\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.GAlignFrame;\r
import jalview.schemes.*;\r
import jalview.datamodel.*;\r
import jalview.analysis.*;\r
import java.util.*;\r
import java.io.InputStreamReader;\r
import java.io.BufferedReader;\r
+import java.net.URL;\r
\r
-public class AlignFrame\r
- extends GAlignFrame\r
+\r
+public class AlignFrame extends Frame\r
{\r
final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
- public static final int NEW_WINDOW_WIDTH = 700;\r
- public static final int NEW_WINDOW_HEIGHT = 500;\r
+ public final AlignViewport viewport;\r
+ int NEW_WINDOW_WIDTH = 700;\r
+ int NEW_WINDOW_HEIGHT = 500;\r
jalview.bin.JalviewLite applet;\r
\r
- public AlignFrame(AlignmentI al)\r
+\r
+ public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)\r
{\r
- this.applet = null;\r
- viewport = new AlignViewport(al, null);\r
+ try{\r
+ jbInit();\r
+ }catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ this.applet = applet;\r
+ viewport = new AlignViewport(al, applet);\r
alignPanel = new AlignmentPanel(this, viewport);\r
add(alignPanel);\r
alignPanel.validate();\r
\r
- this.addWindowListener(new WindowAdapter()\r
+ if(applet!=null)\r
{\r
- public void windowClosing(WindowEvent e)\r
+ String treeFile = applet.getParameter("treeFile");\r
+ if (treeFile != null)\r
{\r
- closeMenuItem_actionPerformed(null);\r
- }\r
- });\r
+ try\r
+ {\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
+ getCodeBase() + treeFile, "URL");\r
+ fin.parse();\r
\r
- }\r
+ if (fin.getTree() != null)\r
+ {\r
+ TreePanel tp = null;\r
+ tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
+ fin, "FromFile", applet.getCodeBase() + treeFile);\r
+ jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
+ addTreeMenuItem(tp, treeFile);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
\r
+ String param = applet.getParameter("sortBy");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("Id"))\r
+ sortIDMenuItem_actionPerformed(null);\r
+ else if (param.equalsIgnoreCase("Pairwise Identity"))\r
+ sortPairwiseMenuItem_actionPerformed(null);\r
+ }\r
\r
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
- {\r
- this.applet = applet;\r
- viewport = new AlignViewport(al, applet);\r
- alignPanel = new AlignmentPanel(this, viewport);\r
- add(alignPanel);\r
- alignPanel.validate();\r
+ param = applet.getParameter("wrap");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("true"))\r
+ {\r
+ wrapMenuItem.setState(true);\r
+ wrapMenuItem_actionPerformed(null);\r
+ }\r
+ }\r
\r
- String treeFile = applet.getParameter("treeFile");\r
- if (treeFile != null)\r
- {\r
try\r
{\r
- treeFile = treeFile;\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
- getCodeBase() + treeFile, "URL");\r
- fin.parse();\r
-\r
- if (fin.getTree() != null)\r
+ param = applet.getParameter("windowWidth");\r
+ if (param != null)\r
+ {\r
+ int width = Integer.parseInt(param);\r
+ NEW_WINDOW_WIDTH = width;\r
+ }\r
+ param = applet.getParameter("windowHeight");\r
+ if (param != null)\r
{\r
- TreePanel tp = null;\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- fin, "FromFile", applet.getCodeBase() + treeFile);\r
- jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
- addTreeMenuItem(tp, treeFile);\r
+ int height = Integer.parseInt(param);\r
+ NEW_WINDOW_HEIGHT = height;\r
}\r
}\r
catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
+ {}\r
+\r
}\r
\r
this.addWindowListener(new WindowAdapter()\r
}\r
});\r
\r
+ viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
+ {\r
+ public void propertyChange(java.beans.PropertyChangeEvent evt)\r
+ {\r
+ if (evt.getPropertyName().equals("alignment"))\r
+ {\r
+ alignmentChanged();\r
+ }\r
+ }\r
+ });\r
+\r
+ jalview.bin.JalviewLite.addFrame(this, title,\r
+ NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
\r
\r
}\r
\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param String DOCUMENT ME!\r
+ */\r
+\r
+ public void parseFeaturesFile(String file)\r
+ {\r
+ try\r
+ {\r
+ URL url = new URL(file);\r
+\r
+ BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));\r
+ SequenceI seq = null;\r
+ String line, type, desc, token;\r
+\r
+ int index, start, end;\r
+ StringTokenizer st;\r
+ SequenceFeature sf;\r
+ FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+ int lineNo = 0;\r
+ while ( (line = in.readLine()) != null)\r
+ {\r
+ lineNo++;\r
+ st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() == 2)\r
+ {\r
+ type = st.nextToken();\r
+ UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ continue;\r
+ }\r
+\r
+ while (st.hasMoreElements())\r
+ {\r
+ desc = st.nextToken();\r
+ token = st.nextToken();\r
+ if (!token.equals("ID_NOT_SPECIFIED"))\r
+ {\r
+ index = viewport.alignment.findIndex(viewport.alignment.findName(\r
+ token));\r
+ st.nextToken();\r
+ }\r
+ else\r
+ {\r
+ index = Integer.parseInt(st.nextToken());\r
+ }\r
+\r
+ start = Integer.parseInt(st.nextToken());\r
+ end = Integer.parseInt(st.nextToken());\r
+\r
+ seq = viewport.alignment.getSequenceAt(index);\r
+ start = seq.findIndex(start) - 1;\r
+ end = seq.findIndex(end) - 1;\r
+\r
+ type = st.nextToken();\r
+\r
+ if(fr.getColour(type)==null)\r
+ {\r
+ // Probably the old style groups file\r
+ UserColourScheme ucs = new UserColourScheme(type);\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ }\r
+\r
+ sf = new SequenceFeature(type, desc, "", start, end);\r
+\r
+ seq.addSequenceFeature(sf);\r
+ }\r
+ }\r
+\r
+ viewport.showSequenceFeatures = true;\r
+ ((Alignment)viewport.alignment).featuresAdded = true;\r
+\r
+ alignPanel.repaint();\r
+\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println("Error parsing groups file: " + ex);\r
+ }\r
+ }\r
+\r
+\r
public void inputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame,\r
"Alignment output - " + e.getActionCommand(),\r
600, 500);\r
- cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
- viewport.getAlignment().\r
- getSequences()));\r
+ cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
+ viewport.getAlignment().getSequences(),\r
+ viewport.showDBPrefix,\r
+ viewport.showJVSuffix));\r
}\r
\r
public void closeMenuItem_actionPerformed(ActionEvent e)\r
{\r
PaintRefresher.components.remove(viewport.alignment);\r
- dispose();\r
+ if(PaintRefresher.components.size()==0 && applet==null)\r
+ System.exit(0);\r
}\r
\r
Stack historyList = new Stack();\r
redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
HistoryItem.HIDE));\r
restoreHistoryItem(hi);\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
protected void redoMenuItem_actionPerformed(ActionEvent e)\r
HistoryItem hi = (HistoryItem) redoList.pop();\r
restoreHistoryItem(hi);\r
updateEditMenuBar();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
// used by undo and redo\r
\r
updateEditMenuBar();\r
\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
public void moveSelectedSequences(boolean up)\r
newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
}\r
\r
- AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
String newtitle = new String("Copied sequences");\r
if (getTitle().startsWith("Copied sequences"))\r
{\r
{\r
newtitle = newtitle.concat("- from " + getTitle());\r
}\r
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);\r
+\r
jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
NEW_WINDOW_HEIGHT);\r
}\r
{\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
}\r
catch (Exception ex)\r
{}\r
}\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
\r
}\r
\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
+ alignPanel.repaint();\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
-\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
}\r
\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
-\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
}\r
\r
viewport.setStartRes(seq.findIndex(startRes)-1);\r
\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- resetAllClustalSchemes();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
seqs = viewport.getSelectionGroup().sequences;\r
start = viewport.getSelectionGroup().getStartRes();\r
- end = viewport.getSelectionGroup().getEndRes();\r
+ end = viewport.getSelectionGroup().getEndRes()+1;\r
}\r
else\r
seqs = viewport.alignment.getSequences();\r
\r
- for (int i = 0; i <seqs.size(); i++)\r
+ for (int i = 0; i < seqs.size(); i++)\r
{\r
- current = (SequenceI)seqs.elementAt(i);\r
+ current = (SequenceI) seqs.elementAt(i);\r
jSize = current.getLength();\r
\r
+ // Removing a range is much quicker than removing gaps\r
+ // one by one for long sequences\r
int j = start;\r
+ int rangeStart=-1, rangeEnd=-1;\r
+\r
do\r
{\r
if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
{\r
- current.deleteCharAt(j);\r
- j--;\r
- jSize--;\r
+ if(rangeStart==-1)\r
+ {\r
+ rangeStart = j;\r
+ rangeEnd = j+1;\r
+ }\r
+ else\r
+ {\r
+ rangeEnd++;\r
+ }\r
+ j++;\r
+ }\r
+ else\r
+ {\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ j-=rangeEnd-rangeStart;\r
+ jSize-=rangeEnd-rangeStart;\r
+ rangeStart = -1;\r
+ rangeEnd = -1;\r
+ }\r
+ else\r
+ j++;\r
}\r
- j++;\r
}\r
- while(j < end && j < jSize) ;\r
+ while (j < end && j < jSize);\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ }\r
}\r
-\r
viewport.setStartRes(seq.findIndex(startRes)-1);\r
- resetAllClustalSchemes();\r
- viewport.updateConservation();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ public void alignmentChanged()\r
+ {\r
viewport.updateConsensus();\r
+ viewport.updateConservation ();\r
+ resetAllColourSchemes();\r
+ if(alignPanel.overviewPanel!=null)\r
+ alignPanel.overviewPanel.updateOverviewImage();\r
alignPanel.repaint();\r
}\r
\r
- void resetAllClustalSchemes()\r
+ void resetAllColourSchemes()\r
{\r
- if(viewport.getGlobalColourScheme()!=null\r
- && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)\r
+ ColourSchemeI cs = viewport.globalColourScheme;\r
+ if(cs!=null)\r
{\r
- ((ClustalxColourScheme)viewport.getGlobalColourScheme()).\r
- resetClustalX(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth());\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
+ resetClustalX(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth());\r
+ }\r
+\r
+ cs.setConsensus(viewport.vconsensus);\r
+ if (cs.conservationApplied())\r
+ {\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+ }\r
}\r
\r
int s, sSize = viewport.alignment.getGroups().size();\r
for(s=0; s<sSize; s++)\r
{\r
SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
- if(sg.cs instanceof ClustalxColourScheme)\r
+ if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
{\r
((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
}\r
+ sg.recalcConservation();\r
}\r
}\r
\r
\r
public void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
- Finder finder = new Finder(alignPanel);\r
+ new Finder(alignPanel);\r
}\r
\r
public void font_actionPerformed(ActionEvent e)\r
{\r
- Frame frame = new Frame();\r
- FontChooser fc = new FontChooser(alignPanel, frame);\r
- frame.add(fc);\r
- jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
+ new FontChooser(alignPanel);\r
+ }\r
\r
+ public void dbref_actionPerformed(ItemEvent e)\r
+ {\r
+ viewport.showDBPrefix = dbref.getState();\r
+ alignPanel.fontChanged();\r
+ alignPanel.repaint();\r
}\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ public void seqLimits_itemStateChanged(ItemEvent e)\r
{\r
- viewport.setShowFullId(fullSeqId.getState());\r
+ viewport.setShowJVSuffix(seqLimits.getState());\r
alignPanel.fontChanged();\r
alignPanel.repaint();\r
}\r
\r
+\r
protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setColourText(colourTextMenuItem.getState());\r
\r
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
- {\r
- annotationPanelMenuItem.setState(false);\r
- return;\r
- }\r
viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
}\r
\r
public void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
+ new UserDefinedColours(alignPanel, null);\r
}\r
\r
public void PIDColour_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
HistoryItem.SORT));\r
- AlignmentSorter.sortByID(viewport.getAlignment());\r
+ AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);\r
alignPanel.repaint();\r
}\r
\r
if (viewport.getSelectionGroup().getSize() > 1)\r
{\r
Frame frame = new Frame();\r
- frame.add(new PairwiseAlignPanel(viewport));\r
+ frame.add(new PairwiseAlignPanel(alignPanel));\r
jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
}\r
}\r
\r
public void PCAMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ //are the sequences aligned?\r
+ if (!viewport.alignment.isAligned())\r
+ {\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+ alignPanel.repaint();\r
+ }\r
\r
if ( (viewport.getSelectionGroup() != null &&\r
viewport.getSelectionGroup().getSize() < 4 &&\r
\r
try\r
{\r
- PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
- Frame frame = new Frame();\r
- frame.add(pcaPanel);\r
- jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
- 400, 400);\r
+ new PCAPanel(viewport);\r
}\r
catch (java.lang.OutOfMemoryError ex)\r
{\r
\r
protected void documentation_actionPerformed(ActionEvent e)\r
{\r
- jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
+ showURL("http://www.jalview.org/help.html");\r
}\r
\r
protected void about_actionPerformed(ActionEvent e)\r
jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
\r
}\r
+\r
+ /**\r
+ * Displays the given URL in a new browser window\r
+ *\r
+ * @param url URL to display in browser window.\r
+ * <br>New window will be named "HELP_WINDOW"\r
+ */\r
+ public void showURL(String url)\r
+ {\r
+ showURL(url, "HELP");\r
+ }\r
+\r
+ public void showURL(String url, String target)\r
+ {\r
+ if (applet == null)\r
+ {\r
+ System.out.println("Not running as applet - no browser available.");\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ applet.getAppletContext().showDocument(new java.net.URL(url),\r
+ target);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ //////////////////////////////////////////////////////////////////////////////////\r
+ //JBuilder Graphics here\r
+\r
+ protected MenuBar alignFrameMenuBar = new MenuBar();\r
+ protected Menu fileMenu = new Menu();\r
+ protected MenuItem closeMenuItem = new MenuItem();\r
+ protected Menu editMenu = new Menu();\r
+ protected Menu viewMenu = new Menu();\r
+ protected Menu colourMenu = new Menu();\r
+ protected Menu calculateMenu = new Menu();\r
+ protected MenuItem selectAllSequenceMenuItem = new MenuItem();\r
+ protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
+ protected MenuItem invertSequenceMenuItem = new MenuItem();\r
+ protected MenuItem remove2LeftMenuItem = new MenuItem();\r
+ protected MenuItem remove2RightMenuItem = new MenuItem();\r
+ protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+ protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+ protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
+ protected MenuItem sortIDMenuItem = new MenuItem();\r
+ protected MenuItem sortGroupMenuItem = new MenuItem();\r
+ protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
+ protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+ protected MenuItem PCAMenuItem = new MenuItem();\r
+ protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+ protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ public Label statusBar = new Label();\r
+ protected Menu outputTextboxMenu = new Menu();\r
+ protected MenuItem clustalColour = new MenuItem();\r
+ protected MenuItem zappoColour = new MenuItem();\r
+ protected MenuItem taylorColour = new MenuItem();\r
+ protected MenuItem hydrophobicityColour = new MenuItem();\r
+ protected MenuItem helixColour = new MenuItem();\r
+ protected MenuItem strandColour = new MenuItem();\r
+ protected MenuItem turnColour = new MenuItem();\r
+ protected MenuItem buriedColour = new MenuItem();\r
+ protected MenuItem userDefinedColour = new MenuItem();\r
+ protected MenuItem PIDColour = new MenuItem();\r
+ protected MenuItem BLOSUM62Colour = new MenuItem();\r
+ MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+ MenuItem overviewMenuItem = new MenuItem();\r
+ protected MenuItem undoMenuItem = new MenuItem();\r
+ protected MenuItem redoMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+ MenuItem noColourmenuItem = new MenuItem();\r
+ protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+ MenuItem findMenuItem = new MenuItem();\r
+ Menu searchMenu = new Menu();\r
+ protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+ protected MenuItem nucleotideColour = new MenuItem();\r
+ MenuItem deleteGroups = new MenuItem();\r
+ MenuItem delete = new MenuItem();\r
+ MenuItem copy = new MenuItem();\r
+ MenuItem cut = new MenuItem();\r
+ Menu Menu1 = new Menu();\r
+ MenuItem pasteNew = new MenuItem();\r
+ MenuItem pasteThis = new MenuItem();\r
+ protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+ protected MenuItem font = new MenuItem();\r
+ protected CheckboxMenuItem dbref = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+ MenuItem modifyPID = new MenuItem();\r
+ MenuItem modifyConservation = new MenuItem();\r
+ protected Menu sortByTreeMenu = new Menu();\r
+ Menu sort = new Menu();\r
+ Menu calculate = new Menu();\r
+ MenuItem inputText = new MenuItem();\r
+ Menu helpMenu = new Menu();\r
+ MenuItem documentation = new MenuItem();\r
+ MenuItem about = new MenuItem();\r
+ protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
+\r
+ private void jbInit() throws Exception {\r
+\r
+ setMenuBar(alignFrameMenuBar);\r
+\r
+ MenuItem item;\r
+\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)\r
+ {\r
+\r
+ item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
+ elementAt(\r
+ i));\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+\r
+\r
+ fileMenu.setLabel("File");\r
+ closeMenuItem.setLabel("Close");\r
+ closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ closeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ editMenu.setLabel("Edit");\r
+ viewMenu.setLabel("View");\r
+ colourMenu.setLabel("Colour");\r
+ calculateMenu.setLabel("Calculate");\r
+ selectAllSequenceMenuItem.setLabel("Select all");\r
+ selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ selectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ deselectAllSequenceMenuItem.setLabel("Deselect All");\r
+ deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ deselectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ invertSequenceMenuItem.setLabel("Invert Selection");\r
+ invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ invertSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2LeftMenuItem.setLabel("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ remove2LeftMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2RightMenuItem.setLabel("Remove Right");\r
+ remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ remove2RightMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeGappedColumnMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeAllGapsMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ viewBoxesMenuItem.setLabel("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ viewBoxesMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ viewTextMenuItem.setLabel("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ viewTextMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortPairwiseMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortIDMenuItem.setLabel("by ID");\r
+ sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortIDMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortGroupMenuItem.setLabel("by Group");\r
+ sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortGroupMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeRedundancyMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pairwiseAlignmentMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ PCAMenuItem.setLabel("Principal Component Analysis");\r
+ PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ PCAMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ averageDistanceTreeMenuItem.setLabel(\r
+ "Average Distance Using % Identity");\r
+ averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ averageDistanceTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
+ neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ neighbourTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setBackground(Color.white);\r
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setText("Status bar");\r
+ outputTextboxMenu.setLabel("Output to Textbox");\r
+ clustalColour.setLabel("Clustalx");\r
+\r
+ clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ clustalColour_actionPerformed(e);\r
+ }\r
+ });\r
+ zappoColour.setLabel("Zappo");\r
+ zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ zappoColour_actionPerformed(e);\r
+ }\r
+ });\r
+ taylorColour.setLabel("Taylor");\r
+ taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ taylorColour_actionPerformed(e);\r
+ }\r
+ });\r
+ hydrophobicityColour.setLabel("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ hydrophobicityColour_actionPerformed(e);\r
+ }\r
+ });\r
+ helixColour.setLabel("Helix Propensity");\r
+ helixColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ helixColour_actionPerformed(e);\r
+ }\r
+ });\r
+ strandColour.setLabel("Strand Propensity");\r
+ strandColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ strandColour_actionPerformed(e);\r
+ }\r
+ });\r
+ turnColour.setLabel("Turn Propensity");\r
+ turnColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ turnColour_actionPerformed(e);\r
+ }\r
+ });\r
+ buriedColour.setLabel("Buried Index");\r
+ buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ buriedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ userDefinedColour.setLabel("User Defined...");\r
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ userDefinedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ PIDColour.setLabel("Percentage Identity");\r
+ PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ PIDColour_actionPerformed(e);\r
+ }\r
+ });\r
+ BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ BLOSUM62Colour_actionPerformed(e);\r
+ }\r
+ });\r
+ avDistanceTreeBlosumMenuItem.setLabel(\r
+ "Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ avTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
+ njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ njTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ annotationPanelMenuItem.setActionCommand("");\r
+ annotationPanelMenuItem.setState(true);\r
+ annotationPanelMenuItem.setLabel("Show Annotations");\r
+ annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ annotationPanelMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ colourTextMenuItem.setLabel("Colour Text");\r
+ colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ colourTextMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ overviewMenuItem.setLabel("Overview Window");\r
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ overviewMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ undoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ redoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ conservationMenuItem.setLabel("by Conservation");\r
+ conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ conservationMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ noColourmenuItem.setLabel("None");\r
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ noColourmenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ wrapMenuItem.setLabel("Wrap");\r
+ wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ wrapMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ renderGapsMenuItem.setLabel("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ renderGapsMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ findMenuItem.setLabel("Find...");\r
+ findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ findMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ searchMenu.setLabel("Search");\r
+\r
+ abovePIDThreshold.setLabel("Above Identity Threshold");\r
+ abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ abovePIDThreshold_actionPerformed(null);\r
+ }\r
+ });\r
+ nucleotideColour.setLabel("Nucleotide");\r
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ nucleotideColour_actionPerformed(e);\r
+ }\r
+ });\r
+ deleteGroups.setLabel("Undefine Groups");\r
+ deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ deleteGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ copy.setLabel("Copy");\r
+ copy.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ copy_actionPerformed(e);\r
+ }\r
+ });\r
+ cut.setLabel("Cut");\r
+ cut.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ delete.setLabel("Delete");\r
+ delete.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ delete_actionPerformed(e);\r
+ }\r
+ });\r
+ Menu1.setLabel("Paste");\r
+ pasteNew.setLabel("To New Alignment");\r
+ pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pasteNew_actionPerformed(e);\r
+ }\r
+ });\r
+ pasteThis.setLabel("Add To This Alignment");\r
+ pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pasteThis_actionPerformed(e);\r
+ }\r
+ });\r
+ applyToAllGroups.setLabel("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ applyToAllGroups_actionPerformed(null);\r
+ }\r
+ });\r
+ font.setLabel("Font...");\r
+ font.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ font_actionPerformed(e);\r
+ }\r
+ });\r
+ dbref.setLabel("ShowSequence DB Refs");\r
+ dbref.setActionCommand("");\r
+ dbref.setState(true);\r
+ dbref.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ dbref_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleAbove.setLabel("Scale Above");\r
+ scaleAbove.setState(true);\r
+ scaleAbove.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ scaleAbove_actionPerformed(null);\r
+ }\r
+ });\r
+ scaleLeft.setEnabled(false);\r
+ scaleLeft.setState(true);\r
+ scaleLeft.setLabel("Scale Left");\r
+ scaleLeft.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ scaleLeft_actionPerformed(null);\r
+ }\r
+ });\r
+ scaleRight.setEnabled(false);\r
+ scaleRight.setState(true);\r
+ scaleRight.setLabel("Scale Right");\r
+ scaleRight.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ scaleRight_actionPerformed(null);\r
+ }\r
+ });\r
+ modifyPID.setLabel("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ modifyPID_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyConservation.setLabel("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ modifyConservation_actionPerformed(e);\r
+ }\r
+ });\r
+ sortByTreeMenu.setLabel("By Tree Order");\r
+ sort.setLabel("Sort");\r
+ calculate.setLabel("Calculate Tree");\r
+ inputText.setLabel("Input from textbox");\r
+ inputText.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ inputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ helpMenu.setLabel("Help");\r
+ documentation.setLabel("Documentation");\r
+ documentation.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ documentation_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ about.setLabel("About...");\r
+ about.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ about_actionPerformed(e);\r
+ }\r
+ });\r
+ seqLimits.setState(true);\r
+ seqLimits.setLabel("Show Sequence Limits");\r
+ seqLimits.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ seqLimits_itemStateChanged(e);\r
+ }\r
+ });\r
+\r
+ alignFrameMenuBar.add(fileMenu);\r
+ alignFrameMenuBar.add(editMenu);\r
+ alignFrameMenuBar.add(searchMenu);\r
+ alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(colourMenu);\r
+ alignFrameMenuBar.add(calculateMenu);\r
+ alignFrameMenuBar.add(helpMenu);\r
+ fileMenu.add(inputText);\r
+ fileMenu.add(outputTextboxMenu);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(closeMenuItem);\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(Menu1);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
+ editMenu.add(selectAllSequenceMenuItem);\r
+ editMenu.add(deselectAllSequenceMenuItem);\r
+ editMenu.add(invertSequenceMenuItem);\r
+ editMenu.add(deleteGroups);\r
+ editMenu.addSeparator();\r
+ editMenu.add(remove2LeftMenuItem);\r
+ editMenu.add(remove2RightMenuItem);\r
+ editMenu.add(removeGappedColumnMenuItem);\r
+ editMenu.add(removeAllGapsMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ searchMenu.add(findMenuItem);\r
+ viewMenu.add(font);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(dbref);\r
+ viewMenu.add(seqLimits);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(wrapMenuItem);\r
+ viewMenu.add(scaleAbove);\r
+ viewMenu.add(scaleLeft);\r
+ viewMenu.add(scaleRight);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(viewBoxesMenuItem);\r
+ viewMenu.add(viewTextMenuItem);\r
+ viewMenu.add(colourTextMenuItem);\r
+ viewMenu.add(renderGapsMenuItem);\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideColour);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(conservationMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(pairwiseAlignmentMenuItem);\r
+ calculateMenu.add(PCAMenuItem);\r
+ this.add(statusBar, BorderLayout.SOUTH);\r
+ Menu1.add(pasteNew);\r
+ Menu1.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortByTreeMenu);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ helpMenu.add(documentation);\r
+ helpMenu.add(about);\r
+ }\r
}\r
+\r
git://source.jalview.org / jalview.git / blobdiff