X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=479d77180df9706629d82684060638065275fdcf;hb=c1e70ea0a01d2c916675aa8020970c6696d0dba5;hp=04d2045a49a2962826640fa93ce66b3f9b32f7cc;hpb=74f2c25a0ad46ce7286cca6d976f3592952d36ad;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 04d2045..479d771 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -49,7 +49,8 @@ public class AlignFrame extends Frame implements ActionListener, boolean embedded) { - jalviewServletURL = applet.getParameter("APPLICATION_URL"); + if (applet != null) + jalviewServletURL = applet.getParameter("APPLICATION_URL"); try{ jbInit(); @@ -336,7 +337,7 @@ public class AlignFrame extends Frame implements ActionListener, if(toggleSeqs) { - if (sg != null && sg.getSize(false) != viewport.alignment.getHeight()) + if (sg != null && sg.getSize() != viewport.alignment.getHeight()) { hide = true; viewport.hideAllSelectedSeqs(); @@ -498,6 +499,12 @@ public void itemStateChanged(ItemEvent evt) loadTree_actionPerformed(); else if(source==loadApplication) launchFullApplication(); + else if (source == loadAnnotations) + loadAnnotations(); + else if (source == outputAnnotations) + outputAnnotations(); + else if(source == outputFeatures) + outputFeatures(true, "Jalview"); else if(source==closeMenuItem) closeMenuItem_actionPerformed(); else if(source==copy) @@ -648,10 +655,61 @@ public void itemStateChanged(ItemEvent evt) "Alignment output - " + e.getActionCommand(), 600, 500); cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(), - viewport.getAlignment().getSequences(), + viewport.getAlignment(), viewport.showJVSuffix)); } + public void loadAnnotations() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + cap.setText("Paste your features / annotations file here."); + cap.setAnnotationImport(); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300); + + } + + public void outputAnnotations() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Annotations", + 600, 500); + cap.setText( new AnnotationFile().printAnnotations( + viewport.alignment.getAlignmentAnnotation() ) ); + } + + public String outputFeatures(boolean displayTextbox, String format) + { + String features; + if (format.equalsIgnoreCase("Jalview")) + features = new FeaturesFile().printJalviewFormat( + viewport.alignment.getSequencesArray(), + viewport.featuresDisplayed); + else + features = new FeaturesFile().printGFFFormat( + viewport.alignment.getSequencesArray(), + viewport.featuresDisplayed); + + + if(displayTextbox) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Features", + 600, 500); + + cap.setText(features); + } + + return features; + } + void launchFullApplication() { StringBuffer url = new StringBuffer(jalviewServletURL); @@ -723,7 +781,10 @@ public void itemStateChanged(ItemEvent evt) public void closeMenuItem_actionPerformed() { - PaintRefresher.components.remove(viewport.alignment); + PaintRefresher.RemoveComponent(alignPanel); + PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); + PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); + if(PaintRefresher.components.size()==0 && viewport.applet==null) System.exit(0); @@ -792,7 +853,7 @@ public void itemStateChanged(ItemEvent evt) originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; updateEditMenuBar(); - originalSource.firePropertyChange("alignment", null,null); + originalSource.firePropertyChange("alignment", null,originalSource.alignment.getSequences()); } /** @@ -813,19 +874,20 @@ public void itemStateChanged(ItemEvent evt) originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null; updateEditMenuBar(); - originalSource.firePropertyChange("alignment", null, null); + originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences()); } AlignViewport getOriginatingSource(CommandI command) { - AlignViewport originalSource = viewport; + AlignViewport originalSource = null; //For sequence removal and addition, we need to fire //the property change event FROM the viewport where the //original alignment was altered + AlignmentI al = null; if (command instanceof EditCommand) { EditCommand editCommand = (EditCommand) command; - AlignmentI al = editCommand.getAlignment(); + al = editCommand.getAlignment(); Vector comps = (Vector) PaintRefresher.components .get(viewport.getSequenceSetId()); for (int i = 0; i < comps.size(); i++) @@ -840,6 +902,18 @@ public void itemStateChanged(ItemEvent evt) } } } + + if (originalSource == null) + { + //The original view is closed, we must validate + //the current view against the closed view first + if (al != null) + PaintRefresher.validateSequences(al, viewport.alignment); + + originalSource = viewport; + } + + return originalSource; } @@ -856,13 +930,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = 1; i < viewport.alignment.getHeight(); i++) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(false).contains(seq)) + if (!sg.getSequences(null).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.getSequences(false).contains(temp)) + if (sg.getSequences(null).contains(temp)) { continue; } @@ -876,13 +950,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(true).contains(seq)) + if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.getSequences(true).contains(temp)) + if (sg.getSequences(viewport.hiddenRepSequences).contains(temp)) { continue; } @@ -907,7 +981,7 @@ public void itemStateChanged(ItemEvent evt) SequenceGroup sg = viewport.getSelectionGroup(); copiedSequences = new StringBuffer(); Hashtable orderedSeqs = new Hashtable(); - for (int i = 0; i < sg.getSize(false); i++) + for (int i = 0; i < sg.getSize(); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.alignment.findIndex(seq); @@ -936,7 +1010,7 @@ public void itemStateChanged(ItemEvent evt) copiedHiddenColumns = null; - for (int i = 0; i < sg.getSize(false); i++) + for (int i = 0; i < sg.getSize(); i++) { SequenceI seq = null; @@ -980,7 +1054,7 @@ public void itemStateChanged(ItemEvent evt) copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes + "\t" + - seq.getSequence(sg.getStartRes(), + seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1) + "\n"); } @@ -1051,24 +1125,7 @@ public void itemStateChanged(ItemEvent evt) } else { - for (int i = 0; i < newSeqs.length; i++) - { - viewport.alignment.addSequence(newSeqs[i]); - } - - //!newAlignment - addHistoryItem(new EditCommand( - "Add sequences", - EditCommand.PASTE, - newSeqs, - 0, - viewport.alignment.getWidth(), - viewport.alignment) - ); - - viewport.setEndSeq(viewport.alignment.getHeight()); - viewport.alignment.getWidth(); - viewport.firePropertyChange("alignment", null, null); + addSequences(newSeqs); } } @@ -1077,6 +1134,30 @@ public void itemStateChanged(ItemEvent evt) } + void addSequences(SequenceI[] seqs) + { + for (int i = 0; i < seqs.length; i++) + { + viewport.alignment.addSequence(seqs[i]); + } + + //!newAlignment + addHistoryItem(new EditCommand( + "Add sequences", + EditCommand.PASTE, + seqs, + 0, + viewport.alignment.getWidth(), + viewport.alignment) + ); + + viewport.setEndSeq(viewport.alignment.getHeight()); + viewport.alignment.getWidth(); + viewport.firePropertyChange("alignment", null, + viewport.alignment.getSequences()); + + } + protected void cut_actionPerformed() { copy_actionPerformed(); @@ -1094,7 +1175,7 @@ public void itemStateChanged(ItemEvent evt) Vector seqs = new Vector(); SequenceI seq; - for (int i = 0; i < sg.getSize(false); i++) + for (int i = 0; i < sg.getSize(); i++) { seq = sg.getSequenceAt(i); seqs.addElement(seq); @@ -1102,7 +1183,7 @@ public void itemStateChanged(ItemEvent evt) // If the cut affects all sequences, remove highlighted columns - if (sg.getSize(false) == viewport.alignment.getHeight()) + if (sg.getSize() == viewport.alignment.getHeight()) { viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); @@ -1200,7 +1281,7 @@ public void itemStateChanged(ItemEvent evt) SequenceI [] seqs; if(viewport.getSelectionGroup()!=null) - seqs = viewport.getSelectionGroup().getSequencesAsArray(true); + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences); else seqs = viewport.alignment.getSequencesArray(); @@ -1259,7 +1340,7 @@ public void itemStateChanged(ItemEvent evt) SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(true); + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -1298,7 +1379,7 @@ public void itemStateChanged(ItemEvent evt) SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(true); + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -1337,11 +1418,9 @@ public void itemStateChanged(ItemEvent evt) else newal = new Alignment(viewport.alignment.getSequencesArray()); - - AlignFrame newaf = new AlignFrame(newal, viewport.applet, - this.getTitle()+" (New View)", + "", false); newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId(); @@ -1354,6 +1433,23 @@ public void itemStateChanged(ItemEvent evt) PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, newaf.alignPanel.av.getSequenceSetId()); + Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId()); + int viewSize = -1; + for (int i = 0; i < comps.size(); i++) + { + if (comps.elementAt(i) instanceof AlignmentPanel) + viewSize++; + } + + String title = new String(this.getTitle()); + if (title.indexOf("(View") > -1) + title = title.substring(0, title.indexOf("(View")); + + title+= "(View "+viewSize+")"; + + newaf.setTitle(title.toString()); + + newaf.viewport.historyList = viewport.historyList; newaf.viewport.redoList = viewport.redoList; @@ -1475,7 +1571,9 @@ public void itemStateChanged(ItemEvent evt) } if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth()); + sg.cs = new ClustalxColourScheme( + sg.getSequences(viewport.hiddenRepSequences), + sg.getWidth()); } else { @@ -1495,7 +1593,8 @@ public void itemStateChanged(ItemEvent evt) || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth())); } else sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); @@ -1504,7 +1603,7 @@ public void itemStateChanged(ItemEvent evt) { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.getSequences(true), 0, + sg.getSequences(viewport.hiddenRepSequences), 0, viewport.alignment.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); @@ -1610,7 +1709,7 @@ public void itemStateChanged(ItemEvent evt) public void pairwiseAlignmentMenuItem_actionPerformed() { if (viewport.getSelectionGroup()!=null - && viewport.getSelectionGroup().getSize(false) > 1) + && viewport.getSelectionGroup().getSize() > 1) { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); @@ -1640,8 +1739,8 @@ public void itemStateChanged(ItemEvent evt) } if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize(false) < 4 && - viewport.getSelectionGroup().getSize(false) > 0) + viewport.getSelectionGroup().getSize() < 4 && + viewport.getSelectionGroup().getSize() > 0) || viewport.getAlignment().getHeight() < 4) { return; @@ -1674,7 +1773,7 @@ public void itemStateChanged(ItemEvent evt) protected void avTreeBlosumMenuItem_actionPerformed() { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID"); + NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); } void NewTreePanel(String type, String pwType, String title) @@ -1700,7 +1799,7 @@ public void itemStateChanged(ItemEvent evt) } if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize(false) > 1) + viewport.getSelectionGroup().getSize() > 1) || (viewport.getSelectionGroup() == null && viewport.alignment.getHeight() > 1)) { @@ -1718,7 +1817,7 @@ public void itemStateChanged(ItemEvent evt) { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); cap.setText("Paste your Newick tree file here."); - cap.treeImport = true; + cap.setTreeImport(); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300); @@ -1856,7 +1955,11 @@ public void itemStateChanged(ItemEvent evt) protected MenuBar alignFrameMenuBar = new MenuBar(); protected Menu fileMenu = new Menu("File"); protected MenuItem loadApplication = new MenuItem("View in Full Application"); - protected MenuItem loadTree = new MenuItem("Load Associated Tree"); + protected MenuItem loadTree = new MenuItem("Load Associated Tree ..."); + protected MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ..."); + protected MenuItem outputFeatures = new MenuItem("Export Features ..."); + protected MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); + protected MenuItem closeMenuItem = new MenuItem("Close"); protected Menu editMenu = new Menu("Edit"); protected Menu viewMenu = new Menu("View"); @@ -1968,6 +2071,9 @@ public void itemStateChanged(ItemEvent evt) loadApplication.addActionListener(this); loadTree.addActionListener(this); + loadAnnotations.addActionListener(this); + outputFeatures.addActionListener(this); + outputAnnotations.addActionListener(this); selectAllSequenceMenuItem.addActionListener(this); deselectAllSequenceMenuItem.addActionListener(this); invertSequenceMenuItem.addActionListener(this); @@ -2002,7 +2108,6 @@ public void itemStateChanged(ItemEvent evt) averageDistanceTreeMenuItem.addActionListener(this); neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); neighbourTreeMenuItem.addActionListener(this); - alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBackground(Color.white); statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setText("Status bar"); @@ -2144,20 +2249,29 @@ public void itemStateChanged(ItemEvent evt) alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); alignFrameMenuBar.add(helpMenu); + fileMenu.add(inputText); + fileMenu.add(loadTree); + fileMenu.add(loadAnnotations); + + fileMenu.addSeparator(); fileMenu.add(outputTextboxMenu); + fileMenu.add(outputFeatures); + fileMenu.add(outputAnnotations); + if(jalviewServletURL!=null) fileMenu.add(loadApplication); + fileMenu.addSeparator(); - fileMenu.add(loadTree); fileMenu.add(closeMenuItem); + editMenu.add(undoMenuItem); editMenu.add(redoMenuItem); editMenu.add(cut); editMenu.add(copy); editMenu.add(pasteMenu); editMenu.add(delete); - editMenu.addSeparator(); + editMenu.addSeparator(); editMenu.add(remove2LeftMenuItem); editMenu.add(remove2RightMenuItem); editMenu.add(removeGappedColumnMenuItem); @@ -2280,14 +2394,12 @@ public void itemStateChanged(ItemEvent evt) embeddedCalculate.addMouseListener(this); embeddedHelp.addMouseListener(this); - // setVisible(false); fileMenu.remove(closeMenuItem); fileMenu.remove(3); // Seperator viewport.applet.setLayout(new BorderLayout()); viewport.applet.add(embeddedMenu, BorderLayout.NORTH); viewport.applet.add(statusBar, BorderLayout.SOUTH); - // viewport.applet.validate(); alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height - embeddedMenu.HEIGHT - statusBar.HEIGHT);