*/\r
package jalview.gui;\r
\r
-import jalview.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.io.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import jalview.schemes.*;\r
-\r
-import jalview.ws.*;\r
+import java.beans.*;\r
+import java.io.*;\r
+import java.util.*;\r
\r
import java.awt.*;\r
import java.awt.datatransfer.*;\r
import java.awt.event.*;\r
import java.awt.print.*;\r
-\r
-import java.io.*;\r
-\r
-import java.beans.*;\r
-\r
-import java.util.*;\r
-\r
import javax.swing.*;\r
import javax.swing.event.*;\r
\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.jbgui.*;\r
+import jalview.schemes.*;\r
+import jalview.ws.*;\r
\r
/**\r
* DOCUMENT ME!\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class AlignFrame extends GAlignFrame\r
+public class AlignFrame\r
+ extends GAlignFrame\r
{\r
- /** DOCUMENT ME!! */\r
- public static final int NEW_WINDOW_WIDTH = 700;\r
-\r
- /** DOCUMENT ME!! */\r
- public static final int NEW_WINDOW_HEIGHT = 500;\r
- final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
-\r
- /** DOCUMENT ME!! */\r
- public String currentFileFormat = null;\r
- Stack historyList = new Stack();\r
- Stack redoList = new Stack();\r
- private int treeCount = 0;\r
-\r
- /**\r
- * Creates a new AlignFrame object.\r
- *\r
- * @param al DOCUMENT ME!\r
- */\r
- public AlignFrame(AlignmentI al)\r
- {\r
- viewport = new AlignViewport(al);\r
-\r
- alignPanel = new AlignmentPanel(this, viewport);\r
- alignPanel.annotationPanel.adjustPanelHeight();\r
- alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
- alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
- alignPanel.setAnnotationVisible(viewport.getShowAnnotation());\r
-\r
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
-\r
- addInternalFrameListener(new InternalFrameAdapter()\r
- {\r
- public void internalFrameActivated(InternalFrameEvent evt)\r
- {\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- alignPanel.requestFocus();\r
- }\r
- });\r
- }\r
- });\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void parseGroupsFile(String file)\r
- {\r
- try{\r
- BufferedReader in = new BufferedReader(new FileReader(file));\r
- SequenceI seq=null;\r
- String line, text, token;\r
- UserColourScheme ucs;\r
- int index, start, end;\r
- StringTokenizer st;\r
- SequenceGroup sg;\r
- while( (line = in.readLine())!=null)\r
+ /** DOCUMENT ME!! */\r
+ public static final int NEW_WINDOW_WIDTH = 700;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int NEW_WINDOW_HEIGHT = 500;\r
+ final AlignmentPanel alignPanel;\r
+ final AlignViewport viewport;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public String currentFileFormat = null;\r
+ Stack historyList = new Stack();\r
+ Stack redoList = new Stack();\r
+ private int treeCount = 0;\r
+\r
+ /**\r
+ * Creates a new AlignFrame object.\r
+ *\r
+ * @param al DOCUMENT ME!\r
+ */\r
+ public AlignFrame(AlignmentI al)\r
+ {\r
+ viewport = new AlignViewport(al);\r
+\r
+ alignPanel = new AlignmentPanel(this, viewport);\r
+ alignPanel.annotationPanel.adjustPanelHeight();\r
+ alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.\r
+ annotationPanel.getPreferredSize());\r
+ alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.\r
+ getPreferredSize());\r
+ alignPanel.setAnnotationVisible(viewport.getShowAnnotation());\r
+\r
+ getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
+\r
+ addInternalFrameListener(new InternalFrameAdapter()\r
+ {\r
+ public void internalFrameActivated(InternalFrameEvent evt)\r
+ {\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
{\r
- st = new StringTokenizer(line, "\t");\r
- if(st.countTokens()!=6)\r
+ public void run()\r
{\r
- System.out.println("Groups file "+file+" is invalid. Read help file.");\r
- System.exit(1);\r
+ alignPanel.requestFocus();\r
}\r
+ });\r
+ }\r
+ });\r
+ addServiceListeners();\r
+ }\r
+\r
+ /* Set up intrinsic listeners for dynamically generated GUI bits. */\r
+ private void addServiceListeners()\r
+ {\r
+\r
+ final AlignFrame thisFrame = this;\r
+ final java.beans.PropertyChangeListener thisListener;\r
+ // Do this once to get current state\r
+ thisFrame.BuildWebServiceMenu();\r
+ Desktop.discoverer.addPropertyChangeListener(\r
+ thisListener = new java.beans.PropertyChangeListener()\r
+ {\r
+ public void propertyChange(PropertyChangeEvent evt)\r
+ {\r
+ // System.out.println("Discoverer property change.");\r
+ if (evt.getPropertyName().equals("services"))\r
+ {\r
+ // System.out.println("Rebuilding web service menu");\r
+ thisFrame.BuildWebServiceMenu();\r
+ }\r
+ }\r
+ });\r
+ addInternalFrameListener(new javax.swing.event.\r
+ InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ // System.out.println("deregistering discoverer listener");\r
+ Desktop.discoverer.removePropertyChangeListener(thisListener);\r
+ }\r
+ ;\r
+ });\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param String DOCUMENT ME!\r
+ */\r
+\r
+ public void parseGroupsFile(String file)\r
+ {\r
+ try\r
+ {\r
+ BufferedReader in = new BufferedReader(new FileReader(file));\r
+ SequenceI seq = null;\r
+ String line, text, token;\r
+ UserColourScheme ucs;\r
+ int index, start, end;\r
+ StringTokenizer st;\r
+ SequenceGroup sg;\r
+ while ( (line = in.readLine()) != null)\r
+ {\r
+ st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() != 6)\r
+ {\r
+ System.out.println("Groups file " + file +\r
+ " is invalid. Read help file.");\r
+ System.exit(1);\r
+ }\r
\r
- while(st.hasMoreElements())\r
+ while (st.hasMoreElements())\r
+ {\r
+ text = st.nextToken();\r
+ token = st.nextToken();\r
+ if (!token.equals("ID_NOT_SPECIFIED"))\r
{\r
- text = 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
- index = Integer.parseInt( st.nextToken() );\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
- ucs = new UserColourScheme(st.nextToken());\r
+ start = Integer.parseInt(st.nextToken());\r
+ end = Integer.parseInt(st.nextToken());\r
+ ucs = new UserColourScheme(st.nextToken());\r
\r
- seq = viewport.alignment.getSequenceAt(index);\r
- start = seq.findIndex(start)-1;\r
- end = seq.findIndex(end)-1;\r
+ seq = viewport.alignment.getSequenceAt(index);\r
+ start = seq.findIndex(start) - 1;\r
+ end = seq.findIndex(end) - 1;\r
\r
- sg = new SequenceGroup(text,ucs,true,true,false,start,end);\r
- sg.addSequence( seq,true);\r
+ sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
+ sg.addSequence(seq, true);\r
\r
- viewport.alignment.addGroup(sg);\r
- }\r
+ viewport.alignment.addGroup(sg);\r
}\r
+ }\r
\r
- }catch(Exception ex){System.out.println("Error parsing groups file: "+ex);}\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+ catch (Exception ex)\r
{\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]\r
- {\r
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
- "jar"\r
- },\r
- new String[]\r
- {\r
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
- }, currentFileFormat);\r
+ System.out.println("Error parsing groups file: " + ex);\r
+ }\r
+ }\r
\r
- chooser.setAcceptAllFileFilterUsed(false);\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save Alignment to file");\r
- chooser.setToolTipText("Save");\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"),\r
+ new String[]\r
+ {\r
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
+ "jar"\r
+ },\r
+ new String[]\r
+ {\r
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
+ }, currentFileFormat);\r
\r
- int value = chooser.showSaveDialog(this);\r
+ chooser.setAcceptAllFileFilterUsed(false);\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save Alignment to file");\r
+ chooser.setToolTipText("Save");\r
\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- currentFileFormat = chooser.getSelectedFormat();\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
- currentFileFormat);\r
+ int value = chooser.showSaveDialog(this);\r
\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ currentFileFormat = chooser.getSelectedFormat();\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
+ currentFileFormat);\r
\r
- saveAlignment(choice, currentFileFormat);\r
- }\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+\r
+ saveAlignment(choice, currentFileFormat);\r
}\r
+ }\r
\r
- public boolean saveAlignment(String file, String format)\r
+ public boolean saveAlignment(String file, String format)\r
+ {\r
+ if (format.equalsIgnoreCase("Jalview"))\r
{\r
- if (format.equalsIgnoreCase("Jalview"))\r
+ String shortName = title;\r
+\r
+ if (shortName.indexOf(java.io.File.separatorChar) > -1)\r
{\r
- String shortName = title;\r
+ shortName = shortName.substring(shortName.lastIndexOf(\r
+ java.io.File.separatorChar) + 1);\r
+ }\r
\r
- if (shortName.indexOf(java.io.File.separatorChar) > -1)\r
- {\r
- shortName = shortName.substring(shortName.lastIndexOf(\r
- java.io.File.separatorChar) + 1);\r
- }\r
+ Jalview2XML.SaveAlignment(this, file, shortName);\r
\r
- Jalview2XML.SaveAlignment(this, file, shortName);\r
+ // USE Jalview2XML to save this file\r
+ return true;\r
+ }\r
+ else\r
+ {\r
+ String output = FormatAdapter.formatSequences(format,\r
+ viewport.getAlignment().\r
+ getSequences());\r
+ if (output == null)\r
+ {\r
+ return false;\r
+ }\r
\r
- // USE Jalview2XML to save this file\r
+ try\r
+ {\r
+ java.io.PrintWriter out = new java.io.PrintWriter(\r
+ new java.io.FileWriter(file));\r
+ out.println(output);\r
+ out.close();\r
return true;\r
}\r
- else\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ Desktop.addInternalFrame(cap,\r
+ "Alignment output - " + e.getActionCommand(), 600,\r
+ 500);\r
+ cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
+ viewport.getAlignment().\r
+ getSequences()));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ new HTMLOutput(viewport);\r
+ }\r
+\r
+ public void createImageMap(File file, String image)\r
+ {\r
+ alignPanel.makePNGImageMap(file, image);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void createPNG(File f)\r
+ {\r
+ alignPanel.makePNG(f);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void createEPS(File f)\r
+ {\r
+ alignPanel.makeEPS(f);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void printMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ //Putting in a thread avoids Swing painting problems\r
+ PrintThread thread = new PrintThread();\r
+ thread.start();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void closeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ void updateEditMenuBar()\r
+ {\r
+ if (historyList.size() > 0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+\r
+ HistoryItem hi = (HistoryItem) historyList.peek();\r
+ undoMenuItem.setText("Undo " + hi.getDescription());\r
+ }\r
+ else\r
+ {\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setText("Undo");\r
+ }\r
+\r
+ if (redoList.size() > 0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+\r
+ HistoryItem hi = (HistoryItem) redoList.peek();\r
+ redoMenuItem.setText("Redo " + hi.getDescription());\r
+ }\r
+ else\r
+ {\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setText("Redo");\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param hi DOCUMENT ME!\r
+ */\r
+ public void addHistoryItem(HistoryItem hi)\r
+ {\r
+ historyList.push(hi);\r
+ updateEditMenuBar();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem) historyList.pop();\r
+ redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
+ HistoryItem.HIDE));\r
+ restoreHistoryItem(hi);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem) redoList.pop();\r
+ restoreHistoryItem(hi);\r
+ updateEditMenuBar();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ alignPanel.repaint();\r
+ }\r
+\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),\r
+ i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
{\r
- String output = FormatAdapter.formatSequences(format,\r
- viewport.getAlignment().\r
- getSequences());\r
- if(output==null)\r
- return false;\r
+ SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
\r
- try\r
+ if (restore.getLength() == 0)\r
{\r
- java.io.PrintWriter out = new java.io.PrintWriter(\r
- new java.io.FileWriter(file));\r
- out.println(output);\r
- out.close();\r
- return true;\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ viewport.alignment.getSequences().insertElementAt(restore,\r
+ hi.getAlignIndex(i));\r
}\r
- catch (Exception ex)\r
+ else\r
{\r
- ex.printStackTrace();\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
}\r
}\r
- return false;\r
- }\r
-\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void outputText_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- Desktop.addInternalFrame(cap,\r
- "Alignment output - " + e.getActionCommand(), 600, 500);\r
- cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
- viewport.getAlignment().getSequences()));\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
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- new HTMLOutput(viewport);\r
- }\r
+ updateEditMenuBar();\r
\r
- public void createImageMap(File file, String image)\r
- {\r
- alignPanel.makePNGImageMap(file, image);\r
- }\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void createPNG(File f)\r
- {\r
- alignPanel.makePNG(f);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param up DOCUMENT ME!\r
+ */\r
+ public void moveSelectedSequences(boolean up)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void createEPS(File f)\r
+ if (sg == null)\r
{\r
- alignPanel.makeEPS(f);\r
+ return;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void printMenuItem_actionPerformed(ActionEvent e)\r
+ if (up)\r
{\r
- //Putting in a thread avoids Swing painting problems\r
- PrintThread thread = new PrintThread();\r
- thread.start();\r
- }\r
+ for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void closeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try\r
+ if (!sg.sequences.contains(seq))\r
{\r
- this.setClosed(true);\r
+ continue;\r
}\r
- catch (Exception ex)\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
+\r
+ if (sg.sequences.contains(temp))\r
{\r
+ continue;\r
}\r
- }\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- void updateEditMenuBar()\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
+ }\r
+ }\r
+ else\r
{\r
- if (historyList.size() > 0)\r
- {\r
- undoMenuItem.setEnabled(true);\r
+ for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
\r
- HistoryItem hi = (HistoryItem) historyList.peek();\r
- undoMenuItem.setText("Undo " + hi.getDescription());\r
- }\r
- else\r
+ if (!sg.sequences.contains(seq))\r
{\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setText("Undo");\r
+ continue;\r
}\r
\r
- if (redoList.size() > 0)\r
- {\r
- redoMenuItem.setEnabled(true);\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
\r
- HistoryItem hi = (HistoryItem) redoList.peek();\r
- redoMenuItem.setText("Redo " + hi.getDescription());\r
- }\r
- else\r
+ if (sg.sequences.contains(temp))\r
{\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setText("Redo");\r
+ continue;\r
}\r
- }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param hi DOCUMENT ME!\r
- */\r
- public void addHistoryItem(HistoryItem hi)\r
- {\r
- historyList.push(hi);\r
- updateEditMenuBar();\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
+ }\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void copy_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getSelectionGroup() == null)\r
{\r
- HistoryItem hi = (HistoryItem) historyList.pop();\r
- redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
- HistoryItem.HIDE));\r
- restoreHistoryItem(hi);\r
+ return;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ StringBuffer buffer = new StringBuffer();\r
+\r
+ Hashtable orderedSeqs = new Hashtable();\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
- HistoryItem hi = (HistoryItem) redoList.pop();\r
- restoreHistoryItem(hi);\r
- updateEditMenuBar();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- alignPanel.repaint();\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.alignment.findIndex(seq);\r
+ orderedSeqs.put(index + "", seq);\r
}\r
\r
- // used by undo and redo\r
- void restoreHistoryItem(HistoryItem hi)\r
+ int index = 0, startRes, endRes;\r
+ char ch;\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
- if (hi.getType() == HistoryItem.SORT)\r
+ SequenceI seq = null;\r
+\r
+ while (seq == null)\r
+ {\r
+ if (orderedSeqs.containsKey(index + ""))\r
{\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
- {\r
- viewport.alignment.getSequences().setElementAt(hi.getSequences()\r
- .elementAt(i),\r
- i);\r
- }\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+\r
+ break;\r
}\r
else\r
{\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
- {\r
- SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
+ index++;\r
+ }\r
+ }\r
+ //FIND START RES\r
+ //Returns residue following index if gap\r
+ startRes = seq.findPosition(sg.getStartRes());\r
\r
- if (restore.getLength() == 0)\r
- {\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
- viewport.alignment.getSequences().insertElementAt(restore,\r
- hi.getAlignIndex(i));\r
- }\r
- else\r
- {\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
- }\r
- }\r
+ //FIND END RES\r
+ //Need to find the residue preceeding index if gap\r
+ endRes = 0;\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
+ for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ endRes++;\r
}\r
+ }\r
\r
- updateEditMenuBar();\r
+ if (endRes > 0)\r
+ {\r
+ endRes += seq.getStart() - 1;\r
+ }\r
\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- alignPanel.repaint();\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
- }\r
+ buffer.append(seq.getName() + "\t" +\r
+ startRes + "\t" +\r
+ endRes + "\t" +\r
+ seq.getSequence(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
+ }\r
+\r
+ c.setContents(new StringSelection(buffer.toString()), null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void pasteNew_actionPerformed(ActionEvent e)\r
+ {\r
+ paste(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void pasteThis_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
+ HistoryItem.PASTE));\r
+ paste(false);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param newAlignment DOCUMENT ME!\r
+ */\r
+ void paste(boolean newAlignment)\r
+ {\r
+ try\r
+ {\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ Transferable contents = c.getContents(this);\r
+\r
+ if (contents == null)\r
+ {\r
+ return;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param up DOCUMENT ME!\r
- */\r
- public void moveSelectedSequences(boolean up)\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
+ String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
+ StringTokenizer st = new StringTokenizer(str);\r
+ ArrayList seqs = new ArrayList();\r
+\r
+ while (st.hasMoreElements())\r
+ {\r
+ String name = st.nextToken();\r
+ int start = Integer.parseInt(st.nextToken());\r
+ int end = Integer.parseInt(st.nextToken());\r
+ Sequence sequence = new Sequence(name, st.nextToken(), start,\r
+ end);\r
\r
- if (sg == null)\r
+ if (!newAlignment)\r
{\r
- return;\r
+ viewport.alignment.addSequence(sequence);\r
}\r
-\r
- if (up)\r
+ else\r
{\r
- for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
- {\r
- SequenceI seq = viewport.alignment.getSequenceAt(i);\r
-\r
- if (!sg.sequences.contains(seq))\r
- {\r
- continue;\r
- }\r
+ seqs.add(sequence);\r
+ }\r
+ }\r
\r
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
+ if (newAlignment)\r
+ {\r
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
+ seqs.toArray(newSeqs);\r
\r
- if (sg.sequences.contains(temp))\r
- {\r
- continue;\r
- }\r
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
+ String newtitle = new String("Copied sequences");\r
\r
- viewport.alignment.getSequences().setElementAt(temp, i);\r
- viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
- }\r
+ if (title.startsWith("Copied sequences"))\r
+ {\r
+ newtitle = title;\r
}\r
else\r
{\r
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
- {\r
- SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+ newtitle = newtitle.concat("- from " + title);\r
+ }\r
\r
- if (!sg.sequences.contains(seq))\r
- {\r
- continue;\r
- }\r
+ Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
+ }\r
+ else\r
+ {\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ viewport.setEndSeq(viewport.alignment.getHeight());\r
+ viewport.alignment.getWidth();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
\r
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
+ // could be anything being pasted in here\r
+ }\r
\r
- if (sg.sequences.contains(temp))\r
- {\r
- continue;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void cut_actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(null);\r
+ delete_actionPerformed(null);\r
+ }\r
\r
- viewport.alignment.getSequences().setElementAt(temp, i);\r
- viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
- }\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void delete_actionPerformed(ActionEvent e)\r
+ {\r
+ boolean seqsdeleted = false;\r
\r
- alignPanel.repaint();\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void copy_actionPerformed(ActionEvent e)\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
{\r
- if (viewport.getSelectionGroup() == null)\r
- {\r
- return;\r
- }\r
+ allSequences = true;\r
+ }\r
+\r
+ for (int i = 0; i < sg.sequences.size(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.getAlignment().findIndex(seq);\r
+ seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (allSequences)\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- StringBuffer buffer = new StringBuffer();\r
+ if (seq.getSequence().length() < 1)\r
+ {\r
+ seqsdeleted = true;\r
+ viewport.getAlignment().deleteSequence(seq);\r
+ }\r
+ else\r
+ {\r
+ viewport.getAlignment().getSequences().setElementAt(seq, index);\r
+ }\r
+ }\r
\r
- Hashtable orderedSeqs = new Hashtable();\r
+ viewport.setSelectionGroup(null);\r
+ viewport.alignment.deleteGroup(sg);\r
\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.alignment.findIndex(seq);\r
- orderedSeqs.put(index + "", seq);\r
- }\r
+ if (seqsdeleted)\r
+ {\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ }\r
\r
- int index = 0, startRes, endRes;\r
- char ch;\r
+ viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ if (viewport.getAlignment().getHeight() < 1)\r
+ {\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.alignment.deleteAllGroups();\r
+ viewport.setSelectionGroup(null);\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = new SequenceGroup();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+\r
+ sg.setEndRes(viewport.alignment.getWidth() - 1);\r
+ viewport.setSelectionGroup(sg);\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setSelectionGroup(null);\r
+ viewport.getColumnSelection().clear();\r
+ viewport.setSelectionGroup(null);\r
+ alignPanel.annotationPanel.activeRes = null;\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ if (sg == null)\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed(null);\r
+\r
+ return;\r
+ }\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
+\r
+ if (colSel.size() > 0)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ int min = colSel.getMin();\r
+ viewport.getAlignment().trimLeft(min);\r
+ colSel.compensateForEdit(0, min);\r
+\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
+ }\r
+\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+\r
+ if (!sg.adjustForRemoveLeft(min))\r
{\r
- SequenceI seq = null;\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+ }\r
\r
- while (seq == null)\r
- {\r
- if (orderedSeqs.containsKey(index + ""))\r
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
+ alignPanel.repaint();\r
+ }\r
+ }\r
\r
- break;\r
- }\r
- else\r
- {\r
- index++;\r
- }\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
\r
- //FIND START RES\r
- //Returns residue following index if gap\r
- startRes = seq.findPosition(sg.getStartRes());\r
+ if (colSel.size() > 0)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
+ HistoryItem.HIDE));\r
\r
- //FIND END RES\r
- //Need to find the residue preceeding index if gap\r
- endRes = 0;\r
+ int max = colSel.getMax();\r
+ viewport.getAlignment().trimRight(max);\r
\r
- for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
- {\r
- ch = seq.getCharAt(j);\r
- if (!jalview.util.Comparison.isGap( (ch)))\r
- {\r
- endRes++;\r
- }\r
- }\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+ }\r
\r
- if(endRes>0)\r
- {\r
- endRes += seq.getStart() -1;\r
- }\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
\r
- buffer.append(seq.getName() + "\t" +\r
- startRes + "\t" +\r
- endRes + "\t" +\r
- seq.getSequence(sg.getStartRes(),\r
- sg.getEndRes() + 1) + "\n");\r
+ if (!sg.adjustForRemoveRight(max))\r
+ {\r
+ viewport.alignment.deleteGroup(sg);\r
}\r
+ }\r
\r
- c.setContents(new StringSelection(buffer.toString()), null);\r
+ alignPanel.repaint();\r
}\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
+ viewport.alignment, HistoryItem.HIDE));\r
+\r
+ viewport.getAlignment().removeGaps();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ SequenceI current;\r
+ int jSize;\r
+\r
+ Vector seqs = null;\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
+ int start = 0;\r
+ int end = viewport.alignment.getWidth();\r
+\r
+ if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().sequences != null\r
+ && viewport.getSelectionGroup().sequences.size() > 0)\r
{\r
- paste(true);\r
+ seqs = viewport.getSelectionGroup().sequences;\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
+ else\r
{\r
- addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
- HistoryItem.PASTE));\r
- paste(false);\r
+ seqs = viewport.alignment.getSequences();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param newAlignment DOCUMENT ME!\r
- */\r
- void paste(boolean newAlignment)\r
+ for (int i = 0; i < seqs.size(); i++)\r
{\r
- try\r
- {\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- Transferable contents = c.getContents(this);\r
+ current = (SequenceI) seqs.elementAt(i);\r
+ jSize = current.getLength();\r
\r
- if (contents == null)\r
- {\r
- return;\r
- }\r
+ int j = start;\r
\r
- String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
- StringTokenizer st = new StringTokenizer(str);\r
- ArrayList seqs = new ArrayList();\r
-\r
- while (st.hasMoreElements())\r
- {\r
- String name = st.nextToken();\r
- int start = Integer.parseInt(st.nextToken());\r
- int end = Integer.parseInt(st.nextToken());\r
- Sequence sequence = new Sequence(name, st.nextToken(), start,\r
- end);\r
-\r
- if (!newAlignment)\r
- {\r
- viewport.alignment.addSequence(sequence);\r
- }\r
- else\r
- {\r
- seqs.add(sequence);\r
- }\r
- }\r
-\r
- if (newAlignment)\r
- {\r
- SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
- seqs.toArray(newSeqs);\r
-\r
- AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
- String newtitle = new String("Copied sequences");\r
-\r
- if (title.startsWith("Copied sequences"))\r
- {\r
- newtitle = title;\r
- }\r
- else\r
- {\r
- newtitle = newtitle.concat("- from " + title);\r
- }\r
-\r
- Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
- NEW_WINDOW_HEIGHT);\r
- }\r
- else\r
- {\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
- viewport.setEndSeq(viewport.alignment.getHeight());\r
- viewport.alignment.getWidth();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
-\r
- // could be anything being pasted in here\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void cut_actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed(null);\r
- delete_actionPerformed(null);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void delete_actionPerformed(ActionEvent e)\r
- {\r
- boolean seqsdeleted = false;\r
-\r
- if (viewport.getSelectionGroup() == null)\r
- {\r
- return;\r
- }\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
- allSequences = true;\r
-\r
- for (int i = 0; i < sg.sequences.size(); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.getAlignment().findIndex(seq);\r
- seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
-\r
- // If the cut affects all sequences, remove highlighted columns\r
- if(allSequences)\r
- {\r
- viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes()+1);\r
- }\r
-\r
-\r
- if (seq.getSequence().length() < 1)\r
- {\r
- seqsdeleted = true;\r
- viewport.getAlignment().deleteSequence(seq);\r
- }\r
- else\r
- {\r
- viewport.getAlignment().getSequences().setElementAt(seq, index);\r
- }\r
- }\r
-\r
- viewport.setSelectionGroup(null);\r
- viewport.alignment.deleteGroup(sg);\r
-\r
- if (seqsdeleted)\r
- {\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
- }\r
-\r
- viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
-\r
- if (viewport.getAlignment().getHeight() < 1)\r
- {\r
- try\r
- {\r
- this.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.alignment.deleteAllGroups();\r
- viewport.setSelectionGroup(null);\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = new SequenceGroup();\r
-\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
- {\r
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
- }\r
-\r
- sg.setEndRes(viewport.alignment.getWidth()-1);\r
- viewport.setSelectionGroup(sg);\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setSelectionGroup(null);\r
- viewport.getColumnSelection().clear();\r
- viewport.setSelectionGroup(null);\r
- alignPanel.annotationPanel.activeRes = null;\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
-\r
- if (sg == null)\r
- {\r
- selectAllSequenceMenuItem_actionPerformed(null);\r
-\r
- return;\r
- }\r
-\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
- {\r
- sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
- }\r
-\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
-\r
- if (colSel.size() > 0)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
- HistoryItem.HIDE));\r
-\r
- int min = colSel.getMin();\r
- viewport.getAlignment().trimLeft(min);\r
- colSel.compensateForEdit(0, min);\r
-\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
- }\r
-\r
- Vector groups = viewport.alignment.getGroups();\r
-\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.get(i);\r
-\r
- if (!sg.adjustForRemoveLeft(min))\r
- {\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
- }\r
-\r
- alignPanel.repaint();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
-\r
- if (colSel.size() > 0)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
- HistoryItem.HIDE));\r
-\r
- int max = colSel.getMax();\r
- viewport.getAlignment().trimRight(max);\r
-\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- viewport.getSelectionGroup().adjustForRemoveRight(max);\r
- }\r
-\r
- Vector groups = viewport.alignment.getGroups();\r
-\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.get(i);\r
-\r
- if (!sg.adjustForRemoveRight(max))\r
- {\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
- }\r
-\r
- alignPanel.repaint();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
- viewport.alignment, HistoryItem.HIDE));\r
-\r
- viewport.getAlignment().removeGaps();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
- HistoryItem.HIDE));\r
-\r
- SequenceI current;\r
- int jSize;\r
-\r
- Vector seqs = null;\r
-\r
- int start = 0;\r
- int end = viewport.alignment.getWidth();\r
-\r
-\r
- if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().sequences != null\r
- && viewport.getSelectionGroup().sequences.size()>0)\r
- {\r
- seqs = viewport.getSelectionGroup().sequences;\r
- start = viewport.getSelectionGroup().getStartRes();\r
- end = viewport.getSelectionGroup().getEndRes();\r
- }\r
- else\r
- {\r
- seqs = viewport.alignment.getSequences();\r
- }\r
-\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- current = (SequenceI) seqs.elementAt(i);\r
- jSize = current.getLength();\r
-\r
- int j = start;\r
-\r
- do\r
- {\r
- if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
- {\r
- current.deleteCharAt(j);\r
- j--;\r
- jSize--;\r
- }\r
-\r
- j++;\r
- }\r
- while (j < end && j < jSize);\r
- }\r
-\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
- HistoryItem.HIDE));\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
-\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JInternalFrame frame = new JInternalFrame();\r
- Finder finder = new Finder(viewport, alignPanel, frame);\r
- frame.setContentPane(finder);\r
- Desktop.addInternalFrame(frame, "Find", 340, 110);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void font_actionPerformed(ActionEvent e)\r
- {\r
- FontChooser fc = new FontChooser(alignPanel);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowFullId(fullSeqId.isSelected());\r
-\r
- alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourText(colourTextMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
- alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
- scaleAbove.setVisible(wrapMenuItem.isSelected());\r
- scaleLeft.setVisible(wrapMenuItem.isSelected());\r
- scaleRight.setVisible(wrapMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleRightWrapped(scaleRight.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowText(viewTextMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
- {\r
- viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
-\r
- if (viewport.showSequenceFeatures &&\r
- !((Alignment) viewport.alignment).featuresAdded)\r
- {\r
- SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment,\r
- alignPanel);\r
- ((Alignment) viewport.alignment).featuresAdded = true;\r
- }\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (annotationPanelMenuItem.isSelected() &&\r
- viewport.getWrapAlignment())\r
- {\r
- annotationPanelMenuItem.setSelected(false);\r
-\r
- return;\r
- }\r
-\r
- viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (alignPanel.overviewPanel != null)\r
- {\r
- return;\r
- }\r
-\r
- JInternalFrame frame = new JInternalFrame();\r
- OverviewPanel overview = new OverviewPanel(alignPanel);\r
- frame.setContentPane(overview);\r
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
- frame.getWidth(), frame.getHeight());\r
- frame.pack();\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(\r
- javax.swing.event.InternalFrameEvent evt)\r
- {\r
- alignPanel.setOverviewPanel(null);\r
- }\r
- ;\r
- });\r
-\r
- alignPanel.setOverviewPanel(overview);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(null);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new ClustalxColourScheme(\r
- viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new ZappoColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TaylorColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HydrophobicColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HelixColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new StrandColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TurnColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new BuriedColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new NucleotideColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param cs DOCUMENT ME!\r
- */\r
- void changeColour(ColourSchemeI cs)\r
- {\r
- int threshold = 0;\r
-\r
- if (viewport.getAbovePIDThreshold())\r
- {\r
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
- "Background");\r
-\r
- if (cs instanceof ResidueColourScheme)\r
- {\r
- ((ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- ((ScoreColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
- }\r
-\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
- else if (cs instanceof ResidueColourScheme)\r
- {\r
- ((ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- ((ScoreColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());\r
- }\r
-\r
- if (viewport.getConservationSelected())\r
- {\r
- ConservationColourScheme ccs = null;\r
-\r
- Alignment al = (Alignment) viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, al.getSequences(), 0,\r
- al.getWidth() - 1);\r
-\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
-\r
- ccs = new ConservationColourScheme(c, cs);\r
-\r
-\r
- viewport.setGlobalColourScheme(ccs);\r
-\r
- ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,\r
- "Background");\r
- }\r
- else\r
- {\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- if (cs != null)\r
- {\r
- cs.setConsensus(viewport.vconsensus);\r
- }\r
-\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
-\r
- if (viewport.getColourAppliesToAllGroups())\r
- {\r
- Vector groups = viewport.alignment.getGroups();\r
-\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
- if (cs == null)\r
- {\r
- sg.cs = null;\r
- }\r
- else if (cs instanceof ClustalxColourScheme)\r
- {\r
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
- }\r
- else if (cs instanceof UserColourScheme)\r
- {\r
- sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());\r
- }\r
- else\r
- {\r
- try\r
- {\r
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- if (viewport.getAbovePIDThreshold())\r
- {\r
- if (sg.cs instanceof ResidueColourScheme)\r
- {\r
- ((ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
- }\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- {\r
- ((ScoreColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
- }\r
-\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- sg.getWidth()));\r
- }\r
-\r
- if (viewport.getConservationSelected())\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3, sg.sequences, 0,\r
- viewport.alignment.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
-\r
- ConservationColourScheme ccs = new ConservationColourScheme(c,\r
- sg.cs);\r
-\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- sg.getWidth()));\r
- sg.cs = ccs;\r
- }\r
- else if (cs != null)\r
- {\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- sg.getWidth()));\r
- }\r
- }\r
- }\r
-\r
- if (alignPanel.getOverviewPanel() != null)\r
- {\r
- alignPanel.getOverviewPanel().updateOverviewImage();\r
- }\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void modifyPID_actionPerformed(ActionEvent e)\r
- {\r
- if (viewport.getAbovePIDThreshold())\r
- {\r
- SliderPanel.setPIDSliderSource(alignPanel,\r
- viewport.getGlobalColourScheme(), "Background");\r
- SliderPanel.showPIDSlider();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void modifyConservation_actionPerformed(ActionEvent e)\r
- {\r
- if (viewport.getConservationSelected())\r
+ do\r
+ {\r
+ if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
{\r
- SliderPanel.setConservationSlider(alignPanel,\r
- viewport.globalColourScheme, "Background");\r
- SliderPanel.showConservationSlider();\r
+ current.deleteCharAt(j);\r
+ j--;\r
+ jSize--;\r
}\r
+ j++;\r
+ }\r
+ while (j < end && j < jSize);\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setConservationSelected(conservationMenuItem.isSelected());\r
-\r
- viewport.setAbovePIDThreshold(false);\r
- abovePIDThreshold.setSelected(false);\r
-\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
\r
- if (cs instanceof ConservationColourScheme)\r
- {\r
- changeColour(((ConservationColourScheme) cs).cs);\r
- }\r
- else\r
- {\r
- changeColour(cs);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
+ HistoryItem.HIDE));\r
\r
- modifyConservation_actionPerformed(null);\r
- }\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
{\r
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
-\r
- conservationMenuItem.setSelected(false);\r
- viewport.setConservationSelected(false);\r
-\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
-\r
- if (cs instanceof ConservationColourScheme)\r
- {\r
- changeColour(((ConservationColourScheme) cs).cs);\r
- }\r
- else\r
- {\r
- changeColour(cs);\r
- }\r
-\r
- modifyPID_actionPerformed(null);\r
- }\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- if(e.getActionCommand().equals("User Defined..."))\r
- new UserDefinedColours(alignPanel, null);\r
- else\r
+ if (current.getLength() < Width)\r
{\r
- UserColourScheme udc = (UserColourScheme)UserDefinedColours.\r
- getUserColourSchemes().get(e.getActionCommand());\r
-\r
- changeColour(udc);\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
}\r
}\r
\r
- public void updateUserColourMenu()\r
- {\r
-\r
- Component [] menuItems = colourMenu.getMenuComponents();\r
- int i, iSize = menuItems.length;\r
- for(i=0; i<iSize; i++)\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void findMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ JInternalFrame frame = new JInternalFrame();\r
+ Finder finder = new Finder(viewport, alignPanel, frame);\r
+ frame.setContentPane(finder);\r
+ Desktop.addInternalFrame(frame, "Find", 340, 110);\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void font_actionPerformed(ActionEvent e)\r
+ {\r
+ FontChooser fc = new FontChooser(alignPanel);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowFullId(fullSeqId.isSelected());\r
+\r
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setColourText(colourTextMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
+ alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
+ scaleAbove.setVisible(wrapMenuItem.isSelected());\r
+ scaleLeft.setVisible(wrapMenuItem.isSelected());\r
+ scaleRight.setVisible(wrapMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void scaleRight_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleRightWrapped(scaleRight.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowText(viewTextMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
+ {\r
+ viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
+\r
+ if (viewport.showSequenceFeatures &&\r
+ ! ( (Alignment) viewport.alignment).featuresAdded)\r
+ {\r
+ SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.\r
+ alignment,\r
+ alignPanel);\r
+ ( (Alignment) viewport.alignment).featuresAdded = true;\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (annotationPanelMenuItem.isSelected() &&\r
+ viewport.getWrapAlignment())\r
+ {\r
+ annotationPanelMenuItem.setSelected(false);\r
+\r
+ return;\r
+ }\r
+\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void overviewMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (alignPanel.overviewPanel != null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ JInternalFrame frame = new JInternalFrame();\r
+ OverviewPanel overview = new OverviewPanel(alignPanel);\r
+ frame.setContentPane(overview);\r
+ Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
+ frame.getWidth(), frame.getHeight());\r
+ frame.pack();\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
{\r
- if( menuItems[i].getName()!=null && menuItems[i].getName().equals("USER_DEFINED"))\r
- {\r
- colourMenu.remove(menuItems[i]);\r
- iSize--;\r
- }\r
+ alignPanel.setOverviewPanel(null);\r
}\r
- if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
+ ;\r
+ });\r
+\r
+ alignPanel.setOverviewPanel(overview);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void clustalColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new ClustalxColourScheme(\r
+ viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void zappoColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new ZappoColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void taylorColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new TaylorColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new HydrophobicColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void helixColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new HelixColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void strandColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new StrandColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void turnColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new TurnColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void buriedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new BuriedColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void nucleotideColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new NucleotideColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param cs DOCUMENT ME!\r
+ */\r
+ void changeColour(ColourSchemeI cs)\r
+ {\r
+ int threshold = 0;\r
+\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
+ "Background");\r
+\r
+ if (cs instanceof ResidueColourScheme)\r
{\r
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
- getUserColourSchemes().keys();\r
-\r
- while (userColours.hasMoreElements())\r
- {\r
- JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
- nextElement().toString());\r
- radioItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- userDefinedColour_actionPerformed(evt);\r
- }\r
- });\r
- colourMenu.insert(radioItem, 15);\r
- colours.add(radioItem);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new PIDColourScheme());\r
- }\r
+ ( (ResidueColourScheme) cs).setThreshold(threshold,\r
+ viewport.\r
+ getIgnoreGapsConsensus());\r
+ }\r
+ else if (cs instanceof ScoreColourScheme)\r
+ {\r
+ ( (ScoreColourScheme) cs).setThreshold(threshold,\r
+ viewport.getIgnoreGapsConsensus());\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new Blosum62ColourScheme());\r
+ viewport.setGlobalColourScheme(cs);\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+ else if (cs instanceof ResidueColourScheme)\r
{\r
- addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
- AlignmentSorter.sortByPID(viewport.getAlignment(),\r
- viewport.getAlignment().getSequenceAt(0));\r
- alignPanel.repaint();\r
+ ( (ResidueColourScheme) cs).setThreshold(0,\r
+ viewport.getIgnoreGapsConsensus());\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ else if (cs instanceof ScoreColourScheme)\r
{\r
- addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
- AlignmentSorter.sortByID(viewport.getAlignment());\r
- alignPanel.repaint();\r
+ ( (ScoreColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+ if (viewport.getConservationSelected())\r
{\r
- addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
+ ConservationColourScheme ccs = null;\r
\r
- AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- alignPanel.repaint();\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
+\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ ccs = new ConservationColourScheme(c, cs);\r
+\r
+ viewport.setGlobalColourScheme(ccs);\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,\r
+ "Background");\r
+ }\r
+ else\r
{\r
- RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(sp);\r
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
- 100, false);\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ if (cs != null)\r
+ {\r
+ cs.setConsensus(viewport.vconsensus);\r
+ }\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+ if (viewport.getColourAppliesToAllGroups())\r
{\r
- if ((viewport.getSelectionGroup() == null) ||\r
- (viewport.getSelectionGroup().getSize() < 2))\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+\r
+ if (cs == null)\r
+ {\r
+ sg.cs = null;\r
+ }\r
+ else if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ }\r
+ else if (cs instanceof UserColourScheme)\r
{\r
- JOptionPane.showInternalMessageDialog(this,\r
- "You must select at least 2 sequences.", "Invalid Selection",\r
- JOptionPane.WARNING_MESSAGE);\r
+ sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());\r
}\r
else\r
{\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(new PairwiseAlignPanel(viewport));\r
- Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
+ try\r
+ {\r
+ sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
}\r
- }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void PCAMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (((viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() < 4) &&\r
- (viewport.getSelectionGroup().getSize() > 0)) ||\r
- (viewport.getAlignment().getHeight() < 4))\r
+ if (viewport.getAbovePIDThreshold())\r
{\r
- JOptionPane.showInternalMessageDialog(this,\r
- "Principal component analysis must take\n" +\r
- "at least 4 input sequences.",\r
- "Sequence selection insufficient", JOptionPane.WARNING_MESSAGE);\r
+ if (sg.cs instanceof ResidueColourScheme)\r
+ {\r
+ ( (ResidueColourScheme) sg.cs).setThreshold(threshold,\r
+ viewport.getIgnoreGapsConsensus());\r
+ }\r
+ else if (sg.cs instanceof ScoreColourScheme)\r
+ {\r
+ ( (ScoreColourScheme) sg.cs).setThreshold(threshold,\r
+ viewport.getIgnoreGapsConsensus());\r
+ }\r
\r
- return;\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.getWidth()));\r
}\r
\r
- try\r
+ if (viewport.getConservationSelected())\r
{\r
- PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(pcaPanel);\r
- Desktop.addInternalFrame(frame, "Principal component analysis",\r
- 400, 400);\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0,\r
+ viewport.alignment.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c,\r
+ sg.cs);\r
+\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.getWidth()));\r
+ sg.cs = ccs;\r
}\r
- catch (java.lang.OutOfMemoryError ex)\r
+ else if (cs != null)\r
{\r
- JOptionPane.showInternalMessageDialog(this,\r
- "Too many sequences selected\nfor Principal Component Analysis!!",\r
- "Out of memory", JOptionPane.WARNING_MESSAGE);\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.getWidth()));\r
}\r
+ }\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+ if (alignPanel.getOverviewPanel() != null)\r
{\r
- NewTreePanel("AV", "PID", "Average distance tree using PID");\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
- }\r
+ alignPanel.repaint();\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void modifyPID_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getAbovePIDThreshold())\r
{\r
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
+ SliderPanel.setPIDSliderSource(alignPanel,\r
+ viewport.getGlobalColourScheme(),\r
+ "Background");\r
+ SliderPanel.showPIDSlider();\r
}\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getConservationSelected())\r
{\r
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
+ SliderPanel.setConservationSlider(alignPanel,\r
+ viewport.globalColourScheme,\r
+ "Background");\r
+ SliderPanel.showConservationSlider();\r
}\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param type DOCUMENT ME!\r
- * @param pwType DOCUMENT ME!\r
- * @param title DOCUMENT ME!\r
- */\r
- void NewTreePanel(String type, String pwType, String title)\r
- {\r
- final TreePanel tp;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
\r
- if ((viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 3))\r
- {\r
- int s = 0;\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
+ viewport.setAbovePIDThreshold(false);\r
+ abovePIDThreshold.setSelected(false);\r
\r
- /* Decide if the selection is a column region */\r
- while (s < sg.sequences.size())\r
- {\r
- if (((SequenceI) sg.sequences.elementAt(s++)).getLength() < sg.getEndRes())\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "The selected region to create a tree may\nonly contain residues or gaps.\n" +\r
- "Try using the Pad function in the edit menu,\n" +\r
- "or one of the multiple sequence alignment web services.",\r
- "Sequences in selection are not aligned",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
- }\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
\r
- title = title + " on region";\r
- tp = new TreePanel(viewport,\r
- viewport.getSelectionGroup().sequences, type, pwType,\r
- sg.getStartRes(), sg.getEndRes());\r
- }\r
- else\r
- {\r
- //are the sequences aligned?\r
- if (!viewport.alignment.isAligned())\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "The sequences must be aligned before creating a tree.\n" +\r
- "Try using the Pad function in the edit menu,\n" +\r
- "or one of the multiple sequence alignment web services.",\r
- "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ changeColour( ( (ConservationColourScheme) cs).cs);\r
+ }\r
+ else\r
+ {\r
+ changeColour(cs);\r
+ }\r
\r
- return;\r
- }\r
+ modifyConservation_actionPerformed(null);\r
+ }\r
\r
- tp = new TreePanel(viewport,\r
- viewport.getAlignment().getSequences(), type, pwType, 0,\r
- viewport.alignment.getWidth());\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
\r
- addTreeMenuItem(tp, title);\r
- viewport.setCurrentTree(tp.getTree());\r
+ conservationMenuItem.setSelected(false);\r
+ viewport.setConservationSelected(false);\r
\r
- Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
- }\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param title DOCUMENT ME!\r
- * @param order DOCUMENT ME!\r
- */\r
- public void addSortByOrderMenuItem(String title, final AlignmentOrder order)\r
+ if (cs instanceof ConservationColourScheme)\r
{\r
- final JMenuItem item = new JMenuItem("by " + title);\r
- sort.add(item);\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
-\r
- // TODO: JBPNote - have to map order entries to curent SequenceI pointers\r
- AlignmentSorter.sortBy(viewport.getAlignment(), order);\r
- alignPanel.repaint();\r
- }\r
- });\r
+ changeColour( ( (ConservationColourScheme) cs).cs);\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param treePanel DOCUMENT ME!\r
- * @param title DOCUMENT ME!\r
- */\r
- void addTreeMenuItem(final TreePanel treePanel, String title)\r
+ else\r
{\r
- final JMenuItem item = new JMenuItem(title);\r
+ changeColour(cs);\r
+ }\r
\r
- treeCount++;\r
+ modifyPID_actionPerformed(null);\r
+ }\r
\r
- if (treeCount == 1)\r
- {\r
- sort.add(sortByTreeMenu);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void userDefinedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ if (e.getActionCommand().equals("User Defined..."))\r
+ {\r
+ new UserDefinedColours(alignPanel, null);\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
+ getUserColourSchemes().get(e.getActionCommand());\r
\r
- sortByTreeMenu.add(item);\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Tree Sort",\r
- viewport.alignment, HistoryItem.SORT));\r
- AlignmentSorter.sortByTree(viewport.getAlignment(),\r
- treePanel.getTree());\r
- alignPanel.repaint();\r
- }\r
- });\r
+ changeColour(udc);\r
+ }\r
+ }\r
\r
- treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(\r
- javax.swing.event.InternalFrameEvent evt)\r
- {\r
- treeCount--;\r
- sortByTreeMenu.remove(item);\r
+ public void updateUserColourMenu()\r
+ {\r
\r
- if (treeCount == 0)\r
- {\r
- sort.remove(sortByTreeMenu);\r
- }\r
- }\r
- ;\r
- });\r
- viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
- {\r
- public void propertyChange(PropertyChangeEvent evt)\r
- {\r
- if (evt.getPropertyName().equals("alignment"))\r
- {\r
- treePanel.getTree().UpdatePlaceHolders((Vector) evt.getNewValue());\r
- treePanel.repaint();\r
- }\r
- }\r
- });\r
+ Component[] menuItems = colourMenu.getMenuComponents();\r
+ int i, iSize = menuItems.length;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ if (menuItems[i].getName() != null &&\r
+ menuItems[i].getName().equals("USER_DEFINED"))\r
+ {\r
+ colourMenu.remove(menuItems[i]);\r
+ iSize--;\r
+ }\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
{\r
- // TODO:resolve which menu item was actually selected\r
- // Now, check we have enough sequences\r
- SequenceI[] msa = null;\r
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
+ getUserColourSchemes().keys();\r
\r
- if ((viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 1))\r
+ while (userColours.hasMoreElements())\r
+ {\r
+ JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
+ nextElement().toString());\r
+ radioItem.addActionListener(new ActionListener()\r
{\r
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
- int sz;\r
- msa = new SequenceI[sz = seqs.getSize()];\r
-\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
- }\r
- else\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+ colourMenu.insert(radioItem, 15);\r
+ colours.add(radioItem);\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void PIDColour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new PIDColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ {\r
+ changeColour(new Blosum62ColourScheme());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByPID(viewport.getAlignment(),\r
+ viewport.getAlignment().getSequenceAt(0));\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByID(viewport.getAlignment());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+\r
+ AlignmentSorter.sortByGroup(viewport.getAlignment());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(sp);\r
+ Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
+ 100, false);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if ( (viewport.getSelectionGroup() == null) ||\r
+ (viewport.getSelectionGroup().getSize() < 2))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ "You must select at least 2 sequences.",\r
+ "Invalid Selection",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ else\r
+ {\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(new PairwiseAlignPanel(viewport));\r
+ Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void PCAMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if ( ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() < 4) &&\r
+ (viewport.getSelectionGroup().getSize() > 0)) ||\r
+ (viewport.getAlignment().getHeight() < 4))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ "Principal component analysis must take\n" +\r
+ "at least 4 input sequences.",\r
+ "Sequence selection insufficient",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ try\r
+ {\r
+ PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(pcaPanel);\r
+ Desktop.addInternalFrame(frame, "Principal component analysis",\r
+ 400, 400);\r
+ }\r
+ catch (java.lang.OutOfMemoryError ex)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ "Too many sequences selected\nfor Principal Component Analysis!!",\r
+ "Out of memory",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("AV", "PID", "Average distance tree using PID");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param type DOCUMENT ME!\r
+ * @param pwType DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ */\r
+ void NewTreePanel(String type, String pwType, String title)\r
+ {\r
+ final TreePanel tp;\r
+\r
+ if ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 3))\r
+ {\r
+ int s = 0;\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ /* Decide if the selection is a column region */\r
+ while (s < sg.sequences.size())\r
+ {\r
+ if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <\r
+ sg.getEndRes())\r
{\r
- Vector seqs = viewport.getAlignment().getSequences();\r
-\r
- if (seqs.size() > 1)\r
- {\r
- msa = new SequenceI[seqs.size()];\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The selected region to create a tree may\nonly contain residues or gaps.\n" +\r
+ "Try using the Pad function in the edit menu,\n" +\r
+ "or one of the multiple sequence alignment web services.",\r
+ "Sequences in selection are not aligned",\r
+ JOptionPane.WARNING_MESSAGE);\r
\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
- }\r
+ return;\r
}\r
+ }\r
\r
- if (msa != null)\r
- {\r
- jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
- title, msa, false, true);\r
- }\r
+ title = title + " on region";\r
+ tp = new TreePanel(viewport,\r
+ viewport.getSelectionGroup().sequences, type, pwType,\r
+ sg.getStartRes(), sg.getEndRes());\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void ClustalRealign_actionPerformed(ActionEvent e)\r
+ else\r
{\r
- // TODO:resolve which menu item was actually selected\r
- // Now, check we have enough sequences\r
- SequenceI[] msa = null;\r
-\r
- if ((viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 1))\r
- {\r
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
- int sz;\r
- msa = new SequenceI[sz = seqs.getSize()];\r
-\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
- }\r
- else\r
- {\r
- Vector seqs = viewport.getAlignment().getSequences();\r
+ //are the sequences aligned?\r
+ if (!viewport.alignment.isAligned())\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "The sequences must be aligned before creating a tree.\n" +\r
+ "Try using the Pad function in the edit menu,\n" +\r
+ "or one of the multiple sequence alignment web services.",\r
+ "Sequences not aligned",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
\r
- if (seqs.size() > 1)\r
- {\r
- msa = new SequenceI[seqs.size()];\r
+ tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(), type, pwType,\r
+ 0,\r
+ viewport.alignment.getWidth());\r
+ }\r
\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
- }\r
- }\r
+ addTreeMenuItem(tp, title);\r
+ viewport.setCurrentTree(tp.getTree());\r
\r
- if (msa != null)\r
- {\r
- jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
- title, msa, true, true);\r
- }\r
- }\r
+ Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void jpred_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param title DOCUMENT ME!\r
+ * @param order DOCUMENT ME!\r
+ */\r
+ public void addSortByOrderMenuItem(String title, final AlignmentOrder order)\r
+ {\r
+ final JMenuItem item = new JMenuItem("by " + title);\r
+ sort.add(item);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
{\r
- SequenceI seq = null;\r
- SequenceI[] msa = null;\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
\r
- if ((viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 0))\r
- {\r
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
+ // TODO: JBPNote - have to map order entries to curent SequenceI pointers\r
+ AlignmentSorter.sortBy(viewport.getAlignment(), order);\r
+ alignPanel.repaint();\r
+ }\r
+ });\r
+ }\r
\r
- if ((seqs.getSize() == 1) || !viewport.alignment.isAligned())\r
- {\r
- seq = (SequenceI) seqs.getSequenceAt(0);\r
- }\r
- else\r
- {\r
- int sz;\r
- msa = new SequenceI[sz = seqs.getSize()];\r
+ /**\r
+ * Maintain the Order by->Displayed Tree menu.\r
+ * Creates a new menu item for a TreePanel with an appropriate\r
+ * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added\r
+ * to remove the menu item when the treePanel is closed, and adjust\r
+ * the tree leaf to sequence mapping when the alignment is modified.\r
+ * @param treePanel Displayed tree window.\r
+ * @param title SortBy menu item title.\r
+ */\r
+ void addTreeMenuItem(final TreePanel treePanel, String title)\r
+ {\r
+ final JMenuItem item = new JMenuItem(title);\r
\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
- }\r
- }\r
- else\r
- {\r
- Vector seqs = viewport.getAlignment().getSequences();\r
+ treeCount++;\r
\r
- if ((seqs.size() == 1) || !viewport.alignment.isAligned())\r
- {\r
- seq = (SequenceI) seqs.elementAt(0);\r
- }\r
- else\r
- {\r
- msa = new SequenceI[seqs.size()];\r
+ if (treeCount == 1)\r
+ {\r
+ sort.add(sortByTreeMenu);\r
+ }\r
\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
- }\r
- }\r
+ sortByTreeMenu.add(item);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Tree Sort",\r
+ viewport.alignment, HistoryItem.SORT));\r
+ AlignmentSorter.sortByTree(viewport.getAlignment(),\r
+ treePanel.getTree());\r
+ alignPanel.repaint();\r
+ }\r
+ });\r
+\r
+ treePanel.addInternalFrameListener(new javax.swing.event.\r
+ InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ treeCount--;\r
+ sortByTreeMenu.remove(item);\r
\r
- if (msa != null)\r
+ if (treeCount == 0)\r
{\r
- JPredClient ct = new JPredClient(title, msa);\r
+ sort.remove(sortByTreeMenu);\r
}\r
- else if (seq != null)\r
+ }\r
+ ;\r
+ });\r
+ viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
+ {\r
+ public void propertyChange(PropertyChangeEvent evt)\r
+ {\r
+ if (evt.getPropertyName().equals("alignment"))\r
{\r
- JPredClient ct = new JPredClient(title, seq);\r
+ treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());\r
+ treePanel.repaint();\r
}\r
- else\r
+ }\r
+ });\r
+ }\r
+\r
+ /**\r
+ * Work out whether the whole set of sequences\r
+ * or just the selected set will be submitted for multiple alignment.\r
+ *\r
+ */\r
+ private SequenceI[] gatherSequencesForAlignment()\r
+ {\r
+ // Now, check we have enough sequences\r
+ SequenceI[] msa = null;\r
+\r
+ if ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 1))\r
+ {\r
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
+ SequenceGroup seqs = viewport.getSelectionGroup();\r
+ int sz;\r
+ msa = new SequenceI[sz = seqs.getSize()];\r
+\r
+ for (int i = 0; i < sz; i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+ if (seqs.size() > 1)\r
+ {\r
+ msa = new SequenceI[seqs.size()];\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
{\r
- System.err.print(\r
- "JALVIEW ERROR! - Unexpected JPred selection state!\n");\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
}\r
+ }\r
}\r
+ return msa;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
+ /**\r
+ * Decides what is submitted to a secondary structure prediction service,\r
+ * the currently selected sequence, or the currently selected alignment\r
+ * (where the first sequence in the set is the one that the prediction\r
+ * will be for).\r
+ */\r
+ SequenceI[] gatherSeqOrMsaForSecStrPrediction()\r
+ {\r
+ SequenceI seq = null;\r
+ SequenceI[] msa = null;\r
+\r
+ if ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 0))\r
{\r
- // TODO:resolve which menu item was actually selected\r
- // Now, check we have enough sequences\r
- SequenceI[] msa = null;\r
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
+ SequenceGroup seqs = viewport.getSelectionGroup();\r
\r
- if ((viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 1))\r
- {\r
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
- int sz;\r
- msa = new SequenceI[sz = seqs.getSize()];\r
+ if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())\r
+ {\r
+ seq = (SequenceI) seqs.getSequenceAt(0);\r
+ }\r
+ else\r
+ {\r
+ int sz;\r
+ msa = new SequenceI[sz = seqs.getSize()];\r
\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
- }\r
- else\r
+ for (int i = 0; i < sz; i++)\r
{\r
- Vector seqs = viewport.getAlignment().getSequences();\r
-\r
- if (seqs.size() > 1)\r
- {\r
- msa = new SequenceI[seqs.size()];\r
-\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
- }\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
}\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+ if ( (seqs.size() == 1) || !viewport.alignment.isAligned())\r
+ {\r
+ seq = (SequenceI) seqs.elementAt(0);\r
+ }\r
+ else\r
+ {\r
+ msa = new SequenceI[seqs.size()];\r
\r
- if (msa != null)\r
+ for (int i = 0; i < seqs.size(); i++)\r
{\r
- MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,\r
- false, true);\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
}\r
+ }\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
+ if (msa != null)\r
+ {\r
+ return msa;\r
+ }\r
+ else\r
{\r
- // Pick the tree file\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"));\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Select a newick-like tree file");\r
- chooser.setToolTipText("Load a tree file");\r
+ if (seq != null)\r
+ {\r
+ return new SequenceI[]\r
+ {\r
+ seq};\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ // Pick the tree file\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Select a newick-like tree file");\r
+ chooser.setToolTipText("Load a tree file");\r
+\r
+ int value = chooser.showOpenDialog(null);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+\r
+ try\r
+ {\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,\r
+ "File");\r
+ viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "Problem reading tree file",\r
+ ex.getMessage(),\r
+ JOptionPane.WARNING_MESSAGE);\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
\r
- int value = chooser.showOpenDialog(null);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param nf DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public TreePanel ShowNewickTree(NewickFile nf, String title)\r
+ {\r
+ TreePanel tp = null;\r
\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+ try\r
+ {\r
+ nf.parse();\r
\r
- try\r
- {\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,\r
- "File");\r
- viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());\r
- }\r
- catch (Exception ex)\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "Problem reading tree file", ex.getMessage(),\r
- JOptionPane.WARNING_MESSAGE);\r
- ex.printStackTrace();\r
- }\r
- }\r
+ if (nf.getTree() != null)\r
+ {\r
+ tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(), nf,\r
+ "FromFile",\r
+ title);\r
+ Desktop.addInternalFrame(tp, title, 600, 500);\r
+ addTreeMenuItem(tp, title);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param nf DOCUMENT ME!\r
- * @param title DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public TreePanel ShowNewickTree(NewickFile nf, String title)\r
+ return tp;\r
+ }\r
+\r
+ class PrintThread\r
+ extends Thread\r
+ {\r
+ public void run()\r
{\r
- TreePanel tp = null;\r
+ PrinterJob printJob = PrinterJob.getPrinterJob();\r
+ PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
+ printJob.setPrintable(alignPanel, pf);\r
\r
+ if (printJob.printDialog())\r
+ {\r
try\r
{\r
- nf.parse();\r
-\r
- if (nf.getTree() != null)\r
- {\r
- tp = new TreePanel(viewport,\r
- viewport.getAlignment().getSequences(), nf, "FromFile",\r
- title);\r
- Desktop.addInternalFrame(tp, title, 600, 500);\r
- addTreeMenuItem(tp, title);\r
- }\r
+ printJob.print();\r
}\r
- catch (Exception ex)\r
+ catch (Exception PrintException)\r
{\r
- ex.printStackTrace();\r
+ PrintException.printStackTrace();\r
}\r
-\r
- return tp;\r
+ }\r
}\r
+ }\r
+\r
+ /**\r
+ * Generates menu items and listener event actions for web service clients\r
+ *\r
+ */\r
+ public void BuildWebServiceMenu()\r
+ {\r
+ if ( (Desktop.discoverer.services != null)\r
+ && (Desktop.discoverer.services.size() > 0))\r
+ {\r
+ Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");\r
+ Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");\r
+ Vector wsmenu = new Vector();\r
+ if (msaws != null)\r
+ {\r
+ // Add any Multiple Sequence Alignment Services\r
+ final JMenu msawsmenu = new JMenu("Alignment");\r
+ for (int i = 0, j = msaws.size(); i < j; i++)\r
+ {\r
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.\r
+ get(i);\r
+ final JMenuItem method = new JMenuItem(sh.getName());\r
+ method.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] msa = gatherSequencesForAlignment();\r
+ MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,\r
+ false, true);\r
\r
- class PrintThread extends Thread\r
- {\r
- public void run()\r
- {\r
- PrinterJob printJob = PrinterJob.getPrinterJob();\r
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
- printJob.setPrintable(alignPanel, pf);\r
+ }\r
\r
- if (printJob.printDialog())\r
+ });\r
+ msawsmenu.add(method);\r
+ // Deal with services that we know accept partial alignments.\r
+ if (sh.getName().indexOf("lustal") > -1)\r
+ {\r
+ // We know that ClustalWS can accept partial alignments for refinement.\r
+ final JMenuItem methodR = new JMenuItem(sh.getName() + " realign");\r
+ methodR.addActionListener(new ActionListener()\r
{\r
- try\r
- {\r
- printJob.print();\r
- }\r
- catch (Exception PrintException)\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] msa = gatherSequencesForAlignment();\r
+ MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,\r
+ true, true);\r
+\r
+ }\r
+\r
+ });\r
+ msawsmenu.add(methodR);\r
+\r
+ }\r
+ }\r
+ wsmenu.add(msawsmenu);\r
+ }\r
+ if (secstrpr != null)\r
+ {\r
+ // Add any secondary structure prediction services\r
+ final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");\r
+ for (int i = 0, j = secstrpr.size(); i < j; i++)\r
+ {\r
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)\r
+ secstrpr.get(i);\r
+ final JMenuItem method = new JMenuItem(sh.getName());\r
+ method.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();\r
+ if (msa.length == 1)\r
+ {\r
+ // Single Sequence prediction\r
+ jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,\r
+ title, msa[0]);\r
+ }\r
+ else\r
+ {\r
+ if (msa.length > 1)\r
{\r
- PrintException.printStackTrace();\r
+ // Single Sequence prediction\r
+ jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,\r
+ title, msa);\r
}\r
+ }\r
}\r
+ });\r
+ secstrmenu.add(method);\r
}\r
+ wsmenu.add(secstrmenu);\r
+ }\r
+ this.webService.removeAll();\r
+ for (int i = 0, j = wsmenu.size(); i < j; i++)\r
+ {\r
+ webService.add( (JMenu) wsmenu.get(i));\r
+ }\r
+ }\r
+ else\r
+ {\r
+ this.webService.removeAll();\r
+ this.webService.add(this.webServiceNoServices);\r
}\r
+ // TODO: add in rediscovery function\r
+ // TODO: reduce code redundancy.\r
+ // TODO: group services by location as well as function.\r
+ }\r
+\r
}\r
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.io.*;\r
-\r
-import java.awt.*;\r
-import java.awt.datatransfer.*;\r
-import java.awt.dnd.*;\r
-import java.awt.event.*;\r
-\r
-import javax.swing.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Desktop extends jalview.jbgui.GDesktop\r
- implements DropTargetListener\r
-{\r
- /** DOCUMENT ME!! */\r
- public static JDesktopPane desktop;\r
- static int openFrameCount = 0;\r
- static final int xOffset = 30;\r
- static final int yOffset = 30;\r
-\r
- /**\r
- * Creates a new Desktop object.\r
- */\r
- public Desktop()\r
- {\r
- Image image = null;\r
-\r
- try\r
- {\r
- java.net.URL url = getClass().getResource("/images/logo.gif");\r
-\r
- if (url != null)\r
- {\r
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
-\r
- MediaTracker mt = new MediaTracker(this);\r
- mt.addImage(image, 0);\r
- mt.waitForID(0);\r
- setIconImage(image);\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
-\r
- setTitle("Jalview 2005");\r
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
- desktop = new JDesktopPane();\r
- desktop.setBackground(Color.white);\r
- setContentPane(desktop);\r
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
-\r
- // This line prevents Windows Look&Feel resizing all new windows to maximum\r
- // if previous window was maximised\r
- desktop.setDesktopManager(new DefaultDesktopManager());\r
-\r
- Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
- String x = jalview.bin.Cache.getProperty("SCREEN_X");\r
- String y = jalview.bin.Cache.getProperty("SCREEN_Y");\r
- String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");\r
- String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");\r
-\r
- if ((x != null) && (y != null) && (width != null) && (height != null))\r
- {\r
- setBounds(Integer.parseInt(x), Integer.parseInt(y),\r
- Integer.parseInt(width), Integer.parseInt(height));\r
- }\r
- else\r
- {\r
- setBounds((int) (screenSize.width - 900) / 2,\r
- (int) (screenSize.height - 650) / 2, 900, 650);\r
- }\r
-\r
- this.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent evt)\r
- {\r
- quit();\r
- }\r
- });\r
-\r
- this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));\r
-\r
- /////////Add a splashscreen on startup\r
- /////////Add a splashscreen on startup\r
- JInternalFrame frame = new JInternalFrame();\r
-\r
- SplashScreen splash = new SplashScreen(frame, image);\r
- frame.setContentPane(splash);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- addInternalFrame(frame, "", 750, 160, false);\r
- frame.setLocation((int) ((getWidth() - 750) / 2),\r
- (int) ((getHeight() - 160) / 2));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param frame DOCUMENT ME!\r
- * @param title DOCUMENT ME!\r
- * @param w DOCUMENT ME!\r
- * @param h DOCUMENT ME!\r
- */\r
- public static void addInternalFrame(final JInternalFrame frame,\r
- String title, int w, int h)\r
- {\r
- addInternalFrame(frame, title, w, h, true);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param frame DOCUMENT ME!\r
- * @param title DOCUMENT ME!\r
- * @param w DOCUMENT ME!\r
- * @param h DOCUMENT ME!\r
- * @param resizable DOCUMENT ME!\r
- */\r
- public static void addInternalFrame(final JInternalFrame frame,\r
- String title, int w, int h, boolean resizable)\r
- {\r
-\r
- frame.setTitle(title);\r
- frame.setSize(w, h);\r
-\r
- // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN\r
- // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN\r
- // IF JALVIEW IS RUNNING HEADLESS\r
- /////////////////////////////////////////////////\r
- if (System.getProperty("java.awt.headless") != null\r
- && System.getProperty("java.awt.headless").equals("true"))\r
- {\r
- return;\r
- }\r
-\r
-\r
- desktop.add(frame);\r
- openFrameCount++;\r
-\r
- try\r
- {\r
- frame.setSelected(true);\r
- }\r
- catch (java.beans.PropertyVetoException e)\r
- {\r
- }\r
-\r
- frame.setClosable(true);\r
- frame.setResizable(resizable);\r
- frame.setMaximizable(resizable);\r
- frame.setIconifiable(resizable);\r
- frame.setFrameIcon(null);\r
- frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount);\r
- frame.toFront();\r
-\r
- final JMenuItem menuItem = new JMenuItem(title);\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(\r
- javax.swing.event.InternalFrameEvent evt)\r
- {\r
- openFrameCount--;\r
- windowMenu.remove(menuItem);\r
- }\r
- ;\r
- });\r
-\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- frame.setSelected(true);\r
- frame.setIcon(false);\r
- }\r
- catch (java.beans.PropertyVetoException ex)\r
- {\r
- }\r
-\r
- ;\r
- }\r
- });\r
-\r
- frame.setVisible(true);\r
- windowMenu.add(menuItem);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void dragEnter(DropTargetDragEvent evt)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void dragExit(DropTargetEvent evt)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void dragOver(DropTargetDragEvent evt)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void dropActionChanged(DropTargetDragEvent evt)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void drop(DropTargetDropEvent evt)\r
- {\r
- Transferable t = evt.getTransferable();\r
-\r
- if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
- {\r
- return;\r
- }\r
-\r
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
-\r
- try\r
- {\r
- java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
-\r
- for (int i = 0; i < files.size(); i++)\r
- {\r
- String file = files.get(i).toString();\r
- String protocol = "File";\r
- String format = null;\r
-\r
- if (file.endsWith(".jar"))\r
- {\r
- format = "Jalview";\r
-\r
- }\r
- else\r
- {\r
- format = jalview.io.IdentifyFile.Identify(file,\r
- protocol);\r
- }\r
- LoadFile(file, protocol, format);\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]\r
- {\r
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
- "jar"\r
- },\r
- new String[]\r
- {\r
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
- }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Open local file");\r
- chooser.setToolTipText("Open");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- String format = null;\r
- if (chooser.getSelectedFormat().equals("Jalview"))\r
- {\r
- format = "Jalview";\r
- }\r
- else\r
- {\r
- format = IdentifyFile.Identify(choice, "File");\r
- }\r
-\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);\r
- LoadFile(choice, "File", format);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param file DOCUMENT ME!\r
- * @param protocol DOCUMENT ME!\r
- * @param format DOCUMENT ME!\r
- */\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- FileLoader fileLoader = new FileLoader();\r
- fileLoader.LoadFile(file, protocol, format);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String url = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Enter url of input file", "Input alignment from URL",\r
- JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")\r
- .toString();\r
-\r
- if (url == null)\r
- {\r
- return;\r
- }\r
-\r
- if (url.trim().toLowerCase().endsWith(".jar"))\r
- {\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");\r
- Jalview2XML.LoadJalviewAlign(url);\r
- }\r
- else\r
- {\r
-\r
- String format = IdentifyFile.Identify(url, "URL");\r
-\r
- if (format.equals("URL NOT FOUND"))\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Couldn't locate " + url,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
-\r
- LoadFile(url, "URL", format);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setForInput();\r
- Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
- }\r
-\r
- /*\r
- * Exit the program\r
- */\r
- public void quit()\r
- {\r
- jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");\r
- jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");\r
- jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");\r
- jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");\r
- System.exit(0);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void aboutMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- StringBuffer message = new StringBuffer("JalView 2005 version " +\r
- jalview.bin.Cache.getProperty(\r
- "VERSION") +\r
- "; last updated: " +\r
- jalview.bin.\r
- Cache.getDefault("BUILD_DATE", "unknown"));\r
-\r
- if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(\r
- jalview.bin.Cache.getProperty("VERSION")))\r
- {\r
- message.append("\n\n!! Jalview version "\r
- + jalview.bin.Cache.getProperty("LATEST_VERSION")\r
- + " is available for download from http://www.jalview.org !!\n");\r
-\r
- }\r
-\r
- message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +\r
- "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +\r
- "\nFor all issues relating to Jalview, email help@jalview.org" +\r
- "\n\nIf you use JalView, please cite:" +\r
- "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +\r
- "\nBioinformatics, 2004 12;426-7.");\r
-\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-\r
- message.toString(), "About Jalview",\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void documentationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");\r
- javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);\r
-\r
- javax.help.HelpBroker hb = hs.createHelpBroker();\r
- hb.setLocation(new Point(200, 50));\r
- hb.setSize(new Dimension(800, 700));\r
- hb.setCurrentID("home");\r
- hb.setDisplayed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void preferences_actionPerformed(ActionEvent e)\r
- {\r
- new Preferences();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void saveState_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "jar" },\r
- new String[] { "Jalview Project" }, "Jalview Project");\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save State");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- java.io.File choice = chooser.getSelectedFile();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
- Jalview2XML.SaveState(choice);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void loadState_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "jar" },\r
- new String[] { "Jalview Project" }, "Jalview Project");\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Restore state");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getAbsolutePath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
- Jalview2XML.LoadJalviewAlign(choice);\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.io.*;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.dnd.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Desktop extends jalview.jbgui.GDesktop
+ implements DropTargetListener
+{
+ /** DOCUMENT ME!! */
+ public static JDesktopPane desktop;
+ static int openFrameCount = 0;
+ static final int xOffset = 30;
+ static final int yOffset = 30;
+ public static jalview.ws.Discoverer discoverer;
+ /**
+ * Creates a new Desktop object.
+ */
+ public Desktop()
+ {
+ Image image = null;
+
+ try
+ {
+ java.net.URL url = getClass().getResource("/images/logo.gif");
+
+ if (url != null)
+ {
+ image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+
+ MediaTracker mt = new MediaTracker(this);
+ mt.addImage(image, 0);
+ mt.waitForID(0);
+ setIconImage(image);
+ }
+ }
+ catch (Exception ex)
+ {
+ }
+
+ setTitle("Jalview 2005");
+ setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ desktop = new JDesktopPane();
+ desktop.setBackground(Color.white);
+ setContentPane(desktop);
+ desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+
+ // This line prevents Windows Look&Feel resizing all new windows to maximum
+ // if previous window was maximised
+ desktop.setDesktopManager(new DefaultDesktopManager());
+
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+ String x = jalview.bin.Cache.getProperty("SCREEN_X");
+ String y = jalview.bin.Cache.getProperty("SCREEN_Y");
+ String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
+ String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
+
+ if ((x != null) && (y != null) && (width != null) && (height != null))
+ {
+ setBounds(Integer.parseInt(x), Integer.parseInt(y),
+ Integer.parseInt(width), Integer.parseInt(height));
+ }
+ else
+ {
+ setBounds((int) (screenSize.width - 900) / 2,
+ (int) (screenSize.height - 650) / 2, 900, 650);
+ }
+
+ this.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent evt)
+ {
+ quit();
+ }
+ });
+
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+
+ /////////Add a splashscreen on startup
+ /////////Add a splashscreen on startup
+ JInternalFrame frame = new JInternalFrame();
+
+ SplashScreen splash = new SplashScreen(frame, image);
+ frame.setContentPane(splash);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ addInternalFrame(frame, "", 750, 160, false);
+ frame.setLocation((int) ((getWidth() - 750) / 2),
+ (int) ((getHeight() - 160) / 2));
+ discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param frame DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param w DOCUMENT ME!
+ * @param h DOCUMENT ME!
+ */
+ public static void addInternalFrame(final JInternalFrame frame,
+ String title, int w, int h)
+ {
+ addInternalFrame(frame, title, w, h, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param frame DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param w DOCUMENT ME!
+ * @param h DOCUMENT ME!
+ * @param resizable DOCUMENT ME!
+ */
+ public static void addInternalFrame(final JInternalFrame frame,
+ String title, int w, int h, boolean resizable)
+ {
+
+ frame.setTitle(title);
+ frame.setSize(w, h);
+
+ // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
+ // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
+ // IF JALVIEW IS RUNNING HEADLESS
+ /////////////////////////////////////////////////
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ return;
+ }
+
+
+ desktop.add(frame);
+ openFrameCount++;
+
+ try
+ {
+ frame.setSelected(true);
+ }
+ catch (java.beans.PropertyVetoException e)
+ {
+ }
+
+ frame.setClosable(true);
+ frame.setResizable(resizable);
+ frame.setMaximizable(resizable);
+ frame.setIconifiable(resizable);
+ frame.setFrameIcon(null);
+ frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount);
+ frame.toFront();
+
+ final JMenuItem menuItem = new JMenuItem(title);
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ openFrameCount--;
+ windowMenu.remove(menuItem);
+ }
+ ;
+ });
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setSelected(true);
+ frame.setIcon(false);
+ }
+ catch (java.beans.PropertyVetoException ex)
+ {
+ }
+
+ ;
+ }
+ });
+
+ frame.setVisible(true);
+ windowMenu.add(menuItem);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void dragEnter(DropTargetDragEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void dragExit(DropTargetEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void dragOver(DropTargetDragEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void dropActionChanged(DropTargetDragEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void drop(DropTargetDropEvent evt)
+ {
+ Transferable t = evt.getTransferable();
+
+ if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+ {
+ return;
+ }
+
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+
+ try
+ {
+ java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+
+ for (int i = 0; i < files.size(); i++)
+ {
+ String file = files.get(i).toString();
+ String protocol = "File";
+ String format = null;
+
+ if (file.endsWith(".jar"))
+ {
+ format = "Jalview";
+
+ }
+ else
+ {
+ format = jalview.io.IdentifyFile.Identify(file,
+ protocol);
+ }
+ LoadFile(file, protocol, format);
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"),
+ new String[]
+ {
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+ "jar"
+ },
+ new String[]
+ {
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+ }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Open local file");
+ chooser.setToolTipText("Open");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+
+ String format = null;
+ if (chooser.getSelectedFormat().equals("Jalview"))
+ {
+ format = "Jalview";
+ }
+ else
+ {
+ format = IdentifyFile.Identify(choice, "File");
+ }
+
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+ LoadFile(choice, "File", format);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param file DOCUMENT ME!
+ * @param protocol DOCUMENT ME!
+ * @param format DOCUMENT ME!
+ */
+ public void LoadFile(String file, String protocol, String format)
+ {
+ FileLoader fileLoader = new FileLoader();
+ fileLoader.LoadFile(file, protocol, format);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void inputURLMenuItem_actionPerformed(ActionEvent e)
+ {
+ String url = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ "Enter url of input file", "Input alignment from URL",
+ JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")
+ .toString();
+
+ if (url == null)
+ {
+ return;
+ }
+
+ if (url.trim().toLowerCase().endsWith(".jar"))
+ {
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
+ Jalview2XML.LoadJalviewAlign(url);
+ }
+ else
+ {
+
+ String format = IdentifyFile.Identify(url, "URL");
+
+ if (format.equals("URL NOT FOUND"))
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Couldn't locate " + url,
+ "URL not found",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+
+ LoadFile(url, "URL", format);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput();
+ Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+ }
+
+ /*
+ * Exit the program
+ */
+ public void quit()
+ {
+ jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
+ jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
+ jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
+ jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
+ System.exit(0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void aboutMenuItem_actionPerformed(ActionEvent e)
+ {
+ StringBuffer message = new StringBuffer("JalView 2005 version " +
+ jalview.bin.Cache.getProperty(
+ "VERSION") +
+ "; last updated: " +
+ jalview.bin.
+ Cache.getDefault("BUILD_DATE", "unknown"));
+
+ if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
+ jalview.bin.Cache.getProperty("VERSION")))
+ {
+ message.append("\n\n!! Jalview version "
+ + jalview.bin.Cache.getProperty("LATEST_VERSION")
+ + " is available for download from http://www.jalview.org !!\n");
+
+ }
+
+ message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
+ "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
+ "\nFor all issues relating to Jalview, email help@jalview.org" +
+ "\n\nIf you use JalView, please cite:" +
+ "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
+ "\nBioinformatics, 2004 12;426-7.");
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+ message.toString(), "About Jalview",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void documentationMenuItem_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+ javax.help.HelpBroker hb = hs.createHelpBroker();
+ hb.setLocation(new Point(200, 50));
+ hb.setSize(new Dimension(800, 700));
+ hb.setCurrentID("home");
+ hb.setDisplayed(true);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void preferences_actionPerformed(ActionEvent e)
+ {
+ new Preferences();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void saveState_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"), new String[] { "jar" },
+ new String[] { "Jalview Project" }, "Jalview Project");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save State");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ java.io.File choice = chooser.getSelectedFile();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+ Jalview2XML.SaveState(choice);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void loadState_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"), new String[] { "jar" },
+ new String[] { "Jalview Project" }, "Jalview Project");
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Restore state");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getAbsolutePath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+ Jalview2XML.LoadJalviewAlign(choice);
+ }
+ }
+
+}
+
git://source.jalview.org / jalview.git / commitdiff