X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=2ee86f1f86a39bc6034e0c905d4825fd1661c278;hb=8b27085fa7fc5f2877e078421284c2636b85b8c6;hp=0d1fd35ef876ad41da9936cfd6199e986071b5f5;hpb=665d49f100089265efdeec7c4a7b500f6d55752d;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 0d1fd35..2ee86f1 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -25,6 +25,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; +import jalview.api.FeatureColourI; import jalview.api.FeatureRenderer; import jalview.api.FeatureSettingsControllerI; import jalview.api.SequenceStructureBinding; @@ -48,7 +49,9 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; import jalview.io.FeaturesFile; +import jalview.io.FileFormat; import jalview.io.TCoffeeScoreFile; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; @@ -218,6 +221,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.setColumnSelection(columnSelection); } + viewport.setScaleAboveWrapped(scaleAbove.getState()); alignPanel = new AlignmentPanel(this, viewport); avc = new jalview.controller.AlignViewController(this, viewport, @@ -234,8 +238,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); applyToAllGroups.setState(viewport.getColourAppliesToAllGroups()); annotationPanelMenuItem.setState(viewport.isShowAnnotation()); - showAlignmentAnnotations.setState(viewport.isShowAnnotation()); - showSequenceAnnotations.setState(viewport.isShowAnnotation()); + showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState()); + showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState()); + showAlignmentAnnotations.setState(true); + showSequenceAnnotations.setState(false); seqLimits.setState(viewport.getShowJVSuffix()); @@ -342,7 +348,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * is protocol for accessing data referred to by file */ - public boolean parseFeaturesFile(String file, String type) + public boolean parseFeaturesFile(String file, DataSourceType type) { return parseFeaturesFile(file, type, true); } @@ -352,28 +358,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * * @param file * file URL, content, or other resolvable path - * @param type + * @param paste * is protocol for accessing data referred to by file * @param autoenabledisplay * when true, display features flag will be automatically enabled if * features are loaded * @return true if data parsed as a features file */ - public boolean parseFeaturesFile(String file, String type, + public boolean parseFeaturesFile(String file, DataSourceType paste, boolean autoenabledisplay) { - // TODO: test if importing a features file onto an alignment which already - // has features with links overwrites the original links. - - Hashtable featureLinks = new Hashtable(); boolean featuresFile = false; try { - featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport - .getAlignment(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().getFeatureColours(), featureLinks, - true, viewport.applet.getDefaultParameter("relaxedidmatch", - false)); + Map colours = alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().getFeatureColours(); + boolean relaxedIdMatching = viewport.applet.getDefaultParameter( + "relaxedidmatch", false); + featuresFile = new FeaturesFile(file, paste).parse( + viewport.getAlignment(), colours, true, relaxedIdMatching); } catch (Exception ex) { ex.printStackTrace(); @@ -381,10 +384,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (featuresFile) { - if (featureLinks.size() > 0) - { - alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks; - } if (autoenabledisplay) { viewport.setShowSequenceFeatures(true); @@ -757,6 +756,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.showAllHiddenColumns(); } + viewport.sendSelection(); } } @@ -816,8 +816,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else if (source == annotationPanelMenuItem) { - viewport.setShowAnnotation(annotationPanelMenuItem.getState()); - alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); + boolean showAnnotations = annotationPanelMenuItem.getState(); + showAlignmentAnnotations.setEnabled(showAnnotations); + showSequenceAnnotations.setEnabled(showAnnotations); + viewport.setShowAnnotation(showAnnotations); + alignPanel.setAnnotationVisible(showAnnotations); } else if (source == sequenceFeatures) { @@ -925,12 +928,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { boolean showForAlignment = showAlignmentAnnotations.getState(); boolean showForSequences = showSequenceAnnotations.getState(); - for (AlignmentAnnotation aa : alignPanel.getAlignment() + if (alignPanel.getAlignment().getAlignmentAnnotation() != null) + { + for (AlignmentAnnotation aa : alignPanel.getAlignment() .getAlignmentAnnotation()) { boolean visible = (aa.sequenceRef == null ? showForAlignment : showForSequences); aa.visible = visible; + } } alignPanel.validateAnnotationDimensions(true); validate(); @@ -1072,11 +1078,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, else if (source == invertSequenceMenuItem) { invertSequenceMenuItem_actionPerformed(); + // uncomment to slave sequence selections in split frame + // viewport.sendSelection(); } else if (source == invertColSel) { viewport.invertColumnSelection(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } else if (source == remove2LeftMenuItem) { @@ -1110,27 +1119,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.showAllHiddenColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } else if (source == showSeqs) { viewport.showAllHiddenSeqs(); alignPanel.paintAlignment(true); + // uncomment if we want to slave sequence selections in split frame + // viewport.sendSelection(); } else if (source == hideColumns) { viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } else if (source == hideSequences && viewport.getSelectionGroup() != null) { viewport.hideAllSelectedSeqs(); alignPanel.paintAlignment(true); + // uncomment if we want to slave sequence selections in split frame + // viewport.sendSelection(); } else if (source == hideAllButSelection) { toggleHiddenRegions(false, false); alignPanel.paintAlignment(true); + viewport.sendSelection(); } else if (source == hideAllSelection) { @@ -1139,12 +1155,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } else if (source == showAllHidden) { viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } else if (source == showGroupConsensus) { @@ -1344,13 +1362,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + JalviewLite.addFrame(frame, MessageManager.formatMessage( "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); - FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer(); + FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand()); cap.setText(new AppletFormatAdapter(alignPanel).formatSequences( - e.getActionCommand(), viewport.getAlignment(), + fileFormat, viewport.getAlignment(), viewport.getShowJVSuffix())); } @@ -1385,7 +1403,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, return annotation; } - private Map getDisplayedFeatureCols() + private Map getDisplayedFeatureCols() { if (alignPanel.getFeatureRenderer() != null && viewport.getFeaturesDisplayed() != null) @@ -1399,15 +1417,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public String outputFeatures(boolean displayTextbox, String format) { String features; + FeaturesFile formatter = new FeaturesFile(); if (format.equalsIgnoreCase("Jalview")) { - features = new FeaturesFile().printJalviewFormat(viewport + features = formatter.printJalviewFormat(viewport .getAlignment().getSequencesArray(), getDisplayedFeatureCols()); } else { - features = new FeaturesFile().printGFFFormat(viewport.getAlignment() + features = formatter.printGffFormat(viewport.getAlignment() .getSequencesArray(), getDisplayedFeatureCols()); } @@ -1747,9 +1766,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport, complement); complement.getAlignment().moveSelectedSequencesByOne(mappedSelection, up ? null : complement.getHiddenRepSequences(), up); - // TODO need to trigger a repaint of the complementary panel - how? - // would prefer to handle in SplitFrame but it is not overriding key - // listener chiz + getSplitFrame().getComplement(this).alignPanel.paintAlignment(true); } } @@ -2072,15 +2089,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getAlignment().getWidth()) ? true : false; if (isEntireAlignWidth) { - String title = MessageManager.getString("label.delete_all"); - Panel mp = new Panel(); - mp.setLayout(new FlowLayout()); - mp.add(new Label(MessageManager.getString("warn.delete_all"))); - - final JVDialog dialog = new JVDialog(this, title, true, 400, - 200); - dialog.setMainPanel(mp); + Panel infoPanel = new Panel(); + infoPanel.setLayout(new FlowLayout()); + infoPanel + .add(new Label(MessageManager.getString("warn.delete_all"))); + + final JVDialog dialog = new JVDialog(this, title, true, 400, 200); + dialog.setMainPanel(infoPanel); + dialog.ok.setLabel(MessageManager.getString("action.ok")); + dialog.cancel.setLabel(MessageManager.getString("action.cancel")); dialog.setVisible(true); if (!dialog.accept) @@ -2218,7 +2236,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); - 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(); } @@ -2235,7 +2256,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.setSelectionGroup(null); alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.seqPanel.seqCanvas.highlightSearchResults(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(); } @@ -2265,7 +2289,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, ColumnSelection colSel = viewport.getColumnSelection(); int column; - if (colSel.size() > 0) + if (!colSel.isEmpty()) { if (trimLeft) { @@ -2290,18 +2314,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, TrimRegionCommand trimRegion; if (trimLeft) { - trimRegion = new TrimRegionCommand("Remove Left", - TrimRegionCommand.TRIM_LEFT, seqs, column, - viewport.getAlignment(), viewport.getColumnSelection(), - viewport.getSelectionGroup()); + trimRegion = new TrimRegionCommand("Remove Left", true, seqs, + column, viewport.getAlignment()); viewport.setStartRes(0); } else { - trimRegion = new TrimRegionCommand("Remove Right", - TrimRegionCommand.TRIM_RIGHT, seqs, column, - viewport.getAlignment(), viewport.getColumnSelection(), - viewport.getSelectionGroup()); + trimRegion = new TrimRegionCommand("Remove Right", false, seqs, + column, viewport.getAlignment()); } statusBar.setText(MessageManager.formatMessage( @@ -2605,6 +2625,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } + @Override public void changeColour(ColourSchemeI cs) { @@ -3498,10 +3519,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, nucleotideColour.setLabel(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(this); modifyPID.setLabel(MessageManager - .getString("label.modify_identity_thereshold")); + .getString("label.modify_identity_threshold")); modifyPID.addActionListener(this); modifyConservation.setLabel(MessageManager - .getString("label.modify_conservation_thereshold")); + .getString("label.modify_conservation_threshold")); modifyConservation.addActionListener(this); annotationColour.setLabel(MessageManager .getString("action.by_annotation")); @@ -3755,6 +3776,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, this.add(statusBar, BorderLayout.SOUTH); } + @Override public void setStatus(String string) { statusBar.setText(string); @@ -4001,7 +4023,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } // resolve data source // TODO: this code should be a refactored to an io package - String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB"); + DataSourceType protocol = AppletFormatAdapter.resolveProtocol( + pdbFile, FileFormat.PDB); if (protocol == null) { return false; @@ -4011,9 +4034,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // make a note of the access mode and add if (pdbentry.getProperty() == null) { - pdbentry.setProperty(new Hashtable()); + pdbentry.setProperty(new Hashtable()); } - pdbentry.getProperty().put("protocol", protocol); + pdbentry.getProperty().put("protocol", protocol.toString()); toaddpdb.addPDBId(pdbentry); alignPanel.getStructureSelectionManager() .registerPDBEntry(pdbentry); @@ -4050,7 +4073,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } public void newStructureView(JalviewLite applet, PDBEntry pdb, - SequenceI[] seqs, String[] chains, String protocol) + SequenceI[] seqs, String[] chains, DataSourceType protocol) { // Scrub any null sequences from the array Object[] sqch = cleanSeqChainArrays(seqs, chains); @@ -4061,10 +4084,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, System.err .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); } - if (protocol == null || protocol.trim().length() == 0 - || protocol.equals("null")) + if (protocol == null) { - protocol = (String) pdb.getProperty().get("protocol"); + String sourceType = pdb.getProperty().get("protocol"); + try + { + protocol = DataSourceType.valueOf(sourceType); + } catch (IllegalArgumentException e) + { + // ignore + } if (protocol == null) { System.err.println("Couldn't work out protocol to open structure: " @@ -4087,12 +4116,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { // can only do alignments with Jmol // find the last jmol window assigned to this alignment - jalview.appletgui.AppletJmol ajm = null, tajm; - Vector jmols = applet - .getAppletWindow(jalview.appletgui.AppletJmol.class); + AppletJmol ajm = null, tajm; + Vector jmols = applet.getAppletWindow(AppletJmol.class); for (int i = 0, iSize = jmols.size(); i < iSize; i++) { - tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i); + tajm = (AppletJmol) jmols.elementAt(i); if (tajm.ap.alignFrame == this) { ajm = tajm; @@ -4111,7 +4139,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // otherwise, create a new window if (applet.jmolAvailable) { - new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel, + new AppletJmol(pdb, seqs, chains, alignPanel, protocol); applet.lastFrameX += 40; applet.lastFrameY += 40;