import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
+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.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.SequenceFetcher;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
@Override
public void fetchSequence_actionPerformed(ActionEvent e)
{
- new SequenceFetcher(this);
+ new jalview.gui.SequenceFetcher(this);
}
@Override
AlignmentI alignmentToExport = null;
AlignExportSettingI settings = exportSettings;
String[] omitHidden = null;
- int[] alignmentStartEnd = new int[2];
HiddenSequences hiddenSeqs = viewport.getAlignment()
.getHiddenSequences();
alignmentToExport = viewport.getAlignment();
- alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
if (settings == null)
omitHidden = viewport.getViewAsString(false);
}
+ int[] alignmentStartEnd = new int[2];
if (hasHiddenSeqs && settings.isExportHiddenSequences())
{
alignmentToExport = hiddenSeqs.getFullAlignment();
else
{
alignmentToExport = viewport.getAlignment();
- alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+ alignmentStartEnd = viewport.getAlignment()
+ .getVisibleStartAndEndIndex(
+ viewport
.getColumnSelection().getHiddenColumns());
}
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
return ed;
}
- public static int[] getStartEnd(int[] aligmentStartEnd,
- List<int[]> hiddenCols)
- {
- int startPos = aligmentStartEnd[0];
- int endPos = aligmentStartEnd[1];
-
- int[] lowestRange = new int[] { -1, -1 };
- int[] higestRange = new int[] { -1, -1 };
-
- for (int[] hiddenCol : hiddenCols)
- {
- lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
- higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
- }
-
- if (lowestRange[0] == -1 && lowestRange[1] == -1)
- {
- startPos = aligmentStartEnd[0];
- }
- else
- {
- startPos = lowestRange[1] + 1;
- }
-
- if (higestRange[0] == -1 && higestRange[1] == -1)
- {
- endPos = aligmentStartEnd[1];
- }
- else
- {
- endPos = higestRange[0] - 1;
- }
-
- // System.out.println("Export range : " + startPos + " - " + endPos);
- return new int[] { startPos, endPos };
- }
-
- public static void main(String[] args)
- {
- ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
- hiddenCols.add(new int[] { 0, 0 });
- hiddenCols.add(new int[] { 6, 9 });
- hiddenCols.add(new int[] { 11, 12 });
- hiddenCols.add(new int[] { 33, 33 });
- hiddenCols.add(new int[] { 50, 50 });
-
- int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
- // System.out.println("Export range : " + x[0] + " - " + x[1]);
- }
/**
* DOCUMENT ME!
new Object[] { source }), sttime);
try
{
- /*
- * 'peer' sequences are any to add to this alignment, for example
- * alternative protein products for my protein's gene
- */
- List<SequenceI> addedPeers = new ArrayList<SequenceI>();
- AlignmentI alignment = AlignFrame.this.getViewport().getAlignment();
- Alignment xrefs = CrossRef.findXrefSequences(sel, dna, source,
- alignment, addedPeers);
+ AlignmentI alignment = AlignFrame.this.getViewport()
+ .getAlignment();
+ AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
+ alignment);
if (xrefs != null)
{
- Alignment al = makeCrossReferencesAlignment(
- alignment.getDataset(), xrefs);
-
/*
- * Copy dna-to-protein mappings to new alignment
+ * get display scheme (if any) to apply to features
*/
- // 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);
- // }
+ FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
+ .getFeatureColourScheme(source);
+
+ AlignmentI al = makeCrossReferencesAlignment(
+ alignment.getDataset(), xrefs);
+
AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
String newtitle = String.format("%s %s %s",
.getString("label.for"), getTitle());
newFrame.setTitle(newtitle);
- boolean asSplitFrame = Cache.getDefault(
- Preferences.ENABLE_SPLIT_FRAME, true);
- if (asSplitFrame)
+ if (!Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
/*
- * Make a copy of this alignment (sharing the same dataset
- * sequences). If we are DNA, drop introns and update mappings
+ * split frame display is turned off in preferences file
*/
- AlignmentI copyAlignment = null;
- final SequenceI[] sequenceSelection = AlignFrame.this.viewport
- .getSequenceSelection();
- List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
- if (dna)
- {
- copyAlignment = AlignmentUtils.makeCdsAlignment(
- sequenceSelection, cf);
- al.getCodonFrames().clear();
- al.getCodonFrames().addAll(cf);
- }
- else
+ Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ return; // via finally clause
+ }
+
+ /*
+ * Make a copy of this alignment (sharing the same dataset
+ * sequences). If we are DNA, drop introns and update mappings
+ */
+ AlignmentI copyAlignment = null;
+ final SequenceI[] sequenceSelection = AlignFrame.this.viewport
+ .getSequenceSelection();
+ List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
+ boolean copyAlignmentIsAligned = false;
+ if (dna)
+ {
+ copyAlignment = AlignmentUtils.makeCdsAlignment(
+ sequenceSelection, cf, alignment);
+ if (copyAlignment.getHeight() == 0)
{
- copyAlignment = new Alignment(new Alignment(
- sequenceSelection));
- copyAlignment.getCodonFrames().addAll(cf);
+ System.err.println("Failed to make CDS alignment");
}
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- ssm.registerMappings(cf);
+ al.getCodonFrames().clear();
+ al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
/*
- * add in any extra 'peer' sequences discovered
- * (e.g. alternative protein products)
+ * pending getting Embl transcripts to 'align',
+ * we are only doing this for Ensembl
*/
- for (SequenceI peer : addedPeers)
+ // TODO proper criteria for 'can align as cdna'
+ if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
+ || AlignmentUtils.looksLikeEnsembl(alignment))
{
- copyAlignment.addSequence(peer);
+ copyAlignment.alignAs(alignment);
+ copyAlignmentIsAligned = true;
}
+ }
+ else
+ {
+ copyAlignment = AlignmentUtils.makeCopyAlignment(
+ sequenceSelection, xrefs.getSequencesArray());
+ copyAlignment.getCodonFrames().addAll(cf);
+ }
+ copyAlignment.setGapCharacter(AlignFrame.this.viewport
+ .getGapCharacter());
- /*
- * align protein to dna
- */
- // TODO needs debugging
- // if (dna)
- // {
- // al.alignAs(copyAlignment);
- // }
- // else
- // {
- // copyAlignment.alignAs(al);
- // }
-
- AlignFrame copyThis = new AlignFrame(copyAlignment,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- copyThis.setTitle(AlignFrame.this.getTitle());
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerMappings(cf);
- 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);
- 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();
+ if (copyAlignment.getHeight() <= 0)
+ {
+ System.err.println("No Sequences generated for xRef type "
+ + source);
+ return;
+ }
+ /*
+ * align protein to dna
+ */
+ if (dna && copyAlignmentIsAligned)
+ {
+ al.alignAs(copyAlignment);
}
else
{
- Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ /*
+ * align cdna to protein - currently only if
+ * fetching and aligning Ensembl transcripts!
+ */
+ if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
+ {
+ copyAlignment.alignAs(al);
+ }
}
- }
- else
- {
- System.err.println("No Sequences generated for xRef type "
- + source);
+
+ 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();
}
} catch (Exception e)
{
- jalview.bin.Cache.log.error(
+ Cache.log.error(
"Exception when finding crossreferences", e);
} catch (OutOfMemoryError e)
{
new OOMWarning("whilst fetching crossreferences", e);
- } catch (Error e)
+ } catch (Throwable e)
{
- jalview.bin.Cache.log.error("Error when finding crossreferences",
+ Cache.log.error("Error when finding crossreferences",
e);
+ } finally
+ {
+ AlignFrame.this.setProgressBar(MessageManager.formatMessage(
+ "status.finished_searching_for_sequences_from",
+ new Object[] { source }), sttime);
}
- AlignFrame.this.setProgressBar(MessageManager.formatMessage(
- "status.finished_searching_for_sequences_from",
- new Object[] { source }), sttime);
}
/**
- * @param alignment
- * @param prods
+ * 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 prods)
+ protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
+ AlignmentI seqs)
{
- SequenceI[] sprods = new SequenceI[prods.getHeight()];
+ boolean sameType = dataset.isNucleotide() == seqs.isNucleotide();
+
+ SequenceI[] sprods = new SequenceI[seqs.getHeight()];
for (int s = 0; s < sprods.length; s++)
{
- sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
- if (dataset.getSequences() == null
- || !dataset.getSequences().contains(
- sprods[s].getDatasetSequence()))
+ sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
+ 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;
}
frunner.start();
}
- public boolean canShowTranslationProducts(SequenceI[] selection,
- AlignmentI alignment)
- {
- // old way
- try
- {
- return (jalview.analysis.Dna.canTranslate(selection,
- viewport.getViewAsVisibleContigs(true)));
- } catch (Exception e)
- {
- jalview.bin.Cache.log
- .warn("canTranslate threw an exception - please report to help@jalview.org",
- e);
- return false;
- }
- }
-
/**
* Construct and display a new frame containing the translation of this
* frame's DNA sequences to their aligned protein (amino acid) equivalents.
alignPanel.paintAlignment(true);
}
}
- else
- {
- new FileLoader().LoadFile(viewport, file, protocol, format);
- }
+ else
+ {
+ new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
}
}
if (isAnnotation)
{
new Thread(new Runnable()
{
-
@Override
public void run()
{
- boolean isNuclueotide = alignPanel.alignFrame
- .getViewport().getAlignment()
- .isNucleotide();
- new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(),
- alignPanel.alignFrame, null,
- alignPanel.alignFrame.featureSettings,
- isNuclueotide)
+ boolean isNucleotide = alignPanel.alignFrame.getViewport()
+ .getAlignment().isNucleotide();
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
+ .getSequenceSelection(), alignPanel.alignFrame, null,
+ alignPanel.alignFrame.featureSettings, isNucleotide);
+ dbRefFetcher.addListener(new FetchFinishedListenerI()
+ {
+ @Override
+ public void finished()
+ {
+ AlignFrame.this.setMenusForViewport();
+ }
+ });
+ dbRefFetcher
.fetchDBRefs(false);
}
}).start();
@Override
public void run()
{
- final jalview.ws.SequenceFetcher sf = SequenceFetcher
+ final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
.getSequenceFetcherSingleton(me);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
- boolean isNuclueotide = alignPanel.alignFrame
+ boolean isNucleotide = alignPanel.alignFrame
.getViewport().getAlignment()
.isNucleotide();
- new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(),
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(
+ alignPanel.av.getSequenceSelection(),
alignPanel.alignFrame, dassource,
alignPanel.alignFrame.featureSettings,
- isNuclueotide)
- .fetchDBRefs(false);
+ isNucleotide);
+ dbRefFetcher
+ .addListener(new FetchFinishedListenerI()
+ {
+ @Override
+ public void finished()
+ {
+ AlignFrame.this.setMenusForViewport();
+ }
+ });
+ dbRefFetcher.fetchDBRefs(false);
}
}).start();
}
@Override
public void run()
{
- boolean isNuclueotide = alignPanel.alignFrame
+ boolean isNucleotide = alignPanel.alignFrame
.getViewport().getAlignment()
.isNucleotide();
- new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(),
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(
+ alignPanel.av.getSequenceSelection(),
alignPanel.alignFrame, dassource,
alignPanel.alignFrame.featureSettings,
- isNuclueotide)
- .fetchDBRefs(false);
+ isNucleotide);
+ dbRefFetcher
+ .addListener(new FetchFinishedListenerI()
+ {
+ @Override
+ public void finished()
+ {
+ AlignFrame.this.setMenusForViewport();
+ }
+ });
+ dbRefFetcher.fetchDBRefs(false);
}
}).start();
}
@Override
public void run()
{
- boolean isNuclueotide = alignPanel.alignFrame
+ boolean isNucleotide = alignPanel.alignFrame
.getViewport().getAlignment()
.isNucleotide();
- new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(),
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(
+ alignPanel.av.getSequenceSelection(),
alignPanel.alignFrame, dassrc,
alignPanel.alignFrame.featureSettings,
- isNuclueotide)
- .fetchDBRefs(false);
+ isNucleotide);
+ dbRefFetcher
+ .addListener(new FetchFinishedListenerI()
+ {
+ @Override
+ public void finished()
+ {
+ AlignFrame.this.setMenusForViewport();
+ }
+ });
+ dbRefFetcher.fetchDBRefs(false);
}
}).start();
}
git://source.jalview.org / jalview.git / blobdiff