X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=5fa168d2e5e3a667ec1a9312ffaa23022302b086;hb=09b8644607fb5b9debbfe39a7177922b0e66aa9a;hp=4e23f2b49f8659ee2c4fb78ce5903ad7c462c92e;hpb=15f319be6f7781efdca23314ec9a13595e938eb9;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 4e23f2b..5fa168d 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -62,6 +62,12 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.hmmer.HMMAlign; +import jalview.hmmer.HMMBuild; +import jalview.hmmer.HMMERParamStore; +import jalview.hmmer.HMMERPreset; +import jalview.hmmer.HMMSearch; +import jalview.hmmer.HmmerCommand; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.BioJsHTMLOutput; @@ -81,6 +87,7 @@ 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; @@ -94,6 +101,9 @@ import jalview.ws.DBRefFetcher.FetchFinishedListenerI; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.params.ArgumentI; +import jalview.ws.params.ParamDatastoreI; +import jalview.ws.params.WsParamSetI; import jalview.ws.seqfetcher.DbSourceProxy; import java.awt.BorderLayout; @@ -123,22 +133,25 @@ import java.awt.print.PrinterJob; import java.beans.PropertyChangeEvent; import java.io.File; import java.io.FileWriter; +import java.io.IOException; import java.io.PrintWriter; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; import java.util.Deque; -import java.util.Enumeration; -import java.util.Hashtable; +import java.util.HashSet; import java.util.List; +import java.util.Set; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; import javax.swing.JEditorPane; +import javax.swing.JFileChooser; import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.JMenu; import javax.swing.JMenuItem; +import javax.swing.JOptionPane; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; @@ -151,7 +164,6 @@ import javax.swing.SwingUtilities; public class AlignFrame extends GAlignFrame implements DropTargetListener, IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener { - public static final int DEFAULT_WIDTH = 700; public static final int DEFAULT_HEIGHT = 500; @@ -163,8 +175,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; - ViewportRanges vpRanges; - public AlignViewControllerI avc; List alignPanels = new ArrayList<>(); @@ -179,6 +189,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ String fileName = null; + /** * Creates a new AlignFrame object with specific width and height. * @@ -336,7 +347,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, progressBar = new ProgressBar(this.statusPanel, this.statusBar); } - vpRanges = viewport.getRanges(); avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) @@ -654,9 +664,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges + ViewportRanges ranges = viewport.getRanges(); + alignPanel.getSeqPanel().seqCanvas.cursorX = ranges .getStartRes(); - alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges + alignPanel.getSeqPanel().seqCanvas.cursorY = ranges .getStartSeq(); } alignPanel.getSeqPanel().seqCanvas.repaint(); @@ -689,10 +700,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, break; } case KeyEvent.VK_PAGE_UP: - vpRanges.pageUp(); + viewport.getRanges().pageUp(); break; case KeyEvent.VK_PAGE_DOWN: - vpRanges.pageDown(); + viewport.getRanges().pageDown(); break; } } @@ -763,6 +774,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ap.av.updateConservation(ap); ap.av.updateConsensus(ap); ap.av.updateStrucConsensus(ap); + ap.av.initInformationWorker(ap); } } @@ -841,6 +853,7 @@ 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); @@ -904,6 +917,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); showSequenceLogo.setSelected(av.isShowSequenceLogo()); normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); + showInformationHistogram.setSelected(av.isShowInformationHistogram()); + showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo()); + normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo()); ColourMenuHelper.setColourSelected(colourMenu, av.getGlobalColourScheme()); @@ -995,6 +1011,198 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override + public void hmmBuild_actionPerformed(boolean withDefaults) + { + if (!alignmentIsSufficient(1)) + { + return; + } + + /* + * get default parameters, and optionally show a dialog + * to allow them to be modified + */ + ParamDatastoreI store = HMMERParamStore.forBuild(viewport); + List args = store.getServiceParameters(); + + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + if (params.showRunDialog()) + { + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + new Thread(new HMMBuild(this, args)).start(); + } + + @Override + public void hmmAlign_actionPerformed(boolean withDefaults) + { + if (!(checkForHMM() && alignmentIsSufficient(2))) + { + return; + } + + /* + * get default parameters, and optionally show a dialog + * to allow them to be modified + */ + ParamDatastoreI store = HMMERParamStore.forAlign(viewport); + List args = store.getServiceParameters(); + + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + if (params.showRunDialog()) + { + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + new Thread(new HMMAlign(this, args)).start(); + } + + @Override + public void hmmSearch_actionPerformed(boolean withDefaults) + { + if (!checkForHMM()) + { + return; + } + + /* + * get default parameters, and (if requested) show + * dialog to allow modification + */ + ParamDatastoreI store = HMMERParamStore.forSearch(viewport); + List args = store.getServiceParameters(); + + if (!withDefaults) + { + WsParamSetI set = new HMMERPreset(); + WsJobParameters params = new WsJobParameters(store, set, args); + if (params.showRunDialog()) + { + args = params.getJobParams(); + } + else + { + return; // user cancelled + } + } + new Thread(new HMMSearch(this, args)).start(); + alignPanel.repaint(); + } + + /** + * Checks if the alignment has at least one hidden Markov model, if not shows + * a dialog advising to run hmmbuild or load an HMM profile + * + * @return + */ + private boolean checkForHMM() + { + if (viewport.getAlignment().getHmmSequences().isEmpty()) + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.no_hmm")); + return false; + } + return true; + } + + /** + * Checks if the alignment contains the required number of sequences. + * + * @param required + * @return + */ + public boolean alignmentIsSufficient(int required) + { + if (getViewport().getAlignment().getSequences().size() < required) + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("label.not_enough_sequences")); + return false; + } + return true; + } + + /** + * Opens a file browser and adds the selected file, if in Fasta, Stockholm or + * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a + * comma-separated list) + */ + @Override + public void addDatabase_actionPerformed() throws IOException + { + if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null) + { + Cache.setProperty(Preferences.HMMSEARCH_DBS, ""); + } + + String path = openFileChooser(false); + if (path != null && new File(path).exists()) + { + IdentifyFile identifier = new IdentifyFile(); + FileFormatI format = identifier.identify(path, DataSourceType.FILE); + if (format == FileFormat.Fasta || format == FileFormat.Stockholm + || format == FileFormat.Pfam) + { + String currentDbPaths = Cache + .getProperty(Preferences.HMMSEARCH_DBS); + currentDbPaths += Preferences.COMMA + path; + Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths); + } + else + { + JOptionPane.showMessageDialog(this, + MessageManager.getString("warn.invalid_format")); + } + } + } + + /** + * Opens a file chooser, optionally restricted to selecting folders + * (directories) only. Answers the path to the selected file or folder, or + * null if none is chosen. + * + * @param + * @return + */ + protected String openFileChooser(boolean forFolder) + { + // TODO duplicates GPreferences method - relocate to JalviewFileChooser? + String choice = null; + JFileChooser chooser = new JFileChooser(); + if (forFolder) + { + chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); + } + chooser.setDialogTitle( + MessageManager.getString("label.open_local_file")); + chooser.setToolTipText(MessageManager.getString("action.open")); + + int value = chooser.showOpenDialog(this); + + if (value == JFileChooser.APPROVE_OPTION) + { + choice = chooser.getSelectedFile().getPath(); + } + return choice; + } + + @Override public void reload_actionPerformed(ActionEvent e) { if (fileName != null) @@ -1392,17 +1600,18 @@ 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 public void associatedData_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( @@ -1711,7 +1920,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } synchronized void slideSequences(boolean right, int size) @@ -1828,7 +2037,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void copy_actionPerformed(ActionEvent e) { - System.gc(); if (viewport.getSelectionGroup() == null) { return; @@ -1889,9 +2097,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param e * DOCUMENT ME! + * @throws InterruptedException + * @throws IOException */ @Override protected void pasteNew_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { paste(true); } @@ -1901,9 +2112,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param e * DOCUMENT ME! + * @throws InterruptedException + * @throws IOException */ @Override protected void pasteThis_actionPerformed(ActionEvent e) + throws IOException, InterruptedException { paste(false); } @@ -1913,8 +2127,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param newAlignment * true to paste to a new alignment, otherwise add to this. + * @throws InterruptedException + * @throws IOException */ - void paste(boolean newAlignment) + void paste(boolean newAlignment) throws IOException, InterruptedException { boolean externalPaste = true; try @@ -2141,7 +2357,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - vpRanges.setEndSeq(alignment.getHeight()); + viewport.getRanges().setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2242,7 +2458,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, System.out.println("Exception whilst pasting: " + ex); // could be anything being pasted in here } - } @Override @@ -2385,7 +2600,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } @@ -2411,7 +2626,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // JAL-2034 - should delegate to // alignPanel to decide if overview needs // updating. - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } @@ -2436,7 +2651,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // JAL-2034 - should delegate to // alignPanel to decide if overview needs // updating. - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2467,7 +2682,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // alignPanel to decide if overview needs // updating. - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2476,7 +2691,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void invertColSel_actionPerformed(ActionEvent e) { viewport.invertColumnSelection(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); viewport.sendSelection(); } @@ -2536,7 +2751,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, column, viewport.getAlignment()); - vpRanges.setStartRes(0); + viewport.getRanges().setStartRes(0); } else { @@ -2601,13 +2816,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(vpRanges.getStartRes()); + ViewportRanges ranges = viewport.getRanges(); + int startRes = seq.findPosition(ranges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); - vpRanges.setStartRes(seq.findIndex(startRes) - 1); + ranges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); @@ -2640,12 +2856,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(vpRanges.getStartRes()); + int startRes = seq.findPosition(viewport.getRanges().getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); - vpRanges.setStartRes(seq.findIndex(startRes) - 1); + viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); @@ -2701,8 +2917,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * Create a new AlignmentPanel (with its own, new Viewport) */ - AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, - true); + AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel); if (!copyAnnotation) { /* @@ -2856,21 +3071,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.getIdPanel().getIdCanvas() .setPreferredSize(alignPanel.calculateIdWidth()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } @Override public void idRightAlign_actionPerformed(ActionEvent e) { viewport.setRightAlignIds(idRightAlign.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } @Override public void centreColumnLabels_actionPerformed(ActionEvent e) { viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /* @@ -2903,7 +3118,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -2932,7 +3147,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void showAllColumns_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3036,7 +3251,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.expandColSelection(sg, false); viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3052,7 +3267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3060,7 +3275,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3081,7 +3296,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); - alignPanel.paintAlignment(true); + // TODO: do we actually need to update overview for scale above change ? + alignPanel.paintAlignment(true, false); } /** @@ -3094,7 +3310,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3107,7 +3323,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3120,7 +3336,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -3133,7 +3349,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -3146,7 +3362,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } public FeatureSettings featureSettings; @@ -3184,7 +3400,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void showSeqFeatures_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } /** @@ -3260,6 +3476,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.setOverviewPanel(null); }; }); + if (getKeyListeners().length > 0) + { + frame.addKeyListener(getKeyListeners()[0]); + } alignPanel.setOverviewPanel(overview); } @@ -3341,7 +3561,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setGlobalColourScheme(cs); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } /** @@ -3426,7 +3646,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment().getSequenceAt(0)); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3442,7 +3662,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignmentSorter.sortByID(viewport.getAlignment()); addHistoryItem( new OrderCommand("ID Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3458,7 +3678,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignmentSorter.sortByLength(viewport.getAlignment()); addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3475,7 +3695,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3632,7 +3852,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } }); } @@ -3661,7 +3881,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment());// ,viewport.getSelectionGroup()); addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } }); } @@ -3687,35 +3907,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.getAlignment().getAlignmentAnnotation() - .hashCode() != _annotationScoreVectorHash) + .hashCode() == _annotationScoreVectorHash) { - sortByAnnotScore.removeAll(); - // almost certainly a quicker way to do this - but we keep it simple - Hashtable scoreSorts = new Hashtable(); - AlignmentAnnotation aann[]; - for (SequenceI sqa : viewport.getAlignment().getSequences()) + return; + } + + sortByAnnotScore.removeAll(); + Set scoreSorts = new HashSet<>(); + for (SequenceI sqa : viewport.getAlignment().getSequences()) + { + AlignmentAnnotation[] anns = sqa.getAnnotation(); + for (int i = 0; anns != null && i < anns.length; i++) { - aann = sqa.getAnnotation(); - for (int i = 0; aann != null && i < aann.length; i++) + AlignmentAnnotation aa = anns[i]; + if (aa != null && aa.hasScore() && aa.sequenceRef != null) { - if (aann[i].hasScore() && aann[i].sequenceRef != null) - { - scoreSorts.put(aann[i].label, aann[i].label); - } + scoreSorts.add(aa.label); } } - Enumeration labels = scoreSorts.keys(); - while (labels.hasMoreElements()) - { - addSortByAnnotScoreMenuItem(sortByAnnotScore, - (String) labels.nextElement()); - } - sortByAnnotScore.setVisible(scoreSorts.size() > 0); - scoreSorts.clear(); - - _annotationScoreVectorHash = viewport.getAlignment() - .getAlignmentAnnotation().hashCode(); } + for (String label : scoreSorts) + { + addSortByAnnotScoreMenuItem(sortByAnnotScore, label); + } + sortByAnnotScore.setVisible(!scoreSorts.isEmpty()); + + _annotationScoreVectorHash = viewport.getAlignment() + .getAlignmentAnnotation().hashCode(); } /** @@ -3776,7 +3994,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment())); } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); return true; } @@ -4247,7 +4465,7 @@ 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(); } @@ -4460,17 +4678,21 @@ 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) { @@ -4491,7 +4713,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, assocfiles++; } } - alignPanel.paintAlignment(true); + // TODO: do we need to update overview ? only if features are + // shown I guess + alignPanel.paintAlignment(true, false); + } + } + else + { + /* + * add declined structures as sequences + */ + for (Object[] o : filesmatched) + { + filesnotmatched.add((String) o[0]); } } } @@ -4539,6 +4773,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param file * either a filename or a URL string. + * @throws InterruptedException + * @throws IOException */ public void loadJalviewDataFile(String file, DataSourceType sourceType, FileFormatI format, SequenceI assocSeq) @@ -4626,11 +4862,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); - SequenceI repseq = viewport.getAlignment().getSequenceAt(0); - viewport.getAlignment().setSeqrep(repseq); - HiddenColumns cs = new HiddenColumns(); - cs.hideInsertionsFor(repseq); - viewport.getAlignment().setHiddenColumns(cs); + viewport.getAlignment().setupJPredAlignment(); isAnnotation = true; } // else if (IdentifyFile.FeaturesFile.equals(format)) @@ -4638,7 +4870,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (parseFeaturesFile(file, sourceType)) { - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } else @@ -4649,11 +4881,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (isAnnotation) { - alignPanel.adjustAnnotationHeight(); viewport.updateSequenceIdColours(); buildSortByAnnotationScoresMenu(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } catch (Exception ex) { @@ -4852,14 +5083,15 @@ 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()); }; }); @@ -5178,7 +5410,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { viewport.setShowUnconserved(showNonconservedMenuItem.getState()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /* @@ -5267,7 +5499,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } @@ -5279,7 +5511,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment().setSeqrep(null); PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } @@ -5369,7 +5601,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder()); this.alignPanel.av .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -5572,6 +5804,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new CalculationChooser(AlignFrame.this); } } + + /** + * Sets the status of the HMMER menu + */ + public void updateHMMERStatus() + { + hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable()); + } + + @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