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.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.SequenceFetcher;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
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.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.StringSelection;
import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
import java.awt.dnd.DropTargetDragEvent;
import java.awt.dnd.DropTargetDropEvent;
import java.awt.dnd.DropTargetEvent;
import java.awt.dnd.DropTargetListener;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyAdapter;
{
formatMenu.add(vsel);
}
+ addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ Jalview.setCurrentAlignFrame(AlignFrame.this);
+ }
+ });
}
showGroupConservation.setEnabled(!nucleotide);
rnahelicesColour.setEnabled(nucleotide);
purinePyrimidineColour.setEnabled(nucleotide);
- showComplementMenuItem.setText(MessageManager
- .getString(nucleotide ? "label.protein" : "label.nucleotide"));
+ showComplementMenuItem.setText(nucleotide ? MessageManager
+ .getString("label.protein") : MessageManager
+ .getString("label.nucleotide"));
setColourSelected(jalview.bin.Cache.getDefault(
nucleotide ? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT, "None"));
.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
showProducts.setEnabled(canShowProducts());
+ setGroovyEnabled(Desktop.getGroovyConsole() != null);
updateEditMenuBar();
}
+ /**
+ * Set the enabled state of the 'Run Groovy' option in the Calculate menu
+ *
+ * @param b
+ */
+ public void setGroovyEnabled(boolean b)
+ {
+ runGroovy.setEnabled(b);
+ }
+
private IProgressIndicator progressBar;
/*
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)
if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
{
- omitHidden = viewport.getViewAsString(false);
+ omitHidden = viewport.getViewAsString(false,
+ settings.isExportHiddenSequences());
}
+ int[] alignmentStartEnd = new int[2];
if (hasHiddenSeqs && settings.isExportHiddenSequences())
{
alignmentToExport = hiddenSeqs.getFullAlignment();
else
{
alignmentToExport = viewport.getAlignment();
- alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
- .getColumnSelection().getHiddenColumns());
}
+ alignmentStartEnd = alignmentToExport
+ .getVisibleStartAndEndIndex(viewport.getColumnSelection()
+ .getHiddenColumns());
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
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!
*
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
viewport.sendSelection();
- alignPanel.paintAlignment(true);
+ // JAL-2034 - should delegate to
+ // alignPanel to decide if overview needs
+ // updating.
+ alignPanel.paintAlignment(false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
viewport.setSelectionGroup(null);
alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
alignPanel.getIdPanel().getIdCanvas().searchResults = null;
- alignPanel.paintAlignment(true);
+ // JAL-2034 - should delegate to
+ // alignPanel to decide if overview needs
+ // updating.
+ alignPanel.paintAlignment(false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
{
sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
}
+ // JAL-2034 - should delegate to
+ // alignPanel to decide if overview needs
+ // updating.
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
@Override
public void expandViews_actionPerformed(ActionEvent e)
{
- Desktop.instance.explodeViews(this);
+ Desktop.explodeViews(this);
}
/**
}
/**
- * Set or clear 'Show Sequence Features'
- *
- * @param evt
- * DOCUMENT ME!
- */
- @Override
- public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
- {
- viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
- .isSelected());
- if (viewport.isShowSequenceFeaturesHeight())
- {
- // ensure we're actually displaying features
- viewport.setShowSequenceFeatures(true);
- showSeqFeatures.setSelected(true);
- }
- alignPanel.paintAlignment(true);
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
- }
-
- /**
* Action on toggle of the 'Show annotations' menu item. This shows or hides
* the annotations panel as a whole.
*
@Override
public void mousePressed(MouseEvent evt)
{
- if (evt.isControlDown()
- || SwingUtilities.isRightMouseButton(evt))
+ if (evt.isPopupTrigger())
{
radioItem.removeActionListener(radioItem.getActionListeners()[0]);
{
JMenuItem tm = new JMenuItem();
ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
- if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
+ if (sm.isDNA() == viewport.getAlignment().isNucleotide()
+ || sm.isProtein() == !viewport.getAlignment()
+ .isNucleotide())
{
String smn = MessageManager.getStringOrReturn(
"label.score_model_", sm.getName());
// object broker mechanism.
final Vector<JMenu> wsmenu = new Vector<JMenu>();
final IProgressIndicator af = me;
+
+ /*
+ * do not i18n these strings - they are hard-coded in class
+ * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
+ * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
+ */
final JMenu msawsmenu = new JMenu("Alignment");
final JMenu secstrmenu = new JMenu(
"Secondary Structure Prediction");
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
final JMenu analymenu = new JMenu("Analysis");
final JMenu dismenu = new JMenu("Protein Disorder");
- // final JMenu msawsmenu = new
- // JMenu(MessageManager.getString("label.alignment"));
- // final JMenu secstrmenu = new
- // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
- // final JMenu seqsrchmenu = new
- // JMenu(MessageManager.getString("label.sequence_database_search"));
- // final JMenu analymenu = new
- // JMenu(MessageManager.getString("label.analysis"));
- // final JMenu dismenu = new
- // JMenu(MessageManager.getString("label.protein_disorder"));
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
}
/**
- * Searches selected sequences for xRef products and builds the Show
- * Cross-References menu (formerly called Show Products)
+ * Searches the alignment sequences for xRefs and builds the Show
+ * Cross-References menu (formerly called Show Products), with database
+ * sources for which cross-references are found (protein sources for a
+ * nucleotide alignment and vice versa)
*
- * @return true if Show Cross-references menu should be enabled.
+ * @return true if Show Cross-references menu should be enabled
*/
public boolean canShowProducts()
{
- SequenceI[] selection = viewport.getSequenceSelection();
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
AlignmentI dataset = viewport.getAlignment().getDataset();
+
+ showProducts.removeAll();
+ final boolean dna = viewport.getAlignment().isNucleotide();
+
+ if (seqs == null || seqs.length == 0)
+ {
+ // nothing to see here.
+ return false;
+ }
+
boolean showp = false;
try
{
- showProducts.removeAll();
- final boolean dna = viewport.getAlignment().isNucleotide();
- String[] ptypes = (selection == null || selection.length == 0) ? null
- : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
+ List<String> ptypes = new CrossRef(seqs, dataset)
+ .findXrefSourcesForSequences(dna);
- for (int t = 0; ptypes != null && t < ptypes.length; t++)
+ for (final String source : ptypes)
{
showp = true;
final AlignFrame af = this;
- final String source = ptypes[t];
- JMenuItem xtype = new JMenuItem(ptypes[t]);
+ JMenuItem xtype = new JMenuItem(source);
xtype.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
showProductsFor(af.viewport.getSequenceSelection(), dna, source);
}
-
});
showProducts.add(xtype);
}
showProducts.setEnabled(showp);
} catch (Exception e)
{
- jalview.bin.Cache.log
+ Cache.log
.warn("canShowProducts threw an exception - please report to help@jalview.org",
e);
return false;
return showp;
}
- protected void showProductsFor(final SequenceI[] sel, final boolean dna,
- final String source)
- {
- Runnable foo = new Runnable()
- {
-
- @Override
- public void run()
- {
- final long sttime = System.currentTimeMillis();
- AlignFrame.this.setProgressBar(MessageManager.formatMessage(
- "status.searching_for_sequences_from",
- 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);
- if (xrefs != null)
- {
- /*
- * 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)
- {
- FeatureSettingsModelI preferredColours = proxy
- .getFeatureColourScheme();
- if (preferredColours != null)
- {
- featureColourScheme = preferredColours;
- break;
- }
- }
- Alignment al = makeCrossReferencesAlignment(
- alignment.getDataset(), xrefs);
-
- AlignFrame newFrame = new AlignFrame(al, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- String newtitle = String.format("%s %s %s",
- MessageManager.getString(dna ? "label.proteins"
- : "label.nucleotides"), MessageManager
- .getString("label.for"), getTitle());
- newFrame.setTitle(newtitle);
-
- boolean asSplitFrame = Cache.getDefault(
- Preferences.ENABLE_SPLIT_FRAME, true);
- if (asSplitFrame)
- {
- /*
- * 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();
- if (dna)
- {
- 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);
- }
- 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();
- }
- }
- else
- {
- Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- }
- }
- else
- {
- System.err.println("No Sequences generated for xRef type "
- + source);
- }
- } catch (Exception e)
- {
- jalview.bin.Cache.log.error(
- "Exception when finding crossreferences", e);
- } catch (OutOfMemoryError e)
- {
- new OOMWarning("whilst fetching crossreferences", e);
- } catch (Error e)
- {
- jalview.bin.Cache.log.error("Error when finding crossreferences",
- e);
- }
- AlignFrame.this.setProgressBar(MessageManager.formatMessage(
- "status.finished_searching_for_sequences_from",
- 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();
- }
-
- public boolean canShowTranslationProducts(SequenceI[] selection,
- AlignmentI alignment)
+ /**
+ * Finds and displays cross-references for the selected sequences (protein
+ * products for nucleotide sequences, dna coding sequences for peptides).
+ *
+ * @param sel
+ * the sequences to show cross-references for
+ * @param dna
+ * true if from a nucleotide alignment (so showing proteins)
+ * @param source
+ * the database to show cross-references for
+ */
+ protected void showProductsFor(final SequenceI[] sel,
+ final boolean _odna, final String source)
{
- // 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;
- }
+ new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+ .start();
}
/**
.getString("label.error_when_translating_sequences_submit_bug_report");
final String errorTitle = MessageManager
.getString("label.implementation_error")
- + MessageManager.getString("translation_failed");
+ + MessageManager.getString("label.translation_failed");
JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.ERROR_MESSAGE);
return;
public void drop(DropTargetDropEvent evt)
{
Transferable t = evt.getTransferable();
- java.util.List files = null;
+ java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
try
{
- DataFlavor uriListFlavor = new DataFlavor(
- "text/uri-list;class=java.lang.String");
- if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
- {
- // Works on Windows and MacOSX
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- files = (java.util.List) t
- .getTransferData(DataFlavor.javaFileListFlavor);
- }
- else if (t.isDataFlavorSupported(uriListFlavor))
- {
- // This is used by Unix drag system
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- String data = (String) t.getTransferData(uriListFlavor);
- files = new java.util.ArrayList(1);
- for (java.util.StringTokenizer st = new java.util.StringTokenizer(
- data, "\r\n"); st.hasMoreTokens();)
- {
- String s = st.nextToken();
- if (s.startsWith("#"))
- {
- // the line is a comment (as per the RFC 2483)
- continue;
- }
-
- java.net.URI uri = new java.net.URI(s);
- // check to see if we can handle this kind of URI
- if (uri.getScheme().toLowerCase().startsWith("http"))
- {
- files.add(uri.toString());
- }
- else
- {
- // otherwise preserve old behaviour: catch all for file objects
- java.io.File file = new java.io.File(uri);
- files.add(file.toString());
- }
- }
- }
+ Desktop.transferFromDropTarget(files, protocols, evt, t);
} catch (Exception e)
{
e.printStackTrace();
@Override
public void tabbedPane_mousePressed(MouseEvent e)
{
- if (SwingUtilities.isRightMouseButton(e))
+ if (e.isPopupTrigger())
{
String msg = MessageManager.getString("label.enter_view_name");
String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
{
new Thread(new Runnable()
{
-
@Override
public void run()
{
- boolean isNuclueotide = alignPanel.alignFrame.getViewport()
+ boolean isNucleotide = alignPanel.alignFrame.getViewport()
.getAlignment().isNucleotide();
- new jalview.ws.DBRefFetcher(alignPanel.av
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
.getSequenceSelection(), alignPanel.alignFrame, null,
- alignPanel.alignFrame.featureSettings, isNuclueotide)
- .fetchDBRefs(false);
+ alignPanel.alignFrame.featureSettings, 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, 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();
}
protected void setAnnotationsVisibility(boolean visible,
boolean forSequences, boolean forAlignment)
{
- for (AlignmentAnnotation aa : alignPanel.getAlignment()
- .getAlignmentAnnotation())
+ AlignmentAnnotation[] anns = alignPanel.getAlignment()
+ .getAlignmentAnnotation();
+ if (anns == null)
+ {
+ return;
+ }
+ for (AlignmentAnnotation aa : anns)
{
/*
* don't display non-positional annotations on an alignment
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
-
al = dna.reverseCdna(complement);
viewport.addAlignment(al, "");
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"),
+ Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
+ viewport.getAlignment()));
} catch (Exception ex)
{
System.err.println(ex.getMessage());
return;
}
}
+
+ /**
+ * Try to run a script in the Groovy console, having first ensured that this
+ * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
+ * be targeted at this alignment.
+ */
+ @Override
+ protected void runGroovy_actionPerformed()
+ {
+ Jalview.setCurrentAlignFrame(this);
+ groovy.ui.Console console = Desktop.getGroovyConsole();
+ if (console != null)
+ {
+ try
+ {
+ console.runScript();
+ } catch (Exception ex)
+ {
+ System.err.println((ex.toString()));
+ JOptionPane
+ .showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.couldnt_run_groovy_script"),
+ MessageManager
+ .getString("label.groovy_support_failed"),
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ else
+ {
+ System.err.println("Can't run Groovy script as console not found");
+ }
+ }
+
+ /**
+ * Hides columns containing (or not containing) a specified feature, provided
+ * that would not leave all columns hidden
+ *
+ * @param featureType
+ * @param columnsContaining
+ * @return
+ */
+ public boolean hideFeatureColumns(String featureType,
+ boolean columnsContaining)
+ {
+ boolean notForHiding = avc.markColumnsContainingFeatures(
+ columnsContaining, false, false, featureType);
+ if (notForHiding)
+ {
+ if (avc.markColumnsContainingFeatures(!columnsContaining, false,
+ false, featureType))
+ {
+ getViewport().hideSelectedColumns();
+ return true;
+ }
+ }
+ return false;
+ }
}
class PrintThread extends Thread