mitochondrialAminoAcidTable.put("ATA", METHIONINE);
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mitochondrialAminoAcidTable.put("TGA", TRYPTOPHAN);
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}
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/**
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* Returns the amino acid encoded by the given codon in a eukaryotic genome.
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*
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* @param codon The 3-letter mRNA nucleotide codon 5' to 3'. Expects T's instead of U's. Not case sensitive.
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*
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* @return The amino acid matching the given codon, or the UNKNOWN amino acid if the codon string doesn't match anything
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*/
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public static AminoAcid getEukaryoticAA(String codon) {
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codon = codon.toUpperCase();
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final AminoAcid aa = aminoAcidTable.get(codon);
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return aa == null ? UNKNOWN : aa;
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}
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/**
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* Returns the amino acid encoded by the given codon in a mitochondrial genome.
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*
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* @param codon The 3-letter mRNA nucleotide codon 5' to 3'. Expects T's instead of U's. Not case sensitive.
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* @param isFirstCodon If this is the 1st codon in the gene, then "ATT" encodes Methyonine
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*
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* @return The amino acid matching the given codon in mitochondrial genes, or the UNKNOWN amino acid if the codon string doesn't match anything
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*/
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public static AminoAcid getMitochondrialAA(String codon, boolean isFirstCodon) {
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codon = codon.toUpperCase();
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final AminoAcid aa = mitochondrialAminoAcidTable.get(codon);
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if(aa == null) {
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return UNKNOWN;
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} else if(isFirstCodon && codon.equals("ATT")) {
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return METHIONINE; //special case - 'ATT' in the first codon of a mitochondrial gene codes for methionine instead of isoleucine
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} else {
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return aa;
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}
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}
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}
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@ -1,68 +0,0 @@
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
*
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
|
||||
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
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package org.broadinstitute.sting.utils.sam;
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import net.sf.samtools.SAMRecord;
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public class ComparableSAMRecord implements Comparable<ComparableSAMRecord> {
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private SAMRecord record;
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public ComparableSAMRecord(SAMRecord record) {
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this.record = record;
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}
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public SAMRecord getRecord() {
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return record;
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}
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public int compareTo(ComparableSAMRecord o) {
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// first sort by start position -- with not coverflow because both are guaranteed to be positive.
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int comparison = record.getAlignmentStart() - o.record.getAlignmentStart();
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// if the reads have the same start position, we must give a non-zero comparison
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// (because java Sets often require "consistency with equals")
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if ( comparison == 0 )
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comparison = record.getReadName().compareTo(o.getRecord().getReadName());
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// if the read names are the same, use the first of the pair if appropriate
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if ( comparison == 0 && record.getReadPairedFlag() )
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comparison = ( record.getFirstOfPairFlag() ? -1 : 1);
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return comparison;
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}
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public boolean equals(Object obj) {
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if ( !(obj instanceof ComparableSAMRecord) )
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return false;
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if ( this == obj )
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return true;
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ComparableSAMRecord csr = (ComparableSAMRecord)obj;
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if(record.getAlignmentStart() != csr.record.getAlignmentStart())
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return false;
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if ( !record.getReadName().equals(csr.getRecord().getReadName()) )
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return false;
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return ( record.getFirstOfPairFlag() == csr.record.getFirstOfPairFlag() );
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}
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}
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