-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Softwarechang\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\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
-\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 java.awt.dnd.*;\r
-import org.biojava.dasobert.eventmodel.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class AlignFrame\r
- extends GAlignFrame implements DropTargetListener, FeatureListener\r
-{\r
- /** DOCUMENT ME!! */\r
- public static final int NEW_WINDOW_WIDTH = 700;\r
-\r
- /** DOCUMENT ME!! */\r
- public static final int NEW_WINDOW_HEIGHT = 500;\r
- AlignmentPanel alignPanel;\r
- 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
- * new alignment window with hidden columns\r
- * @param al AlignmentI\r
- * @param hiddenColumns ColumnSelection or null\r
- */\r
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {\r
-\r
- viewport = new AlignViewport(al, hiddenColumns);\r
-\r
- this.setDropTarget(new java.awt.dnd.DropTarget(this, this));\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
-\r
- alignPanel = new AlignmentPanel(this, viewport);\r
-\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
- // remove(tabbedPane);\r
- getContentPane().add(alignPanel, BorderLayout.CENTER);\r
-\r
-\r
-\r
- // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);\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
- if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))\r
- {\r
- wrapMenuItem.setSelected(true);\r
- wrapMenuItem_actionPerformed(null);\r
- }\r
-\r
- }\r
-\r
-\r
- /**\r
- * Creates a new AlignFrame object.\r
- *\r
- * @param al DOCUMENT ME!\r
- */\r
- public AlignFrame(AlignmentI al)\r
- {\r
- this(al, null);\r
- }\r
-\r
- public AlignViewport getViewport()\r
- {\r
- return viewport;\r
- }\r
-\r
- /* Set up intrinsic listeners for dynamically generated GUI bits. */\r
- private void addServiceListeners()\r
- {\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
- 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
- //Remember AlignFrame always starts as protein\r
- if(!nucleotide)\r
- {\r
- calculateMenu.remove(calculateMenu.getItemCount()-2);\r
- }\r
- }\r
-\r
- public void comeBackLater(FeatureEvent evt)\r
- {}\r
-\r
- public void newFeatures(FeatureEvent evt)\r
- {\r
- if (evt.getFeatures().length > 0)\r
- {\r
- alignPanel.seqPanel.seqCanvas.fr.featuresAdded();\r
- alignPanel.repaint();\r
- }\r
- }\r
-\r
- Hashtable progressBars;\r
- public void setProgressBar(String message, long id)\r
- {\r
- if(progressBars == null)\r
- progressBars = new Hashtable();\r
-\r
- JPanel progressPanel;\r
- GridLayout layout = (GridLayout) statusPanel.getLayout();\r
- if(progressBars.get( new Long(id) )!=null)\r
- {\r
- progressPanel = (JPanel)progressBars.get( new Long(id) );\r
- statusPanel.remove(progressPanel);\r
- progressBars.remove( progressPanel );\r
- progressPanel = null;\r
- if(message!=null)\r
- statusBar.setText(message);\r
-\r
- layout.setRows(layout.getRows() - 1);\r
- }\r
- else\r
- {\r
- progressPanel = new JPanel(new BorderLayout(10, 5));\r
-\r
- JProgressBar progressBar = new JProgressBar();\r
- progressBar.setIndeterminate(true);\r
-\r
- progressPanel.add(new JLabel(message), BorderLayout.WEST);\r
- progressPanel.add(progressBar, BorderLayout.CENTER);\r
-\r
- layout.setRows(layout.getRows() + 1);\r
- statusPanel.add(progressPanel);\r
-\r
- progressBars.put(new Long(id), progressPanel);\r
- }\r
-\r
- validate();\r
- }\r
-\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
- public FeatureRenderer getFeatureRenderer()\r
- {\r
- return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
- }\r
-\r
-\r
- public void fetchSequence_actionPerformed(ActionEvent e)\r
- {\r
- new SequenceFetcher(this);\r
- }\r
-\r
- public void addFromFile_actionPerformed(ActionEvent e)\r
- {\r
- Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);\r
- }\r
-\r
- public void addFromText_actionPerformed(ActionEvent e)\r
- {\r
- Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);\r
- }\r
-\r
- public void addFromURL_actionPerformed(ActionEvent e)\r
- {\r
- Desktop.instance.inputURLMenuItem_actionPerformed(viewport);\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( "LAST_DIRECTORY"),\r
- new String[]\r
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },\r
- new String[]\r
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },\r
- currentFileFormat,\r
- false);\r
-\r
-\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
- 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
-\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
-\r
- new Jalview2XML().SaveAlignment(this, file, shortName);\r
-\r
- // USE Jalview2XML to save this file\r
- return true;\r
- }\r
- else\r
- {\r
-\r
- String[] omitHidden = null;\r
-\r
- if (viewport.hasHiddenColumns)\r
- {\r
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
- "The Alignment contains hidden columns."\r
- + "\nDo you want to save only the visible alignment?",\r
- "Save / Omit Hidden Columns",\r
- JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
-\r
- if (reply == JOptionPane.YES_OPTION)\r
- omitHidden = viewport.getViewAsString(false);\r
- }\r
-\r
- String output = new FormatAdapter().formatSequences(\r
- format,\r
- viewport.alignment.getSequencesArray(),\r
- omitHidden);\r
-\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
- this.setTitle(file);\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
- String [] omitHidden = null;\r
-\r
- if(viewport.hasHiddenColumns)\r
- {\r
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
- "The Alignment contains hidden columns."\r
- +"\nDo you want to output only the visible alignment?",\r
- "Save / Omit Hidden Columns",\r
- JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
-\r
- if(reply==JOptionPane.YES_OPTION)\r
- {\r
- omitHidden = viewport.getViewAsString(false);\r
- }\r
- }\r
-\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- Desktop.addInternalFrame(cap,\r
- "Alignment output - " + e.getActionCommand(), 600,\r
- 500);\r
-\r
-\r
- cap.setText(new FormatAdapter().formatSequences(\r
- e.getActionCommand(),\r
- viewport.alignment.getSequencesArray(),\r
- omitHidden));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- new HTMLOutput(viewport,\r
- alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),\r
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
- }\r
-\r
- public void createImageMap(File file, String image)\r
- {\r
- alignPanel.makePNGImageMap(file, image);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void createPNG(File f)\r
- {\r
- alignPanel.makePNG(f);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void createEPS(File f)\r
- {\r
- alignPanel.makeEPS(f);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void printMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- //Putting in a thread avoids Swing painting problems\r
- PrintThread thread = new PrintThread();\r
- thread.start();\r
- }\r
-\r
- public void exportFeatures_actionPerformed(ActionEvent e)\r
- {\r
- new AnnotationExporter().exportFeatures(alignPanel);\r
- }\r
-\r
-\r
- public void exportAnnotations_actionPerformed(ActionEvent e)\r
- {\r
- new AnnotationExporter().exportAnnotations(\r
- alignPanel,\r
- viewport.alignment.getAlignmentAnnotation()\r
- );\r
- }\r
-\r
-\r
- public void associatedData_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("Load Jalview Annotations or Features File");\r
- chooser.setToolTipText("Load Jalview Annotations / Features 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
- loadJalviewDataFile(choice);\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
- {\r
- PaintRefresher.components.remove(viewport.alignment);\r
- this.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- void updateEditMenuBar()\r
- {\r
- if (historyList.size() > 0)\r
- {\r
- undoMenuItem.setEnabled(true);\r
-\r
- HistoryItem hi = (HistoryItem) historyList.peek();\r
- undoMenuItem.setText("Undo " + hi.getDescription());\r
- }\r
- else\r
- {\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setText("Undo");\r
- }\r
-\r
- if (redoList.size() > 0)\r
- {\r
- redoMenuItem.setEnabled(true);\r
-\r
- HistoryItem hi = (HistoryItem) redoList.peek();\r
- redoMenuItem.setText("Redo " + hi.getDescription());\r
- }\r
- else\r
- {\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setText("Redo");\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param hi DOCUMENT ME!\r
- */\r
- public void addHistoryItem(HistoryItem hi)\r
- {\r
- historyList.push(hi);\r
- updateEditMenuBar();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- HistoryItem hi = (HistoryItem) historyList.pop();\r
- redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
- HistoryItem.HIDE));\r
- restoreHistoryItem(hi);\r
- 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
-\r
- hi.restore();\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.getSequences(false).contains(seq))\r
- {\r
- continue;\r
- }\r
-\r
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
-\r
- if (sg.getSequences(false).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
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
- {\r
- SequenceI seq = viewport.alignment.getSequenceAt(i);\r
-\r
- if (!sg.getSequences(false).contains(seq))\r
- {\r
- continue;\r
- }\r
-\r
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
-\r
- if (sg.getSequences(false).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
-\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
- SequenceI [] seqs = viewport.getSelectionAsNewSequence();\r
- String[] omitHidden = null;\r
-\r
- if (viewport.hasHiddenColumns)\r
- {\r
- omitHidden = viewport.getViewAsString(true);\r
- }\r
-\r
- String output = new FormatAdapter().formatSequences(\r
- "Fasta",\r
- seqs,\r
- omitHidden);\r
-\r
-\r
- Toolkit.getDefaultToolkit().getSystemClipboard()\r
- .setContents(new StringSelection(output), Desktop.instance);\r
-\r
- Vector hiddenColumns = null;\r
- if(viewport.hasHiddenColumns)\r
- {\r
- hiddenColumns =new Vector();\r
- int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
- for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)\r
- {\r
- int[] region = (int[])\r
- viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
-\r
- hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,\r
- region[1]-hiddenOffset});\r
- }\r
- }\r
-\r
- Desktop.jalviewClipboard = new Object[]{ seqs,\r
- viewport.alignment.getDataset(),\r
- hiddenColumns};\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
- {\r
- paste(true);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
- HistoryItem.PASTE));\r
- paste(false);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param newAlignment DOCUMENT ME!\r
- */\r
- void paste(boolean newAlignment)\r
- {\r
- try\r
- {\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- Transferable contents = c.getContents(this);\r
-\r
- if (contents == null)\r
- {\r
- return;\r
- }\r
-\r
- String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
- if(str.length()<1)\r
- return;\r
-\r
- String format = new IdentifyFile().Identify(str, "Paste");\r
- SequenceI[] sequences;\r
-\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
- AlignmentI alignment = null;\r
-\r
- if (newAlignment)\r
- {\r
- alignment = new Alignment(sequences);\r
-\r
- if(Desktop.jalviewClipboard!=null)\r
- alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );\r
- else\r
- alignment.setDataset( null );\r
-\r
- }\r
- else\r
- {\r
- alignment = viewport.getAlignment();\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
-\r
- alignment.addSequence(newseq);\r
- }\r
-\r
-\r
- viewport.setEndSeq(alignment.getHeight());\r
- alignment.getWidth();\r
- viewport.firePropertyChange("alignment", null, alignment.getSequences());\r
- }\r
-\r
-\r
-\r
-\r
-\r
- // Add any annotations attached to sequences\r
- for (int i = 0; i < sequences.length; i++)\r
- {\r
- if (sequences[i].getAnnotation() != null)\r
- {\r
- for (int a = 0; a < sequences[i].getAnnotation().length; a++)\r
- {\r
- AlignmentAnnotation newAnnot =\r
- new AlignmentAnnotation(\r
- sequences[i].getAnnotation()[a].label,\r
- sequences[i].getAnnotation()[a].description,\r
- sequences[i].getAnnotation()[a].annotations,\r
- sequences[i].getAnnotation()[a].graphMin,\r
- sequences[i].getAnnotation()[a].graphMax,\r
- sequences[i].getAnnotation()[a].graph);\r
-\r
- sequences[i].getAnnotation()[a] = newAnnot;\r
- newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].\r
- sequenceMapping;\r
- newAnnot.sequenceRef = sequences[i];\r
- newAnnot.adjustForAlignment();\r
- alignment.addAnnotation(newAnnot);\r
- alignment.setAnnotationIndex(newAnnot, a);\r
- }\r
-\r
- alignPanel.annotationPanel.adjustPanelHeight();\r
- }\r
- }\r
-\r
- if(newAlignment)\r
- {\r
- AlignFrame af = new AlignFrame(alignment);\r
- String newtitle = new String("Copied sequences");\r
-\r
- if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)\r
- {\r
- Vector hc = (Vector)Desktop.jalviewClipboard[2];\r
- for(int i=0; i<hc.size(); i++)\r
- {\r
- int [] region = (int[]) hc.elementAt(i);\r
- af.viewport.hideColumns(region[0], region[1]);\r
- }\r
- }\r
-\r
-\r
- //>>>This is a fix for the moment, until a better solution is found!!<<<\r
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(\r
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
-\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
- }\r
-\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- System.out.println("Exception whilst pasting: "+ex);\r
- // could be anything being pasted in here\r
- }\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
-\r
- if (viewport.getSelectionGroup() == null)\r
- {\r
- return;\r
- }\r
-\r
-\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
-\r
-\r
-\r
- //Jalview no longer allows deletion of residues.\r
- //Check here whether any residues are in selection area\r
- /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)\r
- {\r
- for (int i = 0; i < sg.sequences.size(); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int j = sg.getStartRes();\r
- do\r
- {\r
- if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
- {\r
- JOptionPane.showInternalMessageDialog(\r
- Desktop.desktop, "Cannot delete residues from alignment!\n"\r
- + "Try hiding columns instead.",\r
- "Deletion of residues not permitted",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
- j++;\r
- }while(j<=sg.getEndRes());\r
- }\r
- }*/\r
-\r
-\r
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
- HistoryItem.HIDE));\r
-\r
-\r
- for (int i = 0; i < sg.getSize(false); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.getAlignment().findIndex(seq);\r
-\r
- seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
-\r
- // If the cut affects all sequences, remove highlighted columns\r
- if (sg.getSize(false) == viewport.alignment.getHeight())\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
- {\r
- viewport.getAlignment().getSequences().setElementAt(seq, index);\r
- }\r
- }\r
-\r
- viewport.setSelectionGroup(null);\r
- viewport.alignment.deleteGroup(sg);\r
-\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
-\r
-\r
-\r
- if (viewport.getAlignment().getHeight() < 1)\r
- {\r
- try\r
- {\r
- this.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.alignment.deleteAllGroups();\r
- viewport.setSelectionGroup(null);\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = new SequenceGroup();\r
-\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
- {\r
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
- }\r
-\r
- sg.setEndRes(viewport.alignment.getWidth() - 1);\r
- viewport.setSelectionGroup(sg);\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.keyboardNo1 = null;\r
- alignPanel.seqPanel.keyboardNo2 = null;\r
- }\r
- viewport.setSelectionGroup(null);\r
- viewport.getColumnSelection().clear();\r
- viewport.setSelectionGroup(null);\r
- alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
- alignPanel.idPanel.idCanvas.searchResults = null;\r
- alignPanel.repaint();\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
-\r
- if (sg == null)\r
- {\r
- selectAllSequenceMenuItem_actionPerformed(null);\r
-\r
- return;\r
- }\r
-\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
- {\r
- sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
- }\r
-\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
- }\r
-\r
- public void invertColSel_actionPerformed(ActionEvent e)\r
- {\r
- viewport.invertColumnSelection();\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
-\r
- if (colSel.size() > 0)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
- HistoryItem.HIDE));\r
-\r
- int min = colSel.getMin();\r
- viewport.getAlignment().trimLeft(min);\r
- colSel.compensateForEdit(0, min);\r
-\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
- }\r
-\r
- Vector groups = viewport.alignment.getGroups();\r
-\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.get(i);\r
-\r
- if (!sg.adjustForRemoveLeft(min))\r
- {\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
- }\r
-\r
- 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
- ColumnSelection colSel = viewport.getColumnSelection();\r
-\r
- if (colSel.size() > 0)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
- HistoryItem.HIDE));\r
-\r
- int max = colSel.getMax();\r
- viewport.getAlignment().trimRight(max);\r
-\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- viewport.getSelectionGroup().adjustForRemoveRight(max);\r
- }\r
-\r
- Vector groups = viewport.alignment.getGroups();\r
-\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.get(i);\r
-\r
- if (!sg.adjustForRemoveRight(max))\r
- {\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
- }\r
-\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
- viewport.alignment, HistoryItem.HIDE));\r
-\r
- //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
-\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(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
-\r
- Vector seqs = null;\r
-\r
- int start = 0;\r
- int end = viewport.alignment.getWidth();\r
-\r
- if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().getSequences(true) != null\r
- && viewport.getSelectionGroup().getSize(true) > 0)\r
- {\r
- seqs = viewport.getSelectionGroup().getSequences(true);\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
-\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
- 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
-\r
- viewport.setStartRes(seq.findIndex(startRes)-1);\r
-\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
-\r
- public void alignmentChanged()\r
- {\r
- if(viewport.padGaps)\r
- viewport.getAlignment().padGaps();\r
-\r
- if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)\r
- {\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- }\r
-\r
- resetAllColourSchemes();\r
- if(alignPanel.overviewPanel!=null)\r
- alignPanel.overviewPanel.updateOverviewImage();\r
-\r
- viewport.alignment.adjustSequenceAnnotations();\r
-\r
- if(alignPanel.overviewPanel!=null)\r
- alignPanel.overviewPanel.updateOverviewImage();\r
-\r
- alignPanel.repaint();\r
- }\r
-\r
- void resetAllColourSchemes()\r
- {\r
- ColourSchemeI cs = viewport.globalColourScheme;\r
- if(cs!=null)\r
- {\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
- resetClustalX(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth());\r
- }\r
-\r
- cs.setConsensus(viewport.vconsensus);\r
- if (cs.conservationApplied())\r
- {\r
- Alignment al = (Alignment) viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
-\r
- cs.setConservation(c);\r
- }\r
- }\r
-\r
- int s, sSize = viewport.alignment.getGroups().size();\r
- for(s=0; s<sSize; s++)\r
- {\r
- SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
- if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
- {\r
- ((ClustalxColourScheme)sg.cs).resetClustalX(\r
- sg.getSequences(true), 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
- viewport.padGaps = padGapsMenuitem.isSelected();\r
-\r
- // if (viewport.padGaps)\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
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- Desktop.addInternalFrame(frame, "Find", 340, 110);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void font_actionPerformed(ActionEvent e)\r
- {\r
- new FontChooser(alignPanel);\r
- }\r
-\r
- public void smoothFont_actionPerformed(ActionEvent e)\r
- {\r
- viewport.antiAlias = smoothFont.isSelected();\r
- alignPanel.annotationPanel.image = null;\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void seqLimit_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowJVSuffix(seqLimits.isSelected());\r
-\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
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\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
- }\r
-\r
- public void showAllSeqs_actionPerformed(ActionEvent e)\r
- {\r
- viewport.showAllHiddenSeqs();\r
- }\r
-\r
- public void showAllColumns_actionPerformed(ActionEvent e)\r
- {\r
- viewport.showAllHiddenColumns();\r
- repaint();\r
- }\r
-\r
- public void hideSelSequences_actionPerformed(ActionEvent e)\r
- {\r
- viewport.hideAllSelectedSeqs();\r
- }\r
-\r
- public void hideSelColumns_actionPerformed(ActionEvent e)\r
- {\r
- viewport.hideSelectedColumns();\r
- alignPanel.repaint();\r
- }\r
-\r
- public void hiddenMarkers_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleRightWrapped(scaleRight.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowText(viewTextMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
- alignPanel.repaint();\r
- }\r
-\r
-\r
- public FeatureSettings featureSettings;\r
- public void featureSettings_actionPerformed(ActionEvent e)\r
- {\r
- if(featureSettings !=null )\r
- {\r
- featureSettings.close();\r
- featureSettings = null;\r
- }\r
- featureSettings = new FeatureSettings(this);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void showSeqFeatures_actionPerformed(ActionEvent evt)\r
- {\r
- viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());\r
- alignPanel.repaint();\r
- if (alignPanel.getOverviewPanel() != null)\r
- {\r
- alignPanel.getOverviewPanel().updateOverviewImage();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (alignPanel.overviewPanel != null)\r
- {\r
- return;\r
- }\r
-\r
- JInternalFrame frame = new JInternalFrame();\r
- OverviewPanel overview = new OverviewPanel(alignPanel);\r
- frame.setContentPane(overview);\r
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
- frame.getWidth(), frame.getHeight());\r
- frame.pack();\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(\r
- javax.swing.event.InternalFrameEvent evt)\r
- {\r
- alignPanel.setOverviewPanel(null);\r
- }\r
- ;\r
- });\r
-\r
- alignPanel.setOverviewPanel(overview);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(null);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new ClustalxColourScheme(\r
- viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new ZappoColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TaylorColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HydrophobicColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HelixColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new StrandColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TurnColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new BuriedColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new NucleotideColourScheme());\r
- }\r
-\r
- public void annotationColour_actionPerformed(ActionEvent e)\r
- {\r
- new AnnotationColourChooser(viewport, alignPanel);\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
- * DOCUMENT ME!\r
- *\r
- * @param cs DOCUMENT ME!\r
- */\r
- public void changeColour(ColourSchemeI cs)\r
- {\r
- int threshold = 0;\r
-\r
- if(cs!=null)\r
- {\r
- if (viewport.getAbovePIDThreshold())\r
- {\r
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
- "Background");\r
-\r
- cs.setThreshold(threshold,\r
- viewport.getIgnoreGapsConsensus());\r
-\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
- else\r
- {\r
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
- }\r
-\r
- if (viewport.getConservationSelected())\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
-\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
-\r
- cs.setConservation(c);\r
-\r
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
- "Background"));\r
- }\r
- else\r
- {\r
- cs.setConservation(null);\r
- }\r
-\r
- cs.setConsensus(viewport.vconsensus);\r
- }\r
-\r
- viewport.setGlobalColourScheme(cs);\r
-\r
- if (viewport.getColourAppliesToAllGroups())\r
- {\r
- Vector groups = viewport.alignment.getGroups();\r
-\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
- if (cs == null)\r
- {\r
- sg.cs = null;\r
- continue;\r
- }\r
-\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- sg.cs = new ClustalxColourScheme(\r
- sg.getSequences(true), 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
- || cs instanceof PIDColourScheme\r
- || cs instanceof Blosum62ColourScheme)\r
- {\r
- sg.cs.setThreshold(threshold,\r
- viewport.getIgnoreGapsConsensus());\r
-\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(true), 0,\r
- sg.getWidth()));\r
- }\r
- else\r
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
-\r
-\r
- if (viewport.getConservationSelected())\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(true), 0,\r
- viewport.alignment.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
- sg.cs.setConservation(c);\r
- }\r
- else\r
- sg.cs.setConservation(null);\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() && 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() && viewport.globalColourScheme!=null)\r
- {\r
- SliderPanel.setConservationSlider(alignPanel,\r
- viewport.globalColourScheme,\r
- "Background");\r
- SliderPanel.showConservationSlider();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setConservationSelected(conservationMenuItem.isSelected());\r
-\r
- viewport.setAbovePIDThreshold(false);\r
- abovePIDThreshold.setSelected(false);\r
-\r
- 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
-\r
- conservationMenuItem.setSelected(false);\r
- viewport.setConservationSelected(false);\r
-\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 updateUserColourMenu()\r
- {\r
-\r
- Component[] menuItems = colourMenu.getMenuComponents();\r
- int i, iSize = menuItems.length;\r
- for (i = 0; i < iSize; i++)\r
- {\r
- if (menuItems[i].getName() != null &&\r
- menuItems[i].getName().equals("USER_DEFINED"))\r
- {\r
- colourMenu.remove(menuItems[i]);\r
- iSize--;\r
- }\r
- }\r
- 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
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new Blosum62ColourScheme());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
- AlignmentSorter.sortByPID(viewport.getAlignment(),\r
- viewport.getAlignment().getSequenceAt(0));\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
- AlignmentSorter.sortByID(viewport.getAlignment());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
-\r
- AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- alignPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- new RedundancyPanel(alignPanel, this);\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if ( (viewport.getSelectionGroup() == null) ||\r
- (viewport.getSelectionGroup().getSize(false) < 2))\r
- {\r
- JOptionPane.showInternalMessageDialog(this,\r
- "You must select at least 2 sequences.",\r
- "Invalid Selection",\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
- else\r
- {\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(new PairwiseAlignPanel(viewport));\r
- Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void PCAMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if ( ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize(false) < 4) &&\r
- (viewport.getSelectionGroup().getSize(false) > 0)) ||\r
- (viewport.getAlignment().getHeight() < 4))\r
- {\r
- JOptionPane.showInternalMessageDialog(this,\r
- "Principal component analysis must take\n" +\r
- "at least 4 input sequences.",\r
- "Sequence selection insufficient",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
-\r
- new PCAPanel(viewport);\r
- }\r
-\r
-\r
- public void autoCalculate_actionPerformed(ActionEvent e)\r
- {\r
- viewport.autoCalculateConsensus = autoCalculate.isSelected();\r
- if(viewport.autoCalculateConsensus)\r
- {\r
- alignmentChanged();\r
- }\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("AV", "PID", "Average distance tree using PID");\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param type DOCUMENT ME!\r
- * @param pwType DOCUMENT ME!\r
- * @param title DOCUMENT ME!\r
- */\r
- void NewTreePanel(String type, String pwType, String title)\r
- {\r
- TreePanel tp;\r
-\r
- if ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize(false) > 3))\r
- {\r
- int s = 0;\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
-\r
- /* Decide if the selection is a column region */\r
- while (s < sg.getSize(false))\r
- {\r
- if ( ( (SequenceI) sg.getSequences(false).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, type, pwType);\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",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- return;\r
- }\r
-\r
- if(viewport.alignment.getHeight()<2)\r
- return;\r
-\r
- tp = new TreePanel(viewport, type, pwType);\r
- }\r
-\r
- addTreeMenuItem(tp, title);\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
- // 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(new HistoryItem("Tree Sort",\r
- viewport.alignment, HistoryItem.SORT));\r
- AlignmentSorter.sortByTree(viewport.getAlignment(),\r
- treePanel.getTree());\r
- alignPanel.repaint();\r
- }\r
- });\r
-\r
- treePanel.addInternalFrameListener(new javax.swing.event.\r
- InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(\r
- javax.swing.event.InternalFrameEvent evt)\r
- {\r
- treeCount--;\r
- sortByTreeMenu.remove(item);\r
-\r
- if (treeCount == 0)\r
- {\r
- sort.remove(sortByTreeMenu);\r
- }\r
- }\r
- ;\r
- });\r
- }\r
-\r
- /**\r
- * Work out whether the whole set of sequences\r
- * or just the selected set will be submitted for multiple alignment.\r
- *\r
- */\r
- private jalview.datamodel.AlignmentView gatherSequencesForAlignment()\r
- {\r
- // Now, check we have enough sequences\r
- AlignmentView msa = null;\r
-\r
- if ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize(false) > 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(false)];\r
-\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- } */\r
- msa = viewport.getAlignmentView(true);\r
- }\r
- else\r
- {\r
- /*Vector seqs = viewport.getAlignment().getSequences();\r
-\r
- if (seqs.size() > 1)\r
- {\r
- msa = new SequenceI[seqs.size()];\r
-\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
- }*/\r
- msa = viewport.getAlignmentView(false);\r
- }\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 ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize(false) > 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(false) == 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(false)];\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
- 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
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- // Pick the tree file\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty(\r
- "LAST_DIRECTORY"));\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Select a newick-like tree file");\r
- chooser.setToolTipText("Load a tree file");\r
-\r
- int value = chooser.showOpenDialog(null);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
-\r
- try\r
- {\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,\r
- "File");\r
- viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());\r
- }\r
- catch (Exception ex)\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "Problem reading tree file",\r
- ex.getMessage(),\r
- JOptionPane.WARNING_MESSAGE);\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
-\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
- "FromFile",\r
- title,\r
- nf);\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
- final AlignFrame af = this;\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
- AlignmentView msa = gatherSequencesForAlignment();\r
- new jalview.ws.MsaWSClient(sh, title, msa,\r
- false, true, viewport.getAlignment().getDataset(), af);\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
- AlignmentView msa = gatherSequencesForAlignment();\r
- new jalview.ws.MsaWSClient(sh, title, msa,\r
- true, true, viewport.getAlignment().getDataset(), af);\r
-\r
- }\r
-\r
- });\r
- msawsmenu.add(methodR);\r
-\r
- }\r
- }\r
- wsmenu.add(msawsmenu);\r
- }\r
- if (secstrpr != null)\r
- {\r
- // Add any secondary structure prediction services\r
- final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");\r
- for (int i = 0, j = secstrpr.size(); i < j; i++)\r
- {\r
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)\r
- secstrpr.get(i);\r
- final JMenuItem method = new JMenuItem(sh.getName());\r
- method.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();\r
- if (msa.length == 1)\r
- {\r
- // Single Sequence prediction\r
- new jalview.ws.JPredClient(sh, title, msa[0], null);\r
- }\r
- else\r
- {\r
- if (msa.length > 1)\r
- {\r
- // Single Sequence prediction\r
- jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,\r
- title, msa, null);\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
-\r
-\r
-\r
-public void showTranslation_actionPerformed(ActionEvent e)\r
-{\r
- SequenceI [] selection = viewport.getSelectionAsNewSequence();\r
- String [] seqstring = viewport.getViewAsString(true);\r
-\r
- int s, sSize = selection.length;\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("-. ", seqstring[s]);\r
- resSize = seq.length();\r
- resSize -= resSize%3;\r
-\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(selection[s].getName(),\r
- 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
- if(annotations!=null)\r
- {\r
- for (int i = 0; i < annotations.length; i++)\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
- 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
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @param String DOCUMENT ME!\r
- */\r
-public boolean parseFeaturesFile(String file, String type)\r
-{\r
- boolean featuresFile = false;\r
- try{\r
- featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),\r
- alignPanel.seqPanel.seqCanvas.\r
- getFeatureRenderer().featureColours,\r
- false);\r
- }\r
- catch(Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- if(featuresFile)\r
- {\r
- viewport.showSequenceFeatures = true;\r
- showSeqFeatures.setSelected(true);\r
- alignPanel.repaint();\r
- }\r
-\r
- return featuresFile;\r
-}\r
-\r
-public void dragEnter(DropTargetDragEvent evt)\r
-{}\r
-\r
-public void dragExit(DropTargetEvent evt)\r
-{}\r
-\r
-public void dragOver(DropTargetDragEvent evt)\r
-{}\r
-\r
-public void dropActionChanged(DropTargetDragEvent evt)\r
-{}\r
-\r
-public void drop(DropTargetDropEvent evt)\r
-{\r
- Transferable t = evt.getTransferable();\r
- java.util.List files = null;\r
-\r
- try\r
- {\r
- DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");\r
- if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
- {\r
- //Works on Windows and MacOSX\r
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
- files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
- }\r
- else if (t.isDataFlavorSupported(uriListFlavor))\r
- {\r
- // This is used by Unix drag system\r
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
- String data = (String) t.getTransferData(uriListFlavor);\r
- files = new java.util.ArrayList(1);\r
- for (java.util.StringTokenizer st = new java.util.StringTokenizer(\r
- data,\r
- "\r\n");\r
- st.hasMoreTokens(); )\r
- {\r
- String s = st.nextToken();\r
- if (s.startsWith("#"))\r
- {\r
- // the line is a comment (as per the RFC 2483)\r
- continue;\r
- }\r
-\r
- java.net.URI uri = new java.net.URI(s);\r
- java.io.File file = new java.io.File(uri);\r
- files.add(file);\r
- }\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
- if (files != null)\r
- {\r
- try\r
- {\r
-\r
- for (int i = 0; i < files.size(); i++)\r
- {\r
- loadJalviewDataFile(files.get(i).toString());\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-}\r
-\r
- // This method will attempt to load a "dropped" file first by testing\r
- // whether its and Annotation file, then features file. If both are\r
- // false then the user may have dropped an alignment file onto this\r
- // AlignFrame\r
- public void loadJalviewDataFile(String file)\r
- {\r
- try{\r
- boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.\r
- alignment, file);\r
-\r
- if (!isAnnotation)\r
- {\r
- boolean isGroupsFile = parseFeaturesFile(file,\r
- AppletFormatAdapter.FILE);\r
- if (!isGroupsFile)\r
- {\r
- String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);\r
- new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);\r
- }\r
- }\r
- else\r
- {\r
- // (isAnnotation)\r
- alignPanel.adjustAnnotationHeight();\r
- }\r
-\r
- }catch(Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Softwarechang
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import java.beans.*;
+import java.io.*;
+import java.util.*;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.event.*;
+import java.awt.print.*;
+import javax.swing.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.util.ShiftList;
+import jalview.ws.*;
+import java.awt.dnd.*;
+import org.biojava.dasobert.eventmodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignFrame
+ extends GAlignFrame implements DropTargetListener, FeatureListener
+{
+ /** DOCUMENT ME!! */
+ public static final int NEW_WINDOW_WIDTH = 700;
+
+ /** DOCUMENT ME!! */
+ public static final int NEW_WINDOW_HEIGHT = 500;
+ AlignmentPanel alignPanel;
+ AlignViewport viewport;
+
+ /** DOCUMENT ME!! */
+ public String currentFileFormat = null;
+ Stack historyList = new Stack();
+ Stack redoList = new Stack();
+ private int treeCount = 0;
+
+ /**
+ * new alignment window with hidden columns
+ * @param al AlignmentI
+ * @param hiddenColumns ColumnSelection or null
+ */
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {
+
+ viewport = new AlignViewport(al, hiddenColumns);
+
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+
+ if(viewport.vconsensus==null)
+ {
+ //Out of memory calculating consensus.
+ BLOSUM62Colour.setEnabled(false);
+ PIDColour.setEnabled(false);
+ conservationMenuItem.setEnabled(false);
+ modifyConservation.setEnabled(false);
+ abovePIDThreshold.setEnabled(false);
+ modifyPID.setEnabled(false);
+ }
+
+ alignPanel = new AlignmentPanel(this, viewport);
+
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
+
+ if(sortby.equals("Id"))
+ sortIDMenuItem_actionPerformed(null);
+ else if(sortby.equals("Pairwise Identity"))
+ sortPairwiseMenuItem_actionPerformed(null);
+
+ // remove(tabbedPane);
+ getContentPane().add(alignPanel, BorderLayout.CENTER);
+
+
+
+ // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
+
+ ///Dataset tab
+ /////////////////////////
+ if(al.getDataset()==null)
+ {
+ al.setDataset(null);
+ }
+ // AlignViewport ds = new AlignViewport(al.getDataset(), true);
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);
+ // tabbedPane.add("Dataset", dap);
+ // viewports.add(ds);
+ // alignPanels.add(dap);
+ /////////////////////////
+
+
+ viewport.addPropertyChangeListener(new PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ alignmentChanged();
+ }
+ }
+ });
+
+
+ if (Desktop.desktop != null)
+ {
+ addServiceListeners();
+ setGUINucleotide(al.isNucleotide());
+ }
+
+
+ if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
+ {
+ wrapMenuItem.setSelected(true);
+ wrapMenuItem_actionPerformed(null);
+ }
+
+ }
+
+
+ /**
+ * Creates a new AlignFrame object.
+ *
+ * @param al DOCUMENT ME!
+ */
+ public AlignFrame(AlignmentI al)
+ {
+ this(al, null);
+ }
+
+ public AlignViewport getViewport()
+ {
+ return viewport;
+ }
+
+ /* Set up intrinsic listeners for dynamically generated GUI bits. */
+ private void addServiceListeners()
+ {
+ final java.beans.PropertyChangeListener thisListener;
+ // Do this once to get current state
+ BuildWebServiceMenu();
+ Desktop.discoverer.addPropertyChangeListener(
+ thisListener = new java.beans.PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // System.out.println("Discoverer property change.");
+ if (evt.getPropertyName().equals("services"))
+ {
+ // System.out.println("Rebuilding web service menu");
+ BuildWebServiceMenu();
+ }
+ }
+ });
+ addInternalFrameListener(new javax.swing.event.
+ InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ // System.out.println("deregistering discoverer listener");
+ Desktop.discoverer.removePropertyChangeListener(thisListener);
+ closeMenuItem_actionPerformed(null);
+ }
+ ;
+ });
+ }
+
+ public void setGUINucleotide(boolean nucleotide)
+ {
+ showTranslation.setVisible( nucleotide );
+ //sequenceFeatures.setVisible(!nucleotide );
+ //featureSettings.setVisible( !nucleotide );
+ conservationMenuItem.setVisible( !nucleotide );
+ modifyConservation.setVisible( !nucleotide );
+
+ //Remember AlignFrame always starts as protein
+ if(!nucleotide)
+ {
+ calculateMenu.remove(calculateMenu.getItemCount()-2);
+ }
+ }
+
+ public void comeBackLater(FeatureEvent evt)
+ {}
+
+ public void newFeatures(FeatureEvent evt)
+ {
+ if (evt.getFeatures().length > 0)
+ {
+ alignPanel.seqPanel.seqCanvas.fr.featuresAdded();
+ alignPanel.repaint();
+ }
+ }
+
+ Hashtable progressBars;
+ public void setProgressBar(String message, long id)
+ {
+ if(progressBars == null)
+ progressBars = new Hashtable();
+
+ JPanel progressPanel;
+ GridLayout layout = (GridLayout) statusPanel.getLayout();
+ if(progressBars.get( new Long(id) )!=null)
+ {
+ progressPanel = (JPanel)progressBars.get( new Long(id) );
+ statusPanel.remove(progressPanel);
+ progressBars.remove( progressPanel );
+ progressPanel = null;
+ if(message!=null)
+ statusBar.setText(message);
+
+ layout.setRows(layout.getRows() - 1);
+ }
+ else
+ {
+ progressPanel = new JPanel(new BorderLayout(10, 5));
+
+ JProgressBar progressBar = new JProgressBar();
+ progressBar.setIndeterminate(true);
+
+ progressPanel.add(new JLabel(message), BorderLayout.WEST);
+ progressPanel.add(progressBar, BorderLayout.CENTER);
+
+ layout.setRows(layout.getRows() + 1);
+ statusPanel.add(progressPanel);
+
+ progressBars.put(new Long(id), progressPanel);
+ }
+
+ validate();
+ }
+
+
+ /*
+ Added so Castor Mapping file can obtain Jalview Version
+ */
+ public String getVersion()
+ {
+ return jalview.bin.Cache.getProperty("VERSION");
+ }
+
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+ }
+
+
+ public void fetchSequence_actionPerformed(ActionEvent e)
+ {
+ new SequenceFetcher(this);
+ }
+
+ public void addFromFile_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+ }
+
+ public void addFromText_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+ }
+
+ public void addFromURL_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void saveAlignmentMenu_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty( "LAST_DIRECTORY"),
+ new String[]
+ { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
+ new String[]
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
+ currentFileFormat,
+ false);
+
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save Alignment to file");
+ chooser.setToolTipText("Save");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ currentFileFormat = chooser.getSelectedFormat();
+
+ if (currentFileFormat == null)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "You must select a file format before saving!",
+ "File format not specified",
+ JOptionPane.WARNING_MESSAGE);
+ value = chooser.showSaveDialog(this);
+ return;
+ }
+
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+ currentFileFormat);
+
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+
+ saveAlignment(choice, currentFileFormat);
+ }
+ }
+
+ public boolean saveAlignment(String file, String format)
+ {
+ if (format.equalsIgnoreCase("Jalview"))
+ {
+ String shortName = title;
+
+ if (shortName.indexOf(java.io.File.separatorChar) > -1)
+ {
+ shortName = shortName.substring(shortName.lastIndexOf(
+ java.io.File.separatorChar) + 1);
+ }
+
+ new Jalview2XML().SaveAlignment(this, file, shortName);
+
+ // USE Jalview2XML to save this file
+ return true;
+ }
+ else
+ {
+
+ String[] omitHidden = null;
+
+ if (viewport.hasHiddenColumns)
+ {
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "The Alignment contains hidden columns."
+ + "\nDo you want to save only the visible alignment?",
+ "Save / Omit Hidden Columns",
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+ if (reply == JOptionPane.YES_OPTION)
+ omitHidden = viewport.getViewAsString(false);
+ }
+
+ String output = new FormatAdapter().formatSequences(
+ format,
+ viewport.alignment.getSequencesArray(),
+ omitHidden);
+
+ if (output == null)
+ {
+ return false;
+ }
+
+ try
+ {
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(file));
+
+ out.print(output);
+ out.close();
+ this.setTitle(file);
+ return true;
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void outputText_actionPerformed(ActionEvent e)
+ {
+ String [] omitHidden = null;
+
+ if(viewport.hasHiddenColumns)
+ {
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "The Alignment contains hidden columns."
+ +"\nDo you want to output only the visible alignment?",
+ "Save / Omit Hidden Columns",
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+ if(reply==JOptionPane.YES_OPTION)
+ {
+ omitHidden = viewport.getViewAsString(false);
+ }
+ }
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ Desktop.addInternalFrame(cap,
+ "Alignment output - " + e.getActionCommand(), 600,
+ 500);
+
+
+ cap.setText(new FormatAdapter().formatSequences(
+ e.getActionCommand(),
+ viewport.alignment.getSequencesArray(),
+ omitHidden));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ {
+ new HTMLOutput(viewport,
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ }
+
+ public void createImageMap(File file, String image)
+ {
+ alignPanel.makePNGImageMap(file, image);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void createPNG(File f)
+ {
+ alignPanel.makePNG(f);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void createEPS(File f)
+ {
+ alignPanel.makeEPS(f);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void printMenuItem_actionPerformed(ActionEvent e)
+ {
+ //Putting in a thread avoids Swing painting problems
+ PrintThread thread = new PrintThread();
+ thread.start();
+ }
+
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportFeatures(alignPanel);
+ }
+
+
+ public void exportAnnotations_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportAnnotations(
+ alignPanel,
+ viewport.alignment.getAlignmentAnnotation()
+ );
+ }
+
+
+ public void associatedData_actionPerformed(ActionEvent e)
+ {
+ // Pick the tree file
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty(
+ "LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Load Jalview Annotations or Features File");
+ chooser.setToolTipText("Load Jalview Annotations / Features file");
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ loadJalviewDataFile(choice);
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void closeMenuItem_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ PaintRefresher.components.remove(viewport.alignment);
+ this.setClosed(true);
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ void updateEditMenuBar()
+ {
+ if (historyList.size() > 0)
+ {
+ undoMenuItem.setEnabled(true);
+
+ HistoryItem hi = (HistoryItem) historyList.peek();
+ undoMenuItem.setText("Undo " + hi.getDescription());
+ }
+ else
+ {
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setText("Undo");
+ }
+
+ if (redoList.size() > 0)
+ {
+ redoMenuItem.setEnabled(true);
+
+ HistoryItem hi = (HistoryItem) redoList.peek();
+ redoMenuItem.setText("Redo " + hi.getDescription());
+ }
+ else
+ {
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setText("Redo");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param hi DOCUMENT ME!
+ */
+ public void addHistoryItem(HistoryItem hi)
+ {
+ historyList.push(hi);
+ redoList.clear();
+ updateEditMenuBar();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+ HistoryItem nh,hi = (HistoryItem) historyList.pop();
+ redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
+ HistoryItem.HIDE));
+ if (hi.alColumnChanges!=null)
+ nh.alColumnChanges = hi.alColumnChanges.getInverse();
+ restoreHistoryItem(hi);
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
+ HistoryItem nh,hi = (HistoryItem) redoList.pop();
+ historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
+ HistoryItem.HIDE));
+ if (hi.alColumnChanges!=null)
+ nh.alColumnChanges=hi.alColumnChanges.getInverse();
+ restoreHistoryItem(hi);
+ updateEditMenuBar();
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+
+ // used by undo and redo
+ void restoreHistoryItem(HistoryItem hi)
+ {
+
+ hi.restore(viewport.getColumnSelection());
+
+ updateEditMenuBar();
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param up DOCUMENT ME!
+ */
+ public void moveSelectedSequences(boolean up)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ if (sg == null)
+ {
+ return;
+ }
+
+ if (up)
+ {
+ for (int i = 1; i < viewport.alignment.getHeight(); i++)
+ {
+ SequenceI seq = viewport.alignment.getSequenceAt(i);
+
+ if (!sg.getSequences(false).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
+
+ if (sg.getSequences(false).contains(temp))
+ {
+ continue;
+ }
+
+ viewport.alignment.getSequences().setElementAt(temp, i);
+ viewport.alignment.getSequences().setElementAt(seq, i - 1);
+ }
+ }
+ else
+ {
+ for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
+ {
+ SequenceI seq = viewport.alignment.getSequenceAt(i);
+
+ if (!sg.getSequences(false).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
+
+ if (sg.getSequences(false).contains(temp))
+ {
+ continue;
+ }
+
+ viewport.alignment.getSequences().setElementAt(temp, i);
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);
+ }
+ }
+
+ alignPanel.repaint();
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void copy_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getSelectionGroup() == null)
+ {
+ return;
+ }
+
+ SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+ String[] omitHidden = null;
+
+ if (viewport.hasHiddenColumns)
+ {
+ omitHidden = viewport.getViewAsString(true);
+ }
+
+ String output = new FormatAdapter().formatSequences(
+ "Fasta",
+ seqs,
+ omitHidden);
+
+
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(output), Desktop.instance);
+
+ Vector hiddenColumns = null;
+ if(viewport.hasHiddenColumns)
+ {
+ hiddenColumns =new Vector();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
+ {
+ int[] region = (int[])
+ viewport.getColumnSelection().getHiddenColumns().elementAt(i);
+
+ hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
+ region[1]-hiddenOffset});
+ }
+ }
+
+ Desktop.jalviewClipboard = new Object[]{ seqs,
+ viewport.alignment.getDataset(),
+ hiddenColumns};
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void pasteNew_actionPerformed(ActionEvent e)
+ {
+ paste(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void pasteThis_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
+ HistoryItem.PASTE));
+ paste(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newAlignment DOCUMENT ME!
+ */
+ void paste(boolean newAlignment)
+ {
+ try
+ {
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ Transferable contents = c.getContents(this);
+
+ if (contents == null)
+ {
+ return;
+ }
+
+ String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+ if(str.length()<1)
+ return;
+
+ String format = new IdentifyFile().Identify(str, "Paste");
+ SequenceI[] sequences;
+
+
+ if(Desktop.jalviewClipboard!=null)
+ {
+ // The clipboard was filled from within Jalview, we must use the sequences
+ // And dataset from the copied alignment
+ sequences = (SequenceI[])Desktop.jalviewClipboard[0];
+ }
+ else
+ {
+ sequences = new FormatAdapter().readFile(str, "Paste", format);
+ }
+
+ AlignmentI alignment = null;
+
+ if (newAlignment)
+ {
+ alignment = new Alignment(sequences);
+
+ if(Desktop.jalviewClipboard!=null)
+ alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
+ else
+ alignment.setDataset( null );
+
+ }
+ else
+ {
+ alignment = viewport.getAlignment();
+
+ //!newAlignment
+ for (int i = 0; i < sequences.length; i++)
+ {
+ Sequence newseq = new Sequence(sequences[i].getName(),
+ sequences[i].getSequence(), sequences[i].getStart(),
+ sequences[i].getEnd());
+
+ alignment.addSequence(newseq);
+ }
+
+
+ viewport.setEndSeq(alignment.getHeight());
+ alignment.getWidth();
+ viewport.firePropertyChange("alignment", null, alignment.getSequences());
+ }
+
+
+
+
+
+ // Add any annotations attached to sequences
+ for (int i = 0; i < sequences.length; i++)
+ {
+ if (sequences[i].getAnnotation() != null)
+ {
+ for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+ {
+ AlignmentAnnotation newAnnot =
+ new AlignmentAnnotation(
+ sequences[i].getAnnotation()[a].label,
+ sequences[i].getAnnotation()[a].description,
+ sequences[i].getAnnotation()[a].annotations,
+ sequences[i].getAnnotation()[a].graphMin,
+ sequences[i].getAnnotation()[a].graphMax,
+ sequences[i].getAnnotation()[a].graph);
+
+ sequences[i].getAnnotation()[a] = newAnnot;
+ newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
+ sequenceMapping;
+ newAnnot.sequenceRef = sequences[i];
+ newAnnot.adjustForAlignment();
+ alignment.addAnnotation(newAnnot);
+ alignment.setAnnotationIndex(newAnnot, a);
+ }
+
+ alignPanel.annotationPanel.adjustPanelHeight();
+ }
+ }
+
+ if(newAlignment)
+ {
+ AlignFrame af = new AlignFrame(alignment);
+ String newtitle = new String("Copied sequences");
+
+ if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
+ {
+ Vector hc = (Vector)Desktop.jalviewClipboard[2];
+ for(int i=0; i<hc.size(); i++)
+ {
+ int [] region = (int[]) hc.elementAt(i);
+ af.viewport.hideColumns(region[0], region[1]);
+ }
+ }
+
+
+ //>>>This is a fix for the moment, until a better solution is found!!<<<
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
+
+ Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
+ NEW_WINDOW_HEIGHT);
+
+ }
+
+
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ System.out.println("Exception whilst pasting: "+ex);
+ // could be anything being pasted in here
+ }
+
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void cut_actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed(null);
+ delete_actionPerformed(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void delete_actionPerformed(ActionEvent e)
+ {
+
+ if (viewport.getSelectionGroup() == null)
+ {
+ return;
+ }
+
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+
+
+ //Jalview no longer allows deletion of residues.
+ //Check here whether any residues are in selection area
+ /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
+ {
+ for (int i = 0; i < sg.sequences.size(); i++)
+ {
+ SequenceI seq = sg.getSequenceAt(i);
+ int j = sg.getStartRes();
+ do
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+ {
+ JOptionPane.showInternalMessageDialog(
+ Desktop.desktop, "Cannot delete residues from alignment!\n"
+ + "Try hiding columns instead.",
+ "Deletion of residues not permitted",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+ j++;
+ }while(j<=sg.getEndRes());
+ }
+ }*/
+
+
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
+ HistoryItem.HIDE));
+
+
+ for (int i = 0; i < sg.getSize(false); i++)
+ {
+ SequenceI seq = sg.getSequenceAt(i);
+ int index = viewport.getAlignment().findIndex(seq);
+
+ seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
+
+ // If the cut affects all sequences, remove highlighted columns
+ if (sg.getSize(false) == viewport.alignment.getHeight())
+ {
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
+ }
+
+ if (seq.getSequence().length() < 1)
+ {
+ viewport.getAlignment().deleteSequence(seq);
+ }
+ else
+ {
+ viewport.getAlignment().getSequences().setElementAt(seq, index);
+ }
+ }
+
+ viewport.setSelectionGroup(null);
+ viewport.alignment.deleteGroup(sg);
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+
+
+
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ try
+ {
+ this.setClosed(true);
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void deleteGroups_actionPerformed(ActionEvent e)
+ {
+ viewport.alignment.deleteAllGroups();
+ viewport.setSelectionGroup(null);
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = new SequenceGroup();
+
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();
+ i++)
+ {
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
+ }
+
+ sg.setEndRes(viewport.alignment.getWidth() - 1);
+ viewport.setSelectionGroup(sg);
+ PaintRefresher.Refresh(null, viewport.alignment);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ if(viewport.cursorMode)
+ {
+ alignPanel.seqPanel.keyboardNo1 = null;
+ alignPanel.seqPanel.keyboardNo2 = null;
+ }
+ viewport.setSelectionGroup(null);
+ viewport.getColumnSelection().clear();
+ viewport.setSelectionGroup(null);
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
+ alignPanel.idPanel.idCanvas.searchResults = null;
+ alignPanel.repaint();
+ PaintRefresher.Refresh(null, viewport.alignment);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ if (sg == null)
+ {
+ selectAllSequenceMenuItem_actionPerformed(null);
+
+ return;
+ }
+
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();
+ i++)
+ {
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
+ }
+
+ PaintRefresher.Refresh(null, viewport.alignment);
+ }
+
+ public void invertColSel_actionPerformed(ActionEvent e)
+ {
+ viewport.invertColumnSelection();
+ alignPanel.repaint();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+
+ if (colSel.size() > 0)
+ {
+ HistoryItem edit;
+ addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment,
+ HistoryItem.HIDE));
+
+ int min = colSel.getMin();
+ viewport.getAlignment().trimLeft(min);
+ colSel.compensateForEdit(0, min);
+ edit.addShift(0,min);
+ if (viewport.getSelectionGroup() != null)
+ {
+ viewport.getSelectionGroup().adjustForRemoveLeft(min);
+ }
+
+ Vector groups = viewport.alignment.getGroups();
+
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.get(i);
+
+ if (!sg.adjustForRemoveLeft(min))
+ {
+ viewport.alignment.deleteGroup(sg);
+ }
+ }
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+
+ if (colSel.size() > 0)
+ {
+ addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
+ HistoryItem.HIDE));
+
+ int max = colSel.getMax();
+ viewport.getAlignment().trimRight(max);
+ // TODO: delete hidden column entries in colSel to right of max
+ // TODO: record hidden columns in history for undo.
+ if (viewport.getSelectionGroup() != null)
+ {
+ viewport.getSelectionGroup().adjustForRemoveRight(max);
+ }
+
+ Vector groups = viewport.alignment.getGroups();
+
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.get(i);
+
+ if (!sg.adjustForRemoveRight(max))
+ {
+ viewport.alignment.deleteGroup(sg);
+ }
+ }
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ {
+ HistoryItem edit;
+ addHistoryItem(edit=new HistoryItem("Remove Gapped Columns",
+ viewport.alignment, HistoryItem.HIDE));
+
+ //This is to maintain viewport position on first residue
+ //of first sequence
+ SequenceI seq = viewport.alignment.getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+ ShiftList shifts;
+ viewport.getAlignment().removeGaps(shifts=new ShiftList());
+ edit.alColumnChanges=shifts.getInverse();
+ if (viewport.hasHiddenColumns)
+ viewport.getColumnSelection().compensateForEdits(shifts);
+ viewport.setStartRes(seq.findIndex(startRes)-1);
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences
+ // TODO: columnSelection.compensateforedits should be called (and passed to history item)
+ addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
+ HistoryItem.HIDE));
+
+ //This is to maintain viewport position on first residue
+ //of first sequence
+ SequenceI seq = viewport.alignment.getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+
+
+ SequenceI current;
+ int jSize;
+
+ Vector seqs = null;
+
+ int start = 0;
+ int end = viewport.alignment.getWidth();
+
+ if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSequences(true) != null
+ && viewport.getSelectionGroup().getSize(true) > 0)
+ {
+ seqs = viewport.getSelectionGroup().getSequences(true);
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes()+1;
+ }
+ else
+ {
+ seqs = viewport.alignment.getSequences();
+ }
+ /* Commented out regions below are partial implementation of todo above.
+ * divide start,end into visible chunks, and for each:
+ int diff=end-start+1;
+ int diffmax=0;
+ int dr[] = new int[seqs.size()];
+ */
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ current = (SequenceI) seqs.elementAt(i);
+ //dr[i]=
+ current.removeGaps(start, end);
+ /*if (d<diff) // can only shift
+ diff=d;
+ if (diffmax<d)
+ diffmax=d;
+ */
+ }
+ /* // after the end of each chunk -
+ * if (diff>0) {
+ // record shift for history.
+ editgaps.addShift(start, diff);
+ if (viewport.hasHiddenColumns && diffmax>diff) {
+ // pad sequence
+ StringBuffer gaps=new StringBuffer(diffmax);
+ for (int i=0,j=diffmax-diff; i<j; i++)
+ gaps.append(viewport.getGapCharacter());
+ for (int i=0, j=seqs.size(); i<j; i++) {
+ current = (SequenceI) seqs.elementAt(i);
+ if (dr[i]-diff>0) {
+ String sq = current.getSequence();
+ current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring());
+ }
+ }
+ }
+ }*/
+
+ viewport.setStartRes(seq.findIndex(startRes)-1);
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+
+ public void alignmentChanged()
+ {
+ if(viewport.padGaps)
+ viewport.getAlignment().padGaps();
+
+ if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)
+ {
+ viewport.updateConsensus();
+ viewport.updateConservation();
+ }
+
+ resetAllColourSchemes();
+ if(alignPanel.overviewPanel!=null)
+ alignPanel.overviewPanel.updateOverviewImage();
+
+ viewport.alignment.adjustSequenceAnnotations();
+
+ if(alignPanel.overviewPanel!=null)
+ alignPanel.overviewPanel.updateOverviewImage();
+
+ alignPanel.repaint();
+ }
+
+ void resetAllColourSchemes()
+ {
+ ColourSchemeI cs = viewport.globalColourScheme;
+ if(cs!=null)
+ {
+ if (cs instanceof ClustalxColourScheme)
+ {
+ ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
+ resetClustalX(viewport.alignment.getSequences(),
+ viewport.alignment.getWidth());
+ }
+
+ cs.setConsensus(viewport.vconsensus);
+ if (cs.conservationApplied())
+ {
+ Alignment al = (Alignment) viewport.alignment;
+ Conservation c = new Conservation("All",
+ ResidueProperties.propHash, 3,
+ al.getSequences(), 0,
+ al.getWidth() - 1);
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+
+ cs.setConservation(c);
+ }
+ }
+
+ int s, sSize = viewport.alignment.getGroups().size();
+ for(s=0; s<sSize; s++)
+ {
+ SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
+ if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
+ {
+ ((ClustalxColourScheme)sg.cs).resetClustalX(
+ sg.getSequences(true), sg.getWidth());
+ }
+ sg.recalcConservation();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void padGapsMenuitem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
+ HistoryItem.HIDE));
+
+ viewport.padGaps = padGapsMenuitem.isSelected();
+
+ // if (viewport.padGaps)
+ alignmentChanged();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void findMenuItem_actionPerformed(ActionEvent e)
+ {
+ JInternalFrame frame = new JInternalFrame();
+ Finder finder = new Finder(viewport, alignPanel, frame);
+ frame.setContentPane(finder);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame, "Find", 340, 110);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void font_actionPerformed(ActionEvent e)
+ {
+ new FontChooser(alignPanel);
+ }
+
+ public void smoothFont_actionPerformed(ActionEvent e)
+ {
+ viewport.antiAlias = smoothFont.isSelected();
+ alignPanel.annotationPanel.image = null;
+ alignPanel.repaint();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void seqLimit_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowJVSuffix(seqLimits.isSelected());
+
+ alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
+ alignPanel.repaint();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setColourText(colourTextMenuItem.isSelected());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void wrapMenuItem_actionPerformed(ActionEvent e)
+ {
+ scaleAbove.setVisible(wrapMenuItem.isSelected());
+ scaleLeft.setVisible(wrapMenuItem.isSelected());
+ scaleRight.setVisible(wrapMenuItem.isSelected());
+ viewport.setWrapAlignment(wrapMenuItem.isSelected());
+ alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+ }
+
+ public void showAllSeqs_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenSeqs();
+ }
+
+ public void showAllColumns_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenColumns();
+ repaint();
+ }
+
+ public void hideSelSequences_actionPerformed(ActionEvent e)
+ {
+ viewport.hideAllSelectedSeqs();
+ }
+
+ public void hideSelColumns_actionPerformed(ActionEvent e)
+ {
+ viewport.hideSelectedColumns();
+ alignPanel.repaint();
+ }
+
+ public void hiddenMarkers_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void scaleAbove_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void scaleLeft_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void scaleRight_actionPerformed(ActionEvent e)
+ {
+ viewport.setScaleRightWrapped(scaleRight.isSelected());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void viewTextMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowText(viewTextMenuItem.isSelected());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setRenderGaps(renderGapsMenuItem.isSelected());
+ alignPanel.repaint();
+ }
+
+
+ public FeatureSettings featureSettings;
+ public void featureSettings_actionPerformed(ActionEvent e)
+ {
+ if(featureSettings !=null )
+ {
+ featureSettings.close();
+ featureSettings = null;
+ }
+ featureSettings = new FeatureSettings(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void showSeqFeatures_actionPerformed(ActionEvent evt)
+ {
+ viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
+ alignPanel.repaint();
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void overviewMenuItem_actionPerformed(ActionEvent e)
+ {
+ if (alignPanel.overviewPanel != null)
+ {
+ return;
+ }
+
+ JInternalFrame frame = new JInternalFrame();
+ OverviewPanel overview = new OverviewPanel(alignPanel);
+ frame.setContentPane(overview);
+ Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
+ frame.getWidth(), frame.getHeight());
+ frame.pack();
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ alignPanel.setOverviewPanel(null);
+ }
+ ;
+ });
+
+ alignPanel.setOverviewPanel(overview);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ {
+ changeColour(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void clustalColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new ClustalxColourScheme(
+ viewport.alignment.getSequences(), viewport.alignment.getWidth()));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void zappoColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new ZappoColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void taylorColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TaylorColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void hydrophobicityColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new HydrophobicColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void helixColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new HelixColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void strandColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new StrandColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void turnColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TurnColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void buriedColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new BuriedColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void nucleotideColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new NucleotideColourScheme());
+ }
+
+ public void annotationColour_actionPerformed(ActionEvent e)
+ {
+ new AnnotationColourChooser(viewport, alignPanel);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ {
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cs DOCUMENT ME!
+ */
+ public void changeColour(ColourSchemeI cs)
+ {
+ int threshold = 0;
+
+ if(cs!=null)
+ {
+ if (viewport.getAbovePIDThreshold())
+ {
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+ "Background");
+
+ cs.setThreshold(threshold,
+ viewport.getIgnoreGapsConsensus());
+
+ viewport.setGlobalColourScheme(cs);
+ }
+ else
+ {
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ }
+
+ if (viewport.getConservationSelected())
+ {
+
+ Alignment al = (Alignment) viewport.alignment;
+ Conservation c = new Conservation("All",
+ ResidueProperties.propHash, 3,
+ al.getSequences(), 0,
+ al.getWidth() - 1);
+
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+
+ cs.setConservation(c);
+
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+ "Background"));
+ }
+ else
+ {
+ cs.setConservation(null);
+ }
+
+ cs.setConsensus(viewport.vconsensus);
+ }
+
+ viewport.setGlobalColourScheme(cs);
+
+ if (viewport.getColourAppliesToAllGroups())
+ {
+ Vector groups = viewport.alignment.getGroups();
+
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+ if (cs == null)
+ {
+ sg.cs = null;
+ continue;
+ }
+
+ if (cs instanceof ClustalxColourScheme)
+ {
+ sg.cs = new ClustalxColourScheme(
+ sg.getSequences(true), sg.getWidth());
+ }
+ else if (cs instanceof UserColourScheme)
+ {
+ sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
+ }
+ else
+ {
+ try
+ {
+ sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+
+ if (viewport.getAbovePIDThreshold()
+ || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ sg.cs.setThreshold(threshold,
+ viewport.getIgnoreGapsConsensus());
+
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(true), 0,
+ sg.getWidth()));
+ }
+ else
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+
+
+ if (viewport.getConservationSelected())
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3,
+ sg.getSequences(true), 0,
+ viewport.alignment.getWidth() - 1);
+ c.calculate();
+ c.verdict(false, viewport.ConsPercGaps);
+ sg.cs.setConservation(c);
+ }
+ else
+ sg.cs.setConservation(null);
+ }
+ }
+
+ if (alignPanel.getOverviewPanel() != null)
+ {
+ alignPanel.getOverviewPanel().updateOverviewImage();
+ }
+
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void modifyPID_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+ {
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(),
+ "Background");
+ SliderPanel.showPIDSlider();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void modifyConservation_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
+ {
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.globalColourScheme,
+ "Background");
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ {
+ viewport.setConservationSelected(conservationMenuItem.isSelected());
+
+ viewport.setAbovePIDThreshold(false);
+ abovePIDThreshold.setSelected(false);
+
+ changeColour(viewport.getGlobalColourScheme());
+
+ modifyConservation_actionPerformed(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)
+ {
+ viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
+
+ conservationMenuItem.setSelected(false);
+ viewport.setConservationSelected(false);
+
+ changeColour(viewport.getGlobalColourScheme());
+
+ modifyPID_actionPerformed(null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void userDefinedColour_actionPerformed(ActionEvent e)
+ {
+ if (e.getActionCommand().equals("User Defined..."))
+ {
+ new UserDefinedColours(alignPanel, null);
+ }
+ else
+ {
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+ getUserColourSchemes().get(e.getActionCommand());
+
+ changeColour(udc);
+ }
+ }
+
+ public void updateUserColourMenu()
+ {
+
+ Component[] menuItems = colourMenu.getMenuComponents();
+ int i, iSize = menuItems.length;
+ for (i = 0; i < iSize; i++)
+ {
+ if (menuItems[i].getName() != null &&
+ menuItems[i].getName().equals("USER_DEFINED"))
+ {
+ colourMenu.remove(menuItems[i]);
+ iSize--;
+ }
+ }
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+ getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+ nextElement().toString());
+ radioItem.setName("USER_DEFINED");
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+ "Remove from default list?",
+ "Remove user defined colour",
+ JOptionPane.YES_NO_OPTION);
+ if(option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ }
+ }
+ });
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+
+ colourMenu.insert(radioItem, 15);
+ colours.add(radioItem);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void PIDColour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new PIDColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ {
+ changeColour(new Blosum62ColourScheme());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
+ HistoryItem.SORT));
+ AlignmentSorter.sortByPID(viewport.getAlignment(),
+ viewport.getAlignment().getSequenceAt(0));
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void sortIDMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
+ HistoryItem.SORT));
+ AlignmentSorter.sortByID(viewport.getAlignment());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+ HistoryItem.SORT));
+
+ AlignmentSorter.sortByGroup(viewport.getAlignment());
+ alignPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+ {
+ new RedundancyPanel(alignPanel, this);
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ {
+ if ( (viewport.getSelectionGroup() == null) ||
+ (viewport.getSelectionGroup().getSize(false) < 2))
+ {
+ JOptionPane.showInternalMessageDialog(this,
+ "You must select at least 2 sequences.",
+ "Invalid Selection",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ JInternalFrame frame = new JInternalFrame();
+ frame.setContentPane(new PairwiseAlignPanel(viewport));
+ Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void PCAMenuItem_actionPerformed(ActionEvent e)
+ {
+ if ( ( (viewport.getSelectionGroup() != null) &&
+ (viewport.getSelectionGroup().getSize(false) < 4) &&
+ (viewport.getSelectionGroup().getSize(false) > 0)) ||
+ (viewport.getAlignment().getHeight() < 4))
+ {
+ JOptionPane.showInternalMessageDialog(this,
+ "Principal component analysis must take\n" +
+ "at least 4 input sequences.",
+ "Sequence selection insufficient",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+
+ new PCAPanel(viewport);
+ }
+
+
+ public void autoCalculate_actionPerformed(ActionEvent e)
+ {
+ viewport.autoCalculateConsensus = autoCalculate.isSelected();
+ if(viewport.autoCalculateConsensus)
+ {
+ alignmentChanged();
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("AV", "PID", "Average distance tree using PID");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param type DOCUMENT ME!
+ * @param pwType DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ */
+ void NewTreePanel(String type, String pwType, String title)
+ {
+ TreePanel tp;
+
+ if ( (viewport.getSelectionGroup() != null) &&
+ (viewport.getSelectionGroup().getSize(false) > 3))
+ {
+ int s = 0;
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ /* Decide if the selection is a column region */
+ while (s < sg.getSize(false))
+ {
+ if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
+ sg.getEndRes())
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "The selected region to create a tree may\nonly contain residues or gaps.\n" +
+ "Try using the Pad function in the edit menu,\n" +
+ "or one of the multiple sequence alignment web services.",
+ "Sequences in selection are not aligned",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+ }
+
+ title = title + " on region";
+ tp = new TreePanel(viewport, type, pwType);
+ }
+ else
+ {
+ //are the sequences aligned?
+ if (!viewport.alignment.isAligned())
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "The sequences must be aligned before creating a tree.\n" +
+ "Try using the Pad function in the edit menu,\n" +
+ "or one of the multiple sequence alignment web services.",
+ "Sequences not aligned",
+ JOptionPane.WARNING_MESSAGE);
+
+ return;
+ }
+
+ if(viewport.alignment.getHeight()<2)
+ return;
+
+ tp = new TreePanel(viewport, type, pwType);
+ }
+
+ addTreeMenuItem(tp, title);
+
+ Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param title DOCUMENT ME!
+ * @param order DOCUMENT ME!
+ */
+ public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
+ {
+ final JMenuItem item = new JMenuItem("by " + title);
+ sort.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+ HistoryItem.SORT));
+
+ // TODO: JBPNote - have to map order entries to curent SequenceI pointers
+ AlignmentSorter.sortBy(viewport.getAlignment(), order);
+ alignPanel.repaint();
+ }
+ });
+ }
+
+ /**
+ * Maintain the Order by->Displayed Tree menu.
+ * Creates a new menu item for a TreePanel with an appropriate
+ * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
+ * to remove the menu item when the treePanel is closed, and adjust
+ * the tree leaf to sequence mapping when the alignment is modified.
+ * @param treePanel Displayed tree window.
+ * @param title SortBy menu item title.
+ */
+ void addTreeMenuItem(final TreePanel treePanel, String title)
+ {
+ final JMenuItem item = new JMenuItem(title);
+
+ treeCount++;
+
+ if (treeCount == 1)
+ {
+ sort.add(sortByTreeMenu);
+ }
+
+ sortByTreeMenu.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addHistoryItem(new HistoryItem("Tree Sort",
+ viewport.alignment, HistoryItem.SORT));
+ AlignmentSorter.sortByTree(viewport.getAlignment(),
+ treePanel.getTree());
+ alignPanel.repaint();
+ }
+ });
+
+ treePanel.addInternalFrameListener(new javax.swing.event.
+ InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ treeCount--;
+ sortByTreeMenu.remove(item);
+
+ if (treeCount == 0)
+ {
+ sort.remove(sortByTreeMenu);
+ }
+ }
+ ;
+ });
+ }
+
+ /**
+ * Work out whether the whole set of sequences
+ * or just the selected set will be submitted for multiple alignment.
+ *
+ */
+ private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
+ {
+ // Now, check we have enough sequences
+ AlignmentView msa = null;
+
+ if ( (viewport.getSelectionGroup() != null) &&
+ (viewport.getSelectionGroup().getSize(false) > 1))
+ {
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+ /*SequenceGroup seqs = viewport.getSelectionGroup();
+ int sz;
+ msa = new SequenceI[sz = seqs.getSize(false)];
+
+ for (int i = 0; i < sz; i++)
+ {
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);
+ } */
+ msa = viewport.getAlignmentView(true);
+ }
+ else
+ {
+ /*Vector seqs = viewport.getAlignment().getSequences();
+
+ if (seqs.size() > 1)
+ {
+ msa = new SequenceI[seqs.size()];
+
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ msa[i] = (SequenceI) seqs.elementAt(i);
+ }
+ }*/
+ msa = viewport.getAlignmentView(false);
+ }
+ return msa;
+ }
+
+ /**
+ * Decides what is submitted to a secondary structure prediction service,
+ * the currently selected sequence, or the currently selected alignment
+ * (where the first sequence in the set is the one that the prediction
+ * will be for).
+ */
+ AlignmentView gatherSeqOrMsaForSecStrPrediction()
+ {
+ AlignmentView seqs = null;
+
+ if ( (viewport.getSelectionGroup() != null) &&
+ (viewport.getSelectionGroup().getSize(false) > 0))
+ {
+ seqs = viewport.getAlignmentView(true);
+ }
+ else
+ {
+ seqs = viewport.getAlignmentView(false);
+ }
+ // limit sequences - JBPNote in future - could spawn multiple prediction jobs
+ // TODO: viewport.alignment.isAligned is a global state - the local selection may well be aligned - we preserve 2.0.8 behaviour for moment.
+ if (!viewport.alignment.isAligned())
+ {
+ seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] } );
+ }
+ return seqs;
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ {
+ // Pick the tree file
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty(
+ "LAST_DIRECTORY"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Select a newick-like tree file");
+ chooser.setToolTipText("Load a tree file");
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+
+ try
+ {
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
+ "File");
+ viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
+ }
+ catch (Exception ex)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "Problem reading tree file",
+ ex.getMessage(),
+ JOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ }
+ }
+
+
+ public TreePanel ShowNewickTree(NewickFile nf, String title)
+ {
+ return ShowNewickTree(nf,title,600,500,4,5);
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nf DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
+ {
+ TreePanel tp = null;
+
+ try
+ {
+ nf.parse();
+
+ if (nf.getTree() != null)
+ {
+ tp = new TreePanel(viewport,
+ "FromFile",
+ title,
+ nf);
+
+ tp.setSize(w,h);
+
+ if(x>0 && y>0)
+ tp.setLocation(x,y);
+
+
+ Desktop.addInternalFrame(tp, title, w, h);
+ addTreeMenuItem(tp, title);
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ return tp;
+ }
+
+ class PrintThread
+ extends Thread
+ {
+ public void run()
+ {
+ PrinterJob printJob = PrinterJob.getPrinterJob();
+ PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+ printJob.setPrintable(alignPanel, pf);
+
+ if (printJob.printDialog())
+ {
+ try
+ {
+ printJob.print();
+ }
+ catch (Exception PrintException)
+ {
+ PrintException.printStackTrace();
+ }
+ }
+ }
+ }
+
+ /**
+ * Generates menu items and listener event actions for web service clients
+ *
+ */
+ public void BuildWebServiceMenu()
+ {
+ if ( (Discoverer.services != null)
+ && (Discoverer.services.size() > 0))
+ {
+ Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+ Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
+ Vector wsmenu = new Vector();
+ final AlignFrame af = this;
+ if (msaws != null)
+ {
+ // Add any Multiple Sequence Alignment Services
+ final JMenu msawsmenu = new JMenu("Alignment");
+ for (int i = 0, j = msaws.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
+ get(i);
+ final JMenuItem method = new JMenuItem(sh.getName());
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = gatherSequencesForAlignment();
+ new jalview.ws.MsaWSClient(sh, title, msa,
+ false, true, viewport.getAlignment().getDataset(), af);
+
+ }
+
+ });
+ msawsmenu.add(method);
+ // Deal with services that we know accept partial alignments.
+ if (sh.getName().indexOf("lustal") > -1)
+ {
+ // We know that ClustalWS can accept partial alignments for refinement.
+ final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
+ methodR.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = gatherSequencesForAlignment();
+ new jalview.ws.MsaWSClient(sh, title, msa,
+ true, true, viewport.getAlignment().getDataset(), af);
+
+ }
+
+ });
+ msawsmenu.add(methodR);
+
+ }
+ }
+ wsmenu.add(msawsmenu);
+ }
+ if (secstrpr != null)
+ {
+ // Add any secondary structure prediction services
+ final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
+ for (int i = 0, j = secstrpr.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
+ secstrpr.get(i);
+ final JMenuItem method = new JMenuItem(sh.getName());
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
+ if (msa.getSequences().length == 1)
+ {
+ // Single Sequence prediction
+ new jalview.ws.JPredClient(sh, title, false, msa, af);
+ }
+ else
+ {
+ if (msa.getSequences().length > 1)
+ {
+ // Sequence profile based prediction
+ new jalview.ws.JPredClient(sh,
+ title, true, msa, af);
+ }
+ }
+ }
+ });
+ secstrmenu.add(method);
+ }
+ wsmenu.add(secstrmenu);
+ }
+ this.webService.removeAll();
+ for (int i = 0, j = wsmenu.size(); i < j; i++)
+ {
+ webService.add( (JMenu) wsmenu.get(i));
+ }
+ }
+ else
+ {
+ this.webService.removeAll();
+ this.webService.add(this.webServiceNoServices);
+ }
+ // TODO: add in rediscovery function
+ // TODO: reduce code redundancy.
+ // TODO: group services by location as well as function.
+ }
+
+ /* public void vamsasStore_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Export to Vamsas file");
+ chooser.setToolTipText("Export");
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+ //vs.store(chooser.getSelectedFile().getAbsolutePath() );
+ vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
+ }
+ }*/
+
+
+
+
+public void showTranslation_actionPerformed(ActionEvent e)
+{
+ SequenceI [] selection = viewport.getSelectionAsNewSequence();
+ String [] seqstring = viewport.getViewAsString(true);
+
+ int s, sSize = selection.length;
+ SequenceI [] newSeq = new SequenceI[sSize];
+
+ int res, resSize;
+ StringBuffer protein;
+ String seq;
+ for(s=0; s<sSize; s++)
+ {
+ protein = new StringBuffer();
+ seq = AlignSeq.extractGaps("-. ", seqstring[s]);
+ resSize = seq.length();
+ resSize -= resSize%3;
+
+ for(res = 0; res < resSize; res+=3)
+ {
+ String codon = seq.substring(res, res+3);
+ codon = codon.replace('U', 'T');
+ String aa = ResidueProperties.codonTranslate(codon);
+ if(aa==null)
+ protein.append(viewport.getGapCharacter());
+ else if(aa.equals("STOP"))
+ protein.append("X");
+ else
+ protein.append( aa );
+ }
+ newSeq[s] = new Sequence(selection[s].getName(),
+ protein.toString());
+ }
+
+
+ AlignmentI al = new Alignment(newSeq);
+ al.setDataset(null);
+
+
+ ////////////////////////////////
+ // Copy annotations across
+ jalview.datamodel.AlignmentAnnotation[] annotations
+ = viewport.alignment.getAlignmentAnnotation();
+ int a, aSize;
+ if(annotations!=null)
+ {
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i].label.equals("Quality") ||
+ annotations[i].label.equals("Conservation") ||
+ annotations[i].label.equals("Consensus"))
+ {
+ continue;
+ }
+
+ aSize = viewport.alignment.getWidth() / 3;
+ jalview.datamodel.Annotation[] anots =
+ new jalview.datamodel.Annotation[aSize];
+
+ for (a = 0; a < viewport.alignment.getWidth(); a++)
+ {
+ if (annotations[i].annotations[a] == null
+ || annotations[i].annotations[a] == null)
+ continue;
+
+ anots[a / 3] = new Annotation(
+ annotations[i].annotations[a].displayCharacter,
+ annotations[i].annotations[a].description,
+ annotations[i].annotations[a].secondaryStructure,
+ annotations[i].annotations[a].value,
+ annotations[i].annotations[a].colour);
+ }
+
+ jalview.datamodel.AlignmentAnnotation aa
+ = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
+ annotations[i].description, anots);
+ al.addAnnotation(aa);
+ }
+ }
+
+ AlignFrame af = new AlignFrame(al);
+ Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
+ NEW_WINDOW_WIDTH,
+ NEW_WINDOW_HEIGHT);
+
+
+ // AlignViewport newViewport = new AlignViewport(al);
+ // AlignmentPanel ap = new AlignmentPanel(this, newViewport);
+ // tabbedPane.add("Protein", ap);
+ // viewports.add(newViewport);
+ // alignPanels.add(ap);
+
+ ///Dataset tab
+ /////////////////////////
+
+ // AlignViewport ds = new AlignViewport(al.getDataset());
+ // ds.setDataset(true);
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);
+ // tabbedPane.add("Dataset", dap);
+ // viewports.add(ds);
+ // alignPanels.add(dap);
+ /////////////////////////
+
+
+}
+
+/*public void tabSelected()
+ {
+ int index = tabbedPane.getSelectedIndex();
+ viewport = (AlignViewport)viewports.elementAt(index);
+ alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
+ }*/
+
+/**
+ * DOCUMENT ME!
+ *
+ * @param String DOCUMENT ME!
+ */
+public boolean parseFeaturesFile(String file, String type)
+{
+ boolean featuresFile = false;
+ try{
+ featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
+ alignPanel.seqPanel.seqCanvas.
+ getFeatureRenderer().featureColours,
+ false);
+ }
+ catch(Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ if(featuresFile)
+ {
+ viewport.showSequenceFeatures = true;
+ showSeqFeatures.setSelected(true);
+ alignPanel.repaint();
+ }
+
+ return featuresFile;
+}
+
+public void dragEnter(DropTargetDragEvent evt)
+{}
+
+public void dragExit(DropTargetEvent evt)
+{}
+
+public void dragOver(DropTargetDragEvent evt)
+{}
+
+public void dropActionChanged(DropTargetDragEvent evt)
+{}
+
+public void drop(DropTargetDropEvent evt)
+{
+ Transferable t = evt.getTransferable();
+ java.util.List files = null;
+
+ try
+ {
+ DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+ {
+ //Works on Windows and MacOSX
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+ }
+ else if (t.isDataFlavorSupported(uriListFlavor))
+ {
+ // This is used by Unix drag system
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ String data = (String) t.getTransferData(uriListFlavor);
+ files = new java.util.ArrayList(1);
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+ data,
+ "\r\n");
+ st.hasMoreTokens(); )
+ {
+ String s = st.nextToken();
+ if (s.startsWith("#"))
+ {
+ // the line is a comment (as per the RFC 2483)
+ continue;
+ }
+
+ java.net.URI uri = new java.net.URI(s);
+ java.io.File file = new java.io.File(uri);
+ files.add(file);
+ }
+ }
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ if (files != null)
+ {
+ try
+ {
+
+ for (int i = 0; i < files.size(); i++)
+ {
+ loadJalviewDataFile(files.get(i).toString());
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+}
+
+ // This method will attempt to load a "dropped" file first by testing
+ // whether its and Annotation file, then features file. If both are
+ // false then the user may have dropped an alignment file onto this
+ // AlignFrame
+ public void loadJalviewDataFile(String file)
+ {
+ try{
+ boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
+ alignment, file);
+
+ if (!isAnnotation)
+ {
+ boolean isGroupsFile = parseFeaturesFile(file,
+ AppletFormatAdapter.FILE);
+ if (!isGroupsFile)
+ {
+ String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);
+ new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);
+ }
+ }
+ else
+ {
+ // (isAnnotation)
+ alignPanel.adjustAnnotationHeight();
+ }
+
+ }catch(Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+}
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.ws;\r
-\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-\r
-import ext.vamsas.*;\r
-import jalview.analysis.*;\r
-import jalview.bin.*;\r
-import jalview.datamodel.*;\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.AlignmentView;\r
-import jalview.gui.*;\r
-import jalview.io.*;\r
-import jalview.util.*;\r
-import jalview.ws.WSThread.*;\r
-import vamsas.objects.simple.*;\r
-\r
-public class JPredClient\r
- extends WSClient\r
-{\r
- AlignFrame parentFrame=null;\r
- /**\r
- * crate a new GUI JPred Job\r
- * @param sh ServiceHandle\r
- * @param title String\r
- * @param msa boolean - true - submit alignment as a sequence profile\r
- * @param alview AlignmentView\r
- */\r
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, AlignmentView alview, AlignFrame parentFrame) {\r
- wsInfo=setWebService(sh);\r
- this.parentFrame=parentFrame;\r
- startJPredClient(title, msa, alview);\r
-\r
- }\r
-\r
- /**\r
- * startJPredClient\r
- *\r
- * @param title String\r
- * @param msa boolean\r
- * @param alview AlignmentView\r
- */\r
- private void startJPredClient(String title, boolean msa,\r
- jalview.datamodel.AlignmentView alview)\r
- {\r
- }\r
-\r
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq, AlignFrame parentFrame)\r
- {\r
- wsInfo = setWebService(sh);\r
- this.parentFrame=parentFrame;\r
- startJPredClient(title, seq);\r
- }\r
-\r
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa, AlignFrame parentFrame)\r
- {\r
- wsInfo = setWebService(sh);\r
- this.parentFrame=parentFrame;\r
- startJPredClient(title, msa);\r
- }\r
-\r
- public JPredClient(String title, SequenceI[] msf)\r
- {\r
- startJPredClient(title, msf);\r
- }\r
-\r
- public JPredClient(String title, SequenceI seq)\r
- {\r
- startJPredClient(title, seq);\r
- }\r
-\r
- private void startJPredClient(String title, SequenceI[] msf)\r
- {\r
- if (wsInfo == null)\r
- {\r
- wsInfo = setWebService();\r
- }\r
-\r
- SequenceI seq = msf[0];\r
-\r
- String altitle = "JNet prediction on " + seq.getName() +\r
- " using alignment from " + title;\r
-\r
- wsInfo.setProgressText("Job details for MSA based prediction (" +\r
- title + ") on sequence :\n>" + seq.getName() + "\n" +\r
- AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
- "\n");\r
- SequenceI aln[] = new SequenceI[msf.length];\r
- for (int i = 0, j = msf.length; i < j; i++)\r
- {\r
- aln[i] = new jalview.datamodel.Sequence(msf[i]);\r
- }\r
-\r
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);\r
-\r
- Jpred server = locateWebService();\r
- if (server==null)\r
- {\r
- return;\r
- }\r
-\r
- JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln);\r
- wsInfo.setthisService(jthread);\r
- jthread.start();\r
- }\r
-\r
- public void startJPredClient(String title, SequenceI seq)\r
- {\r
- if (wsInfo == null)\r
- {\r
- wsInfo = setWebService();\r
- }\r
- wsInfo.setProgressText("Job details for prediction on sequence :\n>" +\r
- seq.getName() + "\n" +\r
- AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
- "\n");\r
- String altitle = "JNet prediction for sequence " + seq.getName() + " from " +\r
- title;\r
-\r
- Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
-\r
- Jpred server = locateWebService();\r
- if (server==null)\r
- {\r
- return;\r
- }\r
-\r
- JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, seq);\r
- wsInfo.setthisService(jthread);\r
- jthread.start();\r
- }\r
-\r
- private WebserviceInfo setWebService()\r
- {\r
- WebServiceName = "JNetWS";\r
- WebServiceJobTitle = "JNet secondary structure prediction";\r
- WebServiceReference =\r
- "\"Cuff J. A and Barton G.J (2000) Application of " +\r
- "multiple sequence alignment profiles to improve protein secondary structure prediction, " +\r
- "Proteins 40:502-511\".";\r
- WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
-\r
- WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,\r
- WebServiceReference);\r
-\r
- return wsInfo;\r
- }\r
-\r
- private ext.vamsas.Jpred locateWebService()\r
- {\r
- ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default\r
- ext.vamsas.Jpred server=null;\r
- try\r
- {\r
- server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
- ( (JpredSoapBindingStub)server).setTimeout(60000); // one minute stub\r
- //((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE);\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- JOptionPane.showMessageDialog(Desktop.desktop,\r
- "The Secondary Structure Prediction Service named " +\r
- WebServiceName + " at " + WsURL +\r
- " couldn't be located.",\r
- "Internal Jalview Error",\r
- JOptionPane.WARNING_MESSAGE);\r
- wsInfo.setProgressText("Serious! " + WebServiceName +\r
- " Service location failed\nfor URL :" + WsURL +\r
- "\n" +\r
- ex.getMessage());\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
-\r
- }\r
-\r
- return server;\r
- }\r
-\r
- class JPredThread\r
- extends WSThread\r
- implements WSClientI\r
- {\r
- class JPredJob\r
- extends WSThread.WSJob\r
- {\r
-\r
- vamsas.objects.simple.Sequence sequence;\r
- vamsas.objects.simple.Msfalignment msa;\r
- java.util.Hashtable SequenceInfo = null;\r
- /**\r
- *\r
- * @return true if getResultSet will return a valid alignment and prediction result.\r
- */\r
- public boolean hasResults()\r
- {\r
- if (subjobComplete && result != null && result.isFinished()\r
- && ( (JpredResult) result).getPredfile() != null &&\r
- ( (JpredResult) result).getAligfile() != null)\r
- {\r
- return true;\r
- }\r
- return false;\r
- }\r
-\r
- boolean hasValidInput()\r
- {\r
- if (sequence != null)\r
- {\r
- return true;\r
- }\r
- return false;\r
- }\r
-\r
- public Alignment getResultSet()\r
- throws Exception\r
- {\r
- if (result == null || !result.isFinished())\r
- {\r
- return null;\r
- }\r
- Alignment al = null;\r
- int FirstSeq = -1; // the position of the query sequence in Alignment al\r
- boolean noMsa = true; // set if no MSA has been returned by JPred\r
-\r
- JpredResult result = (JpredResult)this.result;\r
-\r
- jalview.bin.Cache.log.debug("Parsing output from JNet job.");\r
- // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
- jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.\r
- getPredfile(),\r
- "Paste");\r
- SequenceI[] preds = prediction.getSeqsAsArray();\r
- jalview.bin.Cache.log.debug("Got prediction profile.");\r
-\r
- if ( (this.msa != null) && (result.getAligfile() != null))\r
- {\r
- jalview.bin.Cache.log.debug("Getting associated alignment.");\r
- // we ignore the returned alignment if we only predicted on a single sequence\r
- String format = new jalview.io.IdentifyFile().Identify(result.\r
- getAligfile(),\r
- "Paste");\r
-\r
- if (jalview.io.FormatAdapter.isValidFormat(format))\r
- {\r
- al = new Alignment(new FormatAdapter().readFile(result.getAligfile(),\r
- "Paste", format));\r
- SequenceI sqs[] = new SequenceI[al.getHeight()];\r
- for (int i = 0, j = al.getHeight(); i < j; i++)\r
- {\r
- sqs[i] = al.getSequenceAt(i);\r
- }\r
- if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)\r
- SequenceInfo, sqs))\r
- {\r
- throw (new Exception(\r
- "Couldn't recover sequence properties for alignment."));\r
- }\r
-\r
- noMsa = false;\r
- FirstSeq = 0;\r
- }\r
- else\r
- {\r
- throw (new Exception(\r
- "Unknown format "+format+" for file : \n" +\r
- result.getAligfile()));\r
- }\r
- }\r
- else\r
- {\r
- al = new Alignment(preds);\r
- FirstSeq = prediction.getQuerySeqPosition();\r
- if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(\r
- al.getSequenceAt(FirstSeq), SequenceInfo))\r
- {\r
- throw (new Exception(\r
- "Couldn't recover sequence properties for JNet Query sequence!"));\r
- }\r
- }\r
-\r
- al.setDataset(null);\r
-\r
- jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,\r
- noMsa);\r
- return al; // , FirstSeq, noMsa};\r
- }\r
- public JPredJob(Hashtable SequenceInfo, SequenceI seq)\r
- {\r
- super();\r
- String sq = AlignSeq.extractGaps(Comparison.GapChars, seq.getSequence());\r
- if (sq.length() >= 20)\r
- {\r
- this.SequenceInfo = SequenceInfo;\r
- sequence = new vamsas.objects.simple.Sequence();\r
- sequence.setId(seq.getName());\r
- sequence.setSeq(sq);\r
- }\r
- }\r
-\r
- public JPredJob(Hashtable SequenceInfo, SequenceI[] msf)\r
- {\r
- this(SequenceInfo, msf[0]);\r
- if (sequence != null)\r
- {\r
- if (msf.length > 1)\r
- {\r
- msa = new vamsas.objects.simple.Msfalignment();\r
- jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();\r
- msa.setMsf(pileup.print(msf));\r
- }\r
- }\r
- }\r
- }\r
- ext.vamsas.Jpred server;\r
- String altitle = "";\r
- JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server) {\r
- this.altitle = altitle;\r
- this.server = server;\r
- this.wsInfo = wsinfo;\r
- }\r
-\r
-// String OutputHeader;\r
-// vamsas.objects.simple.JpredResult result;\r
-\r
- JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo,SequenceI seq)\r
- {\r
- this(wsinfo, altitle, server);\r
- JPredJob job = new JPredJob(SequenceInfo, seq);\r
- if (job.hasValidInput())\r
- {\r
- OutputHeader = wsInfo.getProgressText();\r
- jobs = new WSJob[]\r
- {\r
- job};\r
- job.jobnum = 0;\r
- }\r
- }\r
-\r
- JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf)\r
- {\r
- this(wsinfo, altitle, server);\r
- JPredJob job = new JPredJob(SequenceInfo, msf);\r
- if (job.hasValidInput())\r
- {\r
- jobs = new WSJob[]\r
- {\r
- job};\r
- OutputHeader = wsInfo.getProgressText();\r
- job.jobnum = 0;\r
- }\r
- }\r
-\r
- /*\r
- public void run()\r
- {\r
- StartJob();\r
-\r
- while (!jobComplete && (allowedServerExceptions > 0))\r
- {\r
- try\r
- {\r
- if ( (result = server.getresult(jobId)) == null)\r
- {\r
- throw (new Exception(\r
- "Timed out when communicating with server\nTry again later.\n"));\r
- }\r
- if (result.getState()==0)\r
- jalview.bin.Cache.log.debug("Finished "+jobId);\r
- if (result.isRunning())\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
- }\r
- if (result.isQueued())\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
- }\r
-\r
- wsInfo.setProgressText(OutputHeader + "\n" +\r
- result.getStatus());\r
-\r
- if (result.isFinished())\r
- {\r
-\r
- parseResult();\r
- jobComplete = true;\r
- jobsRunning--;\r
- } else {\r
- // catch exceptions\r
- if (! (result.isJobFailed() || result.isServerError()))\r
- {\r
- try\r
- {\r
- Thread.sleep(5000);\r
- }\r
- catch (InterruptedException ex1)\r
- {\r
- }\r
-\r
- // System.out.println("I'm alive "+seqid+" "+jobid);\r
- }\r
- else\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- jobsRunning--;\r
- jobComplete = true;\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- allowedServerExceptions--;\r
-\r
- wsInfo.appendProgressText("\nJPredWS Server exception!\n" +\r
- ex.getMessage());\r
-\r
- try\r
- {\r
- if (allowedServerExceptions > 0)\r
- {\r
- Thread.sleep(5000);\r
- }\r
- }\r
- catch (InterruptedException ex1)\r
- {\r
- }\r
- }\r
- catch (OutOfMemoryError er)\r
- {\r
- jobComplete = true;\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Out of memory handling result!!"\r
- +\r
- "\nSee help files for increasing Java Virtual Machine memory."\r
- , "Out of memory",\r
- JOptionPane.WARNING_MESSAGE);\r
- System.out.println("JPredClient: "+er);\r
- System.gc();\r
- }\r
- }\r
- if (result!=null)\r
- if (! (result.isJobFailed() || result.isServerError()))\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
- }\r
- else\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- }\r
- }\r
- */\r
- void StartJob(WSJob j)\r
- {\r
- if (! (j instanceof JPredJob))\r
- {\r
- throw new Error("Implementation error - StartJob(JpredJob) called on " +\r
- j.getClass());\r
- }\r
- try\r
- {\r
- JPredJob job = (JPredJob) j;\r
- if (job.msa != null)\r
- {\r
- job.jobId = server.predictOnMsa(job.msa);\r
- }\r
- else\r
- if (job.sequence!=null)\r
- {\r
- job.jobId = server.predict(job.sequence);\r
- }\r
-\r
- if (job.jobId != null)\r
- {\r
- if (job.jobId.startsWith("Broken"))\r
- {\r
- job.result = (vamsas.objects.simple.Result)new JpredResult();\r
- job.result.setInvalid(true);\r
- job.result.setStatus("Submission " + job.jobId);\r
- }\r
- else\r
- {\r
- job.submitted = true;\r
- job.subjobComplete = false;\r
- Cache.log.info(WsURL + " Job Id '" + job.jobId + "'");\r
- }\r
- }\r
- else\r
- {\r
- throw new Exception("Server timed out - try again later\n");\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- if (e.getMessage().indexOf("Exception") > -1)\r
- {\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- wsInfo.setProgressText(j.jobnum,\r
- "Failed to submit the prediction. (Just close the window)\n"\r
- +\r
- "It is most likely that there is a problem with the server.\n");\r
- System.err.println(\r
- "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" +\r
- e.getMessage() + "\n");\r
-\r
- jalview.bin.Cache.log.warn("Server Exception", e);\r
- }\r
- else\r
- {\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
- // JBPNote - this could be a popup informing the user of the problem.\r
- wsInfo.appendProgressText(j.jobnum,\r
- "Failed to submit the prediction:\n"\r
- + e.getMessage() +\r
- wsInfo.getProgressText());\r
-\r
- jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);\r
-\r
- }\r
- j.allowedServerExceptions = -1;\r
- j.subjobComplete = true;\r
- }\r
- }\r
-\r
- /* private void addFloatAnnotations(Alignment al, int[] gapmap,\r
- Vector values, String Symname,\r
- String Visname, float min,\r
- float max, int winLength)\r
- {\r
- Annotation[] annotations = new Annotation[al.getWidth()];\r
-\r
- for (int j = 0; j < values.size(); j++)\r
- {\r
- float value = Float.parseFloat(values.get(j).toString());\r
- annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
- value);\r
- }\r
-\r
- al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
- annotations, min, max, winLength));\r
- }*/\r
-\r
- void parseResult()\r
- {\r
- int results = 0; // number of result sets received\r
- JobStateSummary finalState = new JobStateSummary();\r
- try\r
- {\r
- for (int j = 0; j < jobs.length; j++)\r
- {\r
- finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);\r
- if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())\r
- {\r
- results++;\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
-\r
- Cache.log.error("Unexpected exception when processing results for " +\r
- altitle, ex);\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- }\r
- if (results > 0)\r
- {\r
- wsInfo.showResultsNewFrame\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(\r
- java.awt.event.ActionEvent evt)\r
- {\r
- displayResults(true);\r
- }\r
- });\r
- wsInfo.mergeResults\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(\r
- java.awt.event.ActionEvent evt)\r
- {\r
- displayResults(false);\r
- }\r
- });\r
- wsInfo.setResultsReady();\r
- }\r
- else\r
- {\r
- wsInfo.setFinishedNoResults();\r
- }\r
- }\r
-\r
- void displayResults(boolean newWindow)\r
- {\r
- if (jobs != null)\r
- {\r
- Alignment res = null;\r
- for (int jn = 0; jn < jobs.length; jn++)\r
- {\r
- Alignment jobres = null;\r
- JPredJob j = (JPredJob) jobs[jn];\r
-\r
- if (j.hasResults())\r
- {\r
- try\r
- {\r
- jalview.bin.Cache.log.debug("Parsing output of job " + jn);\r
- jobres = j.getResultSet();\r
- jalview.bin.Cache.log.debug("Finished parsing output.");\r
- if (jobs.length==1)\r
- res = jobres;\r
- else {\r
- // do merge with other job results\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- jalview.bin.Cache.log.error(\r
- "JNet Client: JPred Annotation Parse Error",\r
- e);\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
- wsInfo.appendProgressText(j.jobnum,\r
- OutputHeader + "\n" +\r
- j.result.getStatus() +\r
- "\nInvalid JNet job result data!\n" +\r
- e.getMessage());\r
- j.result.setBroken(true);\r
- }\r
- }\r
- }\r
-\r
- if (res != null)\r
- {\r
- if (newWindow)\r
- {\r
- AlignFrame af = new AlignFrame(res);\r
- Desktop.addInternalFrame(af, altitle,\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- }\r
- else\r
- {\r
- Cache.log.info("Append results onto existing alignment.");\r
- }\r
- }\r
- }\r
- }\r
- void pollJob(WSJob job)\r
- throws Exception\r
- {\r
- job.result = server.getresult(job.jobId);\r
- }\r
- public boolean isCancellable()\r
- {\r
- return false;\r
- }\r
-\r
- public void cancelJob()\r
- {\r
- throw new Error("Implementation error!");\r
- }\r
-\r
- public boolean canMergeResults()\r
- {\r
- return false;\r
- }\r
-\r
- }\r
-}\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.ws;
+
+import java.util.*;
+
+import javax.swing.*;
+
+import ext.vamsas.*;
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.gui.*;
+import jalview.io.*;
+import jalview.util.*;
+import jalview.ws.WSThread.*;
+import vamsas.objects.simple.*;
+
+public class JPredClient
+ extends WSClient
+{
+ /**
+ * crate a new GUI JPred Job
+ * @param sh ServiceHandle
+ * @param title String
+ * @param msa boolean - true - submit alignment as a sequence profile
+ * @param alview AlignmentView
+ */
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, AlignmentView alview, AlignFrame parentFrame) {
+ super();
+ wsInfo=setWebService(sh);
+ startJPredClient(title, msa, alview, parentFrame);
+
+ }
+ /**
+ * startJPredClient
+ * TODO: refine submission to cope with local prediction of visible regions or multiple single sequence jobs
+ * TODO: sequence representative support - could submit alignment of representatives as msa.
+ * TODO: msa hidden region prediction - submit each chunk for prediction. concatenate results of each.
+ * TODO: single seq prediction - submit each contig of each sequence for prediction (but must cope with flanking regions and short seqs)
+ * @param title String
+ * @param msa boolean
+ * @param alview AlignmentView
+ */
+ private void startJPredClient(String title, boolean msa,
+ jalview.datamodel.AlignmentView alview, AlignFrame parentFrame)
+ {
+ AlignmentView input = alview;
+ if (wsInfo == null)
+ {
+ wsInfo = setWebService();
+ }
+ Jpred server = locateWebService();
+ if (server == null)
+ {
+ Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
+ return;
+ }
+
+ SeqCigar[] msf = input.getSequences();
+ SequenceI seq = msf[0].getSeq('-');
+ if (msa && msf.length > 1)
+ {
+
+ String altitle = "JNet prediction on " + seq.getName() +
+ " using alignment from " + title;
+
+ wsInfo.setProgressText("Job details for MSA based prediction (" +
+ title + ") on sequence :\n>" + seq.getName() +
+ "\n" +
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +
+ "\n");
+ SequenceI aln[] = new SequenceI[msf.length];
+ for (int i = 0, j = msf.length; i < j; i++)
+ {
+ aln[i] = msf[i].getSeq('-');
+ }
+
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
+
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server,
+ SequenceInfo, aln, alview, parentFrame);
+ wsInfo.setthisService(jthread);
+ jthread.start();
+ }
+ else
+ {
+ if (!msa && msf.length>1)
+ throw new Error("Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
+ wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
+ seq.getName() + "\n" +
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +
+ "\n");
+ String altitle = "JNet prediction for sequence " + seq.getName() +
+ " from " +
+ title;
+
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(
+ seq);
+
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server,
+ SequenceInfo, seq, alview, parentFrame);
+ wsInfo.setthisService(jthread);
+ jthread.start();
+ }
+ }
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq, AlignFrame parentFrame)
+ {
+ super();
+ wsInfo = setWebService(sh);
+ startJPredClient(title, seq, parentFrame);
+ }
+
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa, AlignFrame parentFrame)
+ {
+ wsInfo = setWebService(sh);
+ startJPredClient(title, msa, parentFrame);
+ }
+
+ public JPredClient(String title, SequenceI[] msf)
+ {
+ startJPredClient(title, msf, null);
+ }
+
+ public JPredClient(String title, SequenceI seq)
+ {
+ startJPredClient(title, seq, null);
+ }
+
+ private void startJPredClient(String title, SequenceI[] msf, AlignFrame parentFrame)
+ {
+ if (wsInfo == null)
+ {
+ wsInfo = setWebService();
+ }
+
+ SequenceI seq = msf[0];
+
+ String altitle = "JNet prediction on " + seq.getName() +
+ " using alignment from " + title;
+
+ wsInfo.setProgressText("Job details for MSA based prediction (" +
+ title + ") on sequence :\n>" + seq.getName() + "\n" +
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +
+ "\n");
+ SequenceI aln[] = new SequenceI[msf.length];
+ for (int i = 0, j = msf.length; i < j; i++)
+ {
+ aln[i] = new jalview.datamodel.Sequence(msf[i]);
+ }
+
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
+
+ Jpred server = locateWebService();
+ if (server==null)
+ {
+ return;
+ }
+
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln,null, parentFrame);
+ wsInfo.setthisService(jthread);
+ jthread.start();
+ }
+
+ public void startJPredClient(String title, SequenceI seq, AlignFrame parentFrame)
+ {
+ if (wsInfo == null)
+ {
+ wsInfo = setWebService();
+ }
+ wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
+ seq.getName() + "\n" +
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +
+ "\n");
+ String altitle = "JNet prediction for sequence " + seq.getName() + " from " +
+ title;
+
+ Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
+
+ Jpred server = locateWebService();
+ if (server==null)
+ {
+ return;
+ }
+
+ JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, seq,null, parentFrame);
+ wsInfo.setthisService(jthread);
+ jthread.start();
+ }
+
+ private WebserviceInfo setWebService()
+ {
+ WebServiceName = "JNetWS";
+ WebServiceJobTitle = "JNet secondary structure prediction";
+ WebServiceReference =
+ "\"Cuff J. A and Barton G.J (2000) Application of " +
+ "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
+ "Proteins 40:502-511\".";
+ WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
+
+ WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
+ WebServiceReference);
+
+ return wsInfo;
+ }
+
+ private ext.vamsas.Jpred locateWebService()
+ {
+ ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
+ ext.vamsas.Jpred server=null;
+ try
+ {
+ server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
+ ( (JpredSoapBindingStub)server).setTimeout(60000); // one minute stub
+ //((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE);
+
+ }
+ catch (Exception ex)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "The Secondary Structure Prediction Service named " +
+ WebServiceName + " at " + WsURL +
+ " couldn't be located.",
+ "Internal Jalview Error",
+ JOptionPane.WARNING_MESSAGE);
+ wsInfo.setProgressText("Serious! " + WebServiceName +
+ " Service location failed\nfor URL :" + WsURL +
+ "\n" +
+ ex.getMessage());
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+
+ }
+
+ return server;
+ }
+
+ class JPredThread
+ extends WSThread
+ implements WSClientI
+ {
+ class JPredJob
+ extends WSThread.WSJob
+ {
+
+ vamsas.objects.simple.Sequence sequence;
+ vamsas.objects.simple.Msfalignment msa;
+ java.util.Hashtable SequenceInfo = null;
+ /**
+ *
+ * @return true if getResultSet will return a valid alignment and prediction result.
+ */
+ public boolean hasResults()
+ {
+ if (subjobComplete && result != null && result.isFinished()
+ && ( (JpredResult) result).getPredfile() != null &&
+ ( (JpredResult) result).getAligfile() != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ boolean hasValidInput()
+ {
+ if (sequence != null)
+ {
+ return true;
+ }
+ return false;
+ }
+
+ public Alignment getResultSet()
+ throws Exception
+ {
+ if (result == null || !result.isFinished())
+ {
+ return null;
+ }
+ Alignment al = null;
+ int FirstSeq = -1; // the position of the query sequence in Alignment al
+
+ JpredResult result = (JpredResult)this.result;
+
+ jalview.bin.Cache.log.debug("Parsing output from JNet job.");
+ // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
+ jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.
+ getPredfile(),
+ "Paste");
+ SequenceI[] preds = prediction.getSeqsAsArray();
+ jalview.bin.Cache.log.debug("Got prediction profile.");
+
+ if ( (this.msa != null) && (result.getAligfile() != null))
+ {
+ jalview.bin.Cache.log.debug("Getting associated alignment.");
+ // we ignore the returned alignment if we only predicted on a single sequence
+ String format = new jalview.io.IdentifyFile().Identify(result.
+ getAligfile(),
+ "Paste");
+
+ if (jalview.io.FormatAdapter.isValidFormat(format))
+ {
+ al = new Alignment(new FormatAdapter().readFile(result.getAligfile(),
+ "Paste", format));
+ SequenceI sqs[] = new SequenceI[al.getHeight()];
+ for (int i = 0, j = al.getHeight(); i < j; i++)
+ {
+ sqs[i] = al.getSequenceAt(i);
+ }
+ if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)
+ SequenceInfo, sqs))
+ {
+ throw (new Exception(
+ "Couldn't recover sequence properties for alignment."));
+ }
+
+ FirstSeq = 0;
+ al.setDataset(null);
+
+ jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
+ false);
+
+ }
+ else
+ {
+ throw (new Exception(
+ "Unknown format "+format+" for file : \n" +
+ result.getAligfile()));
+ }
+ }
+ else
+ {
+ al = new Alignment(preds);
+ FirstSeq = prediction.getQuerySeqPosition();
+ if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
+ al.getSequenceAt(FirstSeq), SequenceInfo))
+ {
+ throw (new Exception(
+ "Couldn't recover sequence properties for JNet Query sequence!"));
+ } else {
+ al.setDataset(null);
+ jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
+ true);
+ }
+ }
+
+ return al; // , FirstSeq, noMsa};
+ }
+ public JPredJob(Hashtable SequenceInfo, SequenceI seq)
+ {
+ super();
+ String sq = AlignSeq.extractGaps(Comparison.GapChars, seq.getSequence());
+ if (sq.length() >= 20)
+ {
+ this.SequenceInfo = SequenceInfo;
+ sequence = new vamsas.objects.simple.Sequence();
+ sequence.setId(seq.getName());
+ sequence.setSeq(sq);
+ }
+ }
+
+ public JPredJob(Hashtable SequenceInfo, SequenceI[] msf)
+ {
+ this(SequenceInfo, msf[0]);
+ if (sequence != null)
+ {
+ if (msf.length > 1)
+ {
+ msa = new vamsas.objects.simple.Msfalignment();
+ jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
+ msa.setMsf(pileup.print(msf));
+ }
+ }
+ }
+ }
+ ext.vamsas.Jpred server;
+ String altitle = "";
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, AlignmentView alview, AlignFrame alframe) {
+ this.altitle = altitle;
+ this.server = server;
+ this.wsInfo = wsinfo;
+ this.input = alview;
+ this.alignFrame = alframe;
+ }
+
+// String OutputHeader;
+// vamsas.objects.simple.JpredResult result;
+
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo,SequenceI seq, AlignmentView alview, AlignFrame alframe)
+ {
+ this(wsinfo, altitle, server,alview, alframe);
+ JPredJob job = new JPredJob(SequenceInfo, seq);
+ if (job.hasValidInput())
+ {
+ OutputHeader = wsInfo.getProgressText();
+ jobs = new WSJob[]
+ {
+ job};
+ job.jobnum = 0;
+ }
+ }
+
+ JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf, AlignmentView alview, AlignFrame alframe)
+ {
+ this(wsinfo, altitle, server,alview, alframe);
+ JPredJob job = new JPredJob(SequenceInfo, msf);
+ if (job.hasValidInput())
+ {
+ jobs = new WSJob[]
+ {
+ job};
+ OutputHeader = wsInfo.getProgressText();
+ job.jobnum = 0;
+ }
+ }
+
+ /*
+ public void run()
+ {
+ StartJob();
+
+ while (!jobComplete && (allowedServerExceptions > 0))
+ {
+ try
+ {
+ if ( (result = server.getresult(jobId)) == null)
+ {
+ throw (new Exception(
+ "Timed out when communicating with server\nTry again later.\n"));
+ }
+ if (result.getState()==0)
+ jalview.bin.Cache.log.debug("Finished "+jobId);
+ if (result.isRunning())
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+ }
+ if (result.isQueued())
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+ }
+
+ wsInfo.setProgressText(OutputHeader + "\n" +
+ result.getStatus());
+
+ if (result.isFinished())
+ {
+
+ parseResult();
+ jobComplete = true;
+ jobsRunning--;
+ } else {
+ // catch exceptions
+ if (! (result.isJobFailed() || result.isServerError()))
+ {
+ try
+ {
+ Thread.sleep(5000);
+ }
+ catch (InterruptedException ex1)
+ {
+ }
+
+ // System.out.println("I'm alive "+seqid+" "+jobid);
+ }
+ else
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ jobsRunning--;
+ jobComplete = true;
+ }
+ }
+ }
+ catch (Exception ex)
+ {
+ allowedServerExceptions--;
+
+ wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
+ ex.getMessage());
+
+ try
+ {
+ if (allowedServerExceptions > 0)
+ {
+ Thread.sleep(5000);
+ }
+ }
+ catch (InterruptedException ex1)
+ {
+ }
+ }
+ catch (OutOfMemoryError er)
+ {
+ jobComplete = true;
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of memory handling result!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ JOptionPane.WARNING_MESSAGE);
+ System.out.println("JPredClient: "+er);
+ System.gc();
+ }
+ }
+ if (result!=null)
+ if (! (result.isJobFailed() || result.isServerError()))
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+ }
+ else
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ }
+ */
+ void StartJob(WSJob j)
+ {
+ if (! (j instanceof JPredJob))
+ {
+ throw new Error("Implementation error - StartJob(JpredJob) called on " +
+ j.getClass());
+ }
+ try
+ {
+ JPredJob job = (JPredJob) j;
+ if (job.msa != null)
+ {
+ job.jobId = server.predictOnMsa(job.msa);
+ }
+ else
+ if (job.sequence!=null)
+ {
+ job.jobId = server.predict(job.sequence);
+ }
+
+ if (job.jobId != null)
+ {
+ if (job.jobId.startsWith("Broken"))
+ {
+ job.result = (vamsas.objects.simple.Result)new JpredResult();
+ job.result.setInvalid(true);
+ job.result.setStatus("Submission " + job.jobId);
+ }
+ else
+ {
+ job.submitted = true;
+ job.subjobComplete = false;
+ Cache.log.info(WsURL + " Job Id '" + job.jobId + "'");
+ }
+ }
+ else
+ {
+ throw new Exception("Server timed out - try again later\n");
+ }
+ }
+ catch (Exception e)
+ {
+ if (e.getMessage().indexOf("Exception") > -1)
+ {
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.setProgressText(j.jobnum,
+ "Failed to submit the prediction. (Just close the window)\n"
+ +
+ "It is most likely that there is a problem with the server.\n");
+ System.err.println(
+ "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" +
+ e.getMessage() + "\n");
+
+ jalview.bin.Cache.log.warn("Server Exception", e);
+ }
+ else
+ {
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+ // JBPNote - this could be a popup informing the user of the problem.
+ wsInfo.appendProgressText(j.jobnum,
+ "Failed to submit the prediction:\n"
+ + e.getMessage() +
+ wsInfo.getProgressText());
+
+ jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);
+
+ }
+ j.allowedServerExceptions = -1;
+ j.subjobComplete = true;
+ }
+ }
+
+ /* private void addFloatAnnotations(Alignment al, int[] gapmap,
+ Vector values, String Symname,
+ String Visname, float min,
+ float max, int winLength)
+ {
+ Annotation[] annotations = new Annotation[al.getWidth()];
+
+ for (int j = 0; j < values.size(); j++)
+ {
+ float value = Float.parseFloat(values.get(j).toString());
+ annotations[gapmap[j]] = new Annotation("", value + "", ' ',
+ value);
+ }
+
+ al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
+ annotations, min, max, winLength));
+ }*/
+
+ void parseResult()
+ {
+ int results = 0; // number of result sets received
+ JobStateSummary finalState = new JobStateSummary();
+ try
+ {
+ for (int j = 0; j < jobs.length; j++)
+ {
+ finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+ if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
+ {
+ results++;
+ }
+ }
+ }
+ catch (Exception ex)
+ {
+
+ Cache.log.error("Unexpected exception when processing results for " +
+ altitle, ex);
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ if (results > 0)
+ {
+ wsInfo.showResultsNewFrame
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(
+ java.awt.event.ActionEvent evt)
+ {
+ displayResults(true);
+ }
+ });
+ wsInfo.mergeResults
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(
+ java.awt.event.ActionEvent evt)
+ {
+ displayResults(false);
+ }
+ });
+ wsInfo.setResultsReady();
+ }
+ else
+ {
+ wsInfo.setFinishedNoResults();
+ }
+ }
+
+ void displayResults(boolean newWindow)
+ {
+ // TODO: cope with multiple subjobs.
+ if (jobs != null)
+ {
+ Alignment res = null;
+ boolean msa=false;
+ for (int jn = 0; jn < jobs.length; jn++)
+ {
+ Alignment jobres = null;
+ JPredJob j = (JPredJob) jobs[jn];
+
+ if (j.hasResults())
+ {
+ // hack - we only deal with all single seuqence predictions or all profile predictions
+ msa = (j.msa!=null) ? true : msa;
+ try
+ {
+ jalview.bin.Cache.log.debug("Parsing output of job " + jn);
+ jobres = j.getResultSet();
+ jalview.bin.Cache.log.debug("Finished parsing output.");
+ if (jobs.length==1)
+ res = jobres;
+ else {
+ // do merge with other job results
+ throw new Error("Multiple JNet subjob merging not yet implemented.");
+ }
+ }
+ catch (Exception e)
+ {
+ jalview.bin.Cache.log.error(
+ "JNet Client: JPred Annotation Parse Error",
+ e);
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+ wsInfo.appendProgressText(j.jobnum,
+ OutputHeader + "\n" +
+ j.result.getStatus() +
+ "\nInvalid JNet job result data!\n" +
+ e.getMessage());
+ j.result.setBroken(true);
+ }
+ }
+ }
+
+ if (res != null)
+ {
+ if (newWindow)
+ {
+ AlignFrame af;
+ if (input==null) {
+ af = new AlignFrame(res);
+ } else {
+ java.lang.Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());
+
+ if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
+ if (msa) {
+ throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");
+ } else {
+ // test this.
+ ((ColumnSelection) alandcolsel[1]).compensateForEdits(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));
+ }
+ }
+ af = new AlignFrame(res, (ColumnSelection) alandcolsel[1]);
+ }
+ Desktop.addInternalFrame(af, altitle,
+ AlignFrame.NEW_WINDOW_WIDTH,
+ AlignFrame.NEW_WINDOW_HEIGHT);
+ }
+ else
+ {
+ Cache.log.info("Append results onto existing alignment.");
+ }
+ }
+ }
+ }
+ void pollJob(WSJob job)
+ throws Exception
+ {
+ job.result = server.getresult(job.jobId);
+ }
+ public boolean isCancellable()
+ {
+ return false;
+ }
+
+ public void cancelJob()
+ {
+ throw new Error("Implementation error!");
+ }
+
+ public boolean canMergeResults()
+ {
+ return false;
+ }
+
+ }
+}
+
git://source.jalview.org / jalview.git / commitdiff