X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=1f1fac0e39a45cd690870156cf5ab0d8bc11cb9e;hb=cf64def09a8b741483854ddd8c034d0aefff15b4;hp=0c452c396b7dd55cce44ff98ef3b9aa961c91c35;hpb=2a66892874abea357a5e5d9ef2f69919453c31d0;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 0c452c3..1f1fac0 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -81,6 +81,7 @@ import jalview.io.JnetAnnotationMaker; import jalview.io.NewickFile; import jalview.io.ScoreMatrixFile; import jalview.io.TCoffeeScoreFile; +import jalview.io.vcf.VCFLoader; import jalview.jbgui.GAlignFrame; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; @@ -732,9 +733,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int aSize = alignPanels.size(); - tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null); + tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null); - if (aSize == 1 && ap.av.viewName == null) + if (aSize == 1 && ap.av.getViewName() == null) { this.getContentPane().add(ap, BorderLayout.CENTER); } @@ -747,7 +748,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, expandViews.setEnabled(true); gatherViews.setEnabled(true); - tabbedPane.addTab(ap.av.viewName, ap); + tabbedPane.addTab(ap.av.getViewName(), ap); ap.setVisible(false); } @@ -770,7 +771,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, gatherViews.setEnabled(true); tabbedPane.setVisible(true); AlignmentPanel first = alignPanels.get(0); - tabbedPane.addTab(first.av.viewName, first); + tabbedPane.addTab(first.av.getViewName(), first); this.getContentPane().add(tabbedPane, BorderLayout.CENTER); } @@ -839,6 +840,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignmentI al = getViewport().getAlignment(); boolean nucleotide = al.isNucleotide(); + loadVcf.setVisible(nucleotide); showTranslation.setVisible(nucleotide); showReverse.setVisible(nucleotide); showReverseComplement.setVisible(nucleotide); @@ -870,7 +872,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param av * AlignViewport */ - void setMenusFromViewport(AlignViewport av) + public void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.isPadGaps()); colourTextMenuItem.setSelected(av.isShowColourText()); @@ -1390,13 +1392,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void exportFeatures_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportFeatures(alignPanel); + new AnnotationExporter(alignPanel).exportFeatures(); } @Override public void exportAnnotations_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations(alignPanel); + new AnnotationExporter(alignPanel).exportAnnotations(); } @Override @@ -1826,7 +1828,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void copy_actionPerformed(ActionEvent e) { - System.gc(); if (viewport.getSelectionGroup() == null) { return; @@ -2712,10 +2713,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newap.av.setGatherViewsHere(false); - if (viewport.viewName == null) + if (viewport.getViewName() == null) { - viewport.viewName = MessageManager - .getString("label.view_name_original"); + viewport.setViewName(MessageManager + .getString("label.view_name_original")); } /* @@ -2739,7 +2740,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newap.refresh(true); // adjust layout of annotations } - newap.av.viewName = getNewViewName(viewTitle); + newap.av.setViewName(getNewViewName(viewTitle)); addAlignmentPanel(newap, true); newap.alignmentChanged(); @@ -2802,9 +2803,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (comp instanceof AlignmentPanel) { AlignmentPanel ap = (AlignmentPanel) comp; - if (!existingNames.contains(ap.av.viewName)) + if (!existingNames.contains(ap.av.getViewName())) { - existingNames.add(ap.av.viewName); + existingNames.add(ap.av.getViewName()); } } } @@ -3259,6 +3260,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.setOverviewPanel(null); }; }); + if (getKeyListeners().length > 0) + { + frame.addKeyListener(getKeyListeners()[0]); + } alignPanel.setOverviewPanel(overview); } @@ -3592,9 +3597,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, frameTitle += " from "; - if (viewport.viewName != null) + if (viewport.getViewName() != null) { - frameTitle += viewport.viewName + " of "; + frameTitle += viewport.getViewName() + " of "; } frameTitle += this.title; @@ -4246,7 +4251,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showProductsFor(final SequenceI[] sel, final boolean _odna, final String source) { - new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this)) + new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this)) .start(); } @@ -4459,17 +4464,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int assocfiles = 0; if (filesmatched.size() > 0) { - if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) - || JvOptionPane.showConfirmDialog(thisaf, - MessageManager.formatMessage( - "label.automatically_associate_structure_files_with_sequences_same_name", - new Object[] - { Integer.valueOf(filesmatched.size()) - .toString() }), - MessageManager.getString( - "label.automatically_associate_structure_files_by_name"), - JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION) - + boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false); + if (!autoAssociate) + { + String msg = MessageManager.formatMessage( + "label.automatically_associate_structure_files_with_sequences_same_name", + new Object[] + { Integer.valueOf(filesmatched.size()) + .toString() }); + String ttl = MessageManager.getString( + "label.automatically_associate_structure_files_by_name"); + int choice = JvOptionPane.showConfirmDialog(thisaf, msg, + ttl, JvOptionPane.YES_NO_OPTION); + autoAssociate = choice == JvOptionPane.YES_OPTION; + } + if (autoAssociate) { for (Object[] fm : filesmatched) { @@ -4495,6 +4504,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true, false); } } + else + { + /* + * add declined structures as sequences + */ + for (Object[] o : filesmatched) + { + filesnotmatched.add((String) o[0]); + } + } } if (filesnotmatched.size() > 0) { @@ -4748,7 +4767,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (reply != null) { - viewport.viewName = reply; + viewport.setViewName(reply); // TODO warn if reply is in getExistingViewNames()? tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); } @@ -4849,14 +4868,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, MessageManager.getString("option.trim_retrieved_seqs")); trimrs.setToolTipText( MessageManager.getString("label.trim_retrieved_sequences")); - trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true)); + trimrs.setSelected( + Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); trimrs.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { trimrs.setSelected(trimrs.isSelected()); - Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", + Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, Boolean.valueOf(trimrs.isSelected()).toString()); }; }); @@ -5285,6 +5305,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (avc.createGroup()) { + if (applyAutoAnnotationSettings.isSelected()) + { + alignPanel.updateAnnotation(true, false); + } alignPanel.alignmentChanged(); } } @@ -5375,7 +5399,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public List getAlignPanels() { - return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + // alignPanels is never null + // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + return alignPanels; } /** @@ -5569,6 +5595,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new CalculationChooser(AlignFrame.this); } } + + @Override + protected void loadVcf_actionPerformed() + { + JalviewFileChooser chooser = new JalviewFileChooser( + Cache.getProperty("LAST_DIRECTORY")); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file")); + chooser.setToolTipText(MessageManager.getString("label.load_vcf_file")); + + int value = chooser.showOpenDialog(null); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", choice); + SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); + new VCFLoader(choice).loadVCF(seqs, this); + } + + } } class PrintThread extends Thread