From: Jim Procter Date: Tue, 27 Feb 2018 11:16:41 +0000 (+0000) Subject: Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104 X-Git-Tag: Release_2_10_4~55^2~1 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=aad3640b07f836362df7ea025fa09127a0a06145 Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104 --- aad3640b07f836362df7ea025fa09127a0a06145 diff --cc src/jalview/gui/AnnotationLabels.java index 15f1fe0,c883071..b58269d --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@@ -50,9 -49,10 +51,11 @@@ import java.awt.event.MouseEvent import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.geom.AffineTransform; + import java.awt.image.BufferedImage; +import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; + import java.util.Iterator; import java.util.regex.Pattern; import javax.swing.JCheckBoxMenuItem; diff --cc src/jalview/viewmodel/OverviewDimensionsShowHidden.java index eaa3413,79e1c47..3aa6e1b --- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java +++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java @@@ -101,10 -97,10 +101,10 @@@ public class OverviewDimensionsShowHidd // get mouse location in viewport coords, add translation in viewport // coords, // convert back to pixel coords - int vpx = Math.round(mousex * widthRatio); - int visXAsRes = hiddenCols.findColumnPosition(vpx) + xdiff; + int vpx = Math.round((float) mousex * alwidth / width); + int visXAsRes = hiddenCols.absoluteToVisibleColumn(vpx) + xdiff; - int vpy = Math.round((float) mousey * alheight / sequencesHeight); + int vpy = Math.round(mousey * heightRatio); int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + ydiff; // update viewport accordingly @@@ -265,14 -246,12 +265,14 @@@ public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs, HiddenColumns hiddenCols) { + resetAlignmentDims(); + // get alignment position of x and box (can get directly from vpranges) and // calculate difference between the positions - int vpx = Math.round((float) x * alwidth / width); - int vpy = Math.round((float) y * alheight / sequencesHeight); + int vpx = Math.round(x * widthRatio); + int vpy = Math.round(y * heightRatio); - xdiff = ranges.getStartRes() - hiddenCols.findColumnPosition(vpx); + xdiff = ranges.getStartRes() - hiddenCols.absoluteToVisibleColumn(vpx); ydiff = ranges.getStartSeq() - hiddenSeqs.findIndexWithoutHiddenSeqs(vpy); } diff --cc test/jalview/datamodel/AlignmentTest.java index 74ac146,ddba949..266b90a --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@@ -1333,21 -1323,134 +1334,152 @@@ public class AlignmentTes // hidden sequences, properties } + /** + * test that calcId == null on findOrCreate doesn't raise an NPE, and yields + * an annotation with a null calcId + * + */ + @Test(groups = "Functional") + public void testFindOrCreateForNullCalcId() + { + SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-"); + AlignmentI alignment = new Alignment(new SequenceI[] { seq }); + + AlignmentAnnotation ala = alignment.findOrCreateAnnotation( + "Temperature Factor", null, false, seq, null); + assertNotNull(ala); + assertEquals(seq, ala.sequenceRef); + assertEquals("", ala.calcId); + } ++ + @Test(groups = "Functional") + public void testPropagateInsertions() + { + // create an alignment with no gaps - this will be the profile seq and other + // JPRED seqs + AlignmentGenerator gen = new AlignmentGenerator(false); + AlignmentI al = gen.generate(25, 10, 1234, 0, 0); + + // get the profileseq + SequenceI profileseq = al.getSequenceAt(0); + SequenceI gappedseq = new Sequence(profileseq); + gappedseq.insertCharAt(5, al.getGapCharacter()); + gappedseq.insertCharAt(6, al.getGapCharacter()); + gappedseq.insertCharAt(7, al.getGapCharacter()); + gappedseq.insertCharAt(8, al.getGapCharacter()); + + // force different kinds of padding + al.getSequenceAt(3).deleteChars(2, 23); + al.getSequenceAt(4).deleteChars(2, 27); + al.getSequenceAt(5).deleteChars(10, 27); + + // create an alignment view with the gapped sequence + SequenceI[] seqs = new SequenceI[1]; + seqs[0] = gappedseq; + AlignmentI newal = new Alignment(seqs); + HiddenColumns hidden = new HiddenColumns(); + hidden.hideColumns(15, 17); + + AlignmentView view = new AlignmentView(newal, hidden, null, true, false, + false); + + // confirm that original contigs are as expected + Iterator visible = hidden.getVisContigsIterator(0, 25, false); + int[] region = visible.next(); + assertEquals("[0, 14]", Arrays.toString(region)); + region = visible.next(); + assertEquals("[18, 24]", Arrays.toString(region)); + + // propagate insertions + HiddenColumns result = al.propagateInsertions(profileseq, view); + + // confirm that the contigs have changed to account for the gaps + visible = result.getVisContigsIterator(0, 25, false); + 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 + assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13])); + assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14])); + + } + + @Test(groups = "Functional") + public void testPropagateInsertionsOverlap() + { + // test propagateInsertions where gaps and hiddenColumns overlap + + // create an alignment with no gaps - this will be the profile seq and other + // JPRED seqs + AlignmentGenerator gen = new AlignmentGenerator(false); + AlignmentI al = gen.generate(20, 10, 1234, 0, 0); + + // get the profileseq + SequenceI profileseq = al.getSequenceAt(0); + SequenceI gappedseq = new Sequence(profileseq); + gappedseq.insertCharAt(5, al.getGapCharacter()); + gappedseq.insertCharAt(6, al.getGapCharacter()); + gappedseq.insertCharAt(7, al.getGapCharacter()); + gappedseq.insertCharAt(8, al.getGapCharacter()); + + // create an alignment view with the gapped sequence + SequenceI[] seqs = new SequenceI[1]; + seqs[0] = gappedseq; + AlignmentI newal = new Alignment(seqs); + + // hide columns so that some overlap with the gaps + HiddenColumns hidden = new HiddenColumns(); + hidden.hideColumns(7, 10); + + AlignmentView view = new AlignmentView(newal, hidden, null, true, false, + false); + + // confirm that original contigs are as expected + Iterator visible = hidden.getVisContigsIterator(0, 20, false); + 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 = al.propagateInsertions(profileseq, view); + + // confirm that the contigs have changed to account for the gaps + visible = result.getVisContigsIterator(0, 20, false); + 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 + assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5])); + assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6])); + assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7])); + } + + @Test(groups = { "Functional" }) + public void testPadGaps() + { + SequenceI seq1 = new Sequence("seq1", "ABCDEF--"); + SequenceI seq2 = new Sequence("seq2", "-JKLMNO--"); + SequenceI seq3 = new Sequence("seq2", "-PQR"); + AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 }); + a.setGapCharacter('.'); // this replaces existing gaps + assertEquals("ABCDEF..", seq1.getSequenceAsString()); + a.padGaps(); + // trailing gaps are pruned, short sequences padded with gap character + assertEquals("ABCDEF.", seq1.getSequenceAsString()); + assertEquals(".JKLMNO", seq2.getSequenceAsString()); + assertEquals(".PQR...", seq3.getSequenceAsString()); + } }