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.SequenceFetcher;
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;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
-import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
public void setGUINucleotide(boolean nucleotide)
{
showTranslation.setVisible(nucleotide);
+ showReverse.setVisible(nucleotide);
+ showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation.setEnabled(!nucleotide);
showGroupConservation.setEnabled(!nucleotide);
rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
rnahelicesColour
.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
- setShowProductsEnabled();
+
+ showProducts.setEnabled(canShowProducts());
+
updateEditMenuBar();
}
@Override
public void fetchSequence_actionPerformed(ActionEvent e)
{
- new SequenceFetcher(this);
+ new jalview.gui.SequenceFetcher(this);
}
@Override
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
bjs.exportJalviewAlignmentAsBioJsHtmlFile();
}
return;
}
- format = new IdentifyFile().Identify(str, "Paste");
+ format = new IdentifyFile().identify(str, "Paste");
} catch (OutOfMemoryError er)
{
ColumnSelection colSel = viewport.getColumnSelection();
int column;
- if (colSel.size() > 0)
+ if (!colSel.isEmpty())
{
if (trimLeft)
{
{
viewport.showAllHiddenColumns();
repaint();
+ viewport.sendSelection();
}
@Override
public void hideAllButSelection_actionPerformed(ActionEvent e)
{
toggleHiddenRegions(false, false);
+ viewport.sendSelection();
}
/*
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
/*
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
@Override
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
@Override
}
}
- /*
- * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
- * chooser = new JalviewFileChooser(jalview.bin.Cache.
- * getProperty("LAST_DIRECTORY"));
- *
- * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
- * to Vamsas file"); chooser.setToolTipText("Export");
- *
- * int value = chooser.showSaveDialog(this);
- *
- * if (value == JalviewFileChooser.APPROVE_OPTION) {
- * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
- * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
- * chooser.getSelectedFile().getAbsolutePath(), this); } }
- */
/**
- * prototype of an automatically enabled/disabled analysis function
+ * Searches selected sequences for xRef products and builds the Show
+ * Cross-References menu (formerly called Show Products)
*
+ * @return true if Show Cross-references menu should be enabled.
*/
- protected void setShowProductsEnabled()
+ public boolean canShowProducts()
{
SequenceI[] selection = viewport.getSequenceSelection();
- if (canShowProducts(selection, viewport.getSelectionGroup() != null,
- viewport.getAlignment().getDataset()))
- {
- showProducts.setEnabled(true);
-
- }
- else
- {
- showProducts.setEnabled(false);
- }
- }
-
- /**
- * search selection for sequence xRef products and build the show products
- * menu.
- *
- * @param selection
- * @param dataset
- * @return true if showProducts menu should be enabled.
- */
- public boolean canShowProducts(SequenceI[] selection,
- boolean isRegionSelection, Alignment dataset)
- {
+ AlignmentI dataset = viewport.getAlignment().getDataset();
boolean showp = false;
try
{
showProducts.removeAll();
final boolean dna = viewport.getAlignment().isNucleotide();
- final Alignment ds = dataset;
String[] ptypes = (selection == null || selection.length == 0) ? null
: CrossRef.findSequenceXrefTypes(dna, selection, dataset);
- // Object[] prods =
- // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
- // selection, dataset, true);
- final SequenceI[] sel = selection;
+
for (int t = 0; ptypes != null && t < ptypes.length; t++)
{
showp = true;
- final boolean isRegSel = isRegionSelection;
final AlignFrame af = this;
final String source = ptypes[t];
JMenuItem xtype = new JMenuItem(ptypes[t]);
@Override
public void actionPerformed(ActionEvent e)
{
- // TODO: new thread for this call with vis-delay
- af.showProductsFor(af.viewport.getSequenceSelection(),
- isRegSel, dna, source);
+ showProductsFor(af.viewport.getSequenceSelection(), dna, source);
}
});
} catch (Exception e)
{
jalview.bin.Cache.log
- .warn("canTranslate threw an exception - please report to help@jalview.org",
+ .warn("canShowProducts threw an exception - please report to help@jalview.org",
e);
return false;
}
return showp;
}
- protected void showProductsFor(final SequenceI[] sel,
- final boolean isRegSel, final boolean dna, final String source)
+ protected void showProductsFor(final SequenceI[] sel, final boolean dna,
+ final String source)
{
Runnable foo = new Runnable()
{
new Object[] { source }), sttime);
try
{
- // update our local dataset reference
- Alignment ds = AlignFrame.this.getViewport().getAlignment()
- .getDataset();
- Alignment prods = CrossRef
- .findXrefSequences(sel, dna, source, ds);
- if (prods != null)
+ /*
+ * '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);
+ if (xrefs != null)
{
- SequenceI[] sprods = new SequenceI[prods.getHeight()];
- for (int s = 0; s < sprods.length; s++)
+ /*
+ * figure out colour scheme if any to apply to features
+ */
+ ASequenceFetcher sftch = new SequenceFetcher();
+ List<DbSourceProxy> proxies = sftch.getSourceProxy(source);
+ FeatureSettingsModelI featureColourScheme = null;
+ for (DbSourceProxy proxy : proxies)
{
- sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
- if (ds.getSequences() == null
- || !ds.getSequences().contains(
- sprods[s].getDatasetSequence()))
+ FeatureSettingsModelI preferredColours = proxy
+ .getFeatureColourScheme();
+ if (preferredColours != null)
{
- ds.addSequence(sprods[s].getDatasetSequence());
+ featureColourScheme = preferredColours;
+ break;
}
- sprods[s].updatePDBIds();
}
- Alignment al = new Alignment(sprods);
- al.setDataset(ds);
+ Alignment 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
- Set<AlignedCodonFrame> cf = prods.getCodonFrames();
- for (AlignedCodonFrame acf : cf)
- {
- al.addCodonFrame(acf);
- }
- AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
+ AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
- String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
- + " for " + ((isRegSel) ? "selected region of " : "")
- + getTitle();
- naf.setTitle(newtitle);
+ String newtitle = String.format("%s %s %s",
+ MessageManager.getString(dna ? "label.proteins"
+ : "label.nucleotides"), MessageManager
+ .getString("label.for"), getTitle());
+ newFrame.setTitle(newtitle);
- // temporary flag until SplitFrame is released
boolean asSplitFrame = Cache.getDefault(
Preferences.ENABLE_SPLIT_FRAME, true);
if (asSplitFrame)
AlignmentI copyAlignment = null;
final SequenceI[] sequenceSelection = AlignFrame.this.viewport
.getSequenceSelection();
+ List<AlignedCodonFrame> cf = xrefs.getCodonFrames();
if (dna)
{
- copyAlignment = AlignmentUtils.makeExonAlignment(
- sequenceSelection, cf);
+ 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);
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- ssm.registerMappings(cf);
}
else
{
copyAlignment = new Alignment(new Alignment(
sequenceSelection));
+ copyAlignment.getCodonFrames().addAll(cf);
+ }
+ copyAlignment.setGapCharacter(AlignFrame.this.viewport
+ .getGapCharacter());
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerMappings(cf);
+
+ /*
+ * add in any extra 'peer' sequences discovered
+ * (e.g. alternative protein products)
+ */
+ for (SequenceI peer : addedPeers)
+ {
+ copyAlignment.addSequence(peer);
+ }
+
+ if (copyAlignment.getHeight() > 0)
+ {
+ /*
+ * 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);
+ }
+ }
+
+ 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();
}
- AlignFrame copyThis = new AlignFrame(copyAlignment,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- copyThis.setTitle(AlignFrame.this.getTitle());
- // SplitFrame with dna above, protein below
- SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
- dna ? naf : copyThis);
- naf.setVisible(true);
- copyThis.setVisible(true);
- String linkedTitle = MessageManager
- .getString("label.linked_view_title");
- Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
}
else
{
- Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+ Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
DEFAULT_HEIGHT);
}
}
new Object[] { source }), sttime);
}
+ /**
+ * 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 seqs)
+ {
+ 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()))
+ {
+ dataset.addSequence(sprods[s].getDatasetSequence());
+ }
+ sprods[s].updatePDBIds();
+ }
+ Alignment al = new Alignment(sprods);
+ al.setDataset(dataset);
+ return al;
+ }
+
};
Thread frunner = new Thread(foo);
frunner.start();
String type = null;
try
{
- type = new IdentifyFile().Identify(file, protocol);
+ type = new IdentifyFile().identify(file, protocol);
} catch (Exception ex)
{
type = null;
/**
* Attempt to load a "dropped" file or URL string: First by testing whether
- * it's and Annotation file, then a JNet file, and finally a features file. If
+ * it's an Annotation file, then a JNet file, and finally a features file. If
* all are false then the user may have dropped an alignment file onto this
* AlignFrame.
*
{
if (protocol == null)
{
- protocol = jalview.io.FormatAdapter.checkProtocol(file);
+ protocol = FormatAdapter.checkProtocol(file);
}
// if the file isn't identified, or not positively identified as some
// other filetype (PFAM is default unidentified alignment file type) then
// try to parse it as a features file
if (format == null)
{
- format = new IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
}
if (format.equalsIgnoreCase("JnetFile"))
{
viewport.setColumnSelection(cs);
isAnnotation = true;
}
- else
+ else if (IdentifyFile.FeaturesFile.equals(format))
{
- /*
- * if (format.equalsIgnoreCase("PDB")) {
- *
- * String pdbfn = ""; // try to match up filename with sequence id
- * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
- * new File(file); pdbfn = fl.getName(); } else if (protocol ==
- * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
- * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
- * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
- * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
- * // attempt to find a match in the alignment SequenceI mtch =
- * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
- * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
- * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
- * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
- * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
- * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
- * { System.err.println("Associated file : " + file + " with " +
- * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
- * TODO: maybe need to load as normal otherwise return; } }
- */
- // try to parse it as a features file
- boolean isGroupsFile = parseFeaturesFile(file, protocol);
- // if it wasn't a features file then we just treat it as a general
- // alignment file to load into the current view.
- if (!isGroupsFile)
- {
- new FileLoader().LoadFile(viewport, file, protocol, format);
- }
- else
+ if (parseFeaturesFile(file, protocol))
{
alignPanel.paintAlignment(true);
}
}
+ else
+ {
+ new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
}
}
if (isAnnotation)
} catch (Exception x)
{
}
- ;
new OOMWarning(
"loading data "
+ (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
@Override
public void run()
{
+ boolean isNuclueotide = alignPanel.alignFrame.getViewport()
+ .getAlignment().isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(), alignPanel.alignFrame)
+ .getSequenceSelection(), alignPanel.alignFrame, null,
+ alignPanel.alignFrame.featureSettings, isNuclueotide)
.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
+ .getViewport().getAlignment()
+ .isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
.getSequenceSelection(),
- alignPanel.alignFrame, dassource)
- .fetchDBRefs(false);
+ alignPanel.alignFrame, dassource,
+ alignPanel.alignFrame.featureSettings,
+ isNuclueotide).fetchDBRefs(false);
}
}).start();
}
@Override
public void run()
{
+ boolean isNuclueotide = alignPanel.alignFrame
+ .getViewport().getAlignment()
+ .isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
.getSequenceSelection(),
- alignPanel.alignFrame, dassource)
- .fetchDBRefs(false);
+ alignPanel.alignFrame, dassource,
+ alignPanel.alignFrame.featureSettings,
+ isNuclueotide).fetchDBRefs(false);
}
}).start();
}
@Override
public void run()
{
+ boolean isNuclueotide = alignPanel.alignFrame
+ .getViewport().getAlignment()
+ .isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
.getSequenceSelection(),
- alignPanel.alignFrame, dassrc)
- .fetchDBRefs(false);
+ alignPanel.alignFrame, dassrc,
+ alignPanel.alignFrame.featureSettings,
+ isNuclueotide).fetchDBRefs(false);
}
}).start();
}
{
// TODO no longer a menu action - refactor as required
final AlignmentI alignment = getViewport().getAlignment();
- Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
+ List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
if (mappings == null)
{
return;
sf.setComplementVisible(this, show);
}
}
+
+ /**
+ * Generate the reverse (optionally complemented) of the selected sequences,
+ * and add them to the alignment
+ */
+ @Override
+ protected void showReverse_actionPerformed(boolean complement)
+ {
+ AlignmentI al = null;
+ try
+ {
+ Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
+
+ al = dna.reverseCdna(complement);
+ viewport.addAlignment(al, "");
+ } catch (Exception ex)
+ {
+ System.err.println(ex.getMessage());
+ return;
+ }
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff