* aligned dna sequences
* @param mappings
* from dna to protein; these are replaced with new mappings
- * @param gapChar
+ * @param al
* @return an alignment whose sequences are the cds-only parts of the dna
* sequences (or null if no mappings are found)
*/
public static AlignmentI makeCdsAlignment(SequenceI[] dna,
- List<AlignedCodonFrame> mappings, char gapChar)
+ List<AlignedCodonFrame> mappings, AlignmentI al)
{
List<int[]> cdsColumns = findCdsColumns(dna);
*/
List<AlignedCodonFrame> newMappings = new ArrayList<AlignedCodonFrame>();
List<SequenceI> cdsSequences = new ArrayList<SequenceI>();
+ char gap = al.getGapCharacter();
for (SequenceI dnaSeq : dna)
{
{
AlignedCodonFrame newMapping = new AlignedCodonFrame();
final List<SequenceI> mappedCds = makeCdsSequences(dnaSeq, acf,
- cdsColumns, newMapping, gapChar);
+ cdsColumns, newMapping, gap);
if (!mappedCds.isEmpty())
{
cdsSequences.addAll(mappedCds);
}
}
}
- AlignmentI al = new Alignment(
+ AlignmentI newAl = new Alignment(
cdsSequences.toArray(new SequenceI[cdsSequences.size()]));
- al.setGapCharacter(gapChar);
- al.setDataset(null);
+
+ /*
+ * add new sequences to the shared dataset, set it on the new alignment
+ */
+ List<SequenceI> dsseqs = al.getDataset().getSequences();
+ for (SequenceI seq : newAl.getSequences())
+ {
+ if (!dsseqs.contains(seq.getDatasetSequence()))
+ {
+ dsseqs.add(seq.getDatasetSequence());
+ }
+ }
+ newAl.setDataset(al.getDataset());
/*
* Replace the old mappings with the new ones
mappings.clear();
mappings.addAll(newMappings);
- return al;
+ return newAl;
}
/**
{
SequenceI cds = makeCdsSequence(dnaSeq, seqMapping,
ungappedCdsColumns, gapChar);
+ cds.createDatasetSequence();
cdsSequences.add(cds);
/*
AlignmentI copyAlignment = null;
final SequenceI[] sequenceSelection = AlignFrame.this.viewport
.getSequenceSelection();
- final char gapChar = AlignFrame.this.viewport
- .getGapCharacter();
List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
if (dna)
{
copyAlignment = AlignmentUtils.makeCdsAlignment(
- sequenceSelection, cf, gapChar);
+ sequenceSelection, cf, alignment);
al.getCodonFrames().clear();
al.getCodonFrames().addAll(cf);
}
copyAlignment = new Alignment(new Alignment(
sequenceSelection));
copyAlignment.getCodonFrames().addAll(cf);
- copyAlignment.setGapCharacter(gapChar);
}
+ copyAlignment.setGapCharacter(AlignFrame.this.viewport
+ .getGapCharacter());
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
ssm.registerMappings(cf);
}
/**
- * @param alignment
- * @param prods
+ * Makes an alignment containing the given sequences; the sequences are
+ * added to the given alignment dataset, and the dataset is set on (shared
+ * by) the new alignment
+ *
+ * @param dataset
+ * @param seqs
* @return
*/
protected Alignment makeCrossReferencesAlignment(Alignment dataset,
- Alignment prods)
+ Alignment seqs)
{
- SequenceI[] sprods = new SequenceI[prods.getHeight()];
+ SequenceI[] sprods = new SequenceI[seqs.getHeight()];
for (int s = 0; s < sprods.length; s++)
{
- sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
+ sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
if (dataset.getSequences() == null
|| !dataset.getSequences().contains(
sprods[s].getDatasetSequence()))
*/
Map<String, SequenceI> seqRefIds = null;
- Vector frefedSequence = null;
+ Vector<Object[]> frefedSequence = null;
boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
int r = 0, rSize = frefedSequence.size();
while (r < rSize)
{
- Object[] ref = (Object[]) frefedSequence.elementAt(r);
+ Object[] ref = frefedSequence.elementAt(r);
if (ref != null)
{
String sref = (String) ref[0];
}
if (frefedSequence == null)
{
- frefedSequence = new Vector();
+ frefedSequence = new Vector<Object[]>();
}
AlignFrame af = null, _af = null;
{
mapping = addMapping(maps[m].getMapping());
}
- if (dnaseq != null)
+ if (dnaseq != null && mapping.getTo() != null)
{
cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
}
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.util.Comparison;
+import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
*/
AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
// TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
- if (mapping.getdnaToProt()[0].getFromRatio() == 3)
+ MapList[] mapLists = mapping.getdnaToProt();
+ // mapLists can be empty if project load has not finished resolving seqs
+ if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
{
if (calculator
.getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
// fudge: check mappings are not protein-to-protein
// TODO: nicer
AlignedCodonFrame mapping = codonMappings.iterator().next();
- if (mapping.getdnaToProt()[0].getFromRatio() == 3)
+ MapList[] mapLists = mapping.getdnaToProt();
+ // mapLists can be empty if project load has not finished resolving seqs
+ if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
{
complementConsensus = new AlignmentAnnotation("cDNA Consensus",
"PID for cDNA", new Annotation[1], 0f, 100f,
null));
dna2.addSequenceFeature(new SequenceFeature("CDS", "cds5", 13, 15, 0f,
null));
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
+ dna.setDataset(null);
List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
mappings.add(acf);
AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
- dna1, dna2 }, mappings, '-');
+ dna1, dna2 }, mappings, dna);
assertEquals(2, cds.getSequences().size());
assertEquals("---GGG---TTT---", cds.getSequenceAt(0)
.getSequenceAsString());
.getSequenceAsString());
/*
+ * verify shared, extended alignment dataset
+ */
+ assertSame(dna.getDataset(), cds.getDataset());
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.getSequenceAt(0).getDatasetSequence()));
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.getSequenceAt(1).getDatasetSequence()));
+
+ /*
* Verify updated mappings
*/
assertEquals(2, mappings.size());
* Create the Exon alignment; also replaces the dna-to-protein mappings with
* exon-to-protein and exon-to-dna mappings
*/
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
+ dna.setDataset(null);
AlignmentI exal = AlignmentUtils.makeCdsAlignment(
- new SequenceI[] { dna1 }, mappings, '-');
+ new SequenceI[] { dna1 }, mappings, dna);
/*
* Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
List<SequenceI> cds = exal.getSequences();
assertEquals(3, cds.size());
+ /*
+ * verify shared, extended alignment dataset
+ */
+ assertSame(exal.getDataset(), dna.getDataset());
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.get(0).getDatasetSequence()));
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.get(1).getDatasetSequence()));
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.get(2).getDatasetSequence()));
+
+ /*
+ * verify aligned cds sequences and their xrefs
+ */
SequenceI cdsSeq = cds.get(0);
assertEquals("---GGG---TTT", cdsSeq.getSequenceAsString());
assertEquals("dna1|A12345", cdsSeq.getName());
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
mappings.add(acf);
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
+ dna.setDataset(null);
AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
- dna1, dna2, dna3 }, mappings, '-');
- assertEquals(2, cds.getSequences().size());
- assertEquals("GGGCCCTTTGGG", cds.getSequenceAt(0).getSequenceAsString());
- assertEquals("GGGCC---TGGG", cds.getSequenceAt(1).getSequenceAsString());
+ dna1, dna2, dna3 }, mappings, dna);
+ List<SequenceI> cdsSeqs = cds.getSequences();
+ assertEquals(2, cdsSeqs.size());
+ assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
+ assertEquals("GGGCC---TGGG", cdsSeqs.get(1).getSequenceAsString());
/*
+ * verify shared, extended alignment dataset
+ */
+ assertSame(dna.getDataset(), cds.getDataset());
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cdsSeqs.get(0).getDatasetSequence()));
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cdsSeqs.get(1).getDatasetSequence()));
+
+ /*
* Verify updated mappings
*/
assertEquals(2, mappings.size());
git://source.jalview.org / jalview.git / commitdiff