import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
-import jalview.api.FeatureSettingsI;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.ScoreModelI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
if (xrefs != null)
{
/*
- * figure out colour scheme if any to apply to features
+ * get display scheme (if any) to apply to features
*/
- ASequenceFetcher sftch = new SequenceFetcher();
- List<DbSourceProxy> proxies = sftch.getSourceProxy(source);
- FeatureSettingsI featureColourScheme = null;
- for (DbSourceProxy proxy : proxies)
- {
- FeatureSettingsI preferredColours = proxy
- .getFeatureColourScheme();
- if (preferredColours != null)
- {
- featureColourScheme = preferredColours;
- break;
- }
- }
- Alignment al = makeCrossReferencesAlignment(
+ FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
+ .getFeatureColourScheme(source);
+
+ AlignmentI al = makeCrossReferencesAlignment(
alignment.getDataset(), xrefs);
- /*
- * Copy dna-to-protein mappings to new alignment
- */
- // TODO 1: no mappings are set up for EMBL product
- // TODO 2: if they were, should add them to protein alignment, not
- // dna
- // List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
- // for (AlignedCodonFrame acf : cf)
- // {
- // al.addCodonFrame(acf);
- // }
AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
String newtitle = String.format("%s %s %s",
{
copyAlignment = AlignmentUtils.makeCdsAlignment(
sequenceSelection, cf, alignment);
+ if (copyAlignment.getHeight() == 0)
+ {
+ System.err.println("Failed to make CDS alignment");
+ }
al.getCodonFrames().clear();
al.getCodonFrames().addAll(cf);
}
copyAlignment.addSequence(peer);
}
- /*
- * align protein to dna
- */
- if (dna)
+ if (copyAlignment.getHeight() > 0)
{
- al.alignAs(copyAlignment);
- }
- else
- {
- copyAlignment.alignAs(al);
- }
-
- AlignFrame copyThis = new AlignFrame(copyAlignment,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- copyThis.setTitle(AlignFrame.this.getTitle());
-
- boolean showSequenceFeatures = viewport
- .isShowSequenceFeatures();
- newFrame.setShowSeqFeatures(showSequenceFeatures);
- copyThis.setShowSeqFeatures(showSequenceFeatures);
- FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer();
-
- /*
- * copy feature rendering settings to split frame
- */
- newFrame.alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer().transferSettings(
- myFeatureStyling);
- copyThis.alignPanel.getSeqPanel().seqCanvas
- .getFeatureRenderer().transferSettings(
- myFeatureStyling);
+ /*
+ * align protein to dna
+ */
+ // FIXME what if the dna is not aligned :-O
+ if (dna)
+ {
+ al.alignAs(copyAlignment);
+ }
+ else
+ {
+ /*
+ * align cdna to protein - currently only if
+ * fetching and aligning Ensembl transcripts!
+ */
+ if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
+ {
+ copyAlignment.alignAs(al);
+ }
+ }
- /*
- * apply 'database source' feature configuration
- * if any was found
- */
- newFrame.getViewport()
- .applyFeaturesStyle(featureColourScheme);
- copyThis.getViewport()
- .applyFeaturesStyle(featureColourScheme);
-
- SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
- dna ? newFrame : copyThis);
- newFrame.setVisible(true);
- copyThis.setVisible(true);
- String linkedTitle = MessageManager
- .getString("label.linked_view_title");
- Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
- sf.adjustDivider();
+ AlignFrame copyThis = new AlignFrame(copyAlignment,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyThis.setTitle(AlignFrame.this.getTitle());
+
+ boolean showSequenceFeatures = viewport
+ .isShowSequenceFeatures();
+ newFrame.setShowSeqFeatures(showSequenceFeatures);
+ copyThis.setShowSeqFeatures(showSequenceFeatures);
+ FeatureRenderer myFeatureStyling = alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer();
+
+ /*
+ * copy feature rendering settings to split frame
+ */
+ newFrame.alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer().transferSettings(
+ myFeatureStyling);
+ copyThis.alignPanel.getSeqPanel().seqCanvas
+ .getFeatureRenderer().transferSettings(
+ myFeatureStyling);
+
+ /*
+ * apply 'database source' feature configuration
+ * if any was found
+ */
+ // TODO is this the feature colouring for the original
+ // alignment or the fetched xrefs? either could be Ensembl
+ newFrame.getViewport().applyFeaturesStyle(
+ featureColourScheme);
+ copyThis.getViewport().applyFeaturesStyle(
+ featureColourScheme);
+
+ SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
+ dna ? newFrame : copyThis);
+ newFrame.setVisible(true);
+ copyThis.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
+ sf.adjustDivider();
+ }
}
else
{
}
/**
- * 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
+ * Makes an alignment containing the given sequences. If this is of the
+ * same type as the given dataset (nucleotide/protein), then the new
+ * alignment shares the same dataset, and its dataset sequences are added
+ * to it. Otherwise a new dataset sequence is created for the
+ * cross-references.
*
* @param dataset
* @param seqs
* @return
*/
- protected Alignment makeCrossReferencesAlignment(Alignment dataset,
- Alignment seqs)
+ protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
+ AlignmentI seqs)
{
+ boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
+
SequenceI[] sprods = new SequenceI[seqs.getHeight()];
for (int s = 0; s < sprods.length; s++)
{
sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
- if (dataset.getSequences() == null
- || !dataset.getSequences().contains(
- sprods[s].getDatasetSequence()))
+ if (sameType)
{
- dataset.addSequence(sprods[s].getDatasetSequence());
+ if (dataset.getSequences() == null
+ || !dataset.getSequences().contains(
+ sprods[s].getDatasetSequence()))
+ {
+ dataset.addSequence(sprods[s].getDatasetSequence());
+ }
}
sprods[s].updatePDBIds();
}
Alignment al = new Alignment(sprods);
- al.setDataset(dataset);
+ if (sameType)
+ {
+ al.setDataset((Alignment) dataset);
+ }
+ else
+ {
+ al.createDatasetAlignment();
+ }
return al;
}
git://source.jalview.org / jalview.git / blobdiff