From: kiramt Date: Fri, 29 Sep 2017 13:22:30 +0000 (+0100) Subject: JAL-2674 finish with iterators for now X-Git-Tag: Release_2_10_4~55^2~1^2~95 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4c1ab51e2c08f85ba8c38486adf4a6ce0b0f25c3;p=jalview.git JAL-2674 finish with iterators for now --- diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java index c3408bd..a6fe541 100644 --- a/src/jalview/analysis/Dna.java +++ b/src/jalview/analysis/Dna.java @@ -44,6 +44,7 @@ import jalview.util.ShiftList; import java.util.ArrayList; import java.util.Arrays; import java.util.Comparator; +import java.util.Iterator; import java.util.List; public class Dna @@ -60,7 +61,7 @@ public class Dna private final String[] seqstring; - private final List contigs; + private final Iterator contigs; private final char gapChar; @@ -91,7 +92,7 @@ public class Dna * @param viewport * @param visibleContigs */ - public Dna(AlignViewportI viewport, List visibleContigs) + public Dna(AlignViewportI viewport, Iterator visibleContigs) { this.selection = Arrays.asList(viewport.getSequenceSelection()); this.seqstring = viewport.getViewAsString(true); @@ -396,11 +397,12 @@ public class Dna ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring // intervals int vc = 0; - int[] scontigs = new int[contigs.size() * 2]; + int npos = 0; int[] lastregion = null; - for (int[] region : contigs) + while (contigs.hasNext()) { + int[] region = contigs.next(); if (lastregion == null) { vismapping.addShift(npos, region[0]); @@ -411,7 +413,14 @@ public class Dna vismapping.addShift(npos, region[0] - lastregion[1] + 1); } lastregion = region; + vc++; + } + int[] scontigs = new int[vc]; + vc = 0; + while (contigs.hasNext()) + { + int[] region = contigs.next(); scontigs[vc] = region[0]; scontigs[vc + 1] = region[1]; vc++; diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java index c77fb7b..5554be0 100644 --- a/src/jalview/datamodel/HiddenColumns.java +++ b/src/jalview/datamodel/HiddenColumns.java @@ -714,70 +714,6 @@ public class HiddenColumns return copy; } - /** - * return all visible segments between the given start and end boundaries - * - * @param start - * (first column inclusive from 0) - * @param end - * (last column - not inclusive) - * @return List {[i_start, i_end], ..} where intervals lie in - * start<=i_start<=i_end getVisibleContigs(int start, int end) - { - try - { - LOCK.readLock().lock(); - List vcontigs = new ArrayList<>(); - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - int vstart = start; - int hideStart; - int hideEnd; - - for (int[] region : hiddenColumns) - { - hideStart = region[0]; - hideEnd = region[1]; - - // navigate to start - if (hideEnd < vstart) - { - continue; - } - if (hideStart > vstart) - { - int[] contig = new int[] { vstart, hideStart - 1 }; - vcontigs.add(contig); - } - vstart = hideEnd + 1; - - // exit if we're past the end - if (vstart >= end) - { - break; - } - } - - if (vstart < end) - { - int[] contig = new int[] { vstart, end - 1 }; - vcontigs.add(contig); - } - } - else - { - int[] contig = new int[] { start, end - 1 }; - vcontigs.add(contig); - } - return vcontigs; - } finally - { - LOCK.readLock().unlock(); - } - } - public String[] getVisibleSequenceStrings(int start, int end, SequenceI[] seqs) { @@ -794,30 +730,18 @@ public class HiddenColumns int blockStart = start; int blockEnd = end; - int hideStart; - int hideEnd; - for (int[] region : hiddenColumns) + Iterator regions = new BoundedHiddenColsIterator(start, + end, false); + while (regions.hasNext()) { - hideStart = region[0]; - hideEnd = region[1]; - - if (hideStart < start) - { - continue; - } - - blockStart = Math.min(blockStart, hideEnd + 1); - blockEnd = Math.min(blockEnd, hideStart); - - if (blockStart > blockEnd) - { - break; - } + int[] region = regions.next(); + blockStart = Math.min(blockStart, region[1] + 1); + blockEnd = Math.min(blockEnd, region[0]); visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd)); - blockStart = hideEnd + 1; + blockStart = region[1] + 1; blockEnd = end; } @@ -962,95 +886,91 @@ public class HiddenColumns try { LOCK.readLock().lock(); - if (alignmentAnnotation.annotations == null) - { - return; - } - if (start == end && end == -1) - { - start = 0; - end = alignmentAnnotation.annotations.length; - } - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - // then mangle the alignmentAnnotation annotation array - Vector annels = new Vector<>(); - Annotation[] els = null; - int blockStart = start; - int blockEnd = end; - int hideStart; - int hideEnd; - int w = 0; - - for (int[] region : hiddenColumns) - { - hideStart = region[0]; - hideEnd = region[1]; - if (hideStart < start) - { - continue; - } - - blockStart = Math.min(blockStart, hideEnd + 1); - blockEnd = Math.min(blockEnd, hideStart); - - if (blockStart > blockEnd) - { - break; - } + int startFrom = start; + int endAt = end; - els = new Annotation[blockEnd - blockStart]; - annels.addElement(els); - System.arraycopy(alignmentAnnotation.annotations, blockStart, els, - 0, els.length); - w += els.length; - blockStart = hideEnd + 1; - blockEnd = end; + if (alignmentAnnotation.annotations != null) + { + if (start == end && end == -1) + { + startFrom = 0; + endAt = alignmentAnnotation.annotations.length; } - - if (end > blockStart) + if (hiddenColumns != null && hiddenColumns.size() > 0) { - els = new Annotation[end - blockStart + 1]; - annels.addElement(els); - if ((els.length - + blockStart) <= alignmentAnnotation.annotations.length) - { - // copy just the visible segment of the annotation row - System.arraycopy(alignmentAnnotation.annotations, blockStart, - els, 0, els.length); - } - else - { - // copy to the end of the annotation row - System.arraycopy(alignmentAnnotation.annotations, blockStart, - els, 0, - (alignmentAnnotation.annotations.length - blockStart)); - } - w += els.length; + removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation); } - if (w == 0) + else { - return; + alignmentAnnotation.restrict(startFrom, endAt); } + } + } finally + { + LOCK.readLock().unlock(); + } + } - alignmentAnnotation.annotations = new Annotation[w]; - w = 0; + private void removeHiddenAnnotation(int start, int end, + AlignmentAnnotation alignmentAnnotation) + { + // mangle the alignmentAnnotation annotation array + Vector annels = new Vector<>(); + Annotation[] els = null; + int blockStart = start; + int blockEnd = end; + int w = 0; + + Iterator regions = new BoundedHiddenColsIterator(start, end, + false); + while (regions.hasNext()) + { + int[] region = regions.next(); + blockStart = Math.min(blockStart, region[1] + 1); + blockEnd = Math.min(blockEnd, region[0]); - for (Annotation[] chnk : annels) - { - System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, - chnk.length); - w += chnk.length; - } + els = new Annotation[blockEnd - blockStart]; + annels.addElement(els); + System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, + els.length); + w += els.length; + + blockStart = region[1] + 1; + blockEnd = end; + } + + if (end > blockStart) + { + els = new Annotation[end - blockStart + 1]; + annels.addElement(els); + if ((els.length + + blockStart) <= alignmentAnnotation.annotations.length) + { + // copy just the visible segment of the annotation row + System.arraycopy(alignmentAnnotation.annotations, blockStart, els, + 0, els.length); } else { - alignmentAnnotation.restrict(start, end); + // copy to the end of the annotation row + System.arraycopy(alignmentAnnotation.annotations, blockStart, els, + 0, (alignmentAnnotation.annotations.length - blockStart)); } - } finally + w += els.length; + } + + if (w != 0) { - LOCK.readLock().unlock(); + alignmentAnnotation.annotations = new Annotation[w]; + + w = 0; + for (Annotation[] chnk : annels) + { + System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, + chnk.length); + w += chnk.length; + } } } @@ -1481,6 +1401,9 @@ public class HiddenColumns } } + /** + * Return an iterator over the hidden regions + */ public Iterator iterator() { if (hiddenColumns != null) @@ -1494,28 +1417,66 @@ public class HiddenColumns } } + /** + * Return a bounded iterator over the hidden regions + * + * @param start + * position to start from (inclusive, absolute column position) + * @param end + * position to end at (inclusive, absolute column position) + * @return + */ public Iterator getBoundedIterator(int start, int end) { return new BoundedHiddenColsIterator(start, end, true); } + /** + * Return a bounded iterator over the *visible* start positions of hidden + * regions + * + * @param start + * position to start from (inclusive, visible column position) + * @param end + * position to end at (inclusive, visible column position) + */ public Iterator getBoundedStartIterator(int start, int end) { return new BoundedStartRegionIterator(start, end, true); } + /** + * Return an iterator over visible columns between the given start and end + * boundaries + * + * @param start + * first column (inclusive) + * @param end + * last column (inclusive) + */ public Iterator getVisibleColsIterator(int start, int end) { return new VisibleColsIterator(start, end, true); } /** - * An iterator which iterates over hidden column regions in a range. + * return an iterator over visible segments between the given start and end + * boundaries * - * @author kmourao - * + * @param start + * (first column inclusive from 0) + * @param end + * (last column - not inclusive) */ - class BoundedHiddenColsIterator implements Iterator + public Iterator getVisContigsIterator(int start, int end) + { + return new VisibleContigsIterator(start, end, true); + } + + /** + * An iterator which iterates over hidden column regions in a range. + */ + private class BoundedHiddenColsIterator implements Iterator { private int start; // start position to iterate from @@ -1616,12 +1577,17 @@ public class HiddenColumns } } - class BoundedStartRegionIterator implements Iterator + /** + * An iterator which iterates over visible start positions of hidden column + * regions in a range. + */ + private class BoundedStartRegionIterator implements Iterator { + // start position to iterate from + private int start; - private int start; // start position to iterate from - - private int end; // end position to iterate to + // end position to iterate to + private int end; // current index in hiddenColumns private int currentPosition = 0; @@ -1701,6 +1667,11 @@ public class HiddenColumns return (currentPosition < positions.size()); } + /** + * Get next hidden region start position + * + * @return the start position in *visible* coordinates + */ @Override public Integer next() { @@ -1710,7 +1681,7 @@ public class HiddenColumns } } - public class VisibleColsIterator implements Iterator + private class VisibleColsIterator implements Iterator { private int last; @@ -1722,7 +1693,7 @@ public class HiddenColumns private int lasthiddenregion; - public VisibleColsIterator(int firstcol, int lastcol, boolean useCopy) + VisibleColsIterator(int firstcol, int lastcol, boolean useCopy) { last = lastcol; current = firstcol; @@ -1838,4 +1809,87 @@ public class HiddenColumns throw new UnsupportedOperationException(); } } + + /** + * An iterator which iterates over visible regions in a range. + */ + private class VisibleContigsIterator implements Iterator + { + private List vcontigs = new ArrayList<>(); + + private int currentPosition = 0; + + VisibleContigsIterator(int start, int end, boolean usecopy) + { + try + { + if (usecopy) + { + LOCK.readLock().lock(); + } + + if (hiddenColumns != null && hiddenColumns.size() > 0) + { + int vstart = start; + int hideStart; + int hideEnd; + + for (int[] region : hiddenColumns) + { + hideStart = region[0]; + hideEnd = region[1]; + + // navigate to start + if (hideEnd < vstart) + { + continue; + } + if (hideStart > vstart) + { + int[] contig = new int[] { vstart, hideStart - 1 }; + vcontigs.add(contig); + } + vstart = hideEnd + 1; + + // exit if we're past the end + if (vstart >= end) + { + break; + } + } + + if (vstart < end) + { + int[] contig = new int[] { vstart, end - 1 }; + vcontigs.add(contig); + } + } + else + { + int[] contig = new int[] { start, end - 1 }; + vcontigs.add(contig); + } + } finally + { + if (usecopy) + { + LOCK.readLock().unlock(); + } + } + } + + @Override + public boolean hasNext() + { + return (currentPosition < vcontigs.size()); + } + + @Override + public int[] next() + { + int[] result = vcontigs.get(currentPosition); + currentPosition++; + return result; + } + } } diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 657f8f3..86dcbca 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -60,6 +60,7 @@ import java.awt.FontMetrics; import java.awt.Rectangle; import java.util.ArrayList; import java.util.Hashtable; +import java.util.Iterator; import java.util.List; import java.util.Vector; @@ -476,10 +477,10 @@ public class AlignViewport extends AlignmentViewport * area * @return */ - public List getViewAsVisibleContigs(boolean selectedRegionOnly) + public Iterator getViewAsVisibleContigs(boolean selectedRegionOnly) { - List viscontigs = null; - int start = 0, end = 0; + int start = 0; + int end = 0; if (selectedRegionOnly && selectionGroup != null) { start = selectionGroup.getStartRes(); @@ -489,8 +490,7 @@ public class AlignViewport extends AlignmentViewport { end = alignment.getWidth(); } - viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end); - return viscontigs; + return (alignment.getHiddenColumns().getVisContigsIterator(start, end)); } /** diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index 3bf7c24..ac72e93 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -42,7 +42,6 @@ import java.io.IOException; import java.util.Hashtable; import java.util.IdentityHashMap; import java.util.Iterator; -import java.util.List; import javax.swing.JInternalFrame; @@ -1075,15 +1074,15 @@ public class VamsasApplication implements SelectionSource, VamsasSource } else { - // int[] intervals = colsel.getVisibleContigs( - // seqsel.getStartRes(), seqsel.getEndRes() + 1); - List intervals = hidden.getVisibleContigs( - seqsel.getStartRes(), seqsel.getEndRes() + 1); - for (int[] region : intervals) + Iterator intervals = hidden + .getVisContigsIterator(seqsel.getStartRes(), + seqsel.getEndRes() + 1); + while (intervals.hasNext()) { + int[] region = intervals.next(); Seg s = new Seg(); - s.setStart(region[0] + 1); // vamsas indices begin at - // 1, not zero. + s.setStart(region[0] + 1); // vamsas indices begin at 1, + // not zero. s.setEnd(region[1] + 1); s.setInclusive(true); range.addSeg(s); diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java index 96ac0c3..1ed846a 100644 --- a/test/jalview/analysis/DnaTest.java +++ b/test/jalview/analysis/DnaTest.java @@ -38,8 +38,7 @@ import jalview.io.FileFormat; import jalview.io.FormatAdapter; import java.io.IOException; -import java.util.ArrayList; -import java.util.List; +import java.util.Iterator; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @@ -137,9 +136,7 @@ public class DnaTest FileFormat.Fasta); HiddenColumns cs = new HiddenColumns(); AlignViewportI av = new AlignViewport(alf, cs); - int[] contig = new int[] { 0, alf.getWidth() - 1 }; - List contigs = new ArrayList<>(); - contigs.add(contig); + Iterator contigs = cs.getVisContigsIterator(0, alf.getWidth()); Dna dna = new Dna(av, contigs); AlignmentI translated = dna.translateCdna(); assertNotNull("Couldn't do a full width translation of test data.", @@ -168,7 +165,8 @@ public class DnaTest cs.hideColumns(0, ipos - 1); } cs.hideColumns(ipos + vwidth, alf.getWidth()); - List vcontigs = cs.getVisibleContigs(0, alf.getWidth()); + Iterator vcontigs = cs.getVisContigsIterator(0, + alf.getWidth()); AlignViewportI av = new AlignViewport(alf, cs); Dna dna = new Dna(av, vcontigs); AlignmentI transAlf = dna.translateCdna(); @@ -195,9 +193,7 @@ public class DnaTest DataSourceType.PASTE, FileFormat.Fasta); HiddenColumns cs = new HiddenColumns(); AlignViewportI av = new AlignViewport(alf, cs); - int[] contig = new int[] { 0, alf.getWidth() - 1 }; - List contigs = new ArrayList<>(); - contigs.add(contig); + Iterator contigs = cs.getVisContigsIterator(0, alf.getWidth()); Dna dna = new Dna(av, contigs); AlignmentI translated = dna.translateCdna(); String aa = translated.getSequenceAt(0).getSequenceAsString(); @@ -221,9 +217,7 @@ public class DnaTest cs.hideColumns(24, 35); // hide codons 9-12 cs.hideColumns(177, 191); // hide codons 60-64 AlignViewportI av = new AlignViewport(alf, cs); - int[] contig = new int[] { 0, alf.getWidth() - 1 }; - List contigs = new ArrayList<>(); - contigs.add(contig); + Iterator contigs = cs.getVisContigsIterator(0, alf.getWidth()); Dna dna = new Dna(av, contigs); AlignmentI translated = dna.translateCdna(); String aa = translated.getSequenceAt(0).getSequenceAsString(); @@ -309,9 +303,7 @@ public class DnaTest .generate(12, 8, 97, 5, 5); HiddenColumns cs = new HiddenColumns(); AlignViewportI av = new AlignViewport(cdna, cs); - int[] contig = new int[] { 0, cdna.getWidth() - 1 }; - List contigs = new ArrayList<>(); - contigs.add(contig); + Iterator contigs = cs.getVisContigsIterator(0, cdna.getWidth()); Dna dna = new Dna(av, contigs); AlignmentI translated = dna.translateCdna(); @@ -327,9 +319,7 @@ public class DnaTest } AlignmentI cdnaReordered = new Alignment(sorted); av = new AlignViewport(cdnaReordered, cs); - contig = new int[] { 0, cdna.getWidth() - 1 }; - contigs = new ArrayList<>(); - contigs.add(contig); + contigs = cs.getVisContigsIterator(0, cdna.getWidth()); dna = new Dna(av, contigs); AlignmentI translated2 = dna.translateCdna(); @@ -561,9 +551,7 @@ public class DnaTest HiddenColumns cs = new HiddenColumns(); AlignViewportI av = new AlignViewport(al, cs); - int[] contig = new int[] { 0, al.getWidth() - 1 }; - List contigs = new ArrayList<>(); - contigs.add(contig); + Iterator contigs = cs.getVisContigsIterator(0, al.getWidth()); Dna testee = new Dna(av, contigs); AlignmentI reversed = testee.reverseCdna(false); assertEquals(1, reversed.getHeight()); diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java index 142762b..a3d4623 100644 --- a/test/jalview/datamodel/HiddenColumnsTest.java +++ b/test/jalview/datamodel/HiddenColumnsTest.java @@ -184,12 +184,14 @@ public class HiddenColumnsTest } @Test(groups = { "Functional" }) - public void testGetVisibleContigs() + public void testVisibleContigsIterator() { HiddenColumns cs = new HiddenColumns(); - List visible = cs.getVisibleContigs(3, 10); - assertEquals("[3, 9]", Arrays.toString(visible.get(0))); + Iterator visible = cs.getVisContigsIterator(3, 10); + int[] region = visible.next(); + assertEquals("[3, 9]", Arrays.toString(region)); + assertFalse(visible.hasNext()); cs.hideColumns(3, 6); cs.hideColumns(8, 9); @@ -198,30 +200,44 @@ public class HiddenColumnsTest // Test both ends visible region // start position is inclusive, end position exclusive - visible = cs.getVisibleContigs(1, 13); - assertEquals("[1, 2]", Arrays.toString(visible.get(0))); - assertEquals("[7, 7]", Arrays.toString(visible.get(1))); - assertEquals("[10, 11]", Arrays.toString(visible.get(2))); + visible = cs.getVisContigsIterator(1, 13); + region = visible.next(); + assertEquals("[1, 2]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[7, 7]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[10, 11]", Arrays.toString(region)); + assertFalse(visible.hasNext()); // Test start hidden, end visible - visible = cs.getVisibleContigs(4, 14); - assertEquals("[7, 7]", Arrays.toString(visible.get(0))); - assertEquals("[10, 11]", Arrays.toString(visible.get(1))); - assertEquals("[13, 13]", Arrays.toString(visible.get(2))); + visible = cs.getVisContigsIterator(4, 14); + region = visible.next(); + assertEquals("[7, 7]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[10, 11]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[13, 13]", Arrays.toString(region)); + assertFalse(visible.hasNext()); // Test start hidden, end hidden - visible = cs.getVisibleContigs(3, 10); - assertEquals("[7, 7]", Arrays.toString(visible.get(0))); + visible = cs.getVisContigsIterator(3, 10); + region = visible.next(); + assertEquals("[7, 7]", Arrays.toString(region)); + assertFalse(visible.hasNext()); // Test start visible, end hidden - visible = cs.getVisibleContigs(0, 13); - assertEquals("[0, 2]", Arrays.toString(visible.get(0))); - assertEquals("[7, 7]", Arrays.toString(visible.get(1))); - assertEquals("[10, 11]", Arrays.toString(visible.get(2))); + visible = cs.getVisContigsIterator(0, 13); + region = visible.next(); + assertEquals("[0, 2]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[7, 7]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[10, 11]", Arrays.toString(region)); + assertFalse(visible.hasNext()); // Test empty result - visible = cs.getVisibleContigs(4, 6); - assertEquals(0, visible.size()); + visible = cs.getVisContigsIterator(4, 6); + assertFalse(visible.hasNext()); } @Test(groups = { "Functional" }) @@ -976,18 +992,22 @@ public class HiddenColumnsTest false); // confirm that original contigs are as expected - List visible = hidden.getVisibleContigs(0, 25); - assertEquals("[0, 14]", Arrays.toString(visible.get(0))); - assertEquals("[18, 24]", Arrays.toString(visible.get(1))); + Iterator visible = hidden.getVisContigsIterator(0, 25); + int[] region = visible.next(); + assertEquals("[0, 14]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[18, 24]", Arrays.toString(region)); // propagate insertions HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al, view); // confirm that the contigs have changed to account for the gaps - visible = result.getVisibleContigs(0, 25); - assertEquals("[0, 10]", Arrays.toString(visible.get(0))); - assertEquals("[14, 24]", Arrays.toString(visible.get(1))); + visible = result.getVisContigsIterator(0, 25); + region = visible.next(); + assertEquals("[0, 10]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[14, 24]", Arrays.toString(region)); // confirm the alignment has been changed so that the other sequences have // gaps inserted where the columns are hidden @@ -1030,18 +1050,24 @@ public class HiddenColumnsTest false); // confirm that original contigs are as expected - List visible = hidden.getVisibleContigs(0, 20); - assertEquals("[0, 6]", Arrays.toString(visible.get(0))); - assertEquals("[11, 19]", Arrays.toString(visible.get(1))); + Iterator visible = hidden.getVisContigsIterator(0, 20); + int[] region = visible.next(); + assertEquals("[0, 6]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[11, 19]", Arrays.toString(region)); + assertFalse(visible.hasNext()); // propagate insertions HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al, view); // confirm that the contigs have changed to account for the gaps - visible = result.getVisibleContigs(0, 20); - assertEquals("[0, 4]", Arrays.toString(visible.get(0))); - assertEquals("[7, 19]", Arrays.toString(visible.get(1))); + visible = result.getVisContigsIterator(0, 20); + region = visible.next(); + assertEquals("[0, 4]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[7, 19]", Arrays.toString(region)); + assertFalse(visible.hasNext()); // confirm the alignment has been changed so that the other sequences have // gaps inserted where the columns are hidden