removed old tests and old code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2995 348d0f76-0448-11de-a6fe-93d51630548a
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aaron
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e7eae9b61d
commit
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@ -242,39 +242,6 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
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}
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}
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/**
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* remove an element from the set. Given a specific genome location, this function will
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* remove all regions in the element set that overlap the specified region.
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*
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* @param e the genomic range to remove
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*
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* @return true if a removal action was performed, false if the collection was unchanged.
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*/
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public boolean removeRegion(GenomeLoc e) {
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// todo -- delete me
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if (e == null) {
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return false;
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}
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// sometimes we can't return right away, this holds the value for those cases
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boolean returnValue = false;
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/**
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* check if the specified element overlaps any current locations, subtract the removed
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* region and reinsert what is left.
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*/
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for (GenomeLoc g : mArray) {
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if (g.overlapsP(e)) {
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returnValue = true;
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boolean finishEarly = removeOverlappingRegion(g, e);
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if ( finishEarly )
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break;
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}
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}
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return returnValue;
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}
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// public boolean removeRegions(GenomeLocSortedSet toRemove) {
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// int i = 0, j = 0;
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@ -309,70 +276,6 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
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// }
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//
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// todo -- delete me
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private boolean removeOverlappingRegion(GenomeLoc g, GenomeLoc e) {
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if (g.equals(e)) {
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mArray.remove(mArray.indexOf(g));
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return true;
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} else if (g.containsP(e)) {
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/**
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* we have to create two new region, one for the before part, one for the after
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* The old region:
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* |----------------- old region (g) -------------|
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* |----- to delete (e) ------|
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*
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* product (two new regions):
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* |------| + |--------|
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*
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*/
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GenomeLoc before = GenomeLocParser.createGenomeLoc(g.getContigIndex(), g.getStart(), e.getStart() - 1);
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GenomeLoc after = GenomeLocParser.createGenomeLoc(g.getContigIndex(), e.getStop() + 1, g.getStop());
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int index = mArray.indexOf(g);
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if (after.getStop() - after.getStart() >= 0) {
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mArray.add(index, after);
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}
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if (before.getStop() - before.getStart() >= 0) {
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mArray.add(index, before);
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}
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mArray.remove(mArray.indexOf(g));
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return true;
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} else if (e.containsP(g)) {
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/**
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* e completely contains g, delete g, but keep looking, there may be more regions
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* i.e.:
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* |--------------------- e --------------------|
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* |--- g ---| |---- others ----|
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*/
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mArray.remove(mArray.indexOf(g));
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return false;
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} else {
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/**
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* otherwise e overlaps some part of g
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*/
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GenomeLoc l;
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/**
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* figure out which region occurs first on the genome. I.e., is it:
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* |------------- g ----------|
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* |------------- e ----------|
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*
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* or:
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* |------------- g ----------|
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* |------------ e -----------|
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*
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*/
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if (e.getStart() < g.getStart()) {
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l = GenomeLocParser.createGenomeLoc(g.getContigIndex(), e.getStop() + 1, g.getStop());
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} else {
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l = GenomeLocParser.createGenomeLoc(g.getContigIndex(), g.getStart(), e.getStart() - 1);
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}
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// replace g with the new region
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mArray.set(mArray.indexOf(g), l);
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return false;
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}
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}
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/**
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* a simple removal of an interval contained in this list. The interval must be identical to one in the list (no partial locations or overlapping)
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* @param location the GenomeLoc to remove
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@ -120,99 +120,10 @@ public class GenomeLocSortedSetTest extends BaseTest {
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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 = GenomeLocParser.createGenomeLoc(1, 0, 50);
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GenomeLoc g = GenomeLocParser.createGenomeLoc(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 = GenomeLocParser.createGenomeLoc(1, 25, 75);
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mSortedSet.removeRegion(d);
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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() == 24);
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assertTrue(loc.getContigIndex() == 1);
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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() == 1);
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}
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@Test
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public void deleteAllButTwoEndBases() {
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GenomeLoc e = GenomeLocParser.createGenomeLoc(1, 1, 50);
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mSortedSet.add(e);
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// now delete the region
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GenomeLoc d = GenomeLocParser.createGenomeLoc(1, 2, 49);
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mSortedSet.removeRegion(d);
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Iterator<GenomeLoc> iter = mSortedSet.iterator();
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// we expect to find the two end bases only, this was added because we were
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// dropping intervals that were of size one.
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GenomeLoc loc = iter.next();
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assertTrue(loc.getStart() == 1);
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assertTrue(loc.getStop() == 1);
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assertTrue(loc.getContigIndex() == 1);
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loc = iter.next();
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assertTrue(loc.getStart() == 50);
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assertTrue(loc.getStop() == 50);
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assertTrue(loc.getContigIndex() == 1);
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}
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@Test
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public void deleteAllByRegion() {
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GenomeLoc e = GenomeLocParser.createGenomeLoc(1, 1, 100);
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mSortedSet.add(e);
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for (int x = 1; x < 101; x++) {
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GenomeLoc del = GenomeLocParser.createGenomeLoc(1,x,x);
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mSortedSet.removeRegion(del);
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}
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assertTrue(mSortedSet.isEmpty());
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}
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@Test
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public void deleteSomeByRegion() {
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GenomeLoc e = GenomeLocParser.createGenomeLoc(1, 1, 100);
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mSortedSet.add(e);
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for (int x = 1; x < 50; x++) {
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GenomeLoc del = GenomeLocParser.createGenomeLoc(1,x,x);
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mSortedSet.removeRegion(del);
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}
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assertTrue(!mSortedSet.isEmpty());
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assertTrue(mSortedSet.size() == 1);
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GenomeLoc loc = mSortedSet.iterator().next();
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assertTrue(loc.getStop() == 100);
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assertTrue(loc.getStart() == 50);
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}
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@Test
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public void deleteSuperRegion() {
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GenomeLoc e = GenomeLocParser.createGenomeLoc(1, 10, 20);
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GenomeLoc g = GenomeLocParser.createGenomeLoc(1, 70, 100);
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mSortedSet.add(g);
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mSortedSet.addRegion(e);
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assertTrue(mSortedSet.size() == 2);
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// now delete a region
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GenomeLoc d = GenomeLocParser.createGenomeLoc(1, 15, 75);
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mSortedSet.removeRegion(d);
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Iterator<GenomeLoc> iter = mSortedSet.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() == 1);
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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() == 1);
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}
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@Test
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public void fromSequenceDictionary() {
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