-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\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
- * AM Waterhouse\r
- *******************/\r
-\r
-\r
-\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 Softwarechang\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.jbgui.GAlignFrame;\r
-import jalview.schemes.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.io.*;\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
import javax.swing.*;\r
-import javax.swing.event.*;\r
-import java.util.*;\r
-import java.awt.datatransfer.*;\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
+import javax.swing.event.AncestorEvent;\r
\r
-public class AlignFrame extends GAlignFrame\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class AlignFrame\r
+ extends GAlignFrame implements ClipboardOwner\r
{\r
- final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\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
+ AlignmentPanel alignPanel;\r
+ AlignViewport viewport;\r
+\r
+ Vector viewports = new Vector();\r
+ Vector alignPanels = new Vector();\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
+ /**\r
+ * Creates a new AlignFrame object.\r
+ *\r
+ * @param al DOCUMENT ME!\r
+ */\r
public AlignFrame(AlignmentI al)\r
{\r
- try{\r
- String ip = java.net.InetAddress.getLocalHost().getHostAddress();\r
- if( !ip.startsWith("10."))\r
- alignMenu.setVisible(false);\r
+ viewport = new AlignViewport(al);\r
+ viewports.add(viewport);\r
+\r
+\r
+ if(viewport.vconsensus==null)\r
+ {\r
+ //Out of memory calculating consensus.\r
+ BLOSUM62Colour.setEnabled(false);\r
+ PIDColour.setEnabled(false);\r
+ conservationMenuItem.setEnabled(false);\r
+ modifyConservation.setEnabled(false);\r
+ abovePIDThreshold.setEnabled(false);\r
+ modifyPID.setEnabled(false);\r
}\r
- catch(java.net.UnknownHostException e){}\r
- viewport = new AlignViewport(al,true,true,false);\r
\r
- String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
- String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");\r
- String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");\r
- if(fontName!=null && fontStyle!=null && fontSize!=null)\r
- viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
+ alignPanel = new AlignmentPanel(this, viewport);\r
+ alignPanels.add(alignPanel);\r
\r
- // add conservation graph to alignment\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");\r
\r
+ if(sortby.equals("Id"))\r
+ sortIDMenuItem_actionPerformed(null);\r
+ else if(sortby.equals("Pairwise Identity"))\r
+ sortPairwiseMenuItem_actionPerformed(null);\r
\r
- alignPanel = new AlignmentPanel(this, viewport);\r
+ // remove(tabbedPane);\r
+ getContentPane().add(alignPanel, BorderLayout.CENTER);\r
\r
- alignPanel.annotationPanel.adjustPanelHeight();\r
- alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
- alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
\r
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
\r
+ // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);\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
- { alignPanel.requestFocus(); }\r
- });\r
+ ///Dataset tab\r
+ /////////////////////////\r
+ if(al.getDataset()==null)\r
+ {\r
+ al.setDataset(null);\r
+ }\r
+ // AlignViewport ds = new AlignViewport(al.getDataset(), true);\r
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ // tabbedPane.add("Dataset", dap);\r
+ // viewports.add(ds);\r
+ // alignPanels.add(dap);\r
+ /////////////////////////\r
\r
+\r
+ viewport.addPropertyChangeListener(new PropertyChangeListener()\r
+ {\r
+ public void propertyChange(PropertyChangeEvent evt)\r
+ {\r
+ if (evt.getPropertyName().equals("alignment"))\r
+ {\r
+ alignmentChanged();\r
+ }\r
}\r
});\r
\r
+\r
+ if (Desktop.desktop != null)\r
+ {\r
+ addServiceListeners();\r
+ setGUINucleotide(al.isNucleotide());\r
+ }\r
}\r
\r
- protected void saveAs_actionPerformed(ActionEvent e)\r
+ /* Set up intrinsic listeners for dynamically generated GUI bits. */\r
+ private void addServiceListeners()\r
{\r
- String suffix [] = null;\r
- if(e.getActionCommand().equals("FASTA"))\r
- suffix = new String[]{"fa", "fasta"};\r
- else if(e.getActionCommand().equals("MSF"))\r
- suffix = new String[]{"msf"};\r
- else if(e.getActionCommand().equals("CLUSTAL"))\r
- suffix = new String[]{"aln"};\r
- else if(e.getActionCommand().equals("BLC"))\r
- suffix = new String[]{"blc"};\r
- else if(e.getActionCommand().equals("PIR"))\r
- suffix = new String[]{"pir"};\r
- else if(e.getActionCommand().equals("PFAM"))\r
- suffix = new String[]{"pfam"};\r
+ final java.beans.PropertyChangeListener thisListener;\r
+ // Do this once to get current state\r
+ 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
+ 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
+ closeMenuItem_actionPerformed(null);\r
+ }\r
+ ;\r
+ });\r
+\r
+ }\r
\r
+ public void setGUINucleotide(boolean nucleotide)\r
+ {\r
+ showTranslation.setVisible( nucleotide );\r
+ sequenceFeatures.setVisible(!nucleotide );\r
+ featureSettings.setVisible( !nucleotide );\r
+ conservationMenuItem.setVisible( !nucleotide );\r
+ modifyConservation.setVisible( !nucleotide );\r
+\r
+ //Deal with separators\r
+ //Remember AlignFrame always starts as protein\r
+ if(nucleotide)\r
+ {\r
+ viewMenu.remove(viewMenu.getItemCount()-2);\r
+ }\r
+ else\r
+ {\r
+ calculateMenu.remove(calculateMenu.getItemCount()-2);\r
+ }\r
+ }\r
\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
- , suffix, e.getActionCommand()+" file");\r
+\r
+ /*\r
+ Added so Castor Mapping file can obtain Jalview Version\r
+ */\r
+ public String getVersion()\r
+ {\r
+ return jalview.bin.Cache.getProperty("VERSION");\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, type, desc, token;\r
+\r
+ int index, start, end;\r
+ StringTokenizer st;\r
+ SequenceFeature sf;\r
+ FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+ int lineNo = 0;\r
+ while ( (line = in.readLine()) != null)\r
+ {\r
+ lineNo++;\r
+ st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() == 2)\r
+ {\r
+ type = st.nextToken();\r
+ UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ continue;\r
+ }\r
+\r
+ while (st.hasMoreElements())\r
+ {\r
+ desc = st.nextToken();\r
+ token = st.nextToken();\r
+ if (!token.equals("ID_NOT_SPECIFIED"))\r
+ {\r
+ index = viewport.alignment.findIndex(viewport.alignment.findName(\r
+ token));\r
+ st.nextToken();\r
+ }\r
+ else\r
+ {\r
+ index = Integer.parseInt(st.nextToken());\r
+ }\r
+\r
+ start = Integer.parseInt(st.nextToken());\r
+ end = Integer.parseInt(st.nextToken());\r
+\r
+ seq = viewport.alignment.getSequenceAt(index);\r
+ start = seq.findIndex(start) - 1;\r
+ end = seq.findIndex(end) - 1;\r
+\r
+ type = st.nextToken();\r
+\r
+ if (fr.getColour(type) == null)\r
+ {\r
+ // Probably the old style groups file\r
+ UserColourScheme ucs = new UserColourScheme(type);\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ }\r
+\r
+\r
+ sf = new SequenceFeature(type, desc, "", start, end);\r
+\r
+ seq.addSequenceFeature(sf);\r
+\r
+\r
+ // sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
+ // sg.addSequence(seq, false);\r
+\r
+ // viewport.alignment.addGroup(sg);\r
+\r
+ }\r
+ }\r
+\r
+ viewport.showSequenceFeatures = true;\r
+\r
+ alignPanel.repaint();\r
+\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println("Error parsing groups file: " + ex);\r
+ }\r
+ }\r
+\r
+ public void fetchSequence_actionPerformed(ActionEvent e)\r
+ {\r
+ new SequenceFetcher(this);\r
+ }\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.\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
+ chooser.setAcceptAllFileFilterUsed(false);\r
chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
+ chooser.setDialogTitle("Save Alignment to file");\r
chooser.setToolTipText("Save");\r
+\r
int value = chooser.showSaveDialog(this);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
- String choice = chooser.getSelectedFile().getPath();\r
+ currentFileFormat = chooser.getSelectedFormat();\r
+\r
+ if (currentFileFormat == null)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "You must select a file format before saving!",\r
+ "File format not specified",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ value = chooser.showSaveDialog(this);\r
+ return;\r
+ }\r
+\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
+ currentFileFormat);\r
+\r
+ String choice = chooser.getSelectedFile().getPath();\r
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
- try{\r
- java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );\r
- out.println(output);\r
- out.close();\r
+\r
+ saveAlignment(choice, currentFileFormat);\r
+ }\r
+ }\r
+\r
+ public boolean saveAlignment(String file, String format)\r
+ {\r
+ if (format.equalsIgnoreCase("Jalview"))\r
+ {\r
+ String shortName = title;\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
- catch(Exception ex){}\r
+\r
+ Jalview2XML.SaveAlignment(this, file, shortName);\r
+\r
+ // USE Jalview2XML to save this file\r
+ return true;\r
}\r
+ else\r
+ {\r
+ String output = new FormatAdapter().formatSequences(format,\r
+ viewport.getAlignment().\r
+ getSequences());\r
+ if (output == null)\r
+ {\r
+ return false;\r
+ }\r
\r
+ try\r
+ {\r
+ java.io.PrintWriter out = new java.io.PrintWriter(\r
+ new java.io.FileWriter(file));\r
+\r
+ out.print(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
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- JInternalFrame frame = new JInternalFrame();\r
- cap.formatForOutput();\r
- frame.setContentPane(cap);\r
- Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
- cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ Desktop.addInternalFrame(cap,\r
+ "Alignment output - " + e.getActionCommand(), 600,\r
+ 500);\r
+ cap.setText(new 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
- HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
- htmlOutput = null;\r
+ new HTMLOutput(viewport,\r
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
}\r
\r
- protected void createPNG_actionPerformed(ActionEvent e)\r
+ public void createImageMap(File file, String image)\r
{\r
- alignPanel.makePNG();\r
+ alignPanel.makePNGImageMap(file, image);\r
}\r
\r
- protected void epsFile_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void createPNG(File f)\r
{\r
- alignPanel.makeEPS();\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
thread.start();\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
- 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
-\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void closeMenuItem_actionPerformed(ActionEvent e)\r
{\r
- try{\r
+ try\r
+ {\r
+ PaintRefresher.components.remove(viewport.alignment);\r
this.setClosed(true);\r
- }catch(Exception ex){}\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
}\r
\r
- Stack historyList = new Stack();\r
- Stack redoList = new Stack();\r
- JMenuBar jMenuBar1 = new JMenuBar();\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
void updateEditMenuBar()\r
{\r
- if(historyList.size()>0)\r
- {\r
- undoMenuItem.setEnabled(true);\r
- Object [] history = (Object[])historyList.get(0);\r
- undoMenuItem.setText("Undo "+history[0]);\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
- Object [] history = (Object[])redoList.get(0);\r
- redoMenuItem.setText("Redo "+history[0]);\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
}\r
}\r
\r
- public void addHistoryItem(String type)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param hi DOCUMENT ME!\r
+ */\r
+ public void addHistoryItem(HistoryItem hi)\r
{\r
- // must make sure we add new sequence objects her, not refs to the existing sequences\r
- redoList.clear();\r
- SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
- for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
- {\r
- seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
- viewport.getAlignment().getSequenceAt(i).getSequence());\r
- }\r
-\r
- historyList.add(0, new Object[]{type, seq} );\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
- Object [] history = (Object[])historyList.remove(0);\r
- // add the redo state before continuing!!\r
- SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
- for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
+ HistoryItem hi = (HistoryItem) historyList.pop();\r
+ redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
+ HistoryItem.HIDE));\r
+ restoreHistoryItem(hi);\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ /**\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.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ // used by undo and redo\r
+ void restoreHistoryItem(HistoryItem hi)\r
+ {\r
+ if (hi.getType() == HistoryItem.SORT)\r
{\r
- seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
- viewport.getAlignment().getSequenceAt(i).\r
- getSequence());\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
- /////////\r
+ else\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
+ {\r
+ SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
\r
- redoList.add(0, new Object[] {history[0], seq});\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
- seq = (SequenceI[]) history[1];\r
- viewport.setAlignment( new Alignment(seq) );\r
- updateEditMenuBar();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\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.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\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
+\r
if (sg == null)\r
+ {\r
return;\r
+ }\r
\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
+ {\r
continue;\r
+ }\r
\r
viewport.alignment.getSequences().setElementAt(temp, i);\r
viewport.alignment.getSequences().setElementAt(seq, i - 1);\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
- alignPanel.repaint();\r
- }\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void lostOwnership(Clipboard clipboard, Transferable contents)\r
+ {\r
+ Desktop.jalviewClipboard = null;\r
+ }\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
+ return;\r
+ }\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+\r
+ Hashtable orderedSeqs = new Hashtable();\r
+ SequenceI[] seqs = new SequenceI[sg.getSize()];\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
+\r
+ int index = 0, startRes, endRes;\r
+ char ch;\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\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
+ //FIND START RES\r
+ //Returns residue following index if gap\r
+ startRes = seq.findPosition(sg.getStartRes());\r
\r
+ //FIND END RES\r
+ //Need to find the residue preceeding index if gap\r
+ endRes = 0;\r
\r
- protected void copy_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getSelectionGroup()==null)\r
- return;\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
- SequenceGroup sg = viewport.getSelectionGroup();\r
+ if (endRes > 0)\r
+ {\r
+ endRes += seq.getStart() - 1;\r
+ }\r
\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- StringBuffer buffer= new StringBuffer();\r
+ seqs[i] = new Sequence(seq.getName(),\r
+ seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),\r
+ startRes,\r
+ endRes);\r
+ seqs[i].setDescription(seq.getDescription());\r
+ seqs[i].setDBRef(seq.getDBRef());\r
+ seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
+ seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
\r
- for(int i=0; i<sg.getSize(); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
- +seq.findPosition( sg.getEndRes() )+ "\t"\r
- +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
- }\r
- c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
+ }\r
\r
+ FastaFile ff = new FastaFile();\r
+ ff.addJVSuffix( viewport.showJVSuffix );\r
+ c.setContents(new StringSelection( ff.print(seqs)), this);\r
+ Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};\r
}\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("Paste");\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
+ 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
String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
- StringTokenizer st = new StringTokenizer(str);\r
- ArrayList seqs = new ArrayList();\r
- while (st.hasMoreElements())\r
+ if(str.length()<1)\r
+ return;\r
+\r
+ String format = IdentifyFile.Identify(str, "Paste");\r
+ SequenceI[] sequences;\r
+\r
+ if(Desktop.jalviewClipboard!=null)\r
+ {\r
+ // The clipboard was filled from within Jalview, we must use the sequences\r
+ // And dataset from the copied alignment\r
+ sequences = (SequenceI[])Desktop.jalviewClipboard[0];\r
+ }\r
+ else\r
+ {\r
+ sequences = new FormatAdapter().readFile(str, "Paste", format);\r
+ }\r
+\r
+ if (newAlignment)\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, end);\r
\r
- if(!newAlignment)\r
- viewport.alignment.addSequence(sequence);\r
+ Alignment alignment = new Alignment(sequences);\r
+\r
+ if(Desktop.jalviewClipboard!=null)\r
+ alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );\r
else\r
- seqs.add(sequence);\r
- }\r
+ alignment.setDataset( null );\r
\r
- if(newAlignment)\r
- {\r
- SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
- seqs.toArray(newSeqs);\r
- AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
- Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
+\r
+ AlignFrame af = new AlignFrame(alignment);\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
+ //!newAlignment\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ Sequence newseq = new Sequence(sequences[i].getName(),\r
+ sequences[i].getSequence(), sequences[i].getStart(),\r
+ sequences[i].getEnd());\r
+ viewport.alignment.addSequence(newseq);\r
+ if(sequences[i].getDatasetSequence()==null)\r
+ {\r
+ ////////////////////////////\r
+ //Datset needs extension;\r
+ /////////////////////////////\r
+ Sequence ds = new Sequence(sequences[i].getName(),\r
+ AlignSeq.extractGaps("-. ", sequences[i].getSequence()),\r
+ sequences[i].getStart(),\r
+ sequences[i].getEnd());\r
+ newseq.setDatasetSequence(ds);\r
+ viewport.alignment.getDataset().addSequence(ds);\r
+ }\r
+\r
+ }\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ // could be anything being pasted in here\r
+ }\r
\r
- }catch(Exception ex){}// could be anything being pasted in here\r
\r
}\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
- addHistoryItem("Delete");\r
+\r
if (viewport.getSelectionGroup() == null)\r
+ {\r
return;\r
+ }\r
\r
- SequenceGroup sg = viewport.getSelectionGroup();\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
+ 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
+ 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
- if(seq.getSequence().length()<1)\r
- viewport.getAlignment().deleteSequence(seq);\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
+ if (seq.getSequence().length() < 1)\r
+ {\r
+ viewport.getAlignment().deleteSequence(seq);\r
+ }\r
else\r
- viewport.getAlignment().getSequences().setElementAt(seq, index);\r
- }\r
+ {\r
+ viewport.getAlignment().getSequences().setElementAt(seq, index);\r
+ }\r
+ }\r
\r
- viewport.setSelectionGroup(null);\r
- viewport.alignment.deleteGroup(sg);\r
- viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
- if(viewport.getAlignment().getHeight()<1)\r
- try\r
- {\r
- this.setClosed(true);\r
- }catch(Exception ex){}\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ viewport.setSelectionGroup(null);\r
+ viewport.alignment.deleteGroup(sg);\r
\r
- }\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
\r
\r
\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- Object [] history = (Object[])redoList.remove(0);\r
- SequenceI[] seq = (SequenceI[]) history[1];\r
- viewport.setAlignment( new Alignment(seq) );\r
- updateEditMenuBar();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
- alignPanel.repaint();\r
+ if (viewport.getAlignment().getHeight() < 1)\r
+ {\r
+ try\r
+ {\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
}\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
-\r
alignPanel.repaint();\r
}\r
\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
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
- sg.setEndRes(viewport.alignment.getWidth());\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);\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
- PaintRefresher.Refresh(null);\r
+ viewport.getColumnSelection().clear();\r
+ viewport.setSelectionGroup(null);\r
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(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
- for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
\r
- PaintRefresher.Refresh(null);\r
- }\r
+ if (sg == null)\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed(null);\r
\r
+ return;\r
+ }\r
\r
- public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.getColumnSelection().clear();\r
- repaint();\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
- addHistoryItem("delete columns");\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
+ colSel.compensateForEdit(0, min);\r
\r
- if(viewport.getSelectionGroup()!=null)\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
+ }\r
\r
Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
{\r
SequenceGroup sg = (SequenceGroup) groups.get(i);\r
- if(!sg.adjustForRemoveLeft(min))\r
+\r
+ if (!sg.adjustForRemoveLeft(min))\r
+ {\r
viewport.alignment.deleteGroup(sg);\r
+ }\r
}\r
\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("delete columns");\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
- if(viewport.getSelectionGroup()!=null)\r
+\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+ }\r
\r
Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); 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
+ if (!sg.adjustForRemoveRight(max))\r
+ {\r
viewport.alignment.deleteGroup(sg);\r
+ }\r
}\r
\r
-\r
-\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
-\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("delete gapped columns");\r
+ addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
+ viewport.alignment, HistoryItem.HIDE));\r
+\r
+ //This is to maintain viewport position on first residue\r
+ //of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\r
viewport.getAlignment().removeGaps();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("delete all gaps");\r
+ addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+ //This is to maintain viewport position on first residue\r
+ //of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\r
+\r
SequenceI current;\r
int jSize;\r
- for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
+\r
+ Vector seqs = null;\r
+\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
- current = viewport.getAlignment().getSequenceAt(i);\r
+ seqs = viewport.getSelectionGroup().sequences;\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes()+1;\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
- for (int j=0; j < jSize; j++)\r
- if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
+\r
+ // Removing a range is much quicker than removing gaps\r
+ // one by one for long sequences\r
+ int j = start;\r
+ int rangeStart=-1, rangeEnd=-1;\r
+\r
+ do\r
+ {\r
+ if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
+ {\r
+ if(rangeStart==-1)\r
+ {\r
+ rangeStart = j;\r
+ rangeEnd = j+1;\r
+ }\r
+ else\r
+ {\r
+ rangeEnd++;\r
+ }\r
+ j++;\r
+ }\r
+ else\r
{\r
- current.deleteCharAt(j);\r
- j--;\r
- jSize--;\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ j-=rangeEnd-rangeStart;\r
+ jSize-=rangeEnd-rangeStart;\r
+ rangeStart = -1;\r
+ rangeEnd = -1;\r
+ }\r
+ else\r
+ j++;\r
}\r
+ }\r
+ while (j < end && j < jSize);\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ }\r
}\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes)-1);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
- public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
+ public void alignmentChanged()\r
+ {\r
+ if(viewport.vconsensus!=null)\r
+ {\r
+ viewport.updateConsensus();\r
+ viewport.updateConservation();\r
+ }\r
+ resetAllColourSchemes();\r
+ if(alignPanel.overviewPanel!=null)\r
+ alignPanel.overviewPanel.updateOverviewImage();\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ void resetAllColourSchemes()\r
{\r
- char thisChar = '-';\r
- char nextChar = '.';\r
- if(viewport.getGapCharacter()=='-')\r
+ ColourSchemeI cs = viewport.globalColourScheme;\r
+ if(cs!=null)\r
{\r
- thisChar = '.';\r
- nextChar = '-';\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
+ resetClustalX(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth());\r
+ }\r
+\r
+ cs.setConsensus(viewport.vconsensus);\r
+ if (cs.conservationApplied())\r
+ {\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+ }\r
}\r
- setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
- viewport.setGapCharacter(thisChar);\r
- alignPanel.repaint();\r
+\r
+ int s, sSize = viewport.alignment.getGroups().size();\r
+ for(s=0; s<sSize; s++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
+ if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
+ {\r
+ ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
+ }\r
+ sg.recalcConservation();\r
+ }\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
+ alignmentChanged();\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, false);\r
+ Desktop.addInternalFrame(frame, "Find", 340, 110);\r
frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
-\r
}\r
\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void font_actionPerformed(ActionEvent e)\r
{\r
- JInternalFrame frame = new JInternalFrame();\r
- FontChooser fc = new FontChooser( alignPanel, frame );\r
- frame.setContentPane(fc);\r
- Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ new FontChooser(alignPanel);\r
}\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void seqLimit_actionPerformed(ActionEvent e)\r
{\r
- viewport.setShowFullId( fullSeqId.isSelected() );\r
+ viewport.setShowJVSuffix(seqLimits.isSelected());\r
\r
- alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
alignPanel.repaint();\r
}\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
+ 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
+ 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
-\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
+ 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
+ viewport.setShowText(viewTextMenuItem.isSelected());\r
alignPanel.repaint();\r
}\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
- if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
+\r
+ if (viewport.showSequenceFeatures)\r
{\r
- AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
- ((Alignment)viewport.alignment).featuresAdded = true;\r
+ new SequenceFeatureFetcher(viewport.\r
+ alignment,\r
+ alignPanel);\r
}\r
+\r
+ featureSettings.setEnabled(true);\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() && viewport.getWrapAlignment())\r
- {\r
- annotationPanelMenuItem.setSelected(false);\r
- return;\r
- }\r
- viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
- alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\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 = alignPanel.getOverviewPanel();\r
- try{\r
- overview = new OverviewPanel(alignPanel, viewport);\r
- frame.setContentPane(overview);\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
- { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
{\r
- alignPanel.setOverviewPanel(null);\r
- };\r
+ alignPanel.setOverviewPanel(null);\r
+ }\r
+ ;\r
});\r
- alignPanel.setOverviewPanel( overview );\r
-\r
- }catch(java.lang.OutOfMemoryError ex)\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
- +"\nTry reducing the font size.",\r
- "Out of memory", JOptionPane.WARNING_MESSAGE);\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
+ changeColour(null);\r
}\r
\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void clustalColour_actionPerformed(ActionEvent e)\r
{\r
- abovePIDThreshold.setSelected(false);\r
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour( new HydrophobicColourScheme() );\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
+ changeColour(new HelixColourScheme());\r
}\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
+ /**\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void buriedColour_actionPerformed(ActionEvent e)\r
{\r
- changeColour(new BuriedColourScheme() );\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
+ /**\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
-\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
+ if(cs!=null)\r
{\r
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
-\r
- if (cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) cs).setThreshold(threshold);\r
- else if (cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) cs).setThreshold(threshold);\r
-\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
- else if (cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) cs).setThreshold(0);\r
- else if (cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) cs).setThreshold(0);\r
-\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
+ "Background");\r
\r
+ cs.setThreshold(threshold,\r
+ viewport.getIgnoreGapsConsensus());\r
\r
- if (viewport.getConservationSelected())\r
- {\r
- ConservationColourScheme ccs = null;\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
+ else\r
+ {\r
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+ }\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
+ if (viewport.getConservationSelected())\r
+ {\r
\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\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
- ccs = new ConservationColourScheme(c, cs);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus( viewport.vconsensus );\r
- viewport.setGlobalColourScheme(ccs);\r
+ cs.setConservation(c);\r
\r
- SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
+ "Background"));\r
+ }\r
+ else\r
+ {\r
+ cs.setConservation(null);\r
+ }\r
\r
- }\r
- else\r
- {\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- if (cs != null)\r
- cs.setConsensus(viewport.vconsensus);\r
- viewport.setGlobalColourScheme(cs);\r
+ cs.setConsensus(viewport.vconsensus);\r
}\r
\r
+ viewport.setGlobalColourScheme(cs);\r
\r
- if(viewport.getColourAppliesToAllGroups())\r
+ if (viewport.getColourAppliesToAllGroups())\r
{\r
Vector groups = viewport.alignment.getGroups();\r
- for(int i=0; i<groups.size(); i++)\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
{\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+\r
+ if (cs == null)\r
+ {\r
+ sg.cs = null;\r
+ continue;\r
+ }\r
\r
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
- ex.printStackTrace();\r
- sg.cs = cs;\r
}\r
+ }\r
\r
- if(viewport.getAbovePIDThreshold())\r
+ if (viewport.getAbovePIDThreshold()\r
+ || cs instanceof PIDColourScheme\r
+ || cs instanceof Blosum62ColourScheme)\r
{\r
- if (sg.cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+ sg.cs.setThreshold(threshold,\r
+ viewport.getIgnoreGapsConsensus());\r
+\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.getWidth()));\r
+ }\r
+ else\r
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
\r
- sg.cs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()) );\r
- }\r
\r
- if( viewport.getConservationSelected() )\r
+ if (viewport.getConservationSelected())\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0, viewport.alignment.getWidth()-1);\r
+ sg.sequences, 0,\r
+ viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
-\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
- sg.cs = ccs;\r
+ sg.cs.setConservation(c);\r
}\r
else\r
- {\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
- }\r
-\r
+ sg.cs.setConservation(null);\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, viewport.getGlobalColourScheme(),\r
- "Background");\r
- SliderPanel.showPIDSlider();\r
- }\r
+ if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
+ {\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 modifyConservation_actionPerformed(ActionEvent e)\r
{\r
- if(viewport.getConservationSelected())\r
+ if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
{\r
- SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
+ SliderPanel.setConservationSlider(alignPanel,\r
+ viewport.globalColourScheme,\r
"Background");\r
SliderPanel.showConservationSlider();\r
}\r
}\r
\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\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
- if(cs instanceof ConservationColourScheme )\r
- changeColour( ((ConservationColourScheme)cs).cs );\r
- else\r
- changeColour( cs );\r
+ changeColour(viewport.getGlobalColourScheme());\r
\r
modifyConservation_actionPerformed(null);\r
}\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
conservationMenuItem.setSelected(false);\r
viewport.setConservationSelected(false);\r
\r
- ColourSchemeI cs = viewport.getGlobalColourScheme();\r
-\r
- if(cs instanceof ConservationColourScheme )\r
- changeColour( ((ConservationColourScheme)cs).cs );\r
- else\r
- changeColour( cs );\r
+ changeColour(viewport.getGlobalColourScheme());\r
\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
+ 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
+ changeColour(udc);\r
+ }\r
+ }\r
\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
+ public void updateUserColourMenu()\r
{\r
- JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
- frame.setContentPane(chooser);\r
- Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );\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
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
+ {\r
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
+ getUserColourSchemes().keys();\r
+\r
+ while (userColours.hasMoreElements())\r
+ {\r
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
+ nextElement().toString());\r
+ radioItem.setName("USER_DEFINED");\r
+ radioItem.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
+\r
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
+ "Remove from default list?",\r
+ "Remove user defined colour",\r
+ JOptionPane.YES_NO_OPTION);\r
+ if(option == JOptionPane.YES_OPTION)\r
+ {\r
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
+ colourMenu.remove(radioItem);\r
+ }\r
+ else\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+ }\r
+ }\r
+ });\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\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
+ changeColour(new PIDColourScheme());\r
}\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
+ changeColour(new Blosum62ColourScheme());\r
}\r
\r
-\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\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("sort");\r
- AlignmentSorter.sortByID( viewport.getAlignment() );\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("sort");\r
+ addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
+ HistoryItem.SORT));\r
+\r
AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- AlignmentSorter.sortGroups(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);\r
+ RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
JInternalFrame frame = new JInternalFrame();\r
frame.setContentPane(sp);\r
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);\r
-\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().getSize()<2)\r
- JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\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
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void PCAMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
- if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
- || viewport.getAlignment().getHeight()<4)\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, "Principal component analysis must take\n"\r
- +"at least 4 input sequences.",\r
- "Sequence selection insufficient",\r
- JOptionPane.WARNING_MESSAGE);\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
- PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(pcaPanel);\r
- Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
- }catch(java.lang.OutOfMemoryError ex)\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
- "Out of memory", JOptionPane.WARNING_MESSAGE);\r
- }\r
-\r
-\r
+ new PCAPanel(viewport);\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
+ /**\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 BLOSUM62PID");\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
- //are the sequences aligned?\r
- if(!viewport.alignment.isAligned())\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
- "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-\r
final TreePanel tp;\r
- if (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize() > 3)\r
+\r
+ if ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 3))\r
{\r
- tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
- pwType,\r
- 0, viewport.alignment.getWidth());\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
+ 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
else\r
{\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- type, pwType, 0, viewport.alignment.getWidth());\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
+ tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(), type, pwType,\r
+ 0,\r
+ viewport.alignment.getWidth());\r
}\r
\r
- addTreeMenuItem(tp, title);\r
+ addTreeMenuItem(tp, title);\r
+ viewport.setCurrentTree(tp.getTree());\r
+\r
+ Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
+ }\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
+ {\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
- Desktop.addInternalFrame(tp, title, 600, 500);\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
+ /**\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
+ treeCount++;\r
+\r
+ if (treeCount == 1)\r
+ {\r
+ sort.add(sortByTreeMenu);\r
+ }\r
+\r
sortByTreeMenu.add(item);\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- addHistoryItem("sort");\r
- AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\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
+ treePanel.addInternalFrameListener(new javax.swing.event.\r
+ InternalFrameAdapter()\r
{\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
{\r
+ treeCount--;\r
sortByTreeMenu.remove(item);\r
- };\r
- });\r
\r
+ if (treeCount == 0)\r
+ {\r
+ sort.remove(sortByTreeMenu);\r
+ }\r
+ }\r
+ ;\r
+ });\r
}\r
\r
-\r
- public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\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
- WebserviceInfo info = new WebserviceInfo("Clustal web service",\r
- "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+\r
- " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."\r
- +" Nucleic Acids Research, submitted, June 1994.",\r
- 450, 150);\r
-\r
- ClustalThread thread = new ClustalThread(info);\r
- thread.start();\r
- }\r
+ // Now, check we have enough sequences\r
+ SequenceI[] msa = null;\r
\r
- class ClustalThread extends Thread\r
+ if ( (viewport.getSelectionGroup() != null) &&\r
+ (viewport.getSelectionGroup().getSize() > 1))\r
{\r
- WebserviceInfo info;\r
- public ClustalThread(WebserviceInfo info)\r
- {this.info = info; }\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
- public void run()\r
+ for (int i = 0; i < sz; i++)\r
{\r
- info.setStatus(WebserviceInfo.STATE_RUNNING);\r
- jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
- Vector sv = viewport.getAlignment().getSequences();\r
- SequenceI[] seqs = new SequenceI[sv.size()];\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
\r
- int i = 0;\r
- do\r
- {\r
- seqs[i] = (SequenceI) sv.elementAt(i);\r
- }\r
- while (++i < sv.size());\r
+ if (seqs.size() > 1)\r
+ {\r
+ msa = new SequenceI[seqs.size()];\r
\r
- SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
- if (alignment != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(alignment));\r
- Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),\r
- NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);\r
- af.clustalColour_actionPerformed(null);\r
- af.clustalColour.setSelected(true);\r
- info.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
- }\r
- else\r
+ for (int i = 0; i < seqs.size(); i++)\r
{\r
- info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- info.appendProgressText("Problem obtaining clustal alignment");\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
}\r
}\r
}\r
-\r
- protected void jpred_actionPerformed(ActionEvent e)\r
-{\r
-\r
- if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
+ return msa;\r
+ }\r
+\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 (predictindex==-1) {\r
+\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "The alignment contains no columns or residues usable for prediction!",\r
+ "Invalid Alignment Selection", JOptionPane.WARNING_MESSAGE);\r
+ this.\r
+ return;\r
+ }\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
- if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
+\r
+ if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())\r
{\r
- JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));\r
+ seq = (SequenceI) seqs.getSequenceAt(0);\r
}\r
else\r
{\r
int sz;\r
- SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\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
- JPredClient ct = new JPredClient(msa);\r
}\r
-\r
}\r
else\r
{\r
Vector seqs = viewport.getAlignment().getSequences();\r
\r
- if (seqs.size() == 1 || !viewport.alignment.isAligned())\r
+ if ( (seqs.size() == 1) || !viewport.alignment.isAligned())\r
{\r
- JPredClient ct = new JPredClient( (SequenceI)\r
- seqs.elementAt(0));\r
+ seq = (SequenceI) seqs.elementAt(0);\r
}\r
else\r
{\r
- SequenceI[] msa = new SequenceI[seqs.size()];\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
- JPredClient ct = new JPredClient(msa);\r
}\r
-\r
}\r
+ if (msa != null)\r
+ {\r
+ return msa;\r
+ }\r
+ else\r
+ {\r
+ if (seq != null)\r
+ {\r
+ return new SequenceI[]\r
+ {\r
+ seq};\r
+ }\r
+ }\r
+ return null;\r
}\r
-\r
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\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("LAST_DIRECTORY"));\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
- TreePanel treepanel = null;\r
+\r
try\r
{\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
- fin.parse();\r
-\r
- if (fin.getTree() != null)\r
- {\r
- TreePanel tp = null;\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- fin, "FromFile", choice);\r
- Desktop.addInternalFrame(tp, title, 600, 500);\r
- addTreeMenuItem(tp, title);\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
}\r
}\r
\r
+\r
+ public TreePanel ShowNewickTree(NewickFile nf, String title)\r
+ {\r
+ return ShowNewickTree(nf,title,600,500,4,5);\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, int w,int h,int x, int y)\r
+ {\r
+ TreePanel tp = null;\r
+\r
+ try\r
+ {\r
+ nf.parse();\r
+\r
+ if (nf.getTree() != null)\r
+ {\r
+ tp = new TreePanel(viewport,\r
+ viewport.getAlignment().getSequences(), nf,\r
+ "FromFile",\r
+ title);\r
+\r
+ tp.setSize(w,h);\r
+\r
+ if(x>0 && y>0)\r
+ tp.setLocation(x,y);\r
+\r
+\r
+ Desktop.addInternalFrame(tp, title, w, h);\r
+ addTreeMenuItem(tp, title);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ return tp;\r
+ }\r
+\r
+ class PrintThread\r
+ 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
+ * Generates menu items and listener event actions for web service clients\r
+ *\r
+ */\r
+ public void BuildWebServiceMenu()\r
+ {\r
+ if ( (Discoverer.services != null)\r
+ && (Discoverer.services.size() > 0))\r
+ {\r
+ Vector msaws = (Vector) Discoverer.services.get("MsaWS");\r
+ Vector secstrpr = (Vector) 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
+ new jalview.ws.MsaWSClient(sh, title, msa,\r
+ false, true, viewport.getAlignment().getDataset());\r
+\r
+ }\r
+\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
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] msa = gatherSequencesForAlignment();\r
+ new jalview.ws.MsaWSClient(sh, title, msa,\r
+ true, true, viewport.getAlignment().getDataset());\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 = SeqsetUtils.getNonEmptySequenceSet(gatherSeqOrMsaForSecStrPrediction());\r
+ if (msa==null) {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "There are no columns or residues usable for prediction!\n"\r
+ +"There must be valid residues in at least one\n"\r
+ +"of the sequences in the alignment,\n"\r
+ +"or in the currently selected region.",\r
+ "Invalid Input for Secondary Structure Prediction",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\r
+\r
+ if (msa.length == 1)\r
+ {\r
+ // Single Sequence prediction\r
+ new jalview.ws.JPredClient(sh,title, msa[0]);\r
+ }\r
+ else\r
+ {\r
+ if (msa.length > 1)\r
+ {\r
+ // Aligned Sequences 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
+ /* public void vamsasStore_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty("LAST_DIRECTORY"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Export to Vamsas file");\r
+ chooser.setToolTipText("Export");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);\r
+ //vs.store(chooser.getSelectedFile().getAbsolutePath() );\r
+ vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);\r
+ }\r
+ }*/\r
+\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
+ new FeatureSettings(viewport, alignPanel);\r
+ }\r
+\r
+\r
+\r
+public void showTranslation_actionPerformed(ActionEvent e)\r
+{\r
+ int s, sSize = viewport.alignment.getHeight();\r
+ SequenceI [] newSeq = new SequenceI[sSize];\r
+\r
+ int res, resSize;\r
+ StringBuffer protein;\r
+ String seq;\r
+ for(s=0; s<sSize; s++)\r
+ {\r
+ protein = new StringBuffer();\r
+ seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());\r
+ resSize = seq.length();\r
+ for(res = 0; res < resSize; res+=3)\r
+ {\r
+ String codon = seq.substring(res, res+3);\r
+ codon = codon.replace('U', 'T');\r
+ String aa = ResidueProperties.codonTranslate(codon);\r
+ if(aa==null)\r
+ protein.append(viewport.getGapCharacter());\r
+ else if(aa.equals("STOP"))\r
+ protein.append("X");\r
+ else\r
+ protein.append( aa );\r
+ }\r
+ newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());\r
+ }\r
+\r
+\r
+ AlignmentI al = new Alignment(newSeq);\r
+ al.setDataset(null);\r
+\r
+\r
+ ////////////////////////////////\r
+ // Copy annotations across\r
+ jalview.datamodel.AlignmentAnnotation[] annotations\r
+ = viewport.alignment.getAlignmentAnnotation();\r
+ int a, aSize;\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+\r
+ if (annotations[i].label.equals("Quality") ||\r
+ annotations[i].label.equals("Conservation") ||\r
+ annotations[i].label.equals("Consensus"))\r
+ {\r
+ continue;\r
+ }\r
+\r
+\r
+ aSize = viewport.alignment.getWidth()/3;\r
+ jalview.datamodel.Annotation [] anots =\r
+ new jalview.datamodel.Annotation[aSize];\r
+\r
+ for(a=0; a<viewport.alignment.getWidth(); a++)\r
+ {\r
+ if( annotations[i].annotations[a]==null\r
+ || annotations[i].annotations[a]==null)\r
+ continue;\r
+\r
+ anots[a/3] = new Annotation(\r
+ annotations[i].annotations[a].displayCharacter,\r
+ annotations[i].annotations[a].description,\r
+ annotations[i].annotations[a].secondaryStructure,\r
+ annotations[i].annotations[a].value,\r
+ annotations[i].annotations[a].colour);\r
+ }\r
+\r
+ jalview.datamodel.AlignmentAnnotation aa\r
+ = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,\r
+ annotations[i].description, anots );\r
+ al.addAnnotation(aa);\r
+ }\r
+\r
+\r
+ AlignFrame af = new AlignFrame(al);\r
+ Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
+ NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
+\r
+\r
+ // AlignViewport newViewport = new AlignViewport(al);\r
+ // AlignmentPanel ap = new AlignmentPanel(this, newViewport);\r
+ // tabbedPane.add("Protein", ap);\r
+ // viewports.add(newViewport);\r
+ // alignPanels.add(ap);\r
+\r
+ ///Dataset tab\r
+ /////////////////////////\r
+\r
+ // AlignViewport ds = new AlignViewport(al.getDataset());\r
+ // ds.setDataset(true);\r
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ // tabbedPane.add("Dataset", dap);\r
+ // viewports.add(ds);\r
+ // alignPanels.add(dap);\r
+ /////////////////////////\r
+\r
+\r
+}\r
+\r
+/*public void tabSelected()\r
+ {\r
+ int index = tabbedPane.getSelectedIndex();\r
+ viewport = (AlignViewport)viewports.elementAt(index);\r
+ alignPanel = (AlignmentPanel)alignPanels.elementAt(index);\r
+ }*/\r
}\r
git://source.jalview.org / jalview.git / blobdiff