X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=0670a316159c45d8ca237b0fcb355934e2add4a2;hb=2bab2ead5067d824be9a7716b0fb468b38787cac;hp=bed10a1d09841453881aadef0953e7eb57461e6d;hpb=31def7663858b5ed4840fa3c90d374e0cd798867;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index bed10a1..0670a31 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -19,7 +19,6 @@ package jalview.appletgui; -import jalview.jbappletgui.GAlignFrame; import jalview.schemes.*; import jalview.datamodel.*; import jalview.analysis.*; @@ -29,68 +28,81 @@ import java.awt.event.*; import java.util.*; import java.io.InputStreamReader; import java.io.BufferedReader; +import java.net.URL; -public class AlignFrame - extends GAlignFrame + +public class AlignFrame extends Frame { final AlignmentPanel alignPanel; - final AlignViewport viewport; - public static final int NEW_WINDOW_WIDTH = 700; - public static final int NEW_WINDOW_HEIGHT = 500; + public final AlignViewport viewport; + int NEW_WINDOW_WIDTH = 700; + int NEW_WINDOW_HEIGHT = 500; jalview.bin.JalviewLite applet; - public AlignFrame(AlignmentI al) - { - this.applet = null; - viewport = new AlignViewport(al, null); - alignPanel = new AlignmentPanel(this, viewport); - add(alignPanel); - alignPanel.validate(); - this.addWindowListener(new WindowAdapter() + public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title) + { + try{ + jbInit(); + }catch(Exception ex) { - public void windowClosing(WindowEvent e) - { - closeMenuItem_actionPerformed(null); - } - }); - - } - + ex.printStackTrace(); + } - public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet) - { this.applet = applet; viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); add(alignPanel); alignPanel.validate(); - String treeFile = applet.getParameter("treeFile"); - if (treeFile != null) + if(applet!=null) { - try + String param = applet.getParameter("sortBy"); + if (param != null) { - treeFile = treeFile; - jalview.io.NewickFile fin = new jalview.io.NewickFile(applet. - getCodeBase() + treeFile, "URL"); - fin.parse(); + if (param.equalsIgnoreCase("Id")) + sortIDMenuItem_actionPerformed(null); + else if (param.equalsIgnoreCase("Pairwise Identity")) + sortPairwiseMenuItem_actionPerformed(null); + } - if (fin.getTree() != null) + param = applet.getParameter("wrap"); + if (param != null) + { + if (param.equalsIgnoreCase("true")) { - TreePanel tp = null; - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - fin, "FromFile", applet.getCodeBase() + treeFile); - jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); - addTreeMenuItem(tp, treeFile); + wrapMenuItem.setState(true); + wrapMenuItem_actionPerformed(null); } } - catch (Exception ex) + + try { - ex.printStackTrace(); + param = applet.getParameter("windowWidth"); + if (param != null) + { + int width = Integer.parseInt(param); + NEW_WINDOW_WIDTH = width; + } + param = applet.getParameter("windowHeight"); + if (param != null) + { + int height = Integer.parseInt(param); + NEW_WINDOW_HEIGHT = height; + } } + catch (Exception ex) + {} + } + MyKeyAdapter keyAdapter = new MyKeyAdapter(); + //Some JVMS send keyevents to Top frame or lowest panel, + //Havent worked out why yet. So add to both this frame and seqCanvas for now + this.addKeyListener(keyAdapter); + alignPanel.seqPanel.seqCanvas.addKeyListener(keyAdapter); + alignPanel.idPanel.idCanvas.addKeyListener(keyAdapter); + this.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent e) @@ -99,13 +111,174 @@ public class AlignFrame } }); + viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() + { + public void propertyChange(java.beans.PropertyChangeEvent evt) + { + if (evt.getPropertyName().equals("alignment")) + { + alignmentChanged(); + } + } + }); + + jalview.bin.JalviewLite.addFrame(this, title, + NEW_WINDOW_WIDTH, + NEW_WINDOW_HEIGHT); + } + + public AlignViewport getAlignViewport() + { + return viewport; + } + + public SeqCanvas getSeqcanvas() + { + return alignPanel.seqPanel.seqCanvas; + } + + + /** + * DOCUMENT ME! + * + * @param String DOCUMENT ME! + */ + + public void parseFeaturesFile(String file) + { + try + { + URL url = new URL(file); + + BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); + SequenceI seq = null; + String line, type, desc, token; + + int index, start, end; + StringTokenizer st; + SequenceFeature sf; + FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); + int lineNo = 0; + while ( (line = in.readLine()) != null) + { + lineNo++; + st = new StringTokenizer(line, "\t"); + if (st.countTokens() == 2) + { + type = st.nextToken(); + UserColourScheme ucs = new UserColourScheme(st.nextToken()); + fr.setColour(type, ucs.findColour("A")); + continue; + } + + while (st.hasMoreElements()) + { + desc = st.nextToken(); + token = st.nextToken(); + if (!token.equals("ID_NOT_SPECIFIED")) + { + index = viewport.alignment.findIndex(viewport.alignment.findName( + token)); + st.nextToken(); + } + else + { + index = Integer.parseInt(st.nextToken()); + } + + start = Integer.parseInt(st.nextToken()); + end = Integer.parseInt(st.nextToken()); + + seq = viewport.alignment.getSequenceAt(index); + start = seq.findIndex(start) - 1; + end = seq.findIndex(end) - 1; + + type = st.nextToken(); + + if(fr.getColour(type)==null) + { + // Probably the old style groups file + UserColourScheme ucs = new UserColourScheme(type); + fr.setColour(type, ucs.findColour("A")); + } + + sf = new SequenceFeature(type, desc, "", start, end); + + seq.addSequenceFeature(sf); + } + } + + viewport.showSequenceFeatures = true; + + alignPanel.repaint(); + + } + catch (Exception ex) + { + System.out.println("Error parsing groups file: " + ex); + } + } + + + class MyKeyAdapter extends KeyAdapter + { + public void keyPressed(KeyEvent evt) + { + switch (evt.getKeyCode()) + { + case 27: // escape key + deselectAllSequenceMenuItem_actionPerformed(null); + break; + case KeyEvent.VK_X: + if (evt.isControlDown() || evt.isMetaDown()) + { + cut_actionPerformed(null); + } + break; + case KeyEvent.VK_C: + if (evt.isControlDown() || evt.isMetaDown()) + { + copy_actionPerformed(null); + } + break; + case KeyEvent.VK_V: + if (evt.isControlDown() || evt.isMetaDown()) + { + paste(true); + } + break; + case KeyEvent.VK_A: + if (evt.isControlDown() || evt.isMetaDown()) + { + selectAllSequenceMenuItem_actionPerformed(null); + } + break; + case KeyEvent.VK_DOWN: + moveSelectedSequences(false); + break; + case KeyEvent.VK_UP: + moveSelectedSequences(true); + break; + case KeyEvent.VK_F: + if (evt.isControlDown()) + { + findMenuItem_actionPerformed(null); + } + break; + case KeyEvent.VK_BACK_SPACE: + case KeyEvent.VK_DELETE: + cut_actionPerformed(null); + break; + } + } } + public void inputText_actionPerformed(ActionEvent e) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true); + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); @@ -113,21 +286,22 @@ public class AlignFrame protected void outputText_actionPerformed(ActionEvent e) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Alignment output - " + e.getActionCommand(), 600, 500); - cap.setText(FormatAdapter.formatSequences(e.getActionCommand(), - viewport.getAlignment(). - getSequences())); + cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(), + viewport.getAlignment().getSequences(), + viewport.showJVSuffix)); } public void closeMenuItem_actionPerformed(ActionEvent e) { PaintRefresher.components.remove(viewport.alignment); - dispose(); + if(PaintRefresher.components.size()==0 && applet==null) + System.exit(0); } Stack historyList = new Stack(); @@ -172,7 +346,7 @@ public class AlignFrame redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE)); restoreHistoryItem(hi); - resetAllColourSchemes(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } protected void redoMenuItem_actionPerformed(ActionEvent e) @@ -180,10 +354,7 @@ public class AlignFrame HistoryItem hi = (HistoryItem) redoList.pop(); restoreHistoryItem(hi); updateEditMenuBar(); - viewport.updateConsensus(); - resetAllColourSchemes(); - alignPanel.repaint(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } // used by undo and redo @@ -227,9 +398,7 @@ public class AlignFrame updateEditMenuBar(); - viewport.updateConsensus(); - viewport.updateConservation(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } public void moveSelectedSequences(boolean up) @@ -403,7 +572,6 @@ public class AlignFrame newSeqs[i] = (SequenceI) seqs.elementAt(i); } - AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet); String newtitle = new String("Copied sequences"); if (getTitle().startsWith("Copied sequences")) { @@ -413,6 +581,8 @@ public class AlignFrame { newtitle = newtitle.concat("- from " + getTitle()); } + AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle); + jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); } @@ -420,10 +590,7 @@ public class AlignFrame { viewport.setEndSeq(viewport.alignment.getHeight()); viewport.alignment.getWidth(); - viewport.updateConservation(); - viewport.updateConsensus(); - resetAllColourSchemes(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } @@ -489,10 +656,7 @@ public class AlignFrame catch (Exception ex) {} } - viewport.updateConservation(); - viewport.updateConsensus(); - resetAllColourSchemes(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } @@ -522,6 +686,8 @@ public class AlignFrame viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); + alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); + alignPanel.repaint(); PaintRefresher.Refresh(null, viewport.alignment); } @@ -561,8 +727,7 @@ public class AlignFrame viewport.alignment.deleteGroup(sg); } } - resetAllColourSchemes(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } @@ -589,8 +754,7 @@ public class AlignFrame viewport.alignment.deleteGroup(sg); } } - resetAllColourSchemes(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } @@ -610,10 +774,7 @@ public class AlignFrame viewport.setStartRes(seq.findIndex(startRes)-1); - viewport.updateConservation(); - viewport.updateConsensus(); - resetAllColourSchemes(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) @@ -639,34 +800,67 @@ public class AlignFrame { seqs = viewport.getSelectionGroup().sequences; start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes(); + end = viewport.getSelectionGroup().getEndRes()+1; } else seqs = viewport.alignment.getSequences(); - for (int i = 0; i -1) + { + current.deleteChars(rangeStart, rangeEnd); + j-=rangeEnd-rangeStart; + jSize-=rangeEnd-rangeStart; + rangeStart = -1; + rangeEnd = -1; + } + else + j++; } - j++; } - while(j < end && j < jSize) ; + while (j < end && j < jSize); + if(rangeStart>-1) + { + current.deleteChars(rangeStart, rangeEnd); + } } - viewport.setStartRes(seq.findIndex(startRes)-1); - viewport.updateConservation(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } + + public void alignmentChanged() + { viewport.updateConsensus(); + viewport.updateConservation (); resetAllColourSchemes(); + if(alignPanel.overviewPanel!=null) + alignPanel.overviewPanel.updateOverviewImage(); alignPanel.repaint(); } @@ -675,27 +869,26 @@ public class AlignFrame ColourSchemeI cs = viewport.globalColourScheme; if(cs!=null) { - cs.setConsensus(viewport.vconsensus); - if(cs.conservationApplied()) - { - Alignment al = (Alignment) viewport.alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth() - 1); - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); + if (cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) viewport.getGlobalColourScheme()). + resetClustalX(viewport.alignment.getSequences(), + viewport.alignment.getWidth()); + } - cs.setConservation(c); - } - } + cs.setConsensus(viewport.vconsensus); + if (cs.conservationApplied()) + { + Alignment al = (Alignment) viewport.alignment; + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, + al.getSequences(), 0, + al.getWidth() - 1); + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); - if(viewport.getGlobalColourScheme()!=null - && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme)viewport.getGlobalColourScheme()). - resetClustalX(viewport.alignment.getSequences(), - viewport.alignment.getWidth()); + cs.setConservation(c); + } } int s, sSize = viewport.alignment.getGroups().size(); @@ -706,9 +899,7 @@ public class AlignFrame { ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth()); } - sg.recalcConservation(); - } } @@ -716,25 +907,23 @@ public class AlignFrame public void findMenuItem_actionPerformed(ActionEvent e) { - Finder finder = new Finder(alignPanel); + new Finder(alignPanel); } public void font_actionPerformed(ActionEvent e) { - Frame frame = new Frame(); - FontChooser fc = new FontChooser(alignPanel, frame); - frame.add(fc); - jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100); - + new FontChooser(alignPanel); } - protected void fullSeqId_actionPerformed(ActionEvent e) + + public void seqLimits_itemStateChanged(ItemEvent e) { - viewport.setShowFullId(fullSeqId.getState()); + viewport.setShowJVSuffix(seqLimits.getState()); alignPanel.fontChanged(); alignPanel.repaint(); } + protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.getState()); @@ -789,11 +978,6 @@ public class AlignFrame public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { - if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment()) - { - annotationPanelMenuItem.setState(false); - return; - } viewport.setShowAnnotation(annotationPanelMenuItem.getState()); alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); } @@ -1045,7 +1229,7 @@ public class AlignFrame public void userDefinedColour_actionPerformed(ActionEvent e) { - UserDefinedColours chooser = new UserDefinedColours(alignPanel, null); + new UserDefinedColours(alignPanel, null); } public void PIDColour_actionPerformed(ActionEvent e) @@ -1099,13 +1283,31 @@ public class AlignFrame if (viewport.getSelectionGroup().getSize() > 1) { Frame frame = new Frame(); - frame.add(new PairwiseAlignPanel(viewport)); + frame.add(new PairwiseAlignPanel(alignPanel)); jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500); } } public void PCAMenuItem_actionPerformed(ActionEvent e) { + //are the sequences aligned? + if (!viewport.alignment.isAligned()) + { + SequenceI current; + int Width = viewport.getAlignment().getWidth(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); + i++) + { + current = viewport.getAlignment().getSequenceAt(i); + + if (current.getLength() < Width) + { + current.insertCharAt(Width - 1, viewport.getGapCharacter()); + } + } + alignPanel.repaint(); + } if ( (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() < 4 && @@ -1117,11 +1319,7 @@ public class AlignFrame try { - PCAPanel pcaPanel = new PCAPanel(viewport, null); - Frame frame = new Frame(); - frame.add(pcaPanel); - jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", - 400, 400); + new PCAPanel(viewport); } catch (java.lang.OutOfMemoryError ex) { @@ -1190,7 +1388,7 @@ public class AlignFrame jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); } - void addTreeMenuItem(final TreePanel treePanel, String title) + public void addTreeMenuItem(final TreePanel treePanel, String title) { final MenuItem item = new MenuItem(title); sortByTreeMenu.add(item); @@ -1216,7 +1414,7 @@ public class AlignFrame protected void documentation_actionPerformed(ActionEvent e) { - jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html"); + showURL("http://www.jalview.org/help.html"); } protected void about_actionPerformed(ActionEvent e) @@ -1283,4 +1481,625 @@ public class AlignFrame jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); } + + /** + * Displays the given URL in a new browser window + * + * @param url URL to display in browser window. + *
New window will be named "HELP_WINDOW" + */ + public void showURL(String url) + { + showURL(url, "HELP"); + } + + public void showURL(String url, String target) + { + if (applet == null) + { + System.out.println("Not running as applet - no browser available."); + } + else + { + try + { + applet.getAppletContext().showDocument(new java.net.URL(url), + target); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + + ////////////////////////////////////////////////////////////////////////////////// + //JBuilder Graphics here + + protected MenuBar alignFrameMenuBar = new MenuBar(); + protected Menu fileMenu = new Menu(); + protected MenuItem closeMenuItem = new MenuItem(); + protected Menu editMenu = new Menu(); + protected Menu viewMenu = new Menu(); + protected Menu colourMenu = new Menu(); + protected Menu calculateMenu = new Menu(); + protected MenuItem selectAllSequenceMenuItem = new MenuItem(); + protected MenuItem deselectAllSequenceMenuItem = new MenuItem(); + protected MenuItem invertSequenceMenuItem = new MenuItem(); + protected MenuItem remove2LeftMenuItem = new MenuItem(); + protected MenuItem remove2RightMenuItem = new MenuItem(); + protected MenuItem removeGappedColumnMenuItem = new MenuItem(); + protected MenuItem removeAllGapsMenuItem = new MenuItem(); + protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + protected MenuItem sortPairwiseMenuItem = new MenuItem(); + protected MenuItem sortIDMenuItem = new MenuItem(); + protected MenuItem sortGroupMenuItem = new MenuItem(); + protected MenuItem removeRedundancyMenuItem = new MenuItem(); + protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); + protected MenuItem PCAMenuItem = new MenuItem(); + protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); + protected MenuItem neighbourTreeMenuItem = new MenuItem(); + BorderLayout borderLayout1 = new BorderLayout(); + public Label statusBar = new Label(); + protected Menu outputTextboxMenu = new Menu(); + protected MenuItem clustalColour = new MenuItem(); + protected MenuItem zappoColour = new MenuItem(); + protected MenuItem taylorColour = new MenuItem(); + protected MenuItem hydrophobicityColour = new MenuItem(); + protected MenuItem helixColour = new MenuItem(); + protected MenuItem strandColour = new MenuItem(); + protected MenuItem turnColour = new MenuItem(); + protected MenuItem buriedColour = new MenuItem(); + protected MenuItem userDefinedColour = new MenuItem(); + protected MenuItem PIDColour = new MenuItem(); + protected MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); + MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); + protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + MenuItem overviewMenuItem = new MenuItem(); + protected MenuItem undoMenuItem = new MenuItem(); + protected MenuItem redoMenuItem = new MenuItem(); + protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem noColourmenuItem = new MenuItem(); + protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + MenuItem findMenuItem = new MenuItem(); + Menu searchMenu = new Menu(); + protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); + protected MenuItem nucleotideColour = new MenuItem(); + MenuItem deleteGroups = new MenuItem(); + MenuItem delete = new MenuItem(); + MenuItem copy = new MenuItem(); + MenuItem cut = new MenuItem(); + Menu Menu1 = new Menu(); + MenuItem pasteNew = new MenuItem(); + MenuItem pasteThis = new MenuItem(); + protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); + protected MenuItem font = new MenuItem(); + protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + MenuItem modifyPID = new MenuItem(); + MenuItem modifyConservation = new MenuItem(); + protected Menu sortByTreeMenu = new Menu(); + Menu sort = new Menu(); + Menu calculate = new Menu(); + MenuItem inputText = new MenuItem(); + Menu helpMenu = new Menu(); + MenuItem documentation = new MenuItem(); + MenuItem about = new MenuItem(); + protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); + + private void jbInit() throws Exception { + + setMenuBar(alignFrameMenuBar); + + MenuItem item; + + // dynamically fill save as menu with available formats + for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++) + { + + item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats. + elementAt( + i)); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + outputTextboxMenu.add(item); + } + + + fileMenu.setLabel("File"); + closeMenuItem.setLabel("Close"); + closeMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + closeMenuItem_actionPerformed(e); + } + }); + editMenu.setLabel("Edit"); + viewMenu.setLabel("View"); + colourMenu.setLabel("Colour"); + calculateMenu.setLabel("Calculate"); + selectAllSequenceMenuItem.setLabel("Select all"); + selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + selectAllSequenceMenuItem_actionPerformed(e); + } + }); + deselectAllSequenceMenuItem.setLabel("Deselect All"); + deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + deselectAllSequenceMenuItem_actionPerformed(e); + } + }); + invertSequenceMenuItem.setLabel("Invert Selection"); + invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + invertSequenceMenuItem_actionPerformed(e); + } + }); + remove2LeftMenuItem.setLabel("Remove Left"); + remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + remove2LeftMenuItem_actionPerformed(e); + } + }); + remove2RightMenuItem.setLabel("Remove Right"); + remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + remove2RightMenuItem_actionPerformed(e); + } + }); + removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); + removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + removeGappedColumnMenuItem_actionPerformed(e); + } + }); + removeAllGapsMenuItem.setLabel("Remove All Gaps"); + removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + removeAllGapsMenuItem_actionPerformed(e); + } + }); + viewBoxesMenuItem.setLabel("Boxes"); + viewBoxesMenuItem.setState(true); + viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + viewBoxesMenuItem_actionPerformed(null); + } + }); + viewTextMenuItem.setLabel("Text"); + viewTextMenuItem.setState(true); + viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + viewTextMenuItem_actionPerformed(null); + } + }); + sortPairwiseMenuItem.setLabel("by Pairwise Identity"); + sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + sortPairwiseMenuItem_actionPerformed(e); + } + }); + sortIDMenuItem.setLabel("by ID"); + sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + sortIDMenuItem_actionPerformed(e); + } + }); + sortGroupMenuItem.setLabel("by Group"); + sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + sortGroupMenuItem_actionPerformed(e); + } + }); + removeRedundancyMenuItem.setLabel("Remove Redundancy..."); + removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + removeRedundancyMenuItem_actionPerformed(e); + } + }); + pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); + pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + pairwiseAlignmentMenuItem_actionPerformed(e); + } + }); + PCAMenuItem.setLabel("Principal Component Analysis"); + PCAMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + PCAMenuItem_actionPerformed(e); + } + }); + averageDistanceTreeMenuItem.setLabel( + "Average Distance Using % Identity"); + averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + averageDistanceTreeMenuItem_actionPerformed(e); + } + }); + neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); + neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + neighbourTreeMenuItem_actionPerformed(e); + } + }); + 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"); + outputTextboxMenu.setLabel("Output to Textbox"); + clustalColour.setLabel("Clustalx"); + + clustalColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + clustalColour_actionPerformed(e); + } + }); + zappoColour.setLabel("Zappo"); + zappoColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + zappoColour_actionPerformed(e); + } + }); + taylorColour.setLabel("Taylor"); + taylorColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + taylorColour_actionPerformed(e); + } + }); + hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + hydrophobicityColour_actionPerformed(e); + } + }); + helixColour.setLabel("Helix Propensity"); + helixColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + helixColour_actionPerformed(e); + } + }); + strandColour.setLabel("Strand Propensity"); + strandColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + strandColour_actionPerformed(e); + } + }); + turnColour.setLabel("Turn Propensity"); + turnColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + turnColour_actionPerformed(e); + } + }); + buriedColour.setLabel("Buried Index"); + buriedColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + buriedColour_actionPerformed(e); + } + }); + userDefinedColour.setLabel("User Defined..."); + userDefinedColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + userDefinedColour_actionPerformed(e); + } + }); + PIDColour.setLabel("Percentage Identity"); + PIDColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + PIDColour_actionPerformed(e); + } + }); + BLOSUM62Colour.setLabel("BLOSUM62 Score"); + BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + BLOSUM62Colour_actionPerformed(e); + } + }); + avDistanceTreeBlosumMenuItem.setLabel( + "Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + avTreeBlosumMenuItem_actionPerformed(e); + } + }); + njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); + njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + njTreeBlosumMenuItem_actionPerformed(e); + } + }); + annotationPanelMenuItem.setActionCommand(""); + annotationPanelMenuItem.setState(true); + annotationPanelMenuItem.setLabel("Show Annotations"); + annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + annotationPanelMenuItem_actionPerformed(null); + } + }); + colourTextMenuItem.setLabel("Colour Text"); + colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + colourTextMenuItem_actionPerformed(null); + } + }); + overviewMenuItem.setLabel("Overview Window"); + overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + overviewMenuItem_actionPerformed(e); + } + }); + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + undoMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + undoMenuItem_actionPerformed(e); + } + }); + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + redoMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + redoMenuItem_actionPerformed(e); + } + }); + conservationMenuItem.setLabel("by Conservation"); + conservationMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + conservationMenuItem_actionPerformed(null); + } + }); + noColourmenuItem.setLabel("None"); + noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + noColourmenuItem_actionPerformed(e); + } + }); + wrapMenuItem.setLabel("Wrap"); + wrapMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + wrapMenuItem_actionPerformed(null); + } + }); + renderGapsMenuItem.setLabel("Show Gaps"); + renderGapsMenuItem.setState(true); + renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + renderGapsMenuItem_actionPerformed(null); + } + }); + findMenuItem.setLabel("Find..."); + findMenuItem.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + findMenuItem_actionPerformed(e); + } + }); + searchMenu.setLabel("Search"); + + abovePIDThreshold.setLabel("Above Identity Threshold"); + abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + abovePIDThreshold_actionPerformed(null); + } + }); + nucleotideColour.setLabel("Nucleotide"); + nucleotideColour.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + nucleotideColour_actionPerformed(e); + } + }); + deleteGroups.setLabel("Undefine Groups"); + deleteGroups.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + deleteGroups_actionPerformed(e); + } + }); + copy.setLabel("Copy"); + copy.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + copy_actionPerformed(e); + } + }); + cut.setLabel("Cut"); + cut.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + cut_actionPerformed(e); + } + }); + delete.setLabel("Delete"); + delete.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + delete_actionPerformed(e); + } + }); + Menu1.setLabel("Paste"); + pasteNew.setLabel("To New Alignment"); + pasteNew.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + pasteNew_actionPerformed(e); + } + }); + pasteThis.setLabel("Add To This Alignment"); + pasteThis.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + pasteThis_actionPerformed(e); + } + }); + applyToAllGroups.setLabel("Apply Colour To All Groups"); + applyToAllGroups.setState(true); + applyToAllGroups.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + applyToAllGroups_actionPerformed(null); + } + }); + font.setLabel("Font..."); + font.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + font_actionPerformed(e); + } + }); + scaleAbove.setLabel("Scale Above"); + scaleAbove.setState(true); + scaleAbove.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + scaleAbove_actionPerformed(null); + } + }); + scaleLeft.setEnabled(false); + scaleLeft.setState(true); + scaleLeft.setLabel("Scale Left"); + scaleLeft.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + scaleLeft_actionPerformed(null); + } + }); + scaleRight.setEnabled(false); + scaleRight.setState(true); + scaleRight.setLabel("Scale Right"); + scaleRight.addItemListener(new java.awt.event.ItemListener() { + public void itemStateChanged(ItemEvent e) { + scaleRight_actionPerformed(null); + } + }); + modifyPID.setLabel("Modify Identity Threshold..."); + modifyPID.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + modifyPID_actionPerformed(e); + } + }); + modifyConservation.setLabel("Modify Conservation Threshold..."); + modifyConservation.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + modifyConservation_actionPerformed(e); + } + }); + sortByTreeMenu.setLabel("By Tree Order"); + sort.setLabel("Sort"); + calculate.setLabel("Calculate Tree"); + inputText.setLabel("Input from textbox"); + inputText.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + inputText_actionPerformed(e); + } + }); + + helpMenu.setLabel("Help"); + documentation.setLabel("Documentation"); + documentation.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + documentation_actionPerformed(e); + } + }); + + about.setLabel("About..."); + about.addActionListener(new java.awt.event.ActionListener() { + public void actionPerformed(ActionEvent e) { + about_actionPerformed(e); + } + }); + seqLimits.setState(true); + seqLimits.setLabel("Show Sequence Limits"); + seqLimits.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent e) + { + seqLimits_itemStateChanged(e); + } + }); + + alignFrameMenuBar.add(fileMenu); + alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(searchMenu); + alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(colourMenu); + alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(helpMenu); + fileMenu.add(inputText); + fileMenu.add(outputTextboxMenu); + fileMenu.addSeparator(); + fileMenu.add(closeMenuItem); + editMenu.add(undoMenuItem); + editMenu.add(redoMenuItem); + editMenu.add(cut); + editMenu.add(copy); + editMenu.add(Menu1); + editMenu.add(delete); + editMenu.addSeparator(); + editMenu.add(selectAllSequenceMenuItem); + editMenu.add(deselectAllSequenceMenuItem); + editMenu.add(invertSequenceMenuItem); + editMenu.add(deleteGroups); + editMenu.addSeparator(); + editMenu.add(remove2LeftMenuItem); + editMenu.add(remove2RightMenuItem); + editMenu.add(removeGappedColumnMenuItem); + editMenu.add(removeAllGapsMenuItem); + editMenu.add(removeRedundancyMenuItem); + searchMenu.add(findMenuItem); + viewMenu.add(font); + viewMenu.addSeparator(); + viewMenu.add(seqLimits); + viewMenu.addSeparator(); + viewMenu.add(wrapMenuItem); + viewMenu.add(scaleAbove); + viewMenu.add(scaleLeft); + viewMenu.add(scaleRight); + viewMenu.addSeparator(); + viewMenu.add(viewBoxesMenuItem); + viewMenu.add(viewTextMenuItem); + viewMenu.add(colourTextMenuItem); + viewMenu.add(renderGapsMenuItem); + viewMenu.add(annotationPanelMenuItem); + viewMenu.addSeparator(); + viewMenu.add(overviewMenuItem); + colourMenu.add(applyToAllGroups); + colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + calculateMenu.add(sort); + calculateMenu.add(calculate); + calculateMenu.addSeparator(); + calculateMenu.add(pairwiseAlignmentMenuItem); + calculateMenu.add(PCAMenuItem); + this.add(statusBar, BorderLayout.SOUTH); + Menu1.add(pasteNew); + Menu1.add(pasteThis); + sort.add(sortIDMenuItem); + sort.add(sortByTreeMenu); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + calculate.add(averageDistanceTreeMenuItem); + calculate.add(neighbourTreeMenuItem); + calculate.add(avDistanceTreeBlosumMenuItem); + calculate.add(njTreeBlosumMenuItem); + helpMenu.add(documentation); + helpMenu.add(about); + } } +