\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 implements ActionListener,\r
+ ItemListener, KeyListener, MouseListener\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 AlignmentPanel alignPanel;\r
+ public AlignViewport viewport;\r
+ int NEW_WINDOW_WIDTH = 700;\r
+ int NEW_WINDOW_HEIGHT = 500;\r
jalview.bin.JalviewLite applet;\r
\r
\r
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
+ public AlignFrame(AlignmentI al,\r
+ jalview.bin.JalviewLite applet,\r
+ String title,\r
+ boolean embedded)\r
{\r
+ try{\r
+ jbInit();\r
+ }catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\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
+ annotationPanelMenuItem.setState(viewport.showAnnotation);\r
+\r
+ seqLimits.setState(viewport.showJVSuffix);\r
\r
if(applet!=null)\r
{\r
- String treeFile = applet.getParameter("treeFile");\r
- if (treeFile != null)\r
+ String param = applet.getParameter("sortBy");\r
+ if (param != 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
+ if (param.equalsIgnoreCase("Id"))\r
+ sortIDMenuItem_actionPerformed();\r
+ else if (param.equalsIgnoreCase("Pairwise Identity"))\r
+ sortPairwiseMenuItem_actionPerformed();\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
+ param = applet.getParameter("wrap");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("true"))\r
{\r
- ex.printStackTrace();\r
+ wrapMenuItem.setState(true);\r
+ wrapMenuItem_actionPerformed();\r
}\r
}\r
\r
- String param = applet.getParameter("sortBy");\r
- if (param != null)\r
+ try\r
{\r
- if (param.equalsIgnoreCase("Id"))\r
- sortIDMenuItem_actionPerformed(null);\r
- else if (param.equalsIgnoreCase("Pairwise Identity"))\r
- sortPairwiseMenuItem_actionPerformed(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
+ int height = Integer.parseInt(param);\r
+ NEW_WINDOW_HEIGHT = height;\r
+ }\r
}\r
+ catch (Exception ex)\r
+ {}\r
+\r
}\r
\r
- this.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent e)\r
- {\r
- closeMenuItem_actionPerformed(null);\r
- }\r
- });\r
+ //Some JVMS send keyevents to Top frame or lowest panel,\r
+ //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
+ this.addKeyListener(this);\r
+ alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
+ alignPanel.idPanel.idCanvas.addKeyListener(this);\r
\r
viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
{\r
}\r
}\r
});\r
+\r
+\r
+ if(embedded)\r
+ {\r
+ setEmbedded();\r
+ }\r
+ else\r
+ {\r
+ add(alignPanel, BorderLayout.CENTER);\r
+ jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
+ }\r
+ alignPanel.validate();\r
+ alignPanel.repaint();\r
+ }\r
+ public AlignViewport getAlignViewport()\r
+ {\r
+ return viewport;\r
+ }\r
+\r
+ public SeqCanvas getSeqcanvas()\r
+ {\r
+ return alignPanel.seqPanel.seqCanvas;\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param String DOCUMENT ME!\r
+ */\r
+\r
+ public void parseFeaturesFile(String file, String type)\r
+ {\r
+ Hashtable featureLinks = new Hashtable();\r
+ boolean featuresFile = false;\r
+ try{\r
+ featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,\r
+ alignPanel.seqPanel.seqCanvas.\r
+ getFeatureRenderer().featureColours,\r
+ featureLinks,\r
+ true);\r
+ }\r
+ catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ if(featuresFile)\r
+ {\r
+ if(featureLinks.size()>0)\r
+ alignPanel.seqPanel.seqCanvas\r
+ .getFeatureRenderer().featureLinks = featureLinks;\r
+ viewport.showSequenceFeatures = true;\r
+ sequenceFeatures.setState(true);\r
+ alignPanel.repaint();\r
+ }\r
+\r
}\r
\r
- public void inputText_actionPerformed(ActionEvent e)\r
+\r
+ public void keyPressed(KeyEvent evt)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
+ if (viewport.cursorMode\r
+ && evt.getKeyCode() >= KeyEvent.VK_0\r
+ && evt.getKeyCode() <= KeyEvent.VK_9)\r
+ {\r
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
+ }\r
+\r
+ switch (evt.getKeyCode())\r
+ {\r
+ case 27: // escape key\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ break;\r
+ case KeyEvent.VK_X:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_C:\r
+ if (viewport.cursorMode && !evt.isControlDown())\r
+ {\r
+ alignPanel.seqPanel.setCursorColumn();\r
+ }\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_V:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ paste(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_A:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_DOWN:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0,1);\r
+ }\r
+ else\r
+ moveSelectedSequences(false);\r
+ break;\r
+\r
+ case KeyEvent.VK_UP:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0,-1);\r
+ }\r
+ else\r
+ moveSelectedSequences(true);\r
+ break;\r
+\r
+ case KeyEvent.VK_LEFT:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(-1,0);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_RIGHT:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(1,0);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_SPACE:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_DELETE:\r
+ case KeyEvent.VK_BACK_SPACE:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());\r
+ }\r
+ else\r
+ {\r
+ cut_actionPerformed();\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_S:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRow();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_P:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorPosition();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_ENTER:\r
+ case KeyEvent.VK_COMMA:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRowAndColumn();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Q:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_M:\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_F2:\r
+ viewport.cursorMode = ! viewport.cursorMode;\r
+ statusBar.setText("Keyboard editing mode is "+\r
+ (viewport.cursorMode ? "on" : "off"));\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
+ }\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ break;\r
+\r
+ case KeyEvent.VK_F:\r
+ if (evt.isControlDown())\r
+ {\r
+ findMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+ }\r
+ }\r
+ public void keyReleased(KeyEvent evt)\r
+ {}\r
+ public void keyTyped(KeyEvent evt)\r
+ {}\r
+\r
+public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if(evt.getSource()==colourTextMenuItem)\r
+ colourTextMenuItem_actionPerformed();\r
+ else if(evt.getSource()==wrapMenuItem)\r
+ wrapMenuItem_actionPerformed();\r
+ else if(evt.getSource()==scaleAbove)\r
+ scaleAbove_actionPerformed();\r
+ else if(evt.getSource()==scaleLeft)\r
+ scaleLeft_actionPerformed();\r
+ else if(evt.getSource()==scaleRight)\r
+ scaleRight_actionPerformed();\r
+ else if(evt.getSource()==seqLimits)\r
+ seqLimits_itemStateChanged();\r
+ else if(evt.getSource()==viewBoxesMenuItem)\r
+ viewBoxesMenuItem_actionPerformed();\r
+ else if(evt.getSource()==viewTextMenuItem)\r
+ viewTextMenuItem_actionPerformed();\r
+ else if(evt.getSource()==renderGapsMenuItem)\r
+ renderGapsMenuItem_actionPerformed();\r
+ else if(evt.getSource()==annotationPanelMenuItem)\r
+ annotationPanelMenuItem_actionPerformed();\r
+ else if(evt.getSource()==sequenceFeatures)\r
+ {\r
+ viewport.showSequenceFeatures(sequenceFeatures.getState());\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ else if(evt.getSource()==conservationMenuItem)\r
+ conservationMenuItem_actionPerformed();\r
+ else if(evt.getSource()==abovePIDThreshold)\r
+ abovePIDThreshold_actionPerformed();\r
+ else if(evt.getSource()==applyToAllGroups)\r
+ applyToAllGroups_actionPerformed();\r
+ else if(evt.getSource()==autoCalculate)\r
+ viewport.autocalculateConsensus = autoCalculate.getState();\r
+ }\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ if(evt.getSource()==inputText)\r
+ inputText_actionPerformed();\r
+ else if(evt.getSource()==loadTree)\r
+ loadTree_actionPerformed();\r
+ else if(evt.getSource()==loadApplication)\r
+ launchFullApplication();\r
+ else if(evt.getSource()==closeMenuItem)\r
+ closeMenuItem_actionPerformed();\r
+ else if(evt.getSource()==copy)\r
+ copy_actionPerformed();\r
+ else if(evt.getSource()==undoMenuItem)\r
+ undoMenuItem_actionPerformed();\r
+ else if(evt.getSource()==redoMenuItem)\r
+ redoMenuItem_actionPerformed();\r
+ else if(evt.getSource()==inputText)\r
+ inputText_actionPerformed();\r
+ else if(evt.getSource()==closeMenuItem)\r
+ closeMenuItem_actionPerformed();\r
+ else if(evt.getSource()==undoMenuItem)\r
+ undoMenuItem_actionPerformed();\r
+ else if(evt.getSource()==redoMenuItem)\r
+ redoMenuItem_actionPerformed();\r
+ else if(evt.getSource()==copy)\r
+ copy_actionPerformed();\r
+ else if(evt.getSource()==pasteNew)\r
+ pasteNew_actionPerformed();\r
+ else if(evt.getSource()==pasteThis)\r
+ pasteThis_actionPerformed();\r
+ else if(evt.getSource()==cut)\r
+ cut_actionPerformed();\r
+ else if(evt.getSource()==delete)\r
+ delete_actionPerformed();\r
+ else if(evt.getSource()==deleteGroups)\r
+ deleteGroups_actionPerformed();\r
+ else if(evt.getSource()==selectAllSequenceMenuItem)\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ else if(evt.getSource()==deselectAllSequenceMenuItem)\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ else if(evt.getSource()==invertSequenceMenuItem)\r
+ invertSequenceMenuItem_actionPerformed();\r
+ else if(evt.getSource()==remove2LeftMenuItem)\r
+ remove2LeftMenuItem_actionPerformed();\r
+ else if(evt.getSource()==remove2RightMenuItem)\r
+ remove2RightMenuItem_actionPerformed();\r
+ else if(evt.getSource()==removeGappedColumnMenuItem)\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ else if(evt.getSource()==removeAllGapsMenuItem)\r
+ removeAllGapsMenuItem_actionPerformed();\r
+ else if(evt.getSource()==findMenuItem)\r
+ findMenuItem_actionPerformed();\r
+ else if(evt.getSource()==font)\r
+ font_actionPerformed();\r
+ else if(evt.getSource()==featureSettings)\r
+ featureSettings_actionPerformed();\r
+ else if(evt.getSource()==overviewMenuItem)\r
+ overviewMenuItem_actionPerformed();\r
+ else if(evt.getSource()==noColourmenuItem)\r
+ noColourmenuItem_actionPerformed();\r
+ else if(evt.getSource()==clustalColour)\r
+ clustalColour_actionPerformed();\r
+ else if(evt.getSource()==zappoColour)\r
+ zappoColour_actionPerformed();\r
+ else if(evt.getSource()==taylorColour)\r
+ taylorColour_actionPerformed();\r
+ else if(evt.getSource()==hydrophobicityColour)\r
+ hydrophobicityColour_actionPerformed();\r
+ else if(evt.getSource()==helixColour)\r
+ helixColour_actionPerformed();\r
+ else if(evt.getSource()==strandColour)\r
+ strandColour_actionPerformed();\r
+ else if(evt.getSource()==turnColour)\r
+ turnColour_actionPerformed();\r
+ else if(evt.getSource()==buriedColour)\r
+ buriedColour_actionPerformed();\r
+ else if(evt.getSource()==nucleotideColour)\r
+ nucleotideColour_actionPerformed();\r
+ else if(evt.getSource()==modifyPID)\r
+ modifyPID_actionPerformed();\r
+ else if(evt.getSource()==modifyConservation)\r
+ modifyConservation_actionPerformed();\r
+ else if(evt.getSource()==userDefinedColour)\r
+ userDefinedColour_actionPerformed();\r
+ else if(evt.getSource()==PIDColour)\r
+ PIDColour_actionPerformed();\r
+ else if(evt.getSource()==BLOSUM62Colour)\r
+ BLOSUM62Colour_actionPerformed();\r
+ else if(evt.getSource()==annotationColour)\r
+ new AnnotationColourChooser(viewport, alignPanel);\r
+ else if(evt.getSource()==sortPairwiseMenuItem)\r
+ sortPairwiseMenuItem_actionPerformed();\r
+ else if(evt.getSource()==sortIDMenuItem)\r
+ sortIDMenuItem_actionPerformed();\r
+ else if(evt.getSource()==sortGroupMenuItem)\r
+ sortGroupMenuItem_actionPerformed();\r
+ else if(evt.getSource()==removeRedundancyMenuItem)\r
+ removeRedundancyMenuItem_actionPerformed();\r
+ else if(evt.getSource()==pairwiseAlignmentMenuItem)\r
+ pairwiseAlignmentMenuItem_actionPerformed();\r
+ else if(evt.getSource()==PCAMenuItem)\r
+ PCAMenuItem_actionPerformed();\r
+ else if(evt.getSource()==averageDistanceTreeMenuItem)\r
+ averageDistanceTreeMenuItem_actionPerformed();\r
+ else if(evt.getSource()==neighbourTreeMenuItem)\r
+ neighbourTreeMenuItem_actionPerformed();\r
+ else if(evt.getSource()==njTreeBlosumMenuItem)\r
+ njTreeBlosumMenuItem_actionPerformed();\r
+ else if(evt.getSource()==avDistanceTreeBlosumMenuItem)\r
+ avTreeBlosumMenuItem_actionPerformed();\r
+ else if(evt.getSource()==documentation)\r
+ documentation_actionPerformed();\r
+ else if(evt.getSource()==about)\r
+ about_actionPerformed();\r
+\r
+ }\r
+\r
+ public void inputText_actionPerformed()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\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, applet);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\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.showJVSuffix));\r
+ }\r
+\r
+ void launchFullApplication()\r
+ {\r
+ StringBuffer url = new StringBuffer("http://bug.compbio.dundee.ac.uk:8080/Jalview/jalview?");\r
+\r
+ url.append("open="+\r
+ appendProtocol( applet.getParameter("file") ) );\r
+\r
+ if(applet.getParameter("features")!=null)\r
+ {\r
+ url.append( "&features=" );\r
+ url.append( appendProtocol( applet.getParameter("features") ) );\r
+ }\r
+\r
+ if(applet.getParameter("defaultColour")!=null)\r
+ {\r
+ url.append("&colour=" +\r
+ removeWhiteSpace(applet.getParameter("defaultColour"))\r
+ );\r
+ }\r
+\r
+ if(applet.getParameter("userDefinedColour")!=null)\r
+ {\r
+ url.append( "&colour=" +\r
+ removeWhiteSpace( applet.getParameter("userDefinedColour") )\r
+ );\r
+ }\r
+\r
+ showURL(url.toString(), "FULL_APP");\r
+ }\r
+\r
+\r
+ String removeWhiteSpace(String colour)\r
+ {\r
+ StringBuffer sb = new StringBuffer();\r
+ for (int i = 0; i < colour.length(); i++)\r
+ {\r
+ if (Character.isWhitespace(colour.charAt(i)))\r
+ sb.append("%20");\r
+ else\r
+ sb.append(colour.charAt(i));\r
+ }\r
+\r
+ return sb.toString();\r
+ }\r
+\r
+\r
+ String appendProtocol(String url)\r
+ {\r
+ try{\r
+ new URL(url);\r
+ }catch(java.net.MalformedURLException ex)\r
+ {\r
+ url = applet.getCodeBase()+url;\r
+ }\r
+ return url;\r
}\r
\r
- public void closeMenuItem_actionPerformed(ActionEvent e)\r
+ public void closeMenuItem_actionPerformed()\r
{\r
PaintRefresher.components.remove(viewport.alignment);\r
- dispose();\r
if(PaintRefresher.components.size()==0 && applet==null)\r
System.exit(0);\r
+\r
+ this.dispose();\r
}\r
\r
Stack historyList = new Stack();\r
updateEditMenuBar();\r
}\r
\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ protected void undoMenuItem_actionPerformed()\r
{\r
HistoryItem hi = (HistoryItem) historyList.pop();\r
redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ protected void redoMenuItem_actionPerformed()\r
{\r
HistoryItem hi = (HistoryItem) redoList.pop();\r
restoreHistoryItem(hi);\r
// used by undo and redo\r
void restoreHistoryItem(HistoryItem hi)\r
{\r
- if (hi.getType() == HistoryItem.SORT)\r
- {\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
- {\r
- viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
- elementAt(i), i);\r
- }\r
- }\r
- else\r
- {\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
- {\r
- SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
- if (restore.getLength() == 0)\r
- {\r
- // log.System.out.println(hi.getHidden().elementAt(i));\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
- viewport.alignment.getSequences().insertElementAt(\r
- restore,\r
- hi.getAlignIndex(i));\r
- }\r
- else\r
- {\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
- }\r
- }\r
- if (hi.getType() == HistoryItem.PASTE)\r
- {\r
- for (int i = viewport.alignment.getHeight() - 1;\r
- i > hi.getSequences().size() - 1; i--)\r
- {\r
- viewport.alignment.deleteSequence(i);\r
- }\r
- }\r
- }\r
+ hi.restore();\r
\r
updateEditMenuBar();\r
\r
for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.sequences.contains(seq))\r
+ if (!sg.getSequences(false).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(false).contains(temp))\r
{\r
continue;\r
}\r
for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.sequences.contains(seq))\r
+ if (!sg.getSequences(true).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(true).contains(temp))\r
{\r
continue;\r
}\r
}\r
\r
StringBuffer copiedSequences;\r
- protected void copy_actionPerformed(ActionEvent e)\r
+ protected void copy_actionPerformed()\r
{\r
if (viewport.getSelectionGroup() == null)\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
copiedSequences = new StringBuffer();\r
Hashtable orderedSeqs = new Hashtable();\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.alignment.findIndex(seq);\r
int index = 0, startRes, endRes;\r
char ch;\r
\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
SequenceI seq = null;\r
\r
\r
}\r
\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
+ protected void pasteNew_actionPerformed()\r
{\r
paste(true);\r
}\r
\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
+ protected void pasteThis_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
HistoryItem.PASTE));\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),\r
+ applet,\r
+ newtitle,\r
+ false);\r
+\r
jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
NEW_WINDOW_HEIGHT);\r
}\r
\r
}\r
\r
- protected void cut_actionPerformed(ActionEvent e)\r
+ protected void cut_actionPerformed()\r
{\r
- copy_actionPerformed(null);\r
- delete_actionPerformed(null);\r
+ copy_actionPerformed();\r
+ delete_actionPerformed();\r
}\r
\r
- protected void delete_actionPerformed(ActionEvent e)\r
+ protected void delete_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
HistoryItem.HIDE));\r
\r
SequenceGroup sg = viewport.getSelectionGroup();\r
boolean allSequences = false;\r
- if(sg.sequences.size()==viewport.alignment.getHeight())\r
+ if(sg.getSize(false)==viewport.alignment.getHeight())\r
allSequences = true;\r
\r
- for (int i = 0; i < sg.sequences.size(); i++)\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.getAlignment().findIndex(seq);\r
\r
}\r
\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ protected void deleteGroups_actionPerformed()\r
{\r
viewport.alignment.deleteAllGroups();\r
viewport.setSelectionGroup(null);\r
alignPanel.repaint();\r
}\r
\r
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ public void selectAllSequenceMenuItem_actionPerformed()\r
{\r
SequenceGroup sg = new SequenceGroup();\r
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
- public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ public void deselectAllSequenceMenuItem_actionPerformed()\r
{\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.keyboardNo1=null;\r
+ alignPanel.seqPanel.keyboardNo2=null;\r
+ }\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
+ alignPanel.idPanel.idCanvas.searchResults = null;\r
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
alignPanel.repaint();\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ public void invertSequenceMenuItem_actionPerformed()\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
+ public void remove2LeftMenuItem_actionPerformed()\r
{\r
ColumnSelection colSel = viewport.getColumnSelection();\r
if (colSel.size() > 0)\r
}\r
}\r
\r
- public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+ public void remove2RightMenuItem_actionPerformed()\r
{\r
ColumnSelection colSel = viewport.getColumnSelection();\r
if (colSel.size() > 0)\r
\r
}\r
\r
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
+ public void removeGappedColumnMenuItem_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
viewport.alignment,\r
viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
- public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
+ public void removeAllGapsMenuItem_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
HistoryItem.HIDE));\r
int start=0, end = viewport.alignment.getWidth();\r
\r
if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().sequences != null\r
- && viewport.getSelectionGroup().sequences.size()>0)\r
+ && viewport.getSelectionGroup().getSequences(false) != null\r
+ && viewport.getSelectionGroup().getSize(false)>0)\r
{\r
- seqs = viewport.getSelectionGroup().sequences;\r
+ seqs = viewport.getSelectionGroup().getSequences(true);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes()+1;\r
}\r
\r
public void alignmentChanged()\r
{\r
- viewport.updateConsensus();\r
- viewport.updateConservation ();\r
+ viewport.alignment.padGaps();\r
+ if(viewport.autocalculateConsensus)\r
+ {\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ }\r
+\r
resetAllColourSchemes();\r
if(alignPanel.overviewPanel!=null)\r
alignPanel.overviewPanel.updateOverviewImage();\r
+\r
+ viewport.alignment.adjustSequenceAnnotations();\r
alignPanel.repaint();\r
}\r
\r
SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
{\r
- ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
+ ((ClustalxColourScheme)sg.cs).resetClustalX(\r
+ sg.getSequences(true), sg.getWidth());\r
}\r
sg.recalcConservation();\r
}\r
\r
\r
\r
- public void findMenuItem_actionPerformed(ActionEvent e)\r
+ public void findMenuItem_actionPerformed()\r
{\r
- Finder finder = new Finder(alignPanel);\r
+ new Finder(alignPanel);\r
}\r
\r
- public void font_actionPerformed(ActionEvent e)\r
+ public void font_actionPerformed()\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
-\r
+ new FontChooser(alignPanel);\r
}\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
+\r
+ public void seqLimits_itemStateChanged()\r
{\r
- viewport.setShowFullId(fullSeqId.getState());\r
+ viewport.setShowJVSuffix(seqLimits.getState());\r
alignPanel.fontChanged();\r
alignPanel.repaint();\r
}\r
\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+\r
+ protected void colourTextMenuItem_actionPerformed()\r
{\r
viewport.setColourText(colourTextMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+ protected void wrapMenuItem_actionPerformed()\r
{\r
viewport.setWrapAlignment(wrapMenuItem.getState());\r
alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ protected void scaleAbove_actionPerformed()\r
{\r
viewport.setScaleAboveWrapped(scaleAbove.getState());\r
alignPanel.repaint();\r
}\r
\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ protected void scaleLeft_actionPerformed()\r
{\r
viewport.setScaleLeftWrapped(scaleLeft.getState());\r
alignPanel.repaint();\r
}\r
\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
+ protected void scaleRight_actionPerformed()\r
{\r
viewport.setScaleRightWrapped(scaleRight.getState());\r
alignPanel.repaint();\r
}\r
\r
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
+ public void viewBoxesMenuItem_actionPerformed()\r
{\r
viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
- public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
+ public void viewTextMenuItem_actionPerformed()\r
{\r
viewport.setShowText(viewTextMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ protected void renderGapsMenuItem_actionPerformed()\r
{\r
viewport.setRenderGaps(renderGapsMenuItem.getState());\r
alignPanel.repaint();\r
}\r
\r
- public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
+ public void annotationPanelMenuItem_actionPerformed()\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 overviewMenuItem_actionPerformed(ActionEvent e)\r
+ public void featureSettings_actionPerformed()\r
+ {\r
+ new FeatureSettings(viewport, alignPanel);\r
+ }\r
+\r
+ public void overviewMenuItem_actionPerformed()\r
{\r
if (alignPanel.overviewPanel != null)\r
{\r
\r
}\r
\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ protected void noColourmenuItem_actionPerformed()\r
{\r
changeColour(null);\r
}\r
\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
+ public void clustalColour_actionPerformed()\r
{\r
abovePIDThreshold.setState(false);\r
changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
viewport.alignment.getWidth()));\r
}\r
\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
+ public void zappoColour_actionPerformed()\r
{\r
changeColour(new ZappoColourScheme());\r
}\r
\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
+ public void taylorColour_actionPerformed()\r
{\r
changeColour(new TaylorColourScheme());\r
}\r
\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+ public void hydrophobicityColour_actionPerformed()\r
{\r
changeColour(new HydrophobicColourScheme());\r
}\r
\r
- public void helixColour_actionPerformed(ActionEvent e)\r
+ public void helixColour_actionPerformed()\r
{\r
changeColour(new HelixColourScheme());\r
}\r
\r
- public void strandColour_actionPerformed(ActionEvent e)\r
+ public void strandColour_actionPerformed()\r
{\r
changeColour(new StrandColourScheme());\r
}\r
\r
- public void turnColour_actionPerformed(ActionEvent e)\r
+ public void turnColour_actionPerformed()\r
{\r
changeColour(new TurnColourScheme());\r
}\r
\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
+ public void buriedColour_actionPerformed()\r
{\r
changeColour(new BuriedColourScheme());\r
}\r
\r
- public void nucleotideColour_actionPerformed(ActionEvent e)\r
+ public void nucleotideColour_actionPerformed()\r
{\r
changeColour(new NucleotideColourScheme());\r
}\r
\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+ protected void applyToAllGroups_actionPerformed()\r
{\r
viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
}\r
}\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
}\r
else\r
{\r
|| cs instanceof Blosum62ColourScheme)\r
{\r
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
}\r
else\r
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
+ sg.getSequences(true), 0,\r
viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
\r
\r
\r
- protected void modifyPID_actionPerformed(ActionEvent e)\r
+ protected void modifyPID_actionPerformed()\r
{\r
if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
{\r
}\r
}\r
\r
- protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ protected void modifyConservation_actionPerformed()\r
{\r
if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
{\r
}\r
}\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_actionPerformed()\r
{\r
viewport.setConservationSelected(conservationMenuItem.getState());\r
\r
\r
changeColour(viewport.getGlobalColourScheme());\r
\r
- modifyConservation_actionPerformed(null);\r
+ modifyConservation_actionPerformed();\r
}\r
\r
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ public void abovePIDThreshold_actionPerformed()\r
{\r
viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
\r
\r
changeColour(viewport.getGlobalColourScheme());\r
\r
- modifyPID_actionPerformed(null);\r
+ modifyPID_actionPerformed();\r
}\r
\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
+ public void userDefinedColour_actionPerformed()\r
{\r
- UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
+ new UserDefinedColours(alignPanel, null);\r
}\r
\r
- public void PIDColour_actionPerformed(ActionEvent e)\r
+ public void PIDColour_actionPerformed()\r
{\r
changeColour(new PIDColourScheme());\r
}\r
\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ public void BLOSUM62Colour_actionPerformed()\r
{\r
changeColour(new Blosum62ColourScheme());\r
}\r
\r
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+ public void sortPairwiseMenuItem_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
HistoryItem.SORT));\r
alignPanel.repaint();\r
}\r
\r
- public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ public void sortIDMenuItem_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
HistoryItem.SORT));\r
alignPanel.repaint();\r
}\r
\r
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+ public void sortGroupMenuItem_actionPerformed()\r
{\r
addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
HistoryItem.SORT));\r
\r
}\r
\r
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ public void removeRedundancyMenuItem_actionPerformed()\r
{\r
- RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
- Frame frame = new Frame();\r
- frame.add(sp);\r
- jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
- 400, 120);\r
-\r
+ new RedundancyPanel(alignPanel);\r
}\r
\r
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+ public void pairwiseAlignmentMenuItem_actionPerformed()\r
{\r
- if (viewport.getSelectionGroup().getSize() > 1)\r
+ if (viewport.getSelectionGroup().getSize(false) > 1)\r
{\r
Frame frame = new Frame();\r
frame.add(new PairwiseAlignPanel(alignPanel));\r
}\r
}\r
\r
- public void PCAMenuItem_actionPerformed(ActionEvent e)\r
+ public void PCAMenuItem_actionPerformed()\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
- viewport.getSelectionGroup().getSize() > 0)\r
+ viewport.getSelectionGroup().getSize(false) < 4 &&\r
+ viewport.getSelectionGroup().getSize(false) > 0)\r
|| viewport.getAlignment().getHeight() < 4)\r
{\r
return;\r
\r
try\r
{\r
- PCAPanel pcaPanel = new PCAPanel(viewport);\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
}\r
\r
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+ public void averageDistanceTreeMenuItem_actionPerformed()\r
{\r
NewTreePanel("AV", "PID", "Average distance tree using PID");\r
}\r
\r
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+ public void neighbourTreeMenuItem_actionPerformed()\r
{\r
NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
}\r
\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ protected void njTreeBlosumMenuItem_actionPerformed()\r
{\r
NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
}\r
\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ protected void avTreeBlosumMenuItem_actionPerformed()\r
{\r
NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
}\r
\r
final TreePanel tp;\r
if (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize() > 3)\r
+ viewport.getSelectionGroup().getSize(false) > 3)\r
{\r
- tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
+ tp = new TreePanel(viewport,\r
+ viewport.getSelectionGroup().getSequences(false),\r
+ type,\r
pwType,\r
0, viewport.alignment.getWidth());\r
}\r
jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
}\r
\r
+ void loadTree_actionPerformed()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ cap.setText("Paste your Newick tree file here.");\r
+ cap.treeImport = true;\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
+ }\r
+\r
+ public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
+ {\r
+ TreePanel tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(),\r
+ tree, "From File - ", treeFile);\r
+ jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
+ addTreeMenuItem(tp, treeFile);\r
+ }\r
+\r
void addTreeMenuItem(final TreePanel treePanel, String title)\r
{\r
final MenuItem item = new MenuItem(title);\r
sortByTreeMenu.add(item);\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void actionPerformed(ActionEvent evt)\r
{\r
addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
HistoryItem.SORT));\r
});\r
}\r
\r
- protected void documentation_actionPerformed(ActionEvent e)\r
+ protected void documentation_actionPerformed()\r
{\r
- jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
+ showURL("http://www.jalview.org/help.html", "HELP");\r
}\r
\r
- protected void about_actionPerformed(ActionEvent e)\r
+ protected void about_actionPerformed()\r
{\r
\r
class AboutPanel extends Canvas\r
g.drawString("If you use JalView, please cite:", x, y += fh + 8);\r
g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
x, y += fh);\r
- g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);\r
+ g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);\r
}\r
}\r
\r
jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
\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
+ System.out.println("Show url: "+url);\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("File");\r
+ protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
+ protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
+ protected MenuItem closeMenuItem = new MenuItem("Close");\r
+ protected Menu editMenu = new Menu("Edit");\r
+ protected Menu viewMenu = new Menu("View");\r
+ protected Menu colourMenu = new Menu("Colour");\r
+ protected Menu calculateMenu = new Menu("Calculate");\r
+ protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
+ protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
+ protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\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 pasteMenu = 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 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 CheckboxMenuItem autoCalculate\r
+ = new CheckboxMenuItem("Autocalculate Consensus", true);\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
+ Panel embeddedMenu;\r
+ Label embeddedEdit;\r
+ Label embeddedSearch;\r
+ Label embeddedView;\r
+ Label embeddedColour;\r
+ Label embeddedFile;\r
+ Label embeddedHelp;\r
+ Label embeddedCalculate;\r
+ FlowLayout flowLayout1;\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
+ closeMenuItem.addActionListener(this);\r
+ loadApplication.addActionListener(this);\r
+\r
+ loadTree.addActionListener(this);\r
+ selectAllSequenceMenuItem.addActionListener(this);\r
+ deselectAllSequenceMenuItem.addActionListener(this);\r
+ invertSequenceMenuItem.addActionListener(this);\r
+ remove2LeftMenuItem.setLabel("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(this);\r
+ remove2RightMenuItem.setLabel("Remove Right");\r
+ remove2RightMenuItem.addActionListener(this);\r
+ removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(this);\r
+ removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(this);\r
+ viewBoxesMenuItem.setLabel("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addItemListener(this);\r
+ viewTextMenuItem.setLabel("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addItemListener(this);\r
+ sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(this);\r
+ sortIDMenuItem.setLabel("by ID");\r
+ sortIDMenuItem.addActionListener(this);\r
+ sortGroupMenuItem.setLabel("by Group");\r
+ sortGroupMenuItem.addActionListener(this);\r
+ removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(this);\r
+ pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(this);\r
+ PCAMenuItem.setLabel("Principal Component Analysis");\r
+ PCAMenuItem.addActionListener(this);\r
+ averageDistanceTreeMenuItem.setLabel(\r
+ "Average Distance Using % Identity");\r
+ averageDistanceTreeMenuItem.addActionListener(this);\r
+ neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
+ neighbourTreeMenuItem.addActionListener(this);\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(this);\r
+ zappoColour.setLabel("Zappo");\r
+ zappoColour.addActionListener(this);\r
+ taylorColour.setLabel("Taylor");\r
+ taylorColour.addActionListener(this);\r
+ hydrophobicityColour.setLabel("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(this);\r
+ helixColour.setLabel("Helix Propensity");\r
+ helixColour.addActionListener(this);\r
+ strandColour.setLabel("Strand Propensity");\r
+ strandColour.addActionListener(this);\r
+ turnColour.setLabel("Turn Propensity");\r
+ turnColour.addActionListener(this);\r
+ buriedColour.setLabel("Buried Index");\r
+ buriedColour.addActionListener(this);\r
+ userDefinedColour.setLabel("User Defined...");\r
+ userDefinedColour.addActionListener(this);\r
+ PIDColour.setLabel("Percentage Identity");\r
+ PIDColour.addActionListener(this);\r
+ BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(this);\r
+ avDistanceTreeBlosumMenuItem.setLabel(\r
+ "Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(this);\r
+ njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
+ njTreeBlosumMenuItem.addActionListener(this);\r
+ annotationPanelMenuItem.setLabel("Show Annotations");\r
+ annotationPanelMenuItem.addItemListener(this);\r
+ colourTextMenuItem.setLabel("Colour Text");\r
+ colourTextMenuItem.addItemListener(this);\r
+ overviewMenuItem.setLabel("Overview Window");\r
+ overviewMenuItem.addActionListener(this);\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ undoMenuItem.addActionListener(this);\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ redoMenuItem.addActionListener(this);\r
+ conservationMenuItem.setLabel("by Conservation");\r
+ conservationMenuItem.addItemListener(this);\r
+ noColourmenuItem.setLabel("None");\r
+ noColourmenuItem.addActionListener(this);\r
+ wrapMenuItem.setLabel("Wrap");\r
+ wrapMenuItem.addItemListener(this);\r
+ renderGapsMenuItem.setLabel("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addItemListener(this);\r
+ findMenuItem.setLabel("Find...");\r
+ findMenuItem.addActionListener(this);\r
+ searchMenu.setLabel("Search");\r
+\r
+ abovePIDThreshold.setLabel("Above Identity Threshold");\r
+ abovePIDThreshold.addItemListener(this);\r
+ nucleotideColour.setLabel("Nucleotide");\r
+ nucleotideColour.addActionListener(this);\r
+ deleteGroups.setLabel("Undefine Groups");\r
+ deleteGroups.addActionListener(this);\r
+ copy.setLabel("Copy");\r
+ copy.addActionListener(this);\r
+ cut.setLabel("Cut");\r
+ cut.addActionListener(this);\r
+ delete.setLabel("Delete");\r
+ delete.addActionListener(this);\r
+ pasteMenu.setLabel("Paste");\r
+ pasteNew.setLabel("To New Alignment");\r
+ pasteNew.addActionListener(this);\r
+ pasteThis.setLabel("Add To This Alignment");\r
+ pasteThis.addActionListener(this);\r
+ applyToAllGroups.setLabel("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addItemListener(this);\r
+ font.setLabel("Font...");\r
+ font.addActionListener(this);\r
+ scaleAbove.setLabel("Scale Above");\r
+ scaleAbove.setState(true);\r
+ scaleAbove.setEnabled(false);\r
+ scaleAbove.addItemListener(this);\r
+ scaleLeft.setEnabled(false);\r
+ scaleLeft.setState(true);\r
+ scaleLeft.setLabel("Scale Left");\r
+ scaleLeft.addItemListener(this);\r
+ scaleRight.setEnabled(false);\r
+ scaleRight.setState(true);\r
+ scaleRight.setLabel("Scale Right");\r
+ scaleRight.addItemListener(this);\r
+ modifyPID.setLabel("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(this);\r
+ modifyConservation.setLabel("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(this);\r
+ sortByTreeMenu.setLabel("By Tree Order");\r
+ sort.setLabel("Sort");\r
+ calculate.setLabel("Calculate Tree");\r
+ autoCalculate.addItemListener(this);\r
+ inputText.setLabel("Input from textbox");\r
+ inputText.addActionListener(this);\r
+\r
+ helpMenu.setLabel("Help");\r
+ documentation.setLabel("Documentation");\r
+ documentation.addActionListener(this);\r
+\r
+ about.setLabel("About...");\r
+ about.addActionListener(this);\r
+ seqLimits.setState(true);\r
+ seqLimits.setLabel("Show Sequence Limits");\r
+ seqLimits.addItemListener(this);\r
+ featureSettings.setLabel("Feature Settings...");\r
+ featureSettings.addActionListener(this);\r
+ sequenceFeatures.setLabel("Sequence Features");\r
+ sequenceFeatures.addItemListener(this);\r
+ sequenceFeatures.setState(false);\r
+ annotationColour.setLabel("by Annotation...");\r
+ annotationColour.addActionListener(this);\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.add(loadApplication);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(loadTree);\r
+ fileMenu.add(closeMenuItem);\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(pasteMenu);\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(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(sequenceFeatures);\r
+ viewMenu.add(featureSettings);\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
+ colourMenu.add(annotationColour);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(pairwiseAlignmentMenuItem);\r
+ calculateMenu.add(PCAMenuItem);\r
+ calculateMenu.add(autoCalculate);\r
+ this.add(statusBar, BorderLayout.SOUTH);\r
+ pasteMenu.add(pasteNew);\r
+ pasteMenu.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
+ public void setEmbedded()\r
+ {\r
+\r
+ embeddedMenu = new Panel();\r
+ embeddedEdit = new Label();\r
+ embeddedSearch = new Label();\r
+ embeddedView = new Label();\r
+ embeddedColour = new Label();\r
+ embeddedFile = new Label();\r
+ embeddedHelp = new Label();\r
+ embeddedCalculate = new Label();\r
+ flowLayout1 = new FlowLayout();\r
+ embeddedMenu.setBackground(Color.lightGray);\r
+ embeddedMenu.setLayout(flowLayout1);\r
+ embeddedEdit.setText("Edit");\r
+ embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedSearch.setText("Search");\r
+ embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedView.setText("View");\r
+ embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedColour.setText("Colour");\r
+ embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedFile.setText("File");\r
+ embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedHelp.setText("Help");\r
+ embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedCalculate.setText("Calculate");\r
+ embeddedMenu.add(embeddedFile);\r
+ embeddedMenu.add(embeddedEdit);\r
+ embeddedMenu.add(embeddedSearch);\r
+ embeddedMenu.add(embeddedView);\r
+ embeddedMenu.add(embeddedColour);\r
+ embeddedMenu.add(embeddedCalculate);\r
+ embeddedMenu.add(embeddedHelp);\r
+ flowLayout1.setAlignment(FlowLayout.LEFT);\r
+ flowLayout1.setHgap(2);\r
+ flowLayout1.setVgap(0);\r
+ embeddedFile.addMouseListener(this);\r
+ embeddedEdit.addMouseListener(this);\r
+ embeddedSearch.addMouseListener(this);\r
+ embeddedView.addMouseListener(this);\r
+ embeddedColour.addMouseListener(this);\r
+ embeddedCalculate.addMouseListener(this);\r
+ embeddedHelp.addMouseListener(this);\r
+\r
+ // setVisible(false);\r
+ fileMenu.remove(closeMenuItem);\r
+ fileMenu.remove(3); // Seperator\r
+\r
+ applet.setLayout(new BorderLayout());\r
+ applet.add(embeddedMenu, BorderLayout.NORTH);\r
+ applet.add(statusBar, BorderLayout.SOUTH);\r
+ // applet.validate();\r
+\r
+ alignPanel.setSize(applet.size().width, applet.size().height\r
+ - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
+\r
+ applet.add(alignPanel, BorderLayout.CENTER);\r
+ applet.validate();\r
+\r
+ }\r
+\r
+\r
+\r
+ PopupMenu filePopup, editPopup, searchPopup,\r
+ viewPopup, colourPopup, calculatePopup, helpPopup;\r
+ MenuItem featureSettings = new MenuItem();\r
+ CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
+ MenuItem annotationColour = new MenuItem();\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ PopupMenu popup = null;\r
+ Label source = (Label)evt.getSource();\r
+ if(source==embeddedFile)\r
+ {\r
+ popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
+ }\r
+ else if(source==embeddedEdit)\r
+ {\r
+ popup = editPopup = genPopupMenu(editPopup, editMenu);\r
+ }\r
+ else if(source==embeddedSearch)\r
+ {\r
+ popup = searchPopup = genPopupMenu(searchPopup, searchMenu);\r
+ }\r
+ else if(source==embeddedView)\r
+ {\r
+ popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
+ }\r
+ else if(source==embeddedColour)\r
+ {\r
+ popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
+ }\r
+ else if(source==embeddedCalculate)\r
+ {\r
+ popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
+ }\r
+ else if(source==embeddedHelp)\r
+ {\r
+ popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
+ }\r
+\r
+ embeddedMenu.add(popup);\r
+ popup.show(embeddedMenu,\r
+ source.getBounds().x,\r
+ source.getBounds().y + source.getBounds().getSize().height);\r
+ }\r
+\r
+ PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
+ {\r
+ if(popup!=null)\r
+ {\r
+ return popup;\r
+ }\r
+ popup = new PopupMenu();\r
+ int m, mSize = original.getItemCount();\r
+ for(m=0; m<mSize; m++)\r
+ {\r
+ popup.add(original.getItem(m));\r
+ mSize--;\r
+ m--;\r
+ }\r
+\r
+ return popup;\r
+ }\r
+ public void mouseClicked(MouseEvent evt)\r
+ {}\r
+ public void mouseReleased(MouseEvent evt)\r
+ {}\r
+ public void mouseEntered(MouseEvent evt)\r
+ {}\r
+ public void mouseExited(MouseEvent evt)\r
+ {}\r
+\r
}\r
+\r
git://source.jalview.org / jalview.git / blobdiff