From 2acdd7fdaa575dd5238585ad86597f808b30d281 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 3 Dec 2015 16:26:08 +0000 Subject: [PATCH] JAL-653 mappings always reside on the dataset alignment if there is one --- src/jalview/datamodel/Alignment.java | 104 +++++++++++++++++------------ test/jalview/datamodel/AlignmentTest.java | 64 +++++++++++++++++- 2 files changed, 124 insertions(+), 44 deletions(-) diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 7ea9985..3f9f03f 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -108,7 +108,7 @@ public class Alignment implements AlignmentI * Share the same dataset sequence mappings (if any). TODO: find a better * place for these to live (alignment dataset?). */ - this.codonFrameList = ((Alignment) al).codonFrameList; + this.setCodonFrames(al.getCodonFrames()); initAlignment(seqs); } @@ -991,25 +991,7 @@ public class Alignment implements AlignmentI { if (dataset == null && data == null) { - // Create a new dataset for this alignment. - // Can only be done once, if dataset is not null - // This will not be performed - SequenceI[] seqs = new SequenceI[getHeight()]; - SequenceI currentSeq; - for (int i = 0; i < getHeight(); i++) - { - currentSeq = getSequenceAt(i); - if (currentSeq.getDatasetSequence() != null) - { - seqs[i] = currentSeq.getDatasetSequence(); - } - else - { - seqs[i] = currentSeq.createDatasetSequence(); - } - } - - dataset = new Alignment(seqs); + createDatasetAlignment(); } else if (dataset == null && data != null) { @@ -1040,6 +1022,37 @@ public class Alignment implements AlignmentI } /** + * Creates a new dataset for this alignment. Can only be done once - if + * dataset is not null this will not be performed. + */ + public void createDatasetAlignment() + { + if (dataset != null) + { + return; + } + SequenceI[] seqs = new SequenceI[getHeight()]; + SequenceI currentSeq; + for (int i = 0; i < getHeight(); i++) + { + currentSeq = getSequenceAt(i); + if (currentSeq.getDatasetSequence() != null) + { + seqs[i] = currentSeq.getDatasetSequence(); + } + else + { + seqs[i] = currentSeq.createDatasetSequence(); + } + } + + dataset = new Alignment(seqs); + // move mappings to the dataset alignment + dataset.codonFrameList = this.codonFrameList; + this.codonFrameList = null; + } + + /** * reference count for number of alignments referencing this one. */ int alignmentRefs = 0; @@ -1261,19 +1274,17 @@ public class Alignment implements AlignmentI return alignmentProperties; } - /* - * (non-Javadoc) - * - * @see - * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame - * ) + /** + * Adds the given mapping to the stored set. Note this may be held on the + * dataset alignment. */ @Override public void addCodonFrame(AlignedCodonFrame codons) { - if (codons != null) + Set acfs = getCodonFrames(); + if (codons != null && acfs != null) { - codonFrameList.add(codons); + acfs.add(codons); } } @@ -1291,7 +1302,7 @@ public class Alignment implements AlignmentI return null; } List cframes = new ArrayList(); - for (AlignedCodonFrame acf : codonFrameList) + for (AlignedCodonFrame acf : getCodonFrames()) { if (acf.involvesSequence(seq)) { @@ -1302,42 +1313,50 @@ public class Alignment implements AlignmentI } /** - * Sets the codon frame mappings (replacing any existing mappings). + * Sets the codon frame mappings (replacing any existing mappings). Note the + * mappings are set on the dataset alignment instead if there is one. * * @see jalview.datamodel.AlignmentI#setCodonFrames() */ @Override public void setCodonFrames(Set acfs) { - this.codonFrameList = acfs; + if (dataset != null) + { + dataset.setCodonFrames(acfs); + } + else + { + this.codonFrameList = acfs; + } } /** * Returns the set of codon frame mappings. Any changes to the returned set - * will affect the alignment. + * will affect the alignment. The mappings are held on (and read from) the + * dataset alignment if there is one. * * @see jalview.datamodel.AlignmentI#getCodonFrames() */ @Override public Set getCodonFrames() { - return codonFrameList; + return dataset != null ? dataset.getCodonFrames() : codonFrameList; } - /* - * (non-Javadoc) - * - * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel. - * AlignedCodonFrame) + /** + * Removes the given mapping from the stored set. Note that the mappings are + * held on the dataset alignment if there is one. */ @Override public boolean removeCodonFrame(AlignedCodonFrame codons) { - if (codons == null || codonFrameList == null) + Set acfs = getCodonFrames(); + if (codons == null || acfs == null) { return false; } - return codonFrameList.remove(codons); + return acfs.remove(codons); } @Override @@ -1383,7 +1402,7 @@ public class Alignment implements AlignmentI addAnnotation(alan[a]); } - this.codonFrameList.addAll(toappend.getCodonFrames()); + getCodonFrames().addAll(toappend.getCodonFrames()); List sg = toappend.getGroups(); if (sg != null) @@ -1595,6 +1614,7 @@ public class Alignment implements AlignmentI * * @return the representative sequence for this group */ + @Override public SequenceI getSeqrep() { return seqrep; @@ -1607,6 +1627,7 @@ public class Alignment implements AlignmentI * @param seqrep * the seqrep to set (null means no sequence representative) */ + @Override public void setSeqrep(SequenceI seqrep) { this.seqrep = seqrep; @@ -1616,6 +1637,7 @@ public class Alignment implements AlignmentI * * @return true if group has a sequence representative */ + @Override public boolean hasSeqrep() { return seqrep != null; diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index 5d299bb..ad1d3bf 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -22,6 +22,8 @@ package jalview.datamodel; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; +import static org.testng.AssertJUnit.assertNotNull; +import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; @@ -392,6 +394,7 @@ public class AlignmentTest public void testCopyConstructor() throws IOException { AlignmentI protein = loadAlignment(AA_SEQS_1, FormatAdapter.PASTE); + // create sequence and alignment datasets protein.setDataset(null); AlignedCodonFrame acf = new AlignedCodonFrame(); protein.getDataset().setCodonFrames(Collections.singleton(acf)); @@ -406,8 +409,63 @@ public class AlignmentTest .getSequenceAt(0).getDatasetSequence()); assertSame(copy.getSequenceAt(1).getDatasetSequence(), protein .getSequenceAt(1).getDatasetSequence()); - // and the same alignment dataset (?) - // or a new one with the same dataset sequences? - assertSame(copy.getDataset(), protein.getDataset()); + + // TODO should the copy constructor copy the dataset? + // or make a new one referring to the same dataset sequences?? + assertNull(copy.getDataset()); + // assertArrayEquals(copy.getDataset().getSequencesArray(), protein + // .getDataset().getSequencesArray()); + } + + /** + * Test behaviour of createDataset + * + * @throws IOException + */ + @Test(groups = "Functional") + public void testCreateDatasetAlignment() throws IOException + { + AlignmentI protein = new FormatAdapter().readFile(AA_SEQS_1, + AppletFormatAdapter.PASTE, "FASTA"); + /* + * create a dataset sequence on first sequence + * leave the second without one + */ + protein.getSequenceAt(0).createDatasetSequence(); + assertNotNull(protein.getSequenceAt(0).getDatasetSequence()); + assertNull(protein.getSequenceAt(1).getDatasetSequence()); + + /* + * add a mapping to the alignment + */ + AlignedCodonFrame acf = new AlignedCodonFrame(); + protein.addCodonFrame(acf); + assertNull(protein.getDataset()); + assertTrue(protein.getCodonFrames().contains(acf)); + + /* + * create the alignment dataset + * note this creates sequence datasets where missing + * as a side-effect (in this case, on seq2 + */ + // TODO promote this method to AlignmentI + ((Alignment) protein).createDatasetAlignment(); + + // TODO this method should return AlignmentI not Alignment !! + Alignment ds = protein.getDataset(); + + // side-effect: dataset created on second sequence + assertNotNull(protein.getSequenceAt(1).getDatasetSequence()); + // dataset alignment has references to dataset sequences + assertEquals(ds.getSequenceAt(0), protein.getSequenceAt(0) + .getDatasetSequence()); + assertEquals(ds.getSequenceAt(1), protein.getSequenceAt(1) + .getDatasetSequence()); + + // codon frames should have been moved to the dataset + // getCodonFrames() should delegate to the dataset: + assertTrue(protein.getCodonFrames().contains(acf)); + // prove the codon frames are indeed on the dataset: + assertTrue(ds.getCodonFrames().contains(acf)); } } -- 1.7.10.2