*/\r
package jalview.gui;\r
\r
-import java.beans.*;\r
-import java.util.*;\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
\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
-public class AlignFrame\r
- extends GAlignFrame\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class AlignFrame extends GAlignFrame\r
{\r
- public static final int NEW_WINDOW_WIDTH = 700;\r
- public static final int NEW_WINDOW_HEIGHT = 500;\r
- final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
- public String currentFileFormat = "Jalview";\r
- Stack historyList = new Stack();\r
- Stack redoList = new Stack();\r
- private int treeCount = 0;\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
+ /** 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
{\r
- public void run()\r
+ st = new StringTokenizer(line, "\t");\r
+ if(st.countTokens()!=6)\r
{\r
- alignPanel.requestFocus();\r
+ System.out.println("Groups file "+file+" is invalid. Read help file.");\r
+ System.exit(1);\r
}\r
- });\r
- }\r
- });\r
- }\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
+ while(st.hasMoreElements())\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
+\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
+\r
+ sg = new SequenceGroup(text,ucs,true,true,false,start,end);\r
+ sg.addSequence( seq,true);\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
+ {\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
+\r
+ chooser.setAcceptAllFileFilterUsed(false);\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save Alignment to file");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
- }, currentFileFormat);\r
+ currentFileFormat = chooser.getSelectedFormat();\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
+ currentFileFormat);\r
\r
- chooser.setAcceptAllFileFilterUsed(false);\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save Alignment to file");\r
- chooser.setToolTipText("Save");\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
\r
- int value = chooser.showSaveDialog(this);\r
+ saveAlignment(choice, currentFileFormat);\r
+ }\r
+ }\r
\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ public boolean saveAlignment(String file, String format)\r
{\r
- currentFileFormat = chooser.getSelectedFormat();\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
- currentFileFormat);\r
-\r
- if (currentFileFormat.equals("Jalview"))\r
+ if (format.equalsIgnoreCase("Jalview"))\r
{\r
String shortName = title;\r
\r
java.io.File.separatorChar) + 1);\r
}\r
\r
- String choice = chooser.getSelectedFile().getPath();\r
- Jalview2XML.SaveAlignment(this, choice, shortName);\r
+ Jalview2XML.SaveAlignment(this, file, shortName);\r
\r
// USE Jalview2XML to save this file\r
- return;\r
- }\r
-\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
-\r
- String output = FormatAdapter.formatSequences(currentFileFormat,\r
- viewport.getAlignment().getSequences());\r
-\r
- try\r
- {\r
- java.io.PrintWriter out = new java.io.PrintWriter(new java.io.\r
- FileWriter(\r
- choice));\r
- out.println(output);\r
- out.close();\r
+ return true;\r
}\r
- catch (Exception ex)\r
+ else\r
{\r
+ String output = FormatAdapter.formatSequences(format,\r
+ viewport.getAlignment().\r
+ getSequences());\r
+ if(output==null)\r
+ return false;\r
+\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
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
+ return false;\r
}\r
- }\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
- protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- new HTMLOutput(viewport);\r
- }\r
\r
- protected void createPNG_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.makePNG();\r
- }\r
-\r
- protected void epsFile_actionPerformed(ActionEvent e)\r
- {\r
- alignPanel.makeEPS();\r
- }\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
- public void closeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void outputText_actionPerformed(ActionEvent e)\r
{\r
- this.setClosed(true);\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
}\r
- catch (Exception ex)\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
\r
- void updateEditMenuBar()\r
- {\r
- if (historyList.size() > 0)\r
+ public void createImageMap(File file, String image)\r
{\r
- undoMenuItem.setEnabled(true);\r
-\r
- HistoryItem hi = (HistoryItem) historyList.peek();\r
- undoMenuItem.setText("Undo " + hi.getDescription());\r
+ alignPanel.makePNGImageMap(file, image);\r
}\r
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void createPNG(File f)\r
{\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setText("Undo");\r
+ alignPanel.makePNG(f);\r
}\r
\r
- if (redoList.size() > 0)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void createEPS(File f)\r
{\r
- redoMenuItem.setEnabled(true);\r
-\r
- HistoryItem hi = (HistoryItem) redoList.peek();\r
- redoMenuItem.setText("Redo " + hi.getDescription());\r
+ alignPanel.makeEPS(f);\r
}\r
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void printMenuItem_actionPerformed(ActionEvent e)\r
{\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setText("Redo");\r
+ //Putting in a thread avoids Swing painting problems\r
+ PrintThread thread = new PrintThread();\r
+ thread.start();\r
}\r
- }\r
-\r
- public void addHistoryItem(HistoryItem hi)\r
- {\r
- historyList.push(hi);\r
- updateEditMenuBar();\r
- }\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
- 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
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void closeMenuItem_actionPerformed(ActionEvent e)\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
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
}\r
- else\r
- {\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
- {\r
- SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
\r
- if (restore.getLength() == 0)\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ void updateEditMenuBar()\r
+ {\r
+ if (historyList.size() > 0)\r
{\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
- viewport.alignment.getSequences().insertElementAt(restore,\r
- hi.getAlignIndex(i));\r
+ undoMenuItem.setEnabled(true);\r
+\r
+ HistoryItem hi = (HistoryItem) historyList.peek();\r
+ undoMenuItem.setText("Undo " + hi.getDescription());\r
}\r
else\r
{\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setText("Undo");\r
}\r
- }\r
\r
- if (hi.getType() == HistoryItem.PASTE)\r
- {\r
- for (int i = viewport.alignment.getHeight() - 1;\r
- i > (hi.getSequences().size() - 1); i--)\r
+ if (redoList.size() > 0)\r
{\r
- viewport.alignment.deleteSequence(i);\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
- updateEditMenuBar();\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
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- alignPanel.repaint();\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\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
- public void moveSelectedSequences(boolean up)\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\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
- if (sg == null)\r
+ // used by undo and redo\r
+ void restoreHistoryItem(HistoryItem hi)\r
{\r
- return;\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
+ SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\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
+\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
+ updateEditMenuBar();\r
+\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
}\r
\r
- if (up)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param up DOCUMENT ME!\r
+ */\r
+ public void moveSelectedSequences(boolean up)\r
{\r
- for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
- {\r
- SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
\r
- if (!sg.sequences.contains(seq))\r
+ if (sg == null)\r
{\r
- continue;\r
+ return;\r
}\r
\r
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
+ if (up)\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
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
\r
- if (sg.sequences.contains(temp))\r
+ if (sg.sequences.contains(temp))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
+ }\r
+ }\r
+ else\r
{\r
- continue;\r
+ for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+\r
+ if (!sg.sequences.contains(seq))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
+\r
+ if (sg.sequences.contains(temp))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
+ }\r
}\r
\r
- viewport.alignment.getSequences().setElementAt(temp, i);\r
- viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
- }\r
+ alignPanel.repaint();\r
}\r
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void copy_actionPerformed(ActionEvent e)\r
{\r
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
- {\r
- SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
\r
- if (!sg.sequences.contains(seq))\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
- continue;\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.alignment.findIndex(seq);\r
+ orderedSeqs.put(index + "", seq);\r
}\r
\r
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
+ int index = 0;\r
\r
- if (sg.sequences.contains(temp))\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
- continue;\r
+ SequenceI seq = null;\r
+\r
+ while (seq == null)\r
+ {\r
+ if (orderedSeqs.containsKey(index + ""))\r
+ {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ index++;\r
+ }\r
+ }\r
+\r
+ buffer.append(seq.getName() + "\t" +\r
+ seq.findPosition(sg.getStartRes()) + "\t" +\r
+ seq.findPosition(sg.getEndRes()) + "\t" +\r
+ sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
}\r
\r
- viewport.alignment.getSequences().setElementAt(temp, i);\r
- viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
- }\r
+ c.setContents(new StringSelection(buffer.toString()), null);\r
}\r
\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void copy_actionPerformed(ActionEvent e)\r
- {\r
- if (viewport.getSelectionGroup() == null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void pasteNew_actionPerformed(ActionEvent e)\r
{\r
- return;\r
+ paste(true);\r
}\r
\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
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void pasteThis_actionPerformed(ActionEvent e)\r
{\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.alignment.findIndex(seq);\r
- orderedSeqs.put(index + "", seq);\r
+ addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
+ HistoryItem.PASTE));\r
+ paste(false);\r
}\r
\r
- int index = 0;\r
-\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param newAlignment DOCUMENT ME!\r
+ */\r
+ void paste(boolean newAlignment)\r
{\r
- SequenceI seq = null;\r
-\r
- while (seq == null)\r
- {\r
- if (orderedSeqs.containsKey(index + ""))\r
+ try\r
{\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
-\r
- break;\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ Transferable contents = c.getContents(this);\r
+\r
+ if (contents == null)\r
+ {\r
+ return;\r
+ }\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
- else\r
+ catch (Exception ex)\r
{\r
- index++;\r
}\r
- }\r
\r
- buffer.append(seq.getName() + "\t" +\r
- seq.findPosition(sg.getStartRes()) + "\t" +\r
- seq.findPosition(sg.getEndRes()) + "\t" +\r
- sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
- sg.getEndRes() + 1) + "\n");\r
+ // could be anything being pasted in here\r
}\r
\r
- c.setContents(new StringSelection(buffer.toString()), null);\r
- }\r
-\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
- {\r
- paste(true);\r
- }\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
+ * 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
- void paste(boolean newAlignment)\r
- {\r
- try\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void delete_actionPerformed(ActionEvent e)\r
{\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- Transferable contents = c.getContents(this);\r
+ boolean seqsdeleted = false;\r
\r
- if (contents == null)\r
- {\r
- return;\r
- }\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
\r
- String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
- StringTokenizer st = new StringTokenizer(str);\r
- ArrayList seqs = new ArrayList();\r
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
+ HistoryItem.HIDE));\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
+ SequenceGroup sg = viewport.getSelectionGroup();\r
\r
- if (!newAlignment)\r
+ for (int i = 0; i < sg.sequences.size(); i++)\r
{\r
- viewport.alignment.addSequence(sequence);\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.getAlignment().findIndex(seq);\r
+ seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\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
- 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
+ viewport.setSelectionGroup(null);\r
+ viewport.alignment.deleteGroup(sg);\r
\r
- if (title.startsWith("Copied sequences"))\r
+ if (seqsdeleted)\r
{\r
- newtitle = title;\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
}\r
- else\r
+\r
+ viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
+\r
+ if (viewport.getAlignment().getHeight() < 1)\r
{\r
- newtitle = newtitle.concat("- from " + title);\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\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
+ * 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
- // could be anything being pasted in here\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
- protected void cut_actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed(null);\r
- delete_actionPerformed(null);\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
- protected void delete_actionPerformed(ActionEvent e)\r
- {\r
- boolean seqsdeleted = false;\r
+ sg.setEndRes(viewport.alignment.getWidth());\r
+ viewport.setSelectionGroup(sg);\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
+ }\r
\r
- if (viewport.getSelectionGroup() == null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
- return;\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
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
- HistoryItem.HIDE));\r
-\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
-\r
- for (int i = 0; i < sg.sequences.size(); i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.getAlignment().findIndex(seq);\r
- seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
+ SequenceGroup sg = viewport.getSelectionGroup();\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
+ if (sg == null)\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed(null);\r
\r
- viewport.setSelectionGroup(null);\r
- viewport.alignment.deleteGroup(sg);\r
+ return;\r
+ }\r
\r
- if (seqsdeleted)\r
- {\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\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
- viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
+ PaintRefresher.Refresh(null, viewport.alignment);\r
+ }\r
\r
- if (viewport.getAlignment().getHeight() < 1)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
{\r
- try\r
- {\r
- this.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
+ if (colSel.size() > 0)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
+ HistoryItem.HIDE));\r
\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.alignment.deleteAllGroups();\r
- viewport.setSelectionGroup(null);\r
- alignPanel.repaint();\r
- }\r
+ int min = colSel.getMin();\r
+ viewport.getAlignment().trimLeft(min);\r
+ colSel.compensateForEdit(0, min);\r
\r
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = new SequenceGroup();\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
+ }\r
\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
- {\r
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
- }\r
+ Vector groups = viewport.alignment.getGroups();\r
\r
- sg.setEndRes(viewport.alignment.getWidth());\r
- viewport.setSelectionGroup(sg);\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
- }\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\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
+ if (!sg.adjustForRemoveLeft(min))\r
+ {\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+ }\r
\r
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- if(sg==null)\r
- {\r
- selectAllSequenceMenuItem_actionPerformed(null);\r
- return;\r
+ alignPanel.repaint();\r
+ }\r
}\r
\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
{\r
- sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
- }\r
-\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
- }\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
\r
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
+ if (colSel.size() > 0)\r
+ {\r
+ addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
+ HistoryItem.HIDE));\r
\r
- if (colSel.size() > 0)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
- HistoryItem.HIDE));\r
+ int max = colSel.getMax();\r
+ viewport.getAlignment().trimRight(max);\r
\r
- int min = colSel.getMin();\r
- viewport.getAlignment().trimLeft(min);\r
- colSel.compensateForEdit(0, min);\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+ }\r
\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
- }\r
+ Vector groups = viewport.alignment.getGroups();\r
\r
- Vector groups = viewport.alignment.getGroups();\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+ if (!sg.adjustForRemoveRight(max))\r
+ {\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+ }\r
\r
- if (!sg.adjustForRemoveLeft(min))\r
- {\r
- viewport.alignment.deleteGroup(sg);\r
+ alignPanel.repaint();\r
}\r
- }\r
-\r
- alignPanel.repaint();\r
}\r
- }\r
\r
- public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ColumnSelection colSel = viewport.getColumnSelection();\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
- if (colSel.size() > 0)\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 Right", viewport.alignment,\r
- HistoryItem.HIDE));\r
+ addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
+ HistoryItem.HIDE));\r
\r
- int max = colSel.getMax();\r
- viewport.getAlignment().trimRight(max);\r
+ SequenceI current;\r
+ int jSize;\r
\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- viewport.getSelectionGroup().adjustForRemoveRight(max);\r
- }\r
+ Vector seqs = null;\r
\r
- Vector groups = viewport.alignment.getGroups();\r
+ int start = 0;\r
+ int end = viewport.alignment.getWidth();\r
\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+ if (viewport.getSelectionGroup() != null)\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
- if (!sg.adjustForRemoveRight(max))\r
+ for (int i = 0; i < seqs.size(); i++)\r
{\r
- viewport.alignment.deleteGroup(sg);\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);\r
}\r
- }\r
\r
- alignPanel.repaint();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
}\r
- }\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
- 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
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
{\r
- current = viewport.getAlignment().getSequenceAt(i);\r
- jSize = current.getLength();\r
+ addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
+ HistoryItem.HIDE));\r
\r
- for (int j = 0; j < jSize; j++)\r
- {\r
- if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
- {\r
- current.deleteCharAt(j);\r
- j--;\r
- jSize--;\r
- }\r
- }\r
- }\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
\r
- public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
- HistoryItem.HIDE));\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
\r
- SequenceI current;\r
- int Width = viewport.getAlignment().getWidth();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+ alignPanel.repaint();\r
+ }\r
\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
- current = viewport.getAlignment().getSequenceAt(i);\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
- if (current.getLength() < Width)\r
- {\r
- current.insertCharAt(Width-1, viewport.getGapCharacter());\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
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- }\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
- public void font_actionPerformed(ActionEvent e)\r
- {\r
- FontChooser fc = new FontChooser(alignPanel);\r
- }\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
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourText(colourTextMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\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
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleRightWrapped(scaleRight.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowText(viewTextMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\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
- 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
- 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
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(null);\r
- }\r
-\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new ClustalxColourScheme(\r
- viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
- }\r
-\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new ZappoColourScheme());\r
- }\r
-\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TaylorColourScheme());\r
- }\r
-\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HydrophobicColourScheme());\r
- }\r
-\r
- public void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HelixColourScheme());\r
- }\r
-\r
- public void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new StrandColourScheme());\r
- }\r
-\r
- public void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TurnColourScheme());\r
- }\r
-\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new BuriedColourScheme());\r
- }\r
-\r
- public void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new NucleotideColourScheme());\r
- }\r
-\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
- }\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);\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- ( (ScoreColourScheme) cs).setThreshold(threshold);\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
- viewport.setGlobalColourScheme(cs);\r
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
+ alignPanel.repaint();\r
}\r
- else if (cs instanceof ResidueColourScheme)\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
- ( (ResidueColourScheme) cs).setThreshold(0);\r
+ viewport.setColourText(colourTextMenuItem.isSelected());\r
+ alignPanel.repaint();\r
}\r
- else if (cs instanceof ScoreColourScheme)\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
{\r
- ( (ScoreColourScheme) cs).setThreshold(0);\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
- if (viewport.getConservationSelected())\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
{\r
- ConservationColourScheme ccs = null;\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
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus(viewport.vconsensus);\r
- viewport.setGlobalColourScheme(ccs);\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
- ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,\r
- "Background");\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
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
{\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- if (cs != null)\r
- {\r
- cs.setConsensus(viewport.vconsensus);\r
- }\r
+ viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
\r
- viewport.setGlobalColourScheme(cs);\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
- if (viewport.getColourAppliesToAllGroups())\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
- Vector groups = viewport.alignment.getGroups();\r
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\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 (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
+ if (viewport.showSequenceFeatures &&\r
+ !((Alignment) viewport.alignment).featuresAdded)\r
{\r
- try\r
- {\r
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
+ SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment,\r
+ alignPanel);\r
+ ((Alignment) viewport.alignment).featuresAdded = true;\r
}\r
\r
- if (viewport.getAbovePIDThreshold())\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
- if (sg.cs instanceof ResidueColourScheme)\r
- {\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
- }\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- {\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
- }\r
+ annotationPanelMenuItem.setSelected(false);\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- sg.getWidth()));\r
+ return;\r
}\r
\r
- if (viewport.getConservationSelected())\r
- {\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
+ viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
+ }\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
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void overviewMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if (alignPanel.overviewPanel != null)\r
{\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- sg.getWidth()));\r
+ return;\r
}\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
- if (alignPanel.getOverviewPanel() != null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.getOverviewPanel().updateOverviewImage();\r
+ changeColour(null);\r
}\r
\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void modifyPID_actionPerformed(ActionEvent e)\r
- {\r
- if (viewport.getAbovePIDThreshold())\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void clustalColour_actionPerformed(ActionEvent e)\r
{\r
- SliderPanel.setPIDSliderSource(alignPanel,\r
- viewport.getGlobalColourScheme(),\r
- "Background");\r
- SliderPanel.showPIDSlider();\r
+ changeColour(new ClustalxColourScheme(\r
+ viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
}\r
- }\r
\r
- protected void modifyConservation_actionPerformed(ActionEvent e)\r
- {\r
- if (viewport.getConservationSelected())\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void zappoColour_actionPerformed(ActionEvent e)\r
{\r
- SliderPanel.setConservationSlider(alignPanel,\r
- viewport.globalColourScheme,\r
- "Background");\r
- SliderPanel.showConservationSlider();\r
+ changeColour(new ZappoColourScheme());\r
}\r
- }\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
-\r
- if (cs instanceof ConservationColourScheme)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void taylorColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour( ( (ConservationColourScheme) cs).cs);\r
+ changeColour(new TaylorColourScheme());\r
}\r
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour(cs);\r
+ changeColour(new HydrophobicColourScheme());\r
}\r
\r
- modifyConservation_actionPerformed(null);\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
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\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
- conservationMenuItem.setSelected(false);\r
- viewport.setConservationSelected(false);\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
- ColourSchemeI cs = viewport.getGlobalColourScheme();\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
- if (cs instanceof ConservationColourScheme)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void nucleotideColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour( ( (ConservationColourScheme) cs).cs);\r
+ changeColour(new NucleotideColourScheme());\r
}\r
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
{\r
- changeColour(cs);\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
}\r
\r
- modifyPID_actionPerformed(null);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param cs DOCUMENT ME!\r
+ */\r
+ void changeColour(ColourSchemeI cs)\r
+ {\r
+ int threshold = 0;\r
\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- new UserDefinedColours(alignPanel, null);\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);\r
+ }\r
+ else if (cs instanceof ScoreColourScheme)\r
+ {\r
+ ((ScoreColourScheme) cs).setThreshold(threshold);\r
+ }\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
+ else if (cs instanceof ResidueColourScheme)\r
+ {\r
+ ((ResidueColourScheme) cs).setThreshold(0);\r
+ }\r
+ else if (cs instanceof ScoreColourScheme)\r
+ {\r
+ ((ScoreColourScheme) cs).setThreshold(0);\r
+ }\r
\r
- public void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new PIDColourScheme());\r
- }\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ ConservationColourScheme ccs = null;\r
\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new Blosum62ColourScheme());\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
- 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
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\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
+ ccs = new ConservationColourScheme(c, cs);\r
\r
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
+ // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
+ ccs.setConsensus(viewport.vconsensus);\r
+ viewport.setGlobalColourScheme(ccs);\r
\r
- // AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- AlignmentSorter.sortGroups(viewport.getAlignment());\r
- alignPanel.repaint();\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
- 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
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
\r
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if ( (viewport.getSelectionGroup() == null) ||\r
- (viewport.getSelectionGroup().getSize() < 2))\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);\r
+ }\r
+ else if (sg.cs instanceof ScoreColourScheme)\r
+ {\r
+ ((ScoreColourScheme) sg.cs).setThreshold(threshold);\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
- JOptionPane.showInternalMessageDialog(this,\r
- "You must select at least 2 sequences.",\r
- "Invalid Selection",\r
- JOptionPane.WARNING_MESSAGE);\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ SliderPanel.setPIDSliderSource(alignPanel,\r
+ viewport.getGlobalColourScheme(), "Background");\r
+ SliderPanel.showPIDSlider();\r
+ }\r
}\r
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void modifyConservation_actionPerformed(ActionEvent e)\r
{\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(new PairwiseAlignPanel(viewport));\r
- Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ SliderPanel.setConservationSlider(alignPanel,\r
+ viewport.globalColourScheme, "Background");\r
+ SliderPanel.showConservationSlider();\r
+ }\r
}\r
- }\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
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\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
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
\r
- return;\r
- }\r
+ viewport.setAbovePIDThreshold(false);\r
+ abovePIDThreshold.setSelected(false);\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
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("AV", "PID", "Average distance tree using PID");\r
- }\r
-\r
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
- }\r
-\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
- }\r
-\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
- }\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
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\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
+ if (cs instanceof ConservationColourScheme)\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
+ changeColour(((ConservationColourScheme) cs).cs);\r
+ }\r
+ else\r
+ {\r
+ changeColour(cs);\r
}\r
- }\r
\r
- title = title + " on region";\r
- tp = new TreePanel(viewport,\r
- viewport.getSelectionGroup().sequences, type, pwType,\r
- sg.getStartRes(), sg.getEndRes());\r
+ modifyConservation_actionPerformed(null);\r
}\r
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)\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",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
\r
- tp = new TreePanel(viewport,\r
- viewport.getAlignment().getSequences(), type, pwType,\r
- 0,\r
- viewport.alignment.getWidth());\r
- }\r
+ conservationMenuItem.setSelected(false);\r
+ viewport.setConservationSelected(false);\r
\r
- addTreeMenuItem(tp, title);\r
- viewport.setCurrentTree(tp.getTree());\r
+ ColourSchemeI cs = viewport.getGlobalColourScheme();\r
\r
- Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
- }\r
+ if (cs instanceof ConservationColourScheme)\r
+ {\r
+ changeColour(((ConservationColourScheme) cs).cs);\r
+ }\r
+ else\r
+ {\r
+ changeColour(cs);\r
+ }\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
+ modifyPID_actionPerformed(null);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
+ new UserDefinedColours(alignPanel, null);\r
+ }\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
- }\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
- void addTreeMenuItem(final TreePanel treePanel, String title)\r
- {\r
- final JMenuItem item = new JMenuItem(title);\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
- treeCount++;\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
- if (treeCount == 1)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
{\r
- sort.add(sortByTreeMenu);\r
+ addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+ AlignmentSorter.sortByID(viewport.getAlignment());\r
+ alignPanel.repaint();\r
}\r
\r
- sortByTreeMenu.add(item);\r
- item.addActionListener(new java.awt.event.ActionListener()\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)\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
+ addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+\r
+ AlignmentSorter.sortByGroup(viewport.getAlignment());\r
alignPanel.repaint();\r
- }\r
- });\r
+ }\r
\r
- treePanel.addInternalFrameListener(new javax.swing.event.\r
- InternalFrameAdapter()\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
{\r
- public void internalFrameClosed(\r
- javax.swing.event.InternalFrameEvent evt)\r
- {\r
- treeCount--;\r
- sortByTreeMenu.remove(item);\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
- if (treeCount == 0)\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
- sort.remove(sortByTreeMenu);\r
+ JOptionPane.showInternalMessageDialog(this,\r
+ "You must select at least 2 sequences.", "Invalid Selection",\r
+ JOptionPane.WARNING_MESSAGE);\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
+ else\r
{\r
- treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());\r
- treePanel.repaint();\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(new PairwiseAlignPanel(viewport));\r
+ Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
}\r
- }\r
- });\r
- }\r
-\r
- public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void PCAMenuItem_actionPerformed(ActionEvent e)\r
{\r
- Vector seqs = viewport.getAlignment().getSequences();\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", JOptionPane.WARNING_MESSAGE);\r
\r
- if (seqs.size() > 1)\r
- {\r
- msa = new SequenceI[seqs.size()];\r
+ return;\r
+ }\r
\r
- for (int i = 0; i < seqs.size(); i++)\r
+ try\r
{\r
- msa[i] = (SequenceI) seqs.elementAt(i);\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", JOptionPane.WARNING_MESSAGE);\r
}\r
- }\r
}\r
\r
- if (msa != null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
{\r
- jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
- title, msa, false, true);\r
+ NewTreePanel("AV", "PID", "Average distance tree using PID");\r
}\r
- }\r
\r
- public void ClustalRealign_actionPerformed(ActionEvent e)\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
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\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
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
+ }\r
\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\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
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
{\r
- Vector seqs = viewport.getAlignment().getSequences();\r
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
+ }\r
\r
- if (seqs.size() > 1)\r
- {\r
- msa = new SequenceI[seqs.size()];\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
- for (int i = 0; i < seqs.size(); i++)\r
+ if ((viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 3))\r
{\r
- msa[i] = (SequenceI) seqs.elementAt(i);\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() < 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
+\r
+ title = title + " on region";\r
+ tp = new TreePanel(viewport,\r
+ viewport.getSelectionGroup().sequences, type, pwType,\r
+ sg.getStartRes(), sg.getEndRes());\r
}\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
+\r
+ return;\r
+ }\r
+\r
+ tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(), type, pwType, 0,\r
+ viewport.alignment.getWidth());\r
+ }\r
+\r
+ addTreeMenuItem(tp, title);\r
+ viewport.setCurrentTree(tp.getTree());\r
+\r
+ Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
}\r
\r
- if (msa != null)\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
- jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
- title, msa, true, true);\r
- }\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
- protected void jpred_actionPerformed(ActionEvent e)\r
- {\r
- SequenceI seq = null;\r
- SequenceI[] msa = null;\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 ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 0))\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
{\r
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
+ final JMenuItem item = new JMenuItem(title);\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
+ treeCount++;\r
\r
- for (int i = 0; i < sz; i++)\r
+ if (treeCount == 1)\r
{\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ sort.add(sortByTreeMenu);\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
+ 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.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ treeCount--;\r
+ sortByTreeMenu.remove(item);\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
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\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
\r
- for (int i = 0; i < seqs.size(); i++)\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
+ }\r
+\r
+ if (msa != null)\r
{\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
+ jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
+ title, msa, false, true);\r
}\r
- }\r
}\r
\r
- if (msa != null)\r
- {\r
- JPredClient ct = new JPredClient(title, msa);\r
- }\r
- else if (seq != null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void ClustalRealign_actionPerformed(ActionEvent e)\r
{\r
- JPredClient ct = new JPredClient(title, seq);\r
- }\r
- else\r
- {\r
- System.err.print(\r
- "JALVIEW ERROR! - Unexpected JPred selection state!\n");\r
- }\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
\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- // TODO:resolve which menu item was actually selected\r
- // Now, check we have enough sequences\r
- SequenceI[] msa = null;\r
+ if (seqs.size() > 1)\r
+ {\r
+ msa = new SequenceI[seqs.size()];\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
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+ }\r
+ }\r
\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
+ if (msa != null)\r
+ {\r
+ jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
+ title, msa, true, true);\r
+ }\r
}\r
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void jpred_actionPerformed(ActionEvent e)\r
{\r
- Vector seqs = viewport.getAlignment().getSequences();\r
+ SequenceI seq = null;\r
+ SequenceI[] msa = null;\r
\r
- if (seqs.size() > 1)\r
- {\r
- msa = new SequenceI[seqs.size()];\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
+\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
+ }\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
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+ }\r
+ }\r
\r
- for (int i = 0; i < seqs.size(); i++)\r
+ if (msa != null)\r
{\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
+ JPredClient ct = new JPredClient(title, msa);\r
+ }\r
+ else if (seq != null)\r
+ {\r
+ JPredClient ct = new JPredClient(title, seq);\r
+ }\r
+ else\r
+ {\r
+ System.err.print(\r
+ "JALVIEW ERROR! - Unexpected JPred selection state!\n");\r
}\r
- }\r
}\r
\r
- if (msa != null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
{\r
- MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,\r
- false, true);\r
- }\r
- }\r
+ // TODO:resolve which menu item was actually selected\r
+ // Now, check we have enough sequences\r
+ SequenceI[] msa = null;\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
+ 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
- int value = chooser.showOpenDialog(null);\r
+ if (seqs.size() > 1)\r
+ {\r
+ msa = new SequenceI[seqs.size()];\r
\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+ }\r
+ }\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
+ if (msa != null)\r
+ {\r
+ MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,\r
+ false, true);\r
+ }\r
}\r
- }\r
\r
- public TreePanel ShowNewickTree(NewickFile nf, String title)\r
- {\r
- TreePanel tp = null;\r
- try\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
{\r
- nf.parse();\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
+ // 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
+\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", ex.getMessage(),\r
+ JOptionPane.WARNING_MESSAGE);\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
}\r
- return tp;\r
- }\r
\r
- class PrintThread\r
- extends Thread\r
- {\r
- public void run()\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
- PrinterJob printJob = PrinterJob.getPrinterJob();\r
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
- printJob.setPrintable(alignPanel, pf);\r
+ TreePanel tp = null;\r
\r
- if (printJob.printDialog())\r
- {\r
try\r
{\r
- printJob.print();\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
}\r
- catch (Exception PrintException)\r
+ catch (Exception ex)\r
{\r
- PrintException.printStackTrace();\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ return tp;\r
+ }\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
+ if (printJob.printDialog())\r
+ {\r
+ try\r
+ {\r
+ printJob.print();\r
+ }\r
+ catch (Exception PrintException)\r
+ {\r
+ PrintException.printStackTrace();\r
+ }\r
+ }\r
}\r
- }\r
}\r
- }\r
}\r
git://source.jalview.org / jalview.git / blobdiff