Changed the name to reflect the sorted nature of the set, added some fixes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@810 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron
parent
831d430025
commit
d056f9f3e8
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@ -37,11 +37,11 @@ import java.util.Iterator;
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* partial interval of a region in the collection it will remove the region from
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* partial interval of a region in the collection it will remove the region from
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* that element.
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* that element.
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*/
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*/
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public class GenomeLocSet extends AbstractSet<GenomeLoc> {
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public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
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// our private storage for the GenomeLoc's
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// our private storage for the GenomeLoc's
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private final ArrayList<GenomeLoc> mArray = new ArrayList<GenomeLoc>();
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private final ArrayList<GenomeLoc> mArray = new ArrayList<GenomeLoc>();
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public GenomeLocSet() {}
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public GenomeLocSortedSet() {}
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/**
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/**
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* get an iterator over this collection
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* get an iterator over this collection
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@ -102,6 +102,9 @@ public class GenomeLocSet extends AbstractSet<GenomeLoc> {
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if (e == null) {
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if (e == null) {
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return false;
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return false;
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}
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}
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// have we added it to the collection?
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boolean haveAdded = false;
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/**
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/**
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* check if the specified element overlaps any current locations, if so
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* check if the specified element overlaps any current locations, if so
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* we should merge the two.
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* we should merge the two.
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@ -110,9 +113,9 @@ public class GenomeLocSet extends AbstractSet<GenomeLoc> {
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if (g.contiguousP(e)) {
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if (g.contiguousP(e)) {
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GenomeLoc c = g.merge(e);
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GenomeLoc c = g.merge(e);
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mArray.set(mArray.indexOf(g),c);
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mArray.set(mArray.indexOf(g),c);
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return true;
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haveAdded = true;
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} else if ((g.getContigIndex() == e.getContigIndex()) &&
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} else if ((g.getContigIndex() == e.getContigIndex()) &&
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(g.getStart() > e.getStart())) {
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(e.getStart() < g.getStart()) && !haveAdded) {
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mArray.add(mArray.indexOf(g), e);
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mArray.add(mArray.indexOf(g), e);
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return true;
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return true;
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}
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}
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@ -120,7 +123,9 @@ public class GenomeLocSet extends AbstractSet<GenomeLoc> {
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/** we're at the end and we haven't found locations that should fall after it,
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/** we're at the end and we haven't found locations that should fall after it,
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* so we'll put it at the end
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* so we'll put it at the end
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*/
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*/
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mArray.add(e);
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if (!haveAdded) {
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mArray.add(e);
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}
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return true;
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return true;
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}
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}
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@ -210,11 +215,11 @@ public class GenomeLocSet extends AbstractSet<GenomeLoc> {
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* @param dict the sequence dictionary to create a collection from
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* @param dict the sequence dictionary to create a collection from
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* @return the GenomeLocSet of all references sequences as GenomeLoc's
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* @return the GenomeLocSet of all references sequences as GenomeLoc's
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*/
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*/
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public static GenomeLocSet createSetFromSequenceDictionary(SAMSequenceDictionary dict) {
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public static GenomeLocSortedSet createSetFromSequenceDictionary(SAMSequenceDictionary dict) {
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GenomeLocSet returnSet = new GenomeLocSet();
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GenomeLocSortedSet returnSortedSet = new GenomeLocSortedSet();
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for (SAMSequenceRecord record : dict.getSequences()) {
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for (SAMSequenceRecord record : dict.getSequences()) {
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returnSet.add(new GenomeLoc(record.getSequenceIndex(),1,record.getSequenceLength()));
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returnSortedSet.add(new GenomeLoc(record.getSequenceIndex(),1,record.getSequenceLength()));
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}
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}
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return returnSet;
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return returnSortedSet;
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}
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}
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}
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}
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@ -1,168 +0,0 @@
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package org.broadinstitute.sting.utils;
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import net.sf.samtools.SAMFileHeader;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.sam.ArtificialSamUtils;
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import static org.junit.Assert.assertTrue;
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import org.junit.Before;
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import org.junit.Test;
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import java.util.Iterator;
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/**
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*
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* User: aaron
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* Date: May 22, 2009
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* Time: 2:14:07 PM
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*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*
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*/
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/**
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* @author aaron
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* @version 1.0
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* @date May 22, 2009
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* <p/>
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* Class GenomeLocSetTest
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* <p/>
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* This tests the functions of the GenomeLocSet
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*/
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public class GenomeLocSetTest extends BaseTest {
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private GenomeLocSet mSet = null;
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private SAMFileHeader header = ArtificialSamUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
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private static final int NUMBER_OF_CHROMOSOMES = 5;
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private static final int STARTING_CHROMOSOME = 1;
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private static final int CHROMOSOME_SIZE = 1000;
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@Before
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public void setup() {
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GenomeLoc.setupRefContigOrdering(header.getSequenceDictionary());
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mSet = new GenomeLocSet();
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}
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@Test
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public void testAdd() {
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GenomeLoc g = new GenomeLoc(STARTING_CHROMOSOME, 0, 0);
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assertTrue(mSet.size() == 0);
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mSet.add(g);
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assertTrue(mSet.size() == STARTING_CHROMOSOME);
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}
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@Test
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public void testRemove() {
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assertTrue(mSet.size() == 0);
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GenomeLoc g = new GenomeLoc(STARTING_CHROMOSOME, 0, 0);
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mSet.add(g);
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assertTrue(mSet.size() == STARTING_CHROMOSOME);
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mSet.remove(g);
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assertTrue(mSet.size() == 0);
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}
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@Test(expected = IllegalArgumentException.class)
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public void testAddDupplicate() {
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assertTrue(mSet.size() == 0);
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GenomeLoc g = new GenomeLoc(STARTING_CHROMOSOME, 0, 0);
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mSet.add(g);
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assertTrue(mSet.size() == STARTING_CHROMOSOME);
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mSet.add(g);
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}
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@Test
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public void mergingOverlappingBelow() {
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GenomeLoc g = new GenomeLoc(STARTING_CHROMOSOME, 0, 50);
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GenomeLoc e = new GenomeLoc(STARTING_CHROMOSOME, 49, 100);
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assertTrue(mSet.size() == 0);
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mSet.add(g);
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assertTrue(mSet.size() == STARTING_CHROMOSOME);
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mSet.addRegion(e);
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assertTrue(mSet.size() == STARTING_CHROMOSOME);
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Iterator<GenomeLoc> iter = mSet.iterator();
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GenomeLoc loc = iter.next();
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assertTrue(loc.getStart() == 0);
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assertTrue(loc.getStop() == 100);
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assertTrue(loc.getContigIndex() == STARTING_CHROMOSOME);
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}
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@Test
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public void mergingOverlappingAbove() {
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GenomeLoc e = new GenomeLoc(STARTING_CHROMOSOME, 0, 50);
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GenomeLoc g = new GenomeLoc(STARTING_CHROMOSOME, 49, 100);
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assertTrue(mSet.size() == 0);
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mSet.add(g);
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assertTrue(mSet.size() == STARTING_CHROMOSOME);
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mSet.addRegion(e);
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assertTrue(mSet.size() == STARTING_CHROMOSOME);
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Iterator<GenomeLoc> iter = mSet.iterator();
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GenomeLoc loc = iter.next();
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assertTrue(loc.getStart() == 0);
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assertTrue(loc.getStop() == 100);
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assertTrue(loc.getContigIndex() == STARTING_CHROMOSOME);
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}
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@Test
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public void deleteSubRegion() {
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GenomeLoc e = new GenomeLoc(STARTING_CHROMOSOME, 0, 50);
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GenomeLoc g = new GenomeLoc(STARTING_CHROMOSOME, 49, 100);
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mSet.add(g);
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mSet.addRegion(e);
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// now delete a region
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GenomeLoc d = new GenomeLoc(STARTING_CHROMOSOME, 25, 75);
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mSet.removeRegion(d);
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Iterator<GenomeLoc> iter = mSet.iterator();
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GenomeLoc loc = iter.next();
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assertTrue(loc.getStart() == 0);
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assertTrue(loc.getStop() == 24);
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assertTrue(loc.getContigIndex() == STARTING_CHROMOSOME);
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loc = iter.next();
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assertTrue(loc.getStart() == 76);
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assertTrue(loc.getStop() == 100);
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assertTrue(loc.getContigIndex() == STARTING_CHROMOSOME);
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}
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@Test
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public void deleteSuperRegion() {
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GenomeLoc e = new GenomeLoc(STARTING_CHROMOSOME, 10, 20);
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GenomeLoc g = new GenomeLoc(STARTING_CHROMOSOME, 70, 100);
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mSet.add(g);
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mSet.addRegion(e);
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assertTrue(mSet.size() == 2);
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// now delete a region
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GenomeLoc d = new GenomeLoc(STARTING_CHROMOSOME, 15, 75);
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mSet.removeRegion(d);
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Iterator<GenomeLoc> iter = mSet.iterator();
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GenomeLoc loc = iter.next();
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assertTrue(loc.getStart() == 10);
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assertTrue(loc.getStop() == 14);
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assertTrue(loc.getContigIndex() == STARTING_CHROMOSOME);
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loc = iter.next();
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assertTrue(loc.getStart() == 76);
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assertTrue(loc.getStop() == 100);
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assertTrue(loc.getContigIndex() == STARTING_CHROMOSOME);
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}
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@Test
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public void fromSequenceDictionary() {
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mSet = GenomeLocSet.createSetFromSequenceDictionary(this.header.getSequenceDictionary());
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// we should have sequence
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assertTrue(mSet.size() == GenomeLocSetTest.NUMBER_OF_CHROMOSOMES);
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int seqNumber = 0;
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for (GenomeLoc loc : mSet) {
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assertTrue(loc.getStart() == 1);
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assertTrue(loc.getStop() == GenomeLocSetTest.CHROMOSOME_SIZE);
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assertTrue(loc.getContigIndex() == seqNumber);
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++seqNumber;
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}
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assertTrue(seqNumber == GenomeLocSetTest.NUMBER_OF_CHROMOSOMES);
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}
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}
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@ -0,0 +1,181 @@
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package org.broadinstitute.sting.utils;
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import net.sf.samtools.SAMFileHeader;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.sam.ArtificialSamUtils;
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import static org.junit.Assert.assertTrue;
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import org.junit.Before;
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import org.junit.Test;
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import java.util.Iterator;
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/**
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*
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* User: aaron
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* Date: May 22, 2009
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* Time: 2:14:07 PM
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*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*
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*/
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/**
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* @author aaron
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* @version 1.0
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* @date May 22, 2009
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* <p/>
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* Class GenomeLocSetTest
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* <p/>
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* This tests the functions of the GenomeLocSet
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*/
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public class GenomeLocSortedSetTest extends BaseTest {
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private GenomeLocSortedSet mSortedSet = null;
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private SAMFileHeader header = ArtificialSamUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
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private static final int NUMBER_OF_CHROMOSOMES = 5;
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private static final int STARTING_CHROMOSOME = 1;
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private static final int CHROMOSOME_SIZE = 1000;
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@Before
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public void setup() {
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GenomeLoc.setupRefContigOrdering(header.getSequenceDictionary());
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mSortedSet = new GenomeLocSortedSet();
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}
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@Test
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public void testAdd() {
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GenomeLoc g = new GenomeLoc(1, 0, 0);
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assertTrue(mSortedSet.size() == 0);
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mSortedSet.add(g);
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assertTrue(mSortedSet.size() == 1);
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}
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@Test
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public void testRemove() {
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assertTrue(mSortedSet.size() == 0);
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GenomeLoc g = new GenomeLoc(1, 0, 0);
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mSortedSet.add(g);
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assertTrue(mSortedSet.size() == 1);
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mSortedSet.remove(g);
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assertTrue(mSortedSet.size() == 0);
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}
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@Test
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public void addRegion() {
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assertTrue(mSortedSet.size() == 0);
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GenomeLoc g = new GenomeLoc(1, 1, 50);
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mSortedSet.add(g);
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GenomeLoc f = new GenomeLoc(1, 30, 80);
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mSortedSet.addRegion(f);
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assertTrue(mSortedSet.size() == 1);
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}
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@Test(expected = IllegalArgumentException.class)
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public void testAddDupplicate() {
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assertTrue(mSortedSet.size() == 0);
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GenomeLoc g = new GenomeLoc(1, 0, 0);
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mSortedSet.add(g);
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assertTrue(mSortedSet.size() == 1);
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mSortedSet.add(g);
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}
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@Test
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public void mergingOverlappingBelow() {
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GenomeLoc g = new GenomeLoc(1, 0, 50);
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GenomeLoc e = new GenomeLoc(1, 49, 100);
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assertTrue(mSortedSet.size() == 0);
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mSortedSet.add(g);
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assertTrue(mSortedSet.size() == 1);
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mSortedSet.addRegion(e);
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assertTrue(mSortedSet.size() == 1);
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Iterator<GenomeLoc> iter = mSortedSet.iterator();
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GenomeLoc loc = iter.next();
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assertTrue(loc.getStart() == 0);
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assertTrue(loc.getStop() == 100);
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assertTrue(loc.getContigIndex() == 1);
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}
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@Test
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public void mergingOverlappingAbove() {
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GenomeLoc e = new GenomeLoc(1, 0, 50);
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GenomeLoc g = new GenomeLoc(1, 49, 100);
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assertTrue(mSortedSet.size() == 0);
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mSortedSet.add(g);
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assertTrue(mSortedSet.size() == 1);
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mSortedSet.addRegion(e);
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assertTrue(mSortedSet.size() == 1);
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Iterator<GenomeLoc> iter = mSortedSet.iterator();
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GenomeLoc loc = iter.next();
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assertTrue(loc.getStart() == 0);
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assertTrue(loc.getStop() == 100);
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assertTrue(loc.getContigIndex() == 1);
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}
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@Test
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public void deleteSubRegion() {
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GenomeLoc e = new GenomeLoc(1, 0, 50);
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GenomeLoc g = new GenomeLoc(1, 49, 100);
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mSortedSet.add(g);
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mSortedSet.addRegion(e);
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// now delete a region
|
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|
GenomeLoc d = new GenomeLoc(1, 25, 75);
|
||||||
|
mSortedSet.removeRegion(d);
|
||||||
|
Iterator<GenomeLoc> iter = mSortedSet.iterator();
|
||||||
|
GenomeLoc loc = iter.next();
|
||||||
|
assertTrue(loc.getStart() == 0);
|
||||||
|
assertTrue(loc.getStop() == 24);
|
||||||
|
assertTrue(loc.getContigIndex() == 1);
|
||||||
|
|
||||||
|
loc = iter.next();
|
||||||
|
assertTrue(loc.getStart() == 76);
|
||||||
|
assertTrue(loc.getStop() == 100);
|
||||||
|
assertTrue(loc.getContigIndex() == 1);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void deleteSuperRegion() {
|
||||||
|
GenomeLoc e = new GenomeLoc(1, 10, 20);
|
||||||
|
GenomeLoc g = new GenomeLoc(1, 70, 100);
|
||||||
|
mSortedSet.add(g);
|
||||||
|
mSortedSet.addRegion(e);
|
||||||
|
assertTrue(mSortedSet.size() == 2);
|
||||||
|
// now delete a region
|
||||||
|
GenomeLoc d = new GenomeLoc(1, 15, 75);
|
||||||
|
mSortedSet.removeRegion(d);
|
||||||
|
Iterator<GenomeLoc> iter = mSortedSet.iterator();
|
||||||
|
GenomeLoc loc = iter.next();
|
||||||
|
assertTrue(loc.getStart() == 10);
|
||||||
|
assertTrue(loc.getStop() == 14);
|
||||||
|
assertTrue(loc.getContigIndex() == 1);
|
||||||
|
|
||||||
|
loc = iter.next();
|
||||||
|
assertTrue(loc.getStart() == 76);
|
||||||
|
assertTrue(loc.getStop() == 100);
|
||||||
|
assertTrue(loc.getContigIndex() == 1);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void fromSequenceDictionary() {
|
||||||
|
mSortedSet = GenomeLocSortedSet.createSetFromSequenceDictionary(this.header.getSequenceDictionary());
|
||||||
|
// we should have sequence
|
||||||
|
assertTrue(mSortedSet.size() == GenomeLocSortedSetTest.NUMBER_OF_CHROMOSOMES);
|
||||||
|
int seqNumber = 0;
|
||||||
|
for (GenomeLoc loc : mSortedSet) {
|
||||||
|
assertTrue(loc.getStart() == 1);
|
||||||
|
assertTrue(loc.getStop() == GenomeLocSortedSetTest.CHROMOSOME_SIZE);
|
||||||
|
assertTrue(loc.getContigIndex() == seqNumber);
|
||||||
|
++seqNumber;
|
||||||
|
}
|
||||||
|
assertTrue(seqNumber == GenomeLocSortedSetTest.NUMBER_OF_CHROMOSOMES);
|
||||||
|
}
|
||||||
|
}
|
||||||
Loading…
Reference in New Issue