2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Softwarechang
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.gui;
\r
21 import java.beans.*;
\r
26 import java.awt.datatransfer.*;
\r
27 import java.awt.event.*;
\r
28 import java.awt.print.*;
\r
29 import javax.swing.*;
\r
31 import jalview.analysis.*;
\r
32 import jalview.datamodel.*;
\r
33 import jalview.io.*;
\r
34 import jalview.jbgui.*;
\r
35 import jalview.schemes.*;
\r
36 import jalview.ws.*;
\r
42 * @version $Revision$
\r
44 public class AlignFrame
\r
45 extends GAlignFrame implements ClipboardOwner
\r
47 /** DOCUMENT ME!! */
\r
48 public static final int NEW_WINDOW_WIDTH = 700;
\r
50 /** DOCUMENT ME!! */
\r
51 public static final int NEW_WINDOW_HEIGHT = 500;
\r
52 AlignmentPanel alignPanel;
\r
53 AlignViewport viewport;
\r
55 Vector viewports = new Vector();
\r
56 Vector alignPanels = new Vector();
\r
58 /** DOCUMENT ME!! */
\r
59 public String currentFileFormat = null;
\r
60 Stack historyList = new Stack();
\r
61 Stack redoList = new Stack();
\r
62 private int treeCount = 0;
\r
65 * Creates a new AlignFrame object.
\r
67 * @param al DOCUMENT ME!
\r
69 public AlignFrame(AlignmentI al)
\r
71 viewport = new AlignViewport(al);
\r
72 viewports.add(viewport);
\r
75 if(viewport.vconsensus==null)
\r
77 //Out of memory calculating consensus.
\r
78 BLOSUM62Colour.setEnabled(false);
\r
79 PIDColour.setEnabled(false);
\r
80 conservationMenuItem.setEnabled(false);
\r
81 modifyConservation.setEnabled(false);
\r
82 abovePIDThreshold.setEnabled(false);
\r
83 modifyPID.setEnabled(false);
\r
86 alignPanel = new AlignmentPanel(this, viewport);
\r
87 alignPanels.add(alignPanel);
\r
89 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
\r
91 if(sortby.equals("Id"))
\r
92 sortIDMenuItem_actionPerformed(null);
\r
93 else if(sortby.equals("Pairwise Identity"))
\r
94 sortPairwiseMenuItem_actionPerformed(null);
\r
96 tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
\r
99 /////////////////////////
\r
101 if(al.getDataset()==null)
\r
103 al.setDataset(null);
\r
106 AlignViewport ds = new AlignViewport(al.getDataset(), true);
\r
107 AlignmentPanel dap = new AlignmentPanel(this, ds);
\r
108 tabbedPane.add("Dataset", dap);
\r
110 alignPanels.add(dap);
\r
111 /////////////////////////
\r
114 viewport.addPropertyChangeListener(new PropertyChangeListener()
\r
116 public void propertyChange(PropertyChangeEvent evt)
\r
118 if (evt.getPropertyName().equals("alignment"))
\r
120 alignmentChanged();
\r
126 if(Desktop.desktop!=null)
\r
127 addServiceListeners();
\r
130 /* Set up intrinsic listeners for dynamically generated GUI bits. */
\r
131 private void addServiceListeners()
\r
133 final java.beans.PropertyChangeListener thisListener;
\r
134 // Do this once to get current state
\r
135 BuildWebServiceMenu();
\r
136 Desktop.discoverer.addPropertyChangeListener(
\r
137 thisListener = new java.beans.PropertyChangeListener()
\r
139 public void propertyChange(PropertyChangeEvent evt)
\r
141 // System.out.println("Discoverer property change.");
\r
142 if (evt.getPropertyName().equals("services"))
\r
144 // System.out.println("Rebuilding web service menu");
\r
145 BuildWebServiceMenu();
\r
149 addInternalFrameListener(new javax.swing.event.
\r
150 InternalFrameAdapter()
\r
152 public void internalFrameClosed(
\r
153 javax.swing.event.InternalFrameEvent evt)
\r
155 // System.out.println("deregistering discoverer listener");
\r
156 Desktop.discoverer.removePropertyChangeListener(thisListener);
\r
157 closeMenuItem_actionPerformed(null);
\r
167 * @param String DOCUMENT ME!
\r
170 public void parseGroupsFile(String file)
\r
174 BufferedReader in = new BufferedReader(new FileReader(file));
\r
175 SequenceI seq = null;
\r
176 String line, type, desc, token;
\r
178 int index, start, end;
\r
179 StringTokenizer st;
\r
180 SequenceFeature sf;
\r
181 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
\r
183 while ( (line = in.readLine()) != null)
\r
186 st = new StringTokenizer(line, "\t");
\r
187 if (st.countTokens() == 2)
\r
189 type = st.nextToken();
\r
190 UserColourScheme ucs = new UserColourScheme(st.nextToken());
\r
191 fr.setColour(type, ucs.findColour("A"));
\r
195 while (st.hasMoreElements())
\r
197 desc = st.nextToken();
\r
198 token = st.nextToken();
\r
199 if (!token.equals("ID_NOT_SPECIFIED"))
\r
201 index = viewport.alignment.findIndex(viewport.alignment.findName(
\r
207 index = Integer.parseInt(st.nextToken());
\r
210 start = Integer.parseInt(st.nextToken());
\r
211 end = Integer.parseInt(st.nextToken());
\r
213 seq = viewport.alignment.getSequenceAt(index);
\r
214 start = seq.findIndex(start) - 1;
\r
215 end = seq.findIndex(end) - 1;
\r
217 type = st.nextToken();
\r
219 if (fr.getColour(type) == null)
\r
221 // Probably the old style groups file
\r
222 UserColourScheme ucs = new UserColourScheme(type);
\r
223 fr.setColour(type, ucs.findColour("A"));
\r
227 sf = new SequenceFeature(type, desc, "", start, end);
\r
229 seq.addSequenceFeature(sf);
\r
232 // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
\r
233 // sg.addSequence(seq, false);
\r
235 // viewport.alignment.addGroup(sg);
\r
240 viewport.showSequenceFeatures = true;
\r
241 ((Alignment)viewport.alignment).featuresAdded = true;
\r
243 alignPanel.repaint();
\r
246 catch (Exception ex)
\r
248 System.out.println("Error parsing groups file: " + ex);
\r
255 * @param e DOCUMENT ME!
\r
257 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
\r
259 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
264 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
\r
269 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
\r
270 }, currentFileFormat);
\r
272 chooser.setAcceptAllFileFilterUsed(false);
\r
273 chooser.setFileView(new JalviewFileView());
\r
274 chooser.setDialogTitle("Save Alignment to file");
\r
275 chooser.setToolTipText("Save");
\r
277 int value = chooser.showSaveDialog(this);
\r
279 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
281 currentFileFormat = chooser.getSelectedFormat();
\r
283 if (currentFileFormat == null)
\r
285 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
286 "You must select a file format before saving!",
\r
287 "File format not specified",
\r
288 JOptionPane.WARNING_MESSAGE);
\r
289 value = chooser.showSaveDialog(this);
\r
293 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
\r
294 currentFileFormat);
\r
296 String choice = chooser.getSelectedFile().getPath();
\r
297 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
299 saveAlignment(choice, currentFileFormat);
\r
303 public boolean saveAlignment(String file, String format)
\r
305 if (format.equalsIgnoreCase("Jalview"))
\r
307 String shortName = title;
\r
309 if (shortName.indexOf(java.io.File.separatorChar) > -1)
\r
311 shortName = shortName.substring(shortName.lastIndexOf(
\r
312 java.io.File.separatorChar) + 1);
\r
315 Jalview2XML.SaveAlignment(this, file, shortName);
\r
317 // USE Jalview2XML to save this file
\r
322 String output = new FormatAdapter().formatSequences(format,
\r
323 viewport.getAlignment().
\r
325 if (output == null)
\r
332 java.io.PrintWriter out = new java.io.PrintWriter(
\r
333 new java.io.FileWriter(file));
\r
339 catch (Exception ex)
\r
341 ex.printStackTrace();
\r
350 * @param e DOCUMENT ME!
\r
352 protected void outputText_actionPerformed(ActionEvent e)
\r
354 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
355 Desktop.addInternalFrame(cap,
\r
356 "Alignment output - " + e.getActionCommand(), 600,
\r
358 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
\r
359 viewport.getAlignment().
\r
366 * @param e DOCUMENT ME!
\r
368 protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
370 new HTMLOutput(viewport);
\r
373 public void createImageMap(File file, String image)
\r
375 alignPanel.makePNGImageMap(file, image);
\r
381 * @param e DOCUMENT ME!
\r
383 public void createPNG(File f)
\r
385 alignPanel.makePNG(f);
\r
391 * @param e DOCUMENT ME!
\r
393 public void createEPS(File f)
\r
395 alignPanel.makeEPS(f);
\r
401 * @param e DOCUMENT ME!
\r
403 public void printMenuItem_actionPerformed(ActionEvent e)
\r
405 //Putting in a thread avoids Swing painting problems
\r
406 PrintThread thread = new PrintThread();
\r
413 * @param e DOCUMENT ME!
\r
415 public void closeMenuItem_actionPerformed(ActionEvent e)
\r
419 PaintRefresher.components.remove(viewport.alignment);
\r
420 this.setClosed(true);
\r
422 catch (Exception ex)
\r
430 void updateEditMenuBar()
\r
432 if (historyList.size() > 0)
\r
434 undoMenuItem.setEnabled(true);
\r
436 HistoryItem hi = (HistoryItem) historyList.peek();
\r
437 undoMenuItem.setText("Undo " + hi.getDescription());
\r
441 undoMenuItem.setEnabled(false);
\r
442 undoMenuItem.setText("Undo");
\r
445 if (redoList.size() > 0)
\r
447 redoMenuItem.setEnabled(true);
\r
449 HistoryItem hi = (HistoryItem) redoList.peek();
\r
450 redoMenuItem.setText("Redo " + hi.getDescription());
\r
454 redoMenuItem.setEnabled(false);
\r
455 redoMenuItem.setText("Redo");
\r
462 * @param hi DOCUMENT ME!
\r
464 public void addHistoryItem(HistoryItem hi)
\r
466 historyList.push(hi);
\r
467 updateEditMenuBar();
\r
473 * @param e DOCUMENT ME!
\r
475 protected void undoMenuItem_actionPerformed(ActionEvent e)
\r
477 HistoryItem hi = (HistoryItem) historyList.pop();
\r
478 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
\r
479 HistoryItem.HIDE));
\r
480 restoreHistoryItem(hi);
\r
481 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
487 * @param e DOCUMENT ME!
\r
489 protected void redoMenuItem_actionPerformed(ActionEvent e)
\r
491 HistoryItem hi = (HistoryItem) redoList.pop();
\r
492 restoreHistoryItem(hi);
\r
493 updateEditMenuBar();
\r
494 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
497 // used by undo and redo
\r
498 void restoreHistoryItem(HistoryItem hi)
\r
500 if (hi.getType() == HistoryItem.SORT)
\r
502 for (int i = 0; i < hi.getSequences().size(); i++)
\r
504 viewport.alignment.getSequences().setElementAt(hi.getSequences()
\r
511 for (int i = 0; i < hi.getSequences().size(); i++)
\r
513 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
\r
515 if (restore.getLength() == 0)
\r
517 restore.setSequence(hi.getHidden().elementAt(i).toString());
\r
518 viewport.alignment.getSequences().insertElementAt(restore,
\r
519 hi.getAlignIndex(i));
\r
523 restore.setSequence(hi.getHidden().elementAt(i).toString());
\r
527 if (hi.getType() == HistoryItem.PASTE)
\r
529 for (int i = viewport.alignment.getHeight() - 1;
\r
530 i > (hi.getSequences().size() - 1); i--)
\r
532 viewport.alignment.deleteSequence(i);
\r
537 updateEditMenuBar();
\r
539 viewport.firePropertyChange("alignment", null,
\r
540 viewport.getAlignment().getSequences());
\r
546 * @param up DOCUMENT ME!
\r
548 public void moveSelectedSequences(boolean up)
\r
550 SequenceGroup sg = viewport.getSelectionGroup();
\r
559 for (int i = 1; i < viewport.alignment.getHeight(); i++)
\r
561 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
563 if (!sg.sequences.contains(seq))
\r
568 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
\r
570 if (sg.sequences.contains(temp))
\r
575 viewport.alignment.getSequences().setElementAt(temp, i);
\r
576 viewport.alignment.getSequences().setElementAt(seq, i - 1);
\r
581 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
\r
583 SequenceI seq = viewport.alignment.getSequenceAt(i);
\r
585 if (!sg.sequences.contains(seq))
\r
590 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
\r
592 if (sg.sequences.contains(temp))
\r
597 viewport.alignment.getSequences().setElementAt(temp, i);
\r
598 viewport.alignment.getSequences().setElementAt(seq, i + 1);
\r
602 alignPanel.repaint();
\r
605 public void lostOwnership(Clipboard clipboard, Transferable contents)
\r
607 Desktop.jalviewClipboard = null;
\r
614 * @param e DOCUMENT ME!
\r
616 protected void copy_actionPerformed(ActionEvent e)
\r
618 if (viewport.getSelectionGroup() == null)
\r
623 SequenceGroup sg = viewport.getSelectionGroup();
\r
625 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
\r
627 Hashtable orderedSeqs = new Hashtable();
\r
628 SequenceI[] seqs = new SequenceI[sg.getSize()];
\r
630 for (int i = 0; i < sg.getSize(); i++)
\r
632 SequenceI seq = sg.getSequenceAt(i);
\r
633 int index = viewport.alignment.findIndex(seq);
\r
634 orderedSeqs.put(index + "", seq);
\r
637 int index = 0, startRes, endRes;
\r
640 for (int i = 0; i < sg.getSize(); i++)
\r
642 SequenceI seq = null;
\r
644 while (seq == null)
\r
646 if (orderedSeqs.containsKey(index + ""))
\r
648 seq = (SequenceI) orderedSeqs.get(index + "");
\r
660 //Returns residue following index if gap
\r
661 startRes = seq.findPosition(sg.getStartRes());
\r
664 //Need to find the residue preceeding index if gap
\r
667 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
\r
669 ch = seq.getCharAt(j);
\r
670 if (!jalview.util.Comparison.isGap( (ch)))
\r
678 endRes += seq.getStart() - 1;
\r
681 seqs[i] = new Sequence(seq.getName(),
\r
682 seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),
\r
685 seqs[i].setDescription(seq.getDescription());
\r
686 seqs[i].setDBRef(seq.getDBRef());
\r
687 seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
\r
688 seqs[i].setDatasetSequence(seq.getDatasetSequence());
\r
692 FastaFile ff = new FastaFile();
\r
693 ff.addDBPrefix( viewport.showDBPrefix );
\r
694 ff.addJVSuffix( viewport.showJVSuffix );
\r
695 c.setContents(new StringSelection( ff.print(seqs)), this);
\r
696 Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};
\r
702 * @param e DOCUMENT ME!
\r
704 protected void pasteNew_actionPerformed(ActionEvent e)
\r
712 * @param e DOCUMENT ME!
\r
714 protected void pasteThis_actionPerformed(ActionEvent e)
\r
716 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
\r
717 HistoryItem.PASTE));
\r
724 * @param newAlignment DOCUMENT ME!
\r
726 void paste(boolean newAlignment)
\r
730 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
\r
731 Transferable contents = c.getContents(this);
\r
733 if (contents == null)
\r
738 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
\r
742 String format = IdentifyFile.Identify(str, "Paste");
\r
743 SequenceI[] sequences;
\r
745 if(Desktop.jalviewClipboard!=null)
\r
747 // The clipboard was filled from within Jalview, we must use the sequences
\r
748 // And dataset from the copied alignment
\r
749 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
\r
753 sequences = new FormatAdapter().readFile(str, "Paste", format);
\r
759 Alignment alignment = new Alignment(sequences);
\r
761 if(Desktop.jalviewClipboard!=null)
\r
762 alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
\r
764 alignment.setDataset( null );
\r
767 AlignFrame af = new AlignFrame(alignment);
\r
768 String newtitle = new String("Copied sequences");
\r
770 if (title.startsWith("Copied sequences"))
\r
776 newtitle = newtitle.concat("- from " + title);
\r
779 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
\r
780 NEW_WINDOW_HEIGHT);
\r
785 for (int i = 0; i < sequences.length; i++)
\r
787 viewport.alignment.addSequence(sequences[i]);
\r
788 if(sequences[i].getDatasetSequence()==null)
\r
790 ////////////////////////////
\r
791 //Datset needs extension;
\r
792 /////////////////////////////
\r
793 Sequence ds = new Sequence(sequences[i].getName(),
\r
794 AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
\r
795 sequences[i].getStart(),
\r
796 sequences[i].getEnd());
\r
797 sequences[i].setDatasetSequence(ds);
\r
798 viewport.alignment.getDataset().addSequence(ds);
\r
804 viewport.setEndSeq(viewport.alignment.getHeight());
\r
805 viewport.alignment.getWidth();
\r
806 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
809 catch (Exception ex)
\r
811 // could be anything being pasted in here
\r
820 * @param e DOCUMENT ME!
\r
822 protected void cut_actionPerformed(ActionEvent e)
\r
824 copy_actionPerformed(null);
\r
825 delete_actionPerformed(null);
\r
831 * @param e DOCUMENT ME!
\r
833 protected void delete_actionPerformed(ActionEvent e)
\r
836 if (viewport.getSelectionGroup() == null)
\r
841 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
\r
842 HistoryItem.HIDE));
\r
844 SequenceGroup sg = viewport.getSelectionGroup();
\r
845 boolean allSequences = false;
\r
846 if (sg.sequences.size() == viewport.alignment.getHeight())
\r
848 allSequences = true;
\r
851 for (int i = 0; i < sg.sequences.size(); i++)
\r
853 SequenceI seq = sg.getSequenceAt(i);
\r
854 int index = viewport.getAlignment().findIndex(seq);
\r
855 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
\r
857 // If the cut affects all sequences, remove highlighted columns
\r
860 viewport.getColumnSelection().removeElements(sg.getStartRes(),
\r
861 sg.getEndRes() + 1);
\r
864 if (seq.getSequence().length() < 1)
\r
866 viewport.getAlignment().deleteSequence(seq);
\r
870 viewport.getAlignment().getSequences().setElementAt(seq, index);
\r
874 viewport.setSelectionGroup(null);
\r
875 viewport.alignment.deleteGroup(sg);
\r
877 viewport.firePropertyChange("alignment", null,
\r
878 viewport.getAlignment().getSequences());
\r
882 if (viewport.getAlignment().getHeight() < 1)
\r
886 this.setClosed(true);
\r
888 catch (Exception ex)
\r
897 * @param e DOCUMENT ME!
\r
899 protected void deleteGroups_actionPerformed(ActionEvent e)
\r
901 viewport.alignment.deleteAllGroups();
\r
902 viewport.setSelectionGroup(null);
\r
903 alignPanel.repaint();
\r
909 * @param e DOCUMENT ME!
\r
911 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
913 SequenceGroup sg = new SequenceGroup();
\r
915 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
918 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
921 sg.setEndRes(viewport.alignment.getWidth() - 1);
\r
922 viewport.setSelectionGroup(sg);
\r
923 PaintRefresher.Refresh(null, viewport.alignment);
\r
929 * @param e DOCUMENT ME!
\r
931 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
933 viewport.setSelectionGroup(null);
\r
934 viewport.getColumnSelection().clear();
\r
935 viewport.setSelectionGroup(null);
\r
936 alignPanel.annotationPanel.activeRes = null;
\r
937 PaintRefresher.Refresh(null, viewport.alignment);
\r
943 * @param e DOCUMENT ME!
\r
945 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
\r
947 SequenceGroup sg = viewport.getSelectionGroup();
\r
951 selectAllSequenceMenuItem_actionPerformed(null);
\r
956 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
959 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
962 PaintRefresher.Refresh(null, viewport.alignment);
\r
968 * @param e DOCUMENT ME!
\r
970 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
\r
972 ColumnSelection colSel = viewport.getColumnSelection();
\r
974 if (colSel.size() > 0)
\r
976 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
977 HistoryItem.HIDE));
\r
979 int min = colSel.getMin();
\r
980 viewport.getAlignment().trimLeft(min);
\r
981 colSel.compensateForEdit(0, min);
\r
983 if (viewport.getSelectionGroup() != null)
\r
985 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
988 Vector groups = viewport.alignment.getGroups();
\r
990 for (int i = 0; i < groups.size(); i++)
\r
992 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
994 if (!sg.adjustForRemoveLeft(min))
\r
996 viewport.alignment.deleteGroup(sg);
\r
1000 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1007 * @param e DOCUMENT ME!
\r
1009 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1011 ColumnSelection colSel = viewport.getColumnSelection();
\r
1013 if (colSel.size() > 0)
\r
1015 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
1016 HistoryItem.HIDE));
\r
1018 int max = colSel.getMax();
\r
1019 viewport.getAlignment().trimRight(max);
\r
1021 if (viewport.getSelectionGroup() != null)
\r
1023 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1026 Vector groups = viewport.alignment.getGroups();
\r
1028 for (int i = 0; i < groups.size(); i++)
\r
1030 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1032 if (!sg.adjustForRemoveRight(max))
\r
1034 viewport.alignment.deleteGroup(sg);
\r
1038 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1045 * @param e DOCUMENT ME!
\r
1047 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1049 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1050 viewport.alignment, HistoryItem.HIDE));
\r
1052 //This is to maintain viewport position on first residue
\r
1053 //of first sequence
\r
1054 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1055 int startRes = seq.findPosition(viewport.startRes);
\r
1057 viewport.getAlignment().removeGaps();
\r
1059 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1061 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1067 * @param e DOCUMENT ME!
\r
1069 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1071 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1072 HistoryItem.HIDE));
\r
1074 //This is to maintain viewport position on first residue
\r
1075 //of first sequence
\r
1076 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1077 int startRes = seq.findPosition(viewport.startRes);
\r
1080 SequenceI current;
\r
1083 Vector seqs = null;
\r
1086 int end = viewport.alignment.getWidth();
\r
1088 if (viewport.getSelectionGroup() != null
\r
1089 && viewport.getSelectionGroup().sequences != null
\r
1090 && viewport.getSelectionGroup().sequences.size() > 0)
\r
1092 seqs = viewport.getSelectionGroup().sequences;
\r
1093 start = viewport.getSelectionGroup().getStartRes();
\r
1094 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1098 seqs = viewport.alignment.getSequences();
\r
1101 for (int i = 0; i < seqs.size(); i++)
\r
1103 current = (SequenceI) seqs.elementAt(i);
\r
1104 jSize = current.getLength();
\r
1106 // Removing a range is much quicker than removing gaps
\r
1107 // one by one for long sequences
\r
1109 int rangeStart=-1, rangeEnd=-1;
\r
1113 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1115 if(rangeStart==-1)
\r
1130 current.deleteChars(rangeStart, rangeEnd);
\r
1131 j-=rangeEnd-rangeStart;
\r
1132 jSize-=rangeEnd-rangeStart;
\r
1140 while (j < end && j < jSize);
\r
1143 current.deleteChars(rangeStart, rangeEnd);
\r
1147 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1149 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1152 public void alignmentChanged()
\r
1154 if(viewport.vconsensus!=null)
\r
1156 viewport.updateConsensus();
\r
1157 viewport.updateConservation();
\r
1159 resetAllColourSchemes();
\r
1160 if(alignPanel.overviewPanel!=null)
\r
1161 alignPanel.overviewPanel.updateOverviewImage();
\r
1163 Provenance prov = viewport.alignment.getProvenance();
\r
1166 prov = new Provenance();
\r
1167 viewport.alignment.setProvenance(prov);
\r
1170 prov.addEntry("Me",
\r
1171 "Edited in Jalview", new java.util.Date(), "myID");
\r
1173 alignPanel.repaint();
\r
1176 void resetAllColourSchemes()
\r
1178 ColourSchemeI cs = viewport.globalColourScheme;
\r
1181 if (cs instanceof ClustalxColourScheme)
\r
1183 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1184 resetClustalX(viewport.alignment.getSequences(),
\r
1185 viewport.alignment.getWidth());
\r
1188 cs.setConsensus(viewport.vconsensus);
\r
1189 if (cs.conservationApplied())
\r
1191 Alignment al = (Alignment) viewport.alignment;
\r
1192 Conservation c = new Conservation("All",
\r
1193 ResidueProperties.propHash, 3,
\r
1194 al.getSequences(), 0,
\r
1195 al.getWidth() - 1);
\r
1197 c.verdict(false, viewport.ConsPercGaps);
\r
1199 cs.setConservation(c);
\r
1203 int s, sSize = viewport.alignment.getGroups().size();
\r
1204 for(s=0; s<sSize; s++)
\r
1206 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1207 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1209 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1211 sg.recalcConservation();
\r
1218 * @param e DOCUMENT ME!
\r
1220 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1222 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1223 HistoryItem.HIDE));
\r
1225 SequenceI current;
\r
1226 int Width = viewport.getAlignment().getWidth();
\r
1228 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1231 current = viewport.getAlignment().getSequenceAt(i);
\r
1233 if (current.getLength() < Width)
\r
1235 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1239 alignmentChanged();
\r
1245 * @param e DOCUMENT ME!
\r
1247 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1249 JInternalFrame frame = new JInternalFrame();
\r
1250 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1251 frame.setContentPane(finder);
\r
1252 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1253 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1259 * @param e DOCUMENT ME!
\r
1261 public void font_actionPerformed(ActionEvent e)
\r
1263 new FontChooser(alignPanel);
\r
1269 * @param e DOCUMENT ME!
\r
1271 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1273 viewport.setShowJVSuffix(seqLimits.isSelected());
\r
1275 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1276 alignPanel.repaint();
\r
1279 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1281 viewport.setShowDBPrefix(seqDBRef.isSelected());
\r
1283 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1284 alignPanel.repaint();
\r
1291 * @param e DOCUMENT ME!
\r
1293 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1295 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1296 alignPanel.repaint();
\r
1302 * @param e DOCUMENT ME!
\r
1304 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1306 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1307 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1308 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1309 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1310 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1311 alignPanel.repaint();
\r
1317 * @param e DOCUMENT ME!
\r
1319 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1321 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1322 alignPanel.repaint();
\r
1328 * @param e DOCUMENT ME!
\r
1330 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1332 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1333 alignPanel.repaint();
\r
1339 * @param e DOCUMENT ME!
\r
1341 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1343 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1344 alignPanel.repaint();
\r
1350 * @param e DOCUMENT ME!
\r
1352 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1354 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1355 alignPanel.repaint();
\r
1361 * @param e DOCUMENT ME!
\r
1363 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1365 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1366 alignPanel.repaint();
\r
1372 * @param e DOCUMENT ME!
\r
1374 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1376 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1377 alignPanel.repaint();
\r
1383 * @param evt DOCUMENT ME!
\r
1385 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1387 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1389 if (viewport.showSequenceFeatures &&
\r
1390 ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)
\r
1392 System.out.println("new fetcher");
\r
1393 new SequenceFeatureFetcher(viewport.
\r
1398 featureSettings.setEnabled(true);
\r
1400 alignPanel.repaint();
\r
1406 * @param e DOCUMENT ME!
\r
1408 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1410 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1411 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1417 * @param e DOCUMENT ME!
\r
1419 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1421 if (alignPanel.overviewPanel != null)
\r
1426 JInternalFrame frame = new JInternalFrame();
\r
1427 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1428 frame.setContentPane(overview);
\r
1429 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1430 frame.getWidth(), frame.getHeight());
\r
1432 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1433 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1435 public void internalFrameClosed(
\r
1436 javax.swing.event.InternalFrameEvent evt)
\r
1438 alignPanel.setOverviewPanel(null);
\r
1443 alignPanel.setOverviewPanel(overview);
\r
1449 * @param e DOCUMENT ME!
\r
1451 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1453 changeColour(null);
\r
1459 * @param e DOCUMENT ME!
\r
1461 public void clustalColour_actionPerformed(ActionEvent e)
\r
1463 changeColour(new ClustalxColourScheme(
\r
1464 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1470 * @param e DOCUMENT ME!
\r
1472 public void zappoColour_actionPerformed(ActionEvent e)
\r
1474 changeColour(new ZappoColourScheme());
\r
1480 * @param e DOCUMENT ME!
\r
1482 public void taylorColour_actionPerformed(ActionEvent e)
\r
1484 changeColour(new TaylorColourScheme());
\r
1490 * @param e DOCUMENT ME!
\r
1492 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1494 changeColour(new HydrophobicColourScheme());
\r
1500 * @param e DOCUMENT ME!
\r
1502 public void helixColour_actionPerformed(ActionEvent e)
\r
1504 changeColour(new HelixColourScheme());
\r
1510 * @param e DOCUMENT ME!
\r
1512 public void strandColour_actionPerformed(ActionEvent e)
\r
1514 changeColour(new StrandColourScheme());
\r
1520 * @param e DOCUMENT ME!
\r
1522 public void turnColour_actionPerformed(ActionEvent e)
\r
1524 changeColour(new TurnColourScheme());
\r
1530 * @param e DOCUMENT ME!
\r
1532 public void buriedColour_actionPerformed(ActionEvent e)
\r
1534 changeColour(new BuriedColourScheme());
\r
1540 * @param e DOCUMENT ME!
\r
1542 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1544 changeColour(new NucleotideColourScheme());
\r
1550 * @param e DOCUMENT ME!
\r
1552 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1554 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1560 * @param cs DOCUMENT ME!
\r
1562 void changeColour(ColourSchemeI cs)
\r
1564 int threshold = 0;
\r
1568 if (viewport.getAbovePIDThreshold())
\r
1570 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1573 cs.setThreshold(threshold,
\r
1574 viewport.getIgnoreGapsConsensus());
\r
1576 viewport.setGlobalColourScheme(cs);
\r
1580 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1583 if (viewport.getConservationSelected())
\r
1586 Alignment al = (Alignment) viewport.alignment;
\r
1587 Conservation c = new Conservation("All",
\r
1588 ResidueProperties.propHash, 3,
\r
1589 al.getSequences(), 0,
\r
1590 al.getWidth() - 1);
\r
1593 c.verdict(false, viewport.ConsPercGaps);
\r
1595 cs.setConservation(c);
\r
1597 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1602 cs.setConservation(null);
\r
1605 cs.setConsensus(viewport.vconsensus);
\r
1608 viewport.setGlobalColourScheme(cs);
\r
1610 if (viewport.getColourAppliesToAllGroups())
\r
1612 Vector groups = viewport.alignment.getGroups();
\r
1614 for (int i = 0; i < groups.size(); i++)
\r
1616 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1624 if (cs instanceof ClustalxColourScheme)
\r
1626 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1628 else if (cs instanceof UserColourScheme)
\r
1630 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1636 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1638 catch (Exception ex)
\r
1643 if (viewport.getAbovePIDThreshold()
\r
1644 || cs instanceof PIDColourScheme
\r
1645 || cs instanceof Blosum62ColourScheme)
\r
1647 sg.cs.setThreshold(threshold,
\r
1648 viewport.getIgnoreGapsConsensus());
\r
1650 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1654 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1657 if (viewport.getConservationSelected())
\r
1659 Conservation c = new Conservation("Group",
\r
1660 ResidueProperties.propHash, 3,
\r
1662 viewport.alignment.getWidth() - 1);
\r
1664 c.verdict(false, viewport.ConsPercGaps);
\r
1665 sg.cs.setConservation(c);
\r
1668 sg.cs.setConservation(null);
\r
1672 if (alignPanel.getOverviewPanel() != null)
\r
1674 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1677 alignPanel.repaint();
\r
1683 * @param e DOCUMENT ME!
\r
1685 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1687 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1689 SliderPanel.setPIDSliderSource(alignPanel,
\r
1690 viewport.getGlobalColourScheme(),
\r
1692 SliderPanel.showPIDSlider();
\r
1699 * @param e DOCUMENT ME!
\r
1701 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1703 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1705 SliderPanel.setConservationSlider(alignPanel,
\r
1706 viewport.globalColourScheme,
\r
1708 SliderPanel.showConservationSlider();
\r
1715 * @param e DOCUMENT ME!
\r
1717 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1719 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1721 viewport.setAbovePIDThreshold(false);
\r
1722 abovePIDThreshold.setSelected(false);
\r
1724 changeColour(viewport.getGlobalColourScheme());
\r
1726 modifyConservation_actionPerformed(null);
\r
1732 * @param e DOCUMENT ME!
\r
1734 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1736 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1738 conservationMenuItem.setSelected(false);
\r
1739 viewport.setConservationSelected(false);
\r
1741 changeColour(viewport.getGlobalColourScheme());
\r
1743 modifyPID_actionPerformed(null);
\r
1749 * @param e DOCUMENT ME!
\r
1751 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1753 if (e.getActionCommand().equals("User Defined..."))
\r
1755 new UserDefinedColours(alignPanel, null);
\r
1759 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1760 getUserColourSchemes().get(e.getActionCommand());
\r
1762 changeColour(udc);
\r
1766 public void updateUserColourMenu()
\r
1769 Component[] menuItems = colourMenu.getMenuComponents();
\r
1770 int i, iSize = menuItems.length;
\r
1771 for (i = 0; i < iSize; i++)
\r
1773 if (menuItems[i].getName() != null &&
\r
1774 menuItems[i].getName().equals("USER_DEFINED"))
\r
1776 colourMenu.remove(menuItems[i]);
\r
1780 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1782 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1783 getUserColourSchemes().keys();
\r
1785 while (userColours.hasMoreElements())
\r
1787 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1788 nextElement().toString());
\r
1789 radioItem.setName("USER_DEFINED");
\r
1790 radioItem.addMouseListener(new MouseAdapter()
\r
1792 public void mousePressed(MouseEvent evt)
\r
1794 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1796 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1798 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1799 "Remove from default list?",
\r
1800 "Remove user defined colour",
\r
1801 JOptionPane.YES_NO_OPTION);
\r
1802 if(option == JOptionPane.YES_OPTION)
\r
1804 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1805 colourMenu.remove(radioItem);
\r
1808 radioItem.addActionListener(new ActionListener()
\r
1810 public void actionPerformed(ActionEvent evt)
\r
1812 userDefinedColour_actionPerformed(evt);
\r
1818 radioItem.addActionListener(new ActionListener()
\r
1820 public void actionPerformed(ActionEvent evt)
\r
1822 userDefinedColour_actionPerformed(evt);
\r
1826 colourMenu.insert(radioItem, 15);
\r
1827 colours.add(radioItem);
\r
1835 * @param e DOCUMENT ME!
\r
1837 public void PIDColour_actionPerformed(ActionEvent e)
\r
1839 changeColour(new PIDColourScheme());
\r
1845 * @param e DOCUMENT ME!
\r
1847 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1849 changeColour(new Blosum62ColourScheme());
\r
1855 * @param e DOCUMENT ME!
\r
1857 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1859 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1860 HistoryItem.SORT));
\r
1861 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1862 viewport.getAlignment().getSequenceAt(0));
\r
1863 alignPanel.repaint();
\r
1869 * @param e DOCUMENT ME!
\r
1871 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1873 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1874 HistoryItem.SORT));
\r
1875 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1876 alignPanel.repaint();
\r
1882 * @param e DOCUMENT ME!
\r
1884 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1886 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1887 HistoryItem.SORT));
\r
1889 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1890 alignPanel.repaint();
\r
1896 * @param e DOCUMENT ME!
\r
1898 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1900 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1901 JInternalFrame frame = new JInternalFrame();
\r
1902 frame.setContentPane(sp);
\r
1903 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1910 * @param e DOCUMENT ME!
\r
1912 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1914 if ( (viewport.getSelectionGroup() == null) ||
\r
1915 (viewport.getSelectionGroup().getSize() < 2))
\r
1917 JOptionPane.showInternalMessageDialog(this,
\r
1918 "You must select at least 2 sequences.",
\r
1919 "Invalid Selection",
\r
1920 JOptionPane.WARNING_MESSAGE);
\r
1924 JInternalFrame frame = new JInternalFrame();
\r
1925 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1926 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1933 * @param e DOCUMENT ME!
\r
1935 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1937 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1938 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1939 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1940 (viewport.getAlignment().getHeight() < 4))
\r
1942 JOptionPane.showInternalMessageDialog(this,
\r
1943 "Principal component analysis must take\n" +
\r
1944 "at least 4 input sequences.",
\r
1945 "Sequence selection insufficient",
\r
1946 JOptionPane.WARNING_MESSAGE);
\r
1951 new PCAPanel(viewport);
\r
1957 * @param e DOCUMENT ME!
\r
1959 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1961 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1967 * @param e DOCUMENT ME!
\r
1969 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1971 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1977 * @param e DOCUMENT ME!
\r
1979 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1981 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1987 * @param e DOCUMENT ME!
\r
1989 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1991 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1997 * @param type DOCUMENT ME!
\r
1998 * @param pwType DOCUMENT ME!
\r
1999 * @param title DOCUMENT ME!
\r
2001 void NewTreePanel(String type, String pwType, String title)
\r
2003 final TreePanel tp;
\r
2005 if ( (viewport.getSelectionGroup() != null) &&
\r
2006 (viewport.getSelectionGroup().getSize() > 3))
\r
2009 SequenceGroup sg = viewport.getSelectionGroup();
\r
2011 /* Decide if the selection is a column region */
\r
2012 while (s < sg.sequences.size())
\r
2014 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
2017 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2018 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
2019 "Try using the Pad function in the edit menu,\n" +
\r
2020 "or one of the multiple sequence alignment web services.",
\r
2021 "Sequences in selection are not aligned",
\r
2022 JOptionPane.WARNING_MESSAGE);
\r
2028 title = title + " on region";
\r
2029 tp = new TreePanel(viewport,
\r
2030 viewport.getSelectionGroup().sequences, type, pwType,
\r
2031 sg.getStartRes(), sg.getEndRes());
\r
2035 //are the sequences aligned?
\r
2036 if (!viewport.alignment.isAligned())
\r
2038 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2039 "The sequences must be aligned before creating a tree.\n" +
\r
2040 "Try using the Pad function in the edit menu,\n" +
\r
2041 "or one of the multiple sequence alignment web services.",
\r
2042 "Sequences not aligned",
\r
2043 JOptionPane.WARNING_MESSAGE);
\r
2048 tp = new TreePanel(viewport,
\r
2049 viewport.getAlignment().getSequences(), type, pwType,
\r
2051 viewport.alignment.getWidth());
\r
2054 addTreeMenuItem(tp, title);
\r
2055 viewport.setCurrentTree(tp.getTree());
\r
2057 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
2063 * @param title DOCUMENT ME!
\r
2064 * @param order DOCUMENT ME!
\r
2066 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
2068 final JMenuItem item = new JMenuItem("by " + title);
\r
2070 item.addActionListener(new java.awt.event.ActionListener()
\r
2072 public void actionPerformed(ActionEvent e)
\r
2074 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2075 HistoryItem.SORT));
\r
2077 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
2078 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
2079 alignPanel.repaint();
\r
2085 * Maintain the Order by->Displayed Tree menu.
\r
2086 * Creates a new menu item for a TreePanel with an appropriate
\r
2087 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
2088 * to remove the menu item when the treePanel is closed, and adjust
\r
2089 * the tree leaf to sequence mapping when the alignment is modified.
\r
2090 * @param treePanel Displayed tree window.
\r
2091 * @param title SortBy menu item title.
\r
2093 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
2095 final JMenuItem item = new JMenuItem(title);
\r
2099 if (treeCount == 1)
\r
2101 sort.add(sortByTreeMenu);
\r
2104 sortByTreeMenu.add(item);
\r
2105 item.addActionListener(new java.awt.event.ActionListener()
\r
2107 public void actionPerformed(ActionEvent e)
\r
2109 addHistoryItem(new HistoryItem("Tree Sort",
\r
2110 viewport.alignment, HistoryItem.SORT));
\r
2111 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2112 treePanel.getTree());
\r
2113 alignPanel.repaint();
\r
2117 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2118 InternalFrameAdapter()
\r
2120 public void internalFrameClosed(
\r
2121 javax.swing.event.InternalFrameEvent evt)
\r
2124 sortByTreeMenu.remove(item);
\r
2126 if (treeCount == 0)
\r
2128 sort.remove(sortByTreeMenu);
\r
2136 * Work out whether the whole set of sequences
\r
2137 * or just the selected set will be submitted for multiple alignment.
\r
2140 private SequenceI[] gatherSequencesForAlignment()
\r
2142 // Now, check we have enough sequences
\r
2143 SequenceI[] msa = null;
\r
2145 if ( (viewport.getSelectionGroup() != null) &&
\r
2146 (viewport.getSelectionGroup().getSize() > 1))
\r
2148 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2149 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2151 msa = new SequenceI[sz = seqs.getSize()];
\r
2153 for (int i = 0; i < sz; i++)
\r
2155 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2160 Vector seqs = viewport.getAlignment().getSequences();
\r
2162 if (seqs.size() > 1)
\r
2164 msa = new SequenceI[seqs.size()];
\r
2166 for (int i = 0; i < seqs.size(); i++)
\r
2168 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2176 * Decides what is submitted to a secondary structure prediction service,
\r
2177 * the currently selected sequence, or the currently selected alignment
\r
2178 * (where the first sequence in the set is the one that the prediction
\r
2181 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2183 SequenceI seq = null;
\r
2184 SequenceI[] msa = null;
\r
2186 if ( (viewport.getSelectionGroup() != null) &&
\r
2187 (viewport.getSelectionGroup().getSize() > 0))
\r
2189 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2190 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2192 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2194 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2199 msa = new SequenceI[sz = seqs.getSize()];
\r
2201 for (int i = 0; i < sz; i++)
\r
2203 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2209 Vector seqs = viewport.getAlignment().getSequences();
\r
2211 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2213 seq = (SequenceI) seqs.elementAt(0);
\r
2217 msa = new SequenceI[seqs.size()];
\r
2219 for (int i = 0; i < seqs.size(); i++)
\r
2221 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2233 return new SequenceI[]
\r
2243 * @param e DOCUMENT ME!
\r
2245 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2247 // Pick the tree file
\r
2248 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2250 "LAST_DIRECTORY"));
\r
2251 chooser.setFileView(new JalviewFileView());
\r
2252 chooser.setDialogTitle("Select a newick-like tree file");
\r
2253 chooser.setToolTipText("Load a tree file");
\r
2255 int value = chooser.showOpenDialog(null);
\r
2257 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2259 String choice = chooser.getSelectedFile().getPath();
\r
2260 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2264 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2266 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2268 catch (Exception ex)
\r
2270 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2271 "Problem reading tree file",
\r
2273 JOptionPane.WARNING_MESSAGE);
\r
2274 ex.printStackTrace();
\r
2280 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2282 return ShowNewickTree(nf,title,600,500,4,5);
\r
2287 * @param nf DOCUMENT ME!
\r
2288 * @param title DOCUMENT ME!
\r
2290 * @return DOCUMENT ME!
\r
2292 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2294 TreePanel tp = null;
\r
2300 if (nf.getTree() != null)
\r
2302 tp = new TreePanel(viewport,
\r
2303 viewport.getAlignment().getSequences(), nf,
\r
2310 tp.setLocation(x,y);
\r
2313 Desktop.addInternalFrame(tp, title, w, h);
\r
2314 addTreeMenuItem(tp, title);
\r
2317 catch (Exception ex)
\r
2319 ex.printStackTrace();
\r
2330 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2331 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2332 printJob.setPrintable(alignPanel, pf);
\r
2334 if (printJob.printDialog())
\r
2340 catch (Exception PrintException)
\r
2342 PrintException.printStackTrace();
\r
2349 * Generates menu items and listener event actions for web service clients
\r
2352 public void BuildWebServiceMenu()
\r
2354 if ( (Discoverer.services != null)
\r
2355 && (Discoverer.services.size() > 0))
\r
2357 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
\r
2358 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
\r
2359 Vector wsmenu = new Vector();
\r
2360 if (msaws != null)
\r
2362 // Add any Multiple Sequence Alignment Services
\r
2363 final JMenu msawsmenu = new JMenu("Alignment");
\r
2364 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2366 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2368 final JMenuItem method = new JMenuItem(sh.getName());
\r
2369 method.addActionListener(new ActionListener()
\r
2371 public void actionPerformed(ActionEvent e)
\r
2373 SequenceI[] msa = gatherSequencesForAlignment();
\r
2374 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2380 msawsmenu.add(method);
\r
2381 // Deal with services that we know accept partial alignments.
\r
2382 if (sh.getName().indexOf("lustal") > -1)
\r
2384 // We know that ClustalWS can accept partial alignments for refinement.
\r
2385 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2386 methodR.addActionListener(new ActionListener()
\r
2388 public void actionPerformed(ActionEvent e)
\r
2390 SequenceI[] msa = gatherSequencesForAlignment();
\r
2391 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2397 msawsmenu.add(methodR);
\r
2401 wsmenu.add(msawsmenu);
\r
2403 if (secstrpr != null)
\r
2405 // Add any secondary structure prediction services
\r
2406 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2407 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2409 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2411 final JMenuItem method = new JMenuItem(sh.getName());
\r
2412 method.addActionListener(new ActionListener()
\r
2414 public void actionPerformed(ActionEvent e)
\r
2416 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2417 if (msa.length == 1)
\r
2419 // Single Sequence prediction
\r
2420 new jalview.ws.JPredClient(sh,title, msa[0]);
\r
2424 if (msa.length > 1)
\r
2426 // Single Sequence prediction
\r
2427 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2433 secstrmenu.add(method);
\r
2435 wsmenu.add(secstrmenu);
\r
2437 this.webService.removeAll();
\r
2438 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2440 webService.add( (JMenu) wsmenu.get(i));
\r
2445 this.webService.removeAll();
\r
2446 this.webService.add(this.webServiceNoServices);
\r
2448 // TODO: add in rediscovery function
\r
2449 // TODO: reduce code redundancy.
\r
2450 // TODO: group services by location as well as function.
\r
2453 public void vamsasStore_actionPerformed(ActionEvent e)
\r
2455 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2456 getProperty("LAST_DIRECTORY"));
\r
2458 chooser.setFileView(new JalviewFileView());
\r
2459 chooser.setDialogTitle("Export to Vamsas file");
\r
2460 chooser.setToolTipText("Export");
\r
2462 int value = chooser.showSaveDialog(this);
\r
2464 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2466 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
\r
2467 vs.store(chooser.getSelectedFile().getAbsolutePath()
\r
2472 public void featureSettings_actionPerformed(ActionEvent e)
\r
2474 new FeatureSettings(viewport, alignPanel);
\r
2479 public void showTranslation_actionPerformed(ActionEvent e)
\r
2482 if(!viewport.alignment.isNucleotide())
\r
2485 viewport.showTranslation(showTranslation.isSelected());
\r
2487 if(!viewport.alignment.isNucleotide())
\r
2490 int s, sSize = viewport.alignment.getHeight();
\r
2491 SequenceI [] newSeq = new SequenceI[sSize];
\r
2494 StringBuffer protein;
\r
2496 for(s=0; s<sSize; s++)
\r
2498 protein = new StringBuffer();
\r
2499 seq = (SequenceI)viewport.alignment.getSequenceAt(s);
\r
2500 resSize = seq.getLength();
\r
2501 for(res = 0; res < resSize; res+=3)
\r
2503 String codon = seq.getSequence(res, res+3);
\r
2504 codon = codon.replace('U', 'T');
\r
2505 String aa = ResidueProperties.codonTranslate(codon);
\r
2507 protein.append(viewport.getGapCharacter());
\r
2508 else if(aa.equals("STOP"))
\r
2509 protein.append("X");
\r
2511 protein.append( aa );
\r
2513 newSeq[s] = new Sequence(seq.getName(), protein.toString());
\r
2517 AlignmentI al = new Alignment(newSeq);
\r
2518 al.setDataset(null);
\r
2521 ////////////////////////////////
\r
2522 // Copy annotations across
\r
2523 jalview.datamodel.AlignmentAnnotation[] annotations
\r
2524 = viewport.alignment.getAlignmentAnnotation();
\r
2526 for (int i = 0; i < annotations.length; i++)
\r
2529 if (annotations[i].label.equals("Quality") ||
\r
2530 annotations[i].label.equals("Conservation") ||
\r
2531 annotations[i].label.equals("Consensus"))
\r
2537 aSize = viewport.alignment.getWidth()/3;
\r
2538 jalview.datamodel.Annotation [] anots =
\r
2539 new jalview.datamodel.Annotation[aSize];
\r
2541 for(a=0; a<viewport.alignment.getWidth(); a++)
\r
2543 if( annotations[i].annotations[a]==null
\r
2544 || annotations[i].annotations[a]==null)
\r
2547 anots[a/3] = new Annotation(
\r
2548 annotations[i].annotations[a].displayCharacter,
\r
2549 annotations[i].annotations[a].description,
\r
2550 annotations[i].annotations[a].secondaryStructure,
\r
2551 annotations[i].annotations[a].value,
\r
2552 annotations[i].annotations[a].colour);
\r
2555 jalview.datamodel.AlignmentAnnotation aa
\r
2556 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
\r
2557 annotations[i].description, anots );
\r
2558 al.addAnnotation(aa);
\r
2562 // Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
\r
2563 // NEW_WINDOW_WIDTH,
\r
2564 // NEW_WINDOW_HEIGHT);
\r
2566 AlignViewport newViewport = new AlignViewport(al);
\r
2567 AlignmentPanel ap = new AlignmentPanel(this, newViewport);
\r
2568 tabbedPane.add("Protein", ap);
\r
2569 viewports.add(newViewport);
\r
2570 alignPanels.add(ap);
\r
2573 /////////////////////////
\r
2575 AlignViewport ds = new AlignViewport(al.getDataset());
\r
2576 ds.setDataset(true);
\r
2577 AlignmentPanel dap = new AlignmentPanel(this, ds);
\r
2578 tabbedPane.add("Dataset", dap);
\r
2579 viewports.add(ds);
\r
2580 alignPanels.add(dap);
\r
2581 /////////////////////////
\r
2586 public void tabSelected()
\r
2588 int index = tabbedPane.getSelectedIndex();
\r
2589 viewport = (AlignViewport)viewports.elementAt(index);
\r
2590 alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
\r