2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.appletgui;
26 import java.awt.event.*;
28 import jalview.analysis.*;
29 import jalview.commands.*;
30 import jalview.datamodel.*;
32 import jalview.schemes.*;
34 public class AlignFrame extends EmbmenuFrame implements ActionListener,
35 ItemListener, KeyListener
37 public AlignmentPanel alignPanel;
39 public AlignViewport viewport;
41 int DEFAULT_WIDTH = 700;
43 int DEFAULT_HEIGHT = 500;
45 String jalviewServletURL;
47 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
48 String title, boolean embedded)
53 jalviewServletURL = applet.getParameter("APPLICATION_URL");
59 } catch (Exception ex)
64 viewport = new AlignViewport(al, applet);
65 alignPanel = new AlignmentPanel(this, viewport);
67 viewport.updateConservation(alignPanel);
68 viewport.updateConsensus(alignPanel);
70 annotationPanelMenuItem.setState(viewport.showAnnotation);
71 displayNonconservedMenuItem.setState(viewport.getShowunconserved());
73 seqLimits.setState(viewport.showJVSuffix);
77 String param = applet.getParameter("sortBy");
80 if (param.equalsIgnoreCase("Id"))
82 sortIDMenuItem_actionPerformed();
84 else if (param.equalsIgnoreCase("Pairwise Identity"))
86 sortPairwiseMenuItem_actionPerformed();
90 param = applet.getParameter("wrap");
93 if (param.equalsIgnoreCase("true"))
95 wrapMenuItem.setState(true);
96 wrapMenuItem_actionPerformed();
99 param = applet.getParameter("centrecolumnlabels");
102 centreColumnLabelFlag.setState(true);
103 centreColumnLabelFlag_stateChanged();
107 param = applet.getParameter("windowWidth");
110 int width = Integer.parseInt(param);
111 DEFAULT_WIDTH = width;
113 param = applet.getParameter("windowHeight");
116 int height = Integer.parseInt(param);
117 DEFAULT_HEIGHT = height;
119 } catch (Exception ex)
125 // Some JVMS send keyevents to Top frame or lowest panel,
126 // Havent worked out why yet. So add to both this frame and seqCanvas for
128 this.addKeyListener(this);
129 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
130 alignPanel.idPanel.idCanvas.addKeyListener(this);
131 alignPanel.scalePanel.addKeyListener(this);
132 alignPanel.annotationPanel.addKeyListener(this);
133 createAlignFrameWindow(embedded, title);
134 alignPanel.validate();
135 alignPanel.paintAlignment(true);
138 public AlignViewport getAlignViewport()
143 public SeqCanvas getSeqcanvas()
145 return alignPanel.seqPanel.seqCanvas;
155 public void parseFeaturesFile(String file, String type)
157 Hashtable featureLinks = new Hashtable();
158 boolean featuresFile = false;
161 featuresFile = new jalview.io.FeaturesFile(file, type).parse(
162 viewport.alignment, alignPanel.seqPanel.seqCanvas
163 .getFeatureRenderer().featureColours, featureLinks,
165 } catch (Exception ex)
167 ex.printStackTrace();
172 if (featureLinks.size() > 0)
174 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
176 viewport.showSequenceFeatures = true;
177 sequenceFeatures.setState(true);
178 alignPanel.paintAlignment(true);
183 public void keyPressed(KeyEvent evt)
185 if (viewport.cursorMode
186 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
187 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
188 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
189 && Character.isDigit(evt.getKeyChar()))
190 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
192 switch (evt.getKeyCode())
194 case 27: // escape key
195 deselectAllSequenceMenuItem_actionPerformed();
198 if (evt.isControlDown() || evt.isMetaDown())
200 cut_actionPerformed();
204 if (viewport.cursorMode && !evt.isControlDown())
206 alignPanel.seqPanel.setCursorColumn();
208 if (evt.isControlDown() || evt.isMetaDown())
210 copy_actionPerformed();
214 if (evt.isControlDown())
216 paste(evt.isShiftDown());
220 if (evt.isControlDown() || evt.isMetaDown())
222 selectAllSequenceMenuItem_actionPerformed();
225 case KeyEvent.VK_DOWN:
226 if (viewport.cursorMode)
228 alignPanel.seqPanel.moveCursor(0, 1);
232 moveSelectedSequences(false);
237 if (viewport.cursorMode)
239 alignPanel.seqPanel.moveCursor(0, -1);
243 moveSelectedSequences(true);
247 case KeyEvent.VK_LEFT:
248 if (evt.isAltDown() || !viewport.cursorMode)
249 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
251 alignPanel.seqPanel.moveCursor(-1, 0);
254 case KeyEvent.VK_RIGHT:
255 if (evt.isAltDown() || !viewport.cursorMode)
256 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
258 alignPanel.seqPanel.moveCursor(1, 0);
261 case KeyEvent.VK_SPACE:
262 if (viewport.cursorMode)
264 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
265 || evt.isShiftDown() || evt.isAltDown());
269 case KeyEvent.VK_DELETE:
270 case KeyEvent.VK_BACK_SPACE:
271 if (viewport.cursorMode)
273 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
274 || evt.isShiftDown() || evt.isAltDown());
278 cut_actionPerformed();
279 alignPanel.seqPanel.seqCanvas.repaint();
284 if (viewport.cursorMode)
286 alignPanel.seqPanel.setCursorRow();
290 if (viewport.cursorMode)
292 alignPanel.seqPanel.setCursorPosition();
296 case KeyEvent.VK_ENTER:
297 case KeyEvent.VK_COMMA:
298 if (viewport.cursorMode)
300 alignPanel.seqPanel.setCursorRowAndColumn();
305 if (viewport.cursorMode)
307 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
311 if (viewport.cursorMode)
313 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
318 viewport.cursorMode = !viewport.cursorMode;
319 statusBar.setText("Keyboard editing mode is "
320 + (viewport.cursorMode ? "on" : "off"));
321 if (viewport.cursorMode)
323 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
324 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
329 if (evt.isControlDown())
331 findMenuItem_actionPerformed();
337 boolean toggleSeqs = !evt.isControlDown();
338 boolean toggleCols = !evt.isShiftDown();
339 boolean hide = false;
340 SequenceGroup sg = viewport.getSelectionGroup();
344 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
347 viewport.hideAllSelectedSeqs();
349 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
351 viewport.showAllHiddenSeqs();
357 if (viewport.colSel.getSelected().size() > 0)
359 viewport.hideSelectedColumns();
362 viewport.selectionGroup = sg;
367 viewport.showAllHiddenColumns();
373 case KeyEvent.VK_PAGE_UP:
374 if (viewport.wrapAlignment)
376 alignPanel.scrollUp(true);
380 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
381 - viewport.endSeq + viewport.startSeq);
385 case KeyEvent.VK_PAGE_DOWN:
386 if (viewport.wrapAlignment)
388 alignPanel.scrollUp(false);
392 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
393 + viewport.endSeq - viewport.startSeq);
398 if (evt.isControlDown())
400 undoMenuItem_actionPerformed();
405 if (evt.isControlDown())
407 redoMenuItem_actionPerformed();
412 if (evt.isControlDown())
419 if (evt.isControlDown())
421 trimAlignment(false);
426 if (evt.isControlDown())
428 if (evt.isShiftDown())
430 this.removeAllGapsMenuItem_actionPerformed();
434 removeGappedColumnMenuItem_actionPerformed();
439 if (evt.isControlDown())
443 viewport.invertColumnSelection();
447 this.invertSequenceMenuItem_actionPerformed();
453 if (evt.isControlDown())
455 this.deleteGroups_actionPerformed();
460 if (evt.isControlDown())
467 alignPanel.paintAlignment(true);
470 public void keyReleased(KeyEvent evt)
474 public void keyTyped(KeyEvent evt)
478 public void itemStateChanged(ItemEvent evt)
480 if (evt.getSource() == displayNonconservedMenuItem)
482 displayNonconservedMenuItem_actionPerformed();
484 else if (evt.getSource() == colourTextMenuItem)
486 colourTextMenuItem_actionPerformed();
488 else if (evt.getSource() == wrapMenuItem)
490 wrapMenuItem_actionPerformed();
492 else if (evt.getSource() == scaleAbove)
494 viewport.setScaleAboveWrapped(scaleAbove.getState());
496 else if (evt.getSource() == scaleLeft)
498 viewport.setScaleLeftWrapped(scaleLeft.getState());
500 else if (evt.getSource() == scaleRight)
502 viewport.setScaleRightWrapped(scaleRight.getState());
504 else if (evt.getSource() == seqLimits)
506 seqLimits_itemStateChanged();
508 else if (evt.getSource() == viewBoxesMenuItem)
510 viewport.setShowBoxes(viewBoxesMenuItem.getState());
512 else if (evt.getSource() == viewTextMenuItem)
514 viewport.setShowText(viewTextMenuItem.getState());
516 else if (evt.getSource() == renderGapsMenuItem)
518 viewport.setRenderGaps(renderGapsMenuItem.getState());
520 else if (evt.getSource() == annotationPanelMenuItem)
522 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
523 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
525 else if (evt.getSource() == sequenceFeatures)
527 viewport.showSequenceFeatures(sequenceFeatures.getState());
528 alignPanel.seqPanel.seqCanvas.repaint();
530 else if (evt.getSource() == conservationMenuItem)
532 conservationMenuItem_actionPerformed();
534 else if (evt.getSource() == abovePIDThreshold)
536 abovePIDThreshold_actionPerformed();
538 else if (evt.getSource() == applyToAllGroups)
540 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
542 else if (evt.getSource() == autoCalculate)
544 viewport.autocalculateConsensus = autoCalculate.getState();
546 else if (evt.getSource() == this.centreColumnLabelFlag)
548 centreColumnLabelFlag_stateChanged();
549 } else if (evt.getSource() == this.followMouseOverFlag)
551 mouseOverFlag_stateChanged();
554 alignPanel.paintAlignment(true);
557 private void mouseOverFlag_stateChanged()
559 viewport.followHighlight = followMouseOverFlag.getState();
560 // TODO: could kick the scrollTo mechanism to reset view for current searchresults.
563 private void centreColumnLabelFlag_stateChanged()
565 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
566 this.alignPanel.annotationPanel.repaint();
569 public void actionPerformed(ActionEvent evt)
571 Object source = evt.getSource();
573 if (source == inputText)
575 inputText_actionPerformed();
577 else if (source == loadTree)
579 loadTree_actionPerformed();
581 else if (source == loadApplication)
583 launchFullApplication();
585 else if (source == loadAnnotations)
589 else if (source == outputAnnotations)
591 outputAnnotations(true);
593 else if (source == outputFeatures)
595 outputFeatures(true, "Jalview");
597 else if (source == closeMenuItem)
599 closeMenuItem_actionPerformed();
601 else if (source == copy)
603 copy_actionPerformed();
605 else if (source == undoMenuItem)
607 undoMenuItem_actionPerformed();
609 else if (source == redoMenuItem)
611 redoMenuItem_actionPerformed();
613 else if (source == inputText)
615 inputText_actionPerformed();
617 else if (source == closeMenuItem)
619 closeMenuItem_actionPerformed();
621 else if (source == undoMenuItem)
623 undoMenuItem_actionPerformed();
625 else if (source == redoMenuItem)
627 redoMenuItem_actionPerformed();
629 else if (source == copy)
631 copy_actionPerformed();
633 else if (source == pasteNew)
635 pasteNew_actionPerformed();
637 else if (source == pasteThis)
639 pasteThis_actionPerformed();
641 else if (source == cut)
643 cut_actionPerformed();
645 else if (source == delete)
647 delete_actionPerformed();
649 else if (source == deleteGroups)
651 deleteGroups_actionPerformed();
653 else if (source == selectAllSequenceMenuItem)
655 selectAllSequenceMenuItem_actionPerformed();
657 else if (source == deselectAllSequenceMenuItem)
659 deselectAllSequenceMenuItem_actionPerformed();
661 else if (source == invertSequenceMenuItem)
663 invertSequenceMenuItem_actionPerformed();
665 else if (source == invertColSel)
667 viewport.invertColumnSelection();
668 alignPanel.paintAlignment(true);
670 else if (source == remove2LeftMenuItem)
674 else if (source == remove2RightMenuItem)
676 trimAlignment(false);
678 else if (source == removeGappedColumnMenuItem)
680 removeGappedColumnMenuItem_actionPerformed();
682 else if (source == removeAllGapsMenuItem)
684 removeAllGapsMenuItem_actionPerformed();
686 else if (source == findMenuItem)
688 findMenuItem_actionPerformed();
690 else if (source == font)
692 new FontChooser(alignPanel);
694 else if (source == newView)
698 else if (source == showColumns)
700 viewport.showAllHiddenColumns();
701 alignPanel.paintAlignment(true);
703 else if (source == showSeqs)
705 viewport.showAllHiddenSeqs();
707 else if (source == hideColumns)
709 viewport.hideSelectedColumns();
710 alignPanel.paintAlignment(true);
712 else if (source == hideSequences
713 && viewport.getSelectionGroup() != null)
715 viewport.hideAllSelectedSeqs();
717 else if (source == featureSettings)
719 new FeatureSettings(alignPanel);
721 else if (source == alProperties)
723 StringBuffer contents = new StringBuffer();
726 int min = Integer.MAX_VALUE, max = 0;
727 for (int i = 0; i < viewport.alignment.getHeight(); i++)
729 int size = viewport.alignment.getSequenceAt(i).getEnd()
730 - viewport.alignment.getSequenceAt(i).getStart();
737 avg = avg / (float) viewport.alignment.getHeight();
739 contents.append("\nSequences: " + viewport.alignment.getHeight());
740 contents.append("\nMinimum Sequence Length: " + min);
741 contents.append("\nMaximum Sequence Length: " + max);
742 contents.append("\nAverage Length: " + (int) avg);
744 if (((Alignment) viewport.alignment).alignmentProperties != null)
746 Hashtable props = ((Alignment) viewport.alignment).alignmentProperties;
747 Enumeration en = props.keys();
748 while (en.hasMoreElements())
750 String key = en.nextElement().toString();
751 contents.append("\n" + key + "\t" + props.get(key));
755 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
756 cap.setText(contents.toString());
757 Frame frame = new Frame();
759 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
760 + getTitle(), 400, 250);
762 else if (source == overviewMenuItem)
764 overviewMenuItem_actionPerformed();
766 else if (source == noColourmenuItem)
770 else if (source == clustalColour)
772 abovePIDThreshold.setState(false);
773 changeColour(new ClustalxColourScheme(viewport.alignment
774 .getSequences(), viewport.alignment.getWidth()));
776 else if (source == zappoColour)
778 changeColour(new ZappoColourScheme());
780 else if (source == taylorColour)
782 changeColour(new TaylorColourScheme());
784 else if (source == hydrophobicityColour)
786 changeColour(new HydrophobicColourScheme());
788 else if (source == helixColour)
790 changeColour(new HelixColourScheme());
792 else if (source == strandColour)
794 changeColour(new StrandColourScheme());
796 else if (source == turnColour)
798 changeColour(new TurnColourScheme());
800 else if (source == buriedColour)
802 changeColour(new BuriedColourScheme());
804 else if (source == nucleotideColour)
806 changeColour(new NucleotideColourScheme());
808 else if (source == modifyPID)
810 modifyPID_actionPerformed();
812 else if (source == modifyConservation)
814 modifyConservation_actionPerformed();
816 else if (source == userDefinedColour)
818 new UserDefinedColours(alignPanel, null);
820 else if (source == PIDColour)
822 changeColour(new PIDColourScheme());
824 else if (source == BLOSUM62Colour)
826 changeColour(new Blosum62ColourScheme());
828 else if (source == annotationColour)
830 new AnnotationColourChooser(viewport, alignPanel);
832 else if (source == sortPairwiseMenuItem)
834 sortPairwiseMenuItem_actionPerformed();
836 else if (source == sortIDMenuItem)
838 sortIDMenuItem_actionPerformed();
840 else if (source == sortGroupMenuItem)
842 sortGroupMenuItem_actionPerformed();
844 else if (source == removeRedundancyMenuItem)
846 removeRedundancyMenuItem_actionPerformed();
848 else if (source == pairwiseAlignmentMenuItem)
850 pairwiseAlignmentMenuItem_actionPerformed();
852 else if (source == PCAMenuItem)
854 PCAMenuItem_actionPerformed();
856 else if (source == averageDistanceTreeMenuItem)
858 averageDistanceTreeMenuItem_actionPerformed();
860 else if (source == neighbourTreeMenuItem)
862 neighbourTreeMenuItem_actionPerformed();
864 else if (source == njTreeBlosumMenuItem)
866 njTreeBlosumMenuItem_actionPerformed();
868 else if (source == avDistanceTreeBlosumMenuItem)
870 avTreeBlosumMenuItem_actionPerformed();
872 else if (source == documentation)
874 documentation_actionPerformed();
876 else if (source == about)
878 about_actionPerformed();
883 public void inputText_actionPerformed()
885 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
886 Frame frame = new Frame();
888 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
891 protected void outputText_actionPerformed(ActionEvent e)
893 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
894 Frame frame = new Frame();
896 jalview.bin.JalviewLite.addFrame(frame, "Alignment output - "
897 + e.getActionCommand(), 600, 500);
898 cap.setText(new AppletFormatAdapter().formatSequences(e
899 .getActionCommand(), viewport.getAlignment(),
900 viewport.showJVSuffix));
903 public void loadAnnotations()
905 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
906 cap.setText("Paste your features / annotations file here.");
907 cap.setAnnotationImport();
908 Frame frame = new Frame();
910 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
914 public String outputAnnotations(boolean displayTextbox)
916 String annotation = new AnnotationFile().printAnnotations(
917 viewport.showAnnotation ? viewport.alignment
918 .getAlignmentAnnotation() : null, viewport.alignment
920 ((Alignment) viewport.alignment).alignmentProperties);
924 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
925 Frame frame = new Frame();
927 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
928 cap.setText(annotation);
934 public String outputFeatures(boolean displayTextbox, String format)
937 if (format.equalsIgnoreCase("Jalview"))
939 features = new FeaturesFile().printJalviewFormat(viewport.alignment
940 .getSequencesArray(), viewport.featuresDisplayed);
944 features = new FeaturesFile().printGFFFormat(viewport.alignment
945 .getSequencesArray(), viewport.featuresDisplayed);
950 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
951 Frame frame = new Frame();
953 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
955 cap.setText(features);
961 void launchFullApplication()
963 StringBuffer url = new StringBuffer(jalviewServletURL);
966 + appendProtocol(viewport.applet.getParameter("file")));
968 if (viewport.applet.getParameter("features") != null)
970 url.append("&features=");
971 url.append(appendProtocol(viewport.applet.getParameter("features")));
974 if (viewport.applet.getParameter("annotations") != null)
976 url.append("&annotations=");
978 .append(appendProtocol(viewport.applet
979 .getParameter("annotations")));
982 if (viewport.applet.getParameter("jnetfile") != null)
984 url.append("&annotations=");
985 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
988 if (viewport.applet.getParameter("defaultColour") != null)
990 url.append("&colour="
991 + removeWhiteSpace(viewport.applet
992 .getParameter("defaultColour")));
995 if (viewport.applet.getParameter("userDefinedColour") != null)
997 url.append("&colour="
998 + removeWhiteSpace(viewport.applet
999 .getParameter("userDefinedColour")));
1001 if (viewport.applet.getParameter("tree") != null)
1004 + appendProtocol(viewport.applet.getParameter("tree")));
1006 if (viewport.applet.getParameter("treeFile") != null)
1009 + appendProtocol(viewport.applet.getParameter("treeFile")));
1012 showURL(url.toString(), "FULL_APP");
1015 String removeWhiteSpace(String colour)
1017 StringBuffer sb = new StringBuffer();
1018 for (int i = 0; i < colour.length(); i++)
1020 if (Character.isWhitespace(colour.charAt(i)))
1026 sb.append(colour.charAt(i));
1030 return sb.toString();
1033 String appendProtocol(String url)
1038 url = URLEncoder.encode(url);
1041 * When we finally deprecate 1.1 compatibility, we can start to use
1042 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1043 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1044 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1045 * ex.printStackTrace(); }
1047 catch (java.net.MalformedURLException ex)
1049 url = viewport.applet.getCodeBase() + url;
1054 public void closeMenuItem_actionPerformed()
1056 PaintRefresher.RemoveComponent(alignPanel);
1057 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1058 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1060 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1071 void updateEditMenuBar()
1074 if (viewport.historyList.size() > 0)
1076 undoMenuItem.setEnabled(true);
1077 CommandI command = (CommandI) viewport.historyList.peek();
1078 undoMenuItem.setLabel("Undo " + command.getDescription());
1082 undoMenuItem.setEnabled(false);
1083 undoMenuItem.setLabel("Undo");
1086 if (viewport.redoList.size() > 0)
1088 redoMenuItem.setEnabled(true);
1090 CommandI command = (CommandI) viewport.redoList.peek();
1091 redoMenuItem.setLabel("Redo " + command.getDescription());
1095 redoMenuItem.setEnabled(false);
1096 redoMenuItem.setLabel("Redo");
1100 public void addHistoryItem(CommandI command)
1102 if (command.getSize() > 0)
1104 viewport.historyList.push(command);
1105 viewport.redoList.removeAllElements();
1106 updateEditMenuBar();
1107 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1117 protected void undoMenuItem_actionPerformed()
1119 if (viewport.historyList.size() < 1)
1124 CommandI command = (CommandI) viewport.historyList.pop();
1125 viewport.redoList.push(command);
1126 command.undoCommand(null);
1128 AlignViewport originalSource = getOriginatingSource(command);
1130 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1131 updateEditMenuBar();
1132 originalSource.firePropertyChange("alignment", null,
1133 originalSource.alignment.getSequences());
1142 protected void redoMenuItem_actionPerformed()
1144 if (viewport.redoList.size() < 1)
1149 CommandI command = (CommandI) viewport.redoList.pop();
1150 viewport.historyList.push(command);
1151 command.doCommand(null);
1153 AlignViewport originalSource = getOriginatingSource(command);
1154 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1156 updateEditMenuBar();
1157 originalSource.firePropertyChange("alignment", null,
1158 originalSource.alignment.getSequences());
1161 AlignViewport getOriginatingSource(CommandI command)
1163 AlignViewport originalSource = null;
1164 // For sequence removal and addition, we need to fire
1165 // the property change event FROM the viewport where the
1166 // original alignment was altered
1167 AlignmentI al = null;
1168 if (command instanceof EditCommand)
1170 EditCommand editCommand = (EditCommand) command;
1171 al = editCommand.getAlignment();
1172 Vector comps = (Vector) PaintRefresher.components.get(viewport
1173 .getSequenceSetId());
1174 for (int i = 0; i < comps.size(); i++)
1176 if (comps.elementAt(i) instanceof AlignmentPanel)
1178 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1180 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1187 if (originalSource == null)
1189 // The original view is closed, we must validate
1190 // the current view against the closed view first
1193 PaintRefresher.validateSequences(al, viewport.alignment);
1196 originalSource = viewport;
1199 return originalSource;
1202 public void moveSelectedSequences(boolean up)
1204 SequenceGroup sg = viewport.getSelectionGroup();
1212 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1214 SequenceI seq = viewport.alignment.getSequenceAt(i);
1215 if (!sg.getSequences(null).contains(seq))
1220 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1221 if (sg.getSequences(null).contains(temp))
1226 viewport.alignment.getSequences().setElementAt(temp, i);
1227 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1232 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1234 SequenceI seq = viewport.alignment.getSequenceAt(i);
1235 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
1240 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1241 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
1246 viewport.alignment.getSequences().setElementAt(temp, i);
1247 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1251 alignPanel.paintAlignment(true);
1254 synchronized void slideSequences(boolean right, int size)
1256 Vector sg = new Vector();
1257 if (viewport.cursorMode)
1259 sg.addElement(viewport.alignment
1260 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1262 else if (viewport.getSelectionGroup() != null
1263 && viewport.getSelectionGroup().getSize() != viewport.alignment
1266 sg = viewport.getSelectionGroup().getSequences(
1267 viewport.hiddenRepSequences);
1275 Vector invertGroup = new Vector();
1277 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1279 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1280 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
1283 SequenceI[] seqs1 = new SequenceI[sg.size()];
1284 for (int i = 0; i < sg.size(); i++)
1285 seqs1[i] = (SequenceI) sg.elementAt(i);
1287 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1288 for (int i = 0; i < invertGroup.size(); i++)
1289 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1291 SlideSequencesCommand ssc;
1293 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1294 size, viewport.getGapCharacter());
1296 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1297 size, viewport.getGapCharacter());
1299 int groupAdjustment = 0;
1300 if (ssc.getGapsInsertedBegin() && right)
1302 if (viewport.cursorMode)
1303 alignPanel.seqPanel.moveCursor(size, 0);
1305 groupAdjustment = size;
1307 else if (!ssc.getGapsInsertedBegin() && !right)
1309 if (viewport.cursorMode)
1310 alignPanel.seqPanel.moveCursor(-size, 0);
1312 groupAdjustment = -size;
1315 if (groupAdjustment != 0)
1317 viewport.getSelectionGroup().setStartRes(
1318 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1319 viewport.getSelectionGroup().setEndRes(
1320 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1323 boolean appendHistoryItem = false;
1324 if (viewport.historyList != null && viewport.historyList.size() > 0
1325 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1327 appendHistoryItem = ssc
1328 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1332 if (!appendHistoryItem)
1333 addHistoryItem(ssc);
1338 static StringBuffer copiedSequences;
1340 static Vector copiedHiddenColumns;
1342 protected void copy_actionPerformed()
1344 if (viewport.getSelectionGroup() == null)
1349 SequenceGroup sg = viewport.getSelectionGroup();
1350 copiedSequences = new StringBuffer();
1351 Hashtable orderedSeqs = new Hashtable();
1352 for (int i = 0; i < sg.getSize(); i++)
1354 SequenceI seq = sg.getSequenceAt(i);
1355 int index = viewport.alignment.findIndex(seq);
1356 orderedSeqs.put(index + "", seq);
1359 int index = 0, startRes, endRes;
1362 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
1364 copiedHiddenColumns = new Vector();
1365 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1366 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1369 int[] region = (int[]) viewport.getColumnSelection()
1370 .getHiddenColumns().elementAt(i);
1372 copiedHiddenColumns.addElement(new int[]
1373 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1378 copiedHiddenColumns = null;
1381 for (int i = 0; i < sg.getSize(); i++)
1383 SequenceI seq = null;
1387 if (orderedSeqs.containsKey(index + ""))
1389 seq = (SequenceI) orderedSeqs.get(index + "");
1401 // Returns residue following index if gap
1402 startRes = seq.findPosition(sg.getStartRes());
1405 // Need to find the residue preceeding index if gap
1408 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1410 ch = seq.getCharAt(j);
1411 if (!jalview.util.Comparison.isGap((ch)))
1419 endRes += seq.getStart() - 1;
1422 copiedSequences.append(seq.getName()
1428 + seq.getSequenceAsString(sg.getStartRes(),
1429 sg.getEndRes() + 1) + "\n");
1434 protected void pasteNew_actionPerformed()
1439 protected void pasteThis_actionPerformed()
1444 void paste(boolean newAlignment)
1449 if (copiedSequences == null)
1454 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1455 Vector seqs = new Vector();
1456 while (st.hasMoreElements())
1458 String name = st.nextToken();
1459 int start = Integer.parseInt(st.nextToken());
1460 int end = Integer.parseInt(st.nextToken());
1461 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1463 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1464 for (int i = 0; i < seqs.size(); i++)
1466 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1471 String newtitle = new String("Copied sequences");
1472 if (getTitle().startsWith("Copied sequences"))
1474 newtitle = getTitle();
1478 newtitle = newtitle.concat("- from " + getTitle());
1480 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1481 viewport.applet, newtitle, false);
1482 if (copiedHiddenColumns != null)
1484 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1486 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1487 af.viewport.hideColumns(region[0], region[1]);
1491 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1496 addSequences(newSeqs);
1499 } catch (Exception ex)
1501 } // could be anything being pasted in here
1505 void addSequences(SequenceI[] seqs)
1507 for (int i = 0; i < seqs.length; i++)
1509 viewport.alignment.addSequence(seqs[i]);
1513 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1514 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
1516 viewport.setEndSeq(viewport.alignment.getHeight());
1517 viewport.alignment.getWidth();
1518 viewport.firePropertyChange("alignment", null, viewport.alignment
1523 protected void cut_actionPerformed()
1525 copy_actionPerformed();
1526 delete_actionPerformed();
1529 protected void delete_actionPerformed()
1532 SequenceGroup sg = viewport.getSelectionGroup();
1538 Vector seqs = new Vector();
1540 for (int i = 0; i < sg.getSize(); i++)
1542 seq = sg.getSequenceAt(i);
1543 seqs.addElement(seq);
1546 // If the cut affects all sequences, remove highlighted columns
1547 if (sg.getSize() == viewport.alignment.getHeight())
1549 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1550 sg.getEndRes() + 1);
1553 SequenceI[] cut = new SequenceI[seqs.size()];
1554 for (int i = 0; i < seqs.size(); i++)
1556 cut[i] = (SequenceI) seqs.elementAt(i);
1560 * //ADD HISTORY ITEM
1562 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1563 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1564 viewport.alignment));
1566 viewport.setSelectionGroup(null);
1567 viewport.alignment.deleteGroup(sg);
1569 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1572 if (viewport.getAlignment().getHeight() < 1)
1574 this.setVisible(false);
1578 protected void deleteGroups_actionPerformed()
1580 viewport.alignment.deleteAllGroups();
1581 viewport.sequenceColours = null;
1582 viewport.setSelectionGroup(null);
1584 alignPanel.paintAlignment(true);
1587 public void selectAllSequenceMenuItem_actionPerformed()
1589 SequenceGroup sg = new SequenceGroup();
1590 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1592 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1594 sg.setEndRes(viewport.alignment.getWidth() - 1);
1595 viewport.setSelectionGroup(sg);
1596 alignPanel.paintAlignment(true);
1597 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1600 public void deselectAllSequenceMenuItem_actionPerformed()
1602 if (viewport.cursorMode)
1604 alignPanel.seqPanel.keyboardNo1 = null;
1605 alignPanel.seqPanel.keyboardNo2 = null;
1607 viewport.setSelectionGroup(null);
1608 viewport.getColumnSelection().clear();
1609 viewport.setSelectionGroup(null);
1610 alignPanel.idPanel.idCanvas.searchResults = null;
1611 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1612 alignPanel.paintAlignment(true);
1613 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1616 public void invertSequenceMenuItem_actionPerformed()
1618 SequenceGroup sg = viewport.getSelectionGroup();
1619 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1621 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1624 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1627 void trimAlignment(boolean trimLeft)
1629 ColumnSelection colSel = viewport.getColumnSelection();
1632 if (colSel.size() > 0)
1636 column = colSel.getMin();
1640 column = colSel.getMax();
1644 if (viewport.getSelectionGroup() != null)
1646 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1647 viewport.hiddenRepSequences);
1651 seqs = viewport.alignment.getSequencesArray();
1654 TrimRegionCommand trimRegion;
1657 trimRegion = new TrimRegionCommand("Remove Left",
1658 TrimRegionCommand.TRIM_LEFT, seqs, column,
1659 viewport.alignment, viewport.colSel,
1660 viewport.selectionGroup);
1661 viewport.setStartRes(0);
1665 trimRegion = new TrimRegionCommand("Remove Right",
1666 TrimRegionCommand.TRIM_RIGHT, seqs, column,
1667 viewport.alignment, viewport.colSel,
1668 viewport.selectionGroup);
1671 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
1673 addHistoryItem(trimRegion);
1675 Vector groups = viewport.alignment.getGroups();
1677 for (int i = 0; i < groups.size(); i++)
1679 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1681 if ((trimLeft && !sg.adjustForRemoveLeft(column))
1682 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1684 viewport.alignment.deleteGroup(sg);
1688 viewport.firePropertyChange("alignment", null, viewport
1689 .getAlignment().getSequences());
1693 public void removeGappedColumnMenuItem_actionPerformed()
1695 int start = 0, end = viewport.alignment.getWidth() - 1;
1698 if (viewport.getSelectionGroup() != null)
1700 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1701 viewport.hiddenRepSequences);
1702 start = viewport.getSelectionGroup().getStartRes();
1703 end = viewport.getSelectionGroup().getEndRes();
1707 seqs = viewport.alignment.getSequencesArray();
1710 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
1711 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
1713 addHistoryItem(removeGapCols);
1715 statusBar.setText("Removed " + removeGapCols.getSize()
1716 + " empty columns.");
1718 // This is to maintain viewport position on first residue
1719 // of first sequence
1720 SequenceI seq = viewport.alignment.getSequenceAt(0);
1721 int startRes = seq.findPosition(viewport.startRes);
1722 // ShiftList shifts;
1723 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1724 // edit.alColumnChanges=shifts.getInverse();
1725 // if (viewport.hasHiddenColumns)
1726 // viewport.getColumnSelection().compensateForEdits(shifts);
1727 viewport.setStartRes(seq.findIndex(startRes) - 1);
1728 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1733 public void removeAllGapsMenuItem_actionPerformed()
1735 int start = 0, end = viewport.alignment.getWidth() - 1;
1738 if (viewport.getSelectionGroup() != null)
1740 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1741 viewport.hiddenRepSequences);
1742 start = viewport.getSelectionGroup().getStartRes();
1743 end = viewport.getSelectionGroup().getEndRes();
1747 seqs = viewport.alignment.getSequencesArray();
1750 // This is to maintain viewport position on first residue
1751 // of first sequence
1752 SequenceI seq = viewport.alignment.getSequenceAt(0);
1753 int startRes = seq.findPosition(viewport.startRes);
1755 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
1756 viewport.alignment));
1758 viewport.setStartRes(seq.findIndex(startRes) - 1);
1760 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1765 public void findMenuItem_actionPerformed()
1767 new Finder(alignPanel);
1771 * create a new view derived from the current view
1774 * @return frame for the new view
1776 public AlignFrame newView(String viewtitle)
1779 if (viewport.hasHiddenRows)
1781 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
1782 .getFullAlignment().getSequencesArray());
1786 newal = new Alignment(viewport.alignment.getSequencesArray());
1789 if (viewport.alignment.getAlignmentAnnotation() != null)
1791 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
1793 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
1796 .addAnnotation(viewport.alignment
1797 .getAlignmentAnnotation()[i]);
1802 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
1804 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
1805 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
1806 PaintRefresher.Register(newaf.alignPanel, newaf.alignPanel.av
1807 .getSequenceSetId());
1809 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
1810 newaf.alignPanel.av.getSequenceSetId());
1811 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
1812 newaf.alignPanel.av.getSequenceSetId());
1814 Vector comps = (Vector) PaintRefresher.components.get(viewport
1815 .getSequenceSetId());
1817 for (int i = 0; i < comps.size(); i++)
1819 if (comps.elementAt(i) instanceof AlignmentPanel)
1825 String title = new String(this.getTitle());
1826 if (viewtitle != null)
1828 title = viewtitle + " ( " + title + ")";
1832 if (title.indexOf("(View") > -1)
1834 title = title.substring(0, title.indexOf("(View"));
1836 title += "(View " + viewSize + ")";
1839 newaf.setTitle(title.toString());
1841 newaf.viewport.historyList = viewport.historyList;
1842 newaf.viewport.redoList = viewport.redoList;
1848 * @return list of feature groups on the view
1850 public String[] getFeatureGroups()
1852 FeatureRenderer fr = null;
1853 if (alignPanel != null
1854 && (fr = alignPanel.getFeatureRenderer()) != null)
1856 return fr.getGroups();
1862 * get sequence feature groups that are hidden or shown
1868 public String[] getFeatureGroupsOfState(boolean visible)
1870 FeatureRenderer fr = null;
1871 if (alignPanel != null
1872 && (fr = alignPanel.getFeatureRenderer()) != null)
1874 return fr.getGroups(visible);
1880 * Change the display state for the given feature groups
1883 * list of group strings
1885 * visible or invisible
1887 public void setFeatureGroupState(String[] groups, boolean state)
1889 FeatureRenderer fr = null;
1890 this.sequenceFeatures.setState(true);
1891 viewport.showSequenceFeatures(true);
1892 if (alignPanel != null
1893 && (fr = alignPanel.getFeatureRenderer()) != null)
1895 fr.setGroupState(groups, state);
1896 alignPanel.seqPanel.seqCanvas.repaint();
1897 if (alignPanel.overviewPanel != null)
1899 alignPanel.overviewPanel.updateOverviewImage();
1904 public void seqLimits_itemStateChanged()
1906 viewport.setShowJVSuffix(seqLimits.getState());
1907 alignPanel.fontChanged();
1908 alignPanel.paintAlignment(true);
1911 protected void colourTextMenuItem_actionPerformed()
1913 viewport.setColourText(colourTextMenuItem.getState());
1914 alignPanel.paintAlignment(true);
1917 protected void displayNonconservedMenuItem_actionPerformed()
1919 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
1920 alignPanel.paintAlignment(true);
1923 protected void wrapMenuItem_actionPerformed()
1925 viewport.setWrapAlignment(wrapMenuItem.getState());
1926 alignPanel.setWrapAlignment(wrapMenuItem.getState());
1927 scaleAbove.setEnabled(wrapMenuItem.getState());
1928 scaleLeft.setEnabled(wrapMenuItem.getState());
1929 scaleRight.setEnabled(wrapMenuItem.getState());
1930 alignPanel.paintAlignment(true);
1933 public void overviewMenuItem_actionPerformed()
1935 if (alignPanel.overviewPanel != null)
1940 Frame frame = new Frame();
1941 OverviewPanel overview = new OverviewPanel(alignPanel);
1942 frame.add(overview);
1943 // +50 must allow for applet frame window
1944 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
1945 overview.getPreferredSize().width,
1946 overview.getPreferredSize().height + 50);
1949 frame.addWindowListener(new WindowAdapter()
1951 public void windowClosing(WindowEvent e)
1953 alignPanel.setOverviewPanel(null);
1957 alignPanel.setOverviewPanel(overview);
1961 void changeColour(ColourSchemeI cs)
1967 if (viewport.getAbovePIDThreshold())
1969 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
1972 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
1974 viewport.setGlobalColourScheme(cs);
1978 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
1981 if (viewport.getConservationSelected())
1984 Alignment al = (Alignment) viewport.alignment;
1985 Conservation c = new Conservation("All",
1986 ResidueProperties.propHash, 3, al.getSequences(), 0, al
1990 c.verdict(false, viewport.ConsPercGaps);
1992 cs.setConservation(c);
1994 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2000 cs.setConservation(null);
2003 cs.setConsensus(viewport.hconsensus);
2006 viewport.setGlobalColourScheme(cs);
2008 if (viewport.getColourAppliesToAllGroups())
2010 Vector groups = viewport.alignment.getGroups();
2011 for (int i = 0; i < groups.size(); i++)
2013 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2020 if (cs instanceof ClustalxColourScheme)
2022 sg.cs = new ClustalxColourScheme(sg
2023 .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2029 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2030 } catch (Exception ex)
2032 ex.printStackTrace();
2037 if (viewport.getAbovePIDThreshold()
2038 || cs instanceof PIDColourScheme
2039 || cs instanceof Blosum62ColourScheme)
2041 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2042 sg.cs.setConsensus(AAFrequency.calculate(sg
2043 .getSequences(viewport.hiddenRepSequences), 0, sg
2048 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2051 if (viewport.getConservationSelected())
2053 Conservation c = new Conservation("Group",
2054 ResidueProperties.propHash, 3, sg
2055 .getSequences(viewport.hiddenRepSequences), 0,
2056 viewport.alignment.getWidth() - 1);
2058 c.verdict(false, viewport.ConsPercGaps);
2059 sg.cs.setConservation(c);
2063 sg.cs.setConservation(null);
2064 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2070 if (alignPanel.getOverviewPanel() != null)
2072 alignPanel.getOverviewPanel().updateOverviewImage();
2075 jalview.structure.StructureSelectionManager
2076 .getStructureSelectionManager().sequenceColoursChanged(
2079 alignPanel.paintAlignment(true);
2082 protected void modifyPID_actionPerformed()
2084 if (viewport.getAbovePIDThreshold()
2085 && viewport.globalColourScheme != null)
2087 SliderPanel.setPIDSliderSource(alignPanel, viewport
2088 .getGlobalColourScheme(), "Background");
2089 SliderPanel.showPIDSlider();
2093 protected void modifyConservation_actionPerformed()
2095 if (viewport.getConservationSelected()
2096 && viewport.globalColourScheme != null)
2098 SliderPanel.setConservationSlider(alignPanel,
2099 viewport.globalColourScheme, "Background");
2100 SliderPanel.showConservationSlider();
2104 protected void conservationMenuItem_actionPerformed()
2106 viewport.setConservationSelected(conservationMenuItem.getState());
2108 viewport.setAbovePIDThreshold(false);
2109 abovePIDThreshold.setState(false);
2111 changeColour(viewport.getGlobalColourScheme());
2113 modifyConservation_actionPerformed();
2116 public void abovePIDThreshold_actionPerformed()
2118 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2120 conservationMenuItem.setState(false);
2121 viewport.setConservationSelected(false);
2123 changeColour(viewport.getGlobalColourScheme());
2125 modifyPID_actionPerformed();
2128 public void sortPairwiseMenuItem_actionPerformed()
2130 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2131 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2132 .getAlignment().getSequenceAt(0), null);
2133 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2134 viewport.alignment));
2135 alignPanel.paintAlignment(true);
2138 public void sortIDMenuItem_actionPerformed()
2140 // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
2141 // HistoryItem.SORT));
2142 AlignmentSorter.sortByID(viewport.getAlignment());
2143 alignPanel.paintAlignment(true);
2146 public void sortGroupMenuItem_actionPerformed()
2148 // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
2149 // HistoryItem.SORT));
2150 AlignmentSorter.sortByGroup(viewport.getAlignment());
2151 alignPanel.paintAlignment(true);
2155 public void removeRedundancyMenuItem_actionPerformed()
2157 new RedundancyPanel(alignPanel);
2160 public void pairwiseAlignmentMenuItem_actionPerformed()
2162 if (viewport.getSelectionGroup() != null
2163 && viewport.getSelectionGroup().getSize() > 1)
2165 Frame frame = new Frame();
2166 frame.add(new PairwiseAlignPanel(alignPanel));
2167 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
2172 public void PCAMenuItem_actionPerformed()
2174 // are the sequences aligned?
2175 if (!viewport.alignment.isAligned())
2178 int Width = viewport.getAlignment().getWidth();
2180 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2182 current = viewport.getAlignment().getSequenceAt(i);
2184 if (current.getLength() < Width)
2186 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2189 alignPanel.paintAlignment(true);
2192 if ((viewport.getSelectionGroup() != null
2193 && viewport.getSelectionGroup().getSize() < 4 && viewport
2194 .getSelectionGroup().getSize() > 0)
2195 || viewport.getAlignment().getHeight() < 4)
2202 new PCAPanel(viewport);
2203 } catch (java.lang.OutOfMemoryError ex)
2209 public void averageDistanceTreeMenuItem_actionPerformed()
2211 NewTreePanel("AV", "PID", "Average distance tree using PID");
2214 public void neighbourTreeMenuItem_actionPerformed()
2216 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2219 protected void njTreeBlosumMenuItem_actionPerformed()
2221 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2224 protected void avTreeBlosumMenuItem_actionPerformed()
2226 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2229 void NewTreePanel(String type, String pwType, String title)
2231 // are the sequences aligned?
2232 if (!viewport.alignment.isAligned())
2235 int Width = viewport.getAlignment().getWidth();
2237 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2239 current = viewport.getAlignment().getSequenceAt(i);
2241 if (current.getLength() < Width)
2243 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2246 alignPanel.paintAlignment(true);
2250 if ((viewport.getSelectionGroup() != null && viewport
2251 .getSelectionGroup().getSize() > 1)
2252 || (viewport.getSelectionGroup() == null && viewport.alignment
2255 final TreePanel tp = new TreePanel(viewport, type, pwType);
2257 addTreeMenuItem(tp, title);
2259 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2263 void loadTree_actionPerformed()
2265 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2266 cap.setText("Paste your Newick tree file here.");
2267 cap.setTreeImport();
2268 Frame frame = new Frame();
2270 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
2273 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2275 TreePanel tp = new TreePanel(viewport, treeFile, "From File - ", tree);
2276 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2277 addTreeMenuItem(tp, treeFile);
2280 void addTreeMenuItem(final TreePanel treePanel, String title)
2282 final MenuItem item = new MenuItem(title);
2283 sortByTreeMenu.add(item);
2284 item.addActionListener(new java.awt.event.ActionListener()
2286 public void actionPerformed(ActionEvent evt)
2288 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2289 // HistoryItem.SORT));
2290 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel
2292 alignPanel.paintAlignment(true);
2296 treePanel.addWindowListener(new WindowAdapter()
2298 public void windowClosing(WindowEvent e)
2300 sortByTreeMenu.remove(item);
2305 protected void documentation_actionPerformed()
2307 showURL("http://www.jalview.org/help.html", "HELP");
2310 protected void about_actionPerformed()
2313 class AboutPanel extends Canvas
2317 public AboutPanel(String version)
2319 this.version = version;
2322 public void paint(Graphics g)
2324 g.setColor(Color.white);
2325 g.fillRect(0, 0, getSize().width, getSize().height);
2326 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2327 FontMetrics fm = g.getFontMetrics();
2328 int fh = fm.getHeight();
2330 g.setColor(Color.black);
2331 // TODO: update this text for each release or centrally store it for
2332 // lite and application
2333 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2334 g.drawString("JalviewLite - Release " + version, x, y += fh);
2335 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2338 "Authors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,",
2340 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
2343 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
2347 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
2349 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
2351 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",x,y+=fh);
2352 g.drawString("Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",x,y+=fh);
2353 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",x,y+=fh);
2357 String version = "test";
2358 java.net.URL url = getClass().getResource("/.build_properties");
2363 BufferedReader reader = new BufferedReader(new InputStreamReader(
2366 while ((line = reader.readLine()) != null)
2368 if (line.indexOf("VERSION") > -1)
2370 version = line.substring(line.indexOf("=") + 1);
2373 } catch (Exception ex)
2375 ex.printStackTrace();
2379 Frame frame = new Frame();
2380 frame.add(new AboutPanel(version));
2381 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
2385 public void showURL(String url, String target)
2387 if (viewport.applet == null)
2389 System.out.println("Not running as applet - no browser available.");
2395 if (url.indexOf(":")==-1)
2397 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to form valid URL
2398 if (url.indexOf("/")==0)
2400 String codebase = viewport.applet.getCodeBase().toString();
2401 url = codebase.substring(0,codebase.length()-viewport.applet.getCodeBase().getFile().length())+url;
2403 url = viewport.applet.getCodeBase()+url;
2405 System.out.println("Show url (prepended codebase): " + url);
2407 System.out.println("Show url: " + url);
2409 viewport.applet.getAppletContext().showDocument(
2410 new java.net.URL(url), target);
2411 } catch (Exception ex)
2413 ex.printStackTrace();
2418 // ////////////////////////////////////////////////////////////////////////////////
2419 // JBuilder Graphics here
2421 MenuBar alignFrameMenuBar = new MenuBar();
2423 Menu fileMenu = new Menu("File");
2425 MenuItem loadApplication = new MenuItem("View in Full Application");
2427 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
2429 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
2431 MenuItem outputFeatures = new MenuItem("Export Features ...");
2433 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
2435 MenuItem closeMenuItem = new MenuItem("Close");
2437 Menu editMenu = new Menu("Edit");
2439 Menu viewMenu = new Menu("View");
2441 Menu colourMenu = new Menu("Colour");
2443 Menu calculateMenu = new Menu("Calculate");
2445 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
2447 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
2449 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
2451 MenuItem remove2LeftMenuItem = new MenuItem();
2453 MenuItem remove2RightMenuItem = new MenuItem();
2455 MenuItem removeGappedColumnMenuItem = new MenuItem();
2457 MenuItem removeAllGapsMenuItem = new MenuItem();
2459 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2461 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2463 MenuItem sortPairwiseMenuItem = new MenuItem();
2465 MenuItem sortIDMenuItem = new MenuItem();
2467 MenuItem sortGroupMenuItem = new MenuItem();
2469 MenuItem removeRedundancyMenuItem = new MenuItem();
2471 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2473 MenuItem PCAMenuItem = new MenuItem();
2475 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2477 MenuItem neighbourTreeMenuItem = new MenuItem();
2479 BorderLayout borderLayout1 = new BorderLayout();
2481 public Label statusBar = new Label();
2483 Menu outputTextboxMenu = new Menu();
2485 MenuItem clustalColour = new MenuItem();
2487 MenuItem zappoColour = new MenuItem();
2489 MenuItem taylorColour = new MenuItem();
2491 MenuItem hydrophobicityColour = new MenuItem();
2493 MenuItem helixColour = new MenuItem();
2495 MenuItem strandColour = new MenuItem();
2497 MenuItem turnColour = new MenuItem();
2499 MenuItem buriedColour = new MenuItem();
2501 MenuItem userDefinedColour = new MenuItem();
2503 MenuItem PIDColour = new MenuItem();
2505 MenuItem BLOSUM62Colour = new MenuItem();
2507 MenuItem njTreeBlosumMenuItem = new MenuItem();
2509 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2511 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2513 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2515 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2517 MenuItem alProperties = new MenuItem("Alignment Properties...");
2519 MenuItem overviewMenuItem = new MenuItem();
2521 MenuItem undoMenuItem = new MenuItem();
2523 MenuItem redoMenuItem = new MenuItem();
2525 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2527 MenuItem noColourmenuItem = new MenuItem();
2529 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2531 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2533 MenuItem findMenuItem = new MenuItem();
2535 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2537 MenuItem nucleotideColour = new MenuItem();
2539 MenuItem deleteGroups = new MenuItem();
2541 MenuItem delete = new MenuItem();
2543 MenuItem copy = new MenuItem();
2545 MenuItem cut = new MenuItem();
2547 Menu pasteMenu = new Menu();
2549 MenuItem pasteNew = new MenuItem();
2551 MenuItem pasteThis = new MenuItem();
2553 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2555 MenuItem font = new MenuItem();
2557 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2559 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2561 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2563 MenuItem modifyPID = new MenuItem();
2565 MenuItem modifyConservation = new MenuItem();
2567 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2568 "Autocalculate Consensus", true);
2570 Menu sortByTreeMenu = new Menu();
2572 Menu sort = new Menu();
2574 Menu calculate = new Menu();
2576 MenuItem inputText = new MenuItem();
2578 Menu helpMenu = new Menu();
2580 MenuItem documentation = new MenuItem();
2582 MenuItem about = new MenuItem();
2584 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2586 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2588 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2590 private void jbInit() throws Exception
2593 setMenuBar(alignFrameMenuBar);
2597 // dynamically fill save as menu with available formats
2598 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2601 item = new MenuItem(
2602 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2604 item.addActionListener(new java.awt.event.ActionListener()
2606 public void actionPerformed(ActionEvent e)
2608 outputText_actionPerformed(e);
2612 outputTextboxMenu.add(item);
2614 closeMenuItem.addActionListener(this);
2615 loadApplication.addActionListener(this);
2617 loadTree.addActionListener(this);
2618 loadAnnotations.addActionListener(this);
2619 outputFeatures.addActionListener(this);
2620 outputAnnotations.addActionListener(this);
2621 selectAllSequenceMenuItem.addActionListener(this);
2622 deselectAllSequenceMenuItem.addActionListener(this);
2623 invertSequenceMenuItem.addActionListener(this);
2624 remove2LeftMenuItem.setLabel("Remove Left");
2625 remove2LeftMenuItem.addActionListener(this);
2626 remove2RightMenuItem.setLabel("Remove Right");
2627 remove2RightMenuItem.addActionListener(this);
2628 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2629 removeGappedColumnMenuItem.addActionListener(this);
2630 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2631 removeAllGapsMenuItem.addActionListener(this);
2632 viewBoxesMenuItem.setLabel("Boxes");
2633 viewBoxesMenuItem.setState(true);
2634 viewBoxesMenuItem.addItemListener(this);
2635 viewTextMenuItem.setLabel("Text");
2636 viewTextMenuItem.setState(true);
2637 viewTextMenuItem.addItemListener(this);
2638 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2639 sortPairwiseMenuItem.addActionListener(this);
2640 sortIDMenuItem.setLabel("by ID");
2641 sortIDMenuItem.addActionListener(this);
2642 sortGroupMenuItem.setLabel("by Group");
2643 sortGroupMenuItem.addActionListener(this);
2644 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2645 removeRedundancyMenuItem.addActionListener(this);
2646 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
2647 pairwiseAlignmentMenuItem.addActionListener(this);
2648 PCAMenuItem.setLabel("Principal Component Analysis");
2649 PCAMenuItem.addActionListener(this);
2650 averageDistanceTreeMenuItem
2651 .setLabel("Average Distance Using % Identity");
2652 averageDistanceTreeMenuItem.addActionListener(this);
2653 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
2654 neighbourTreeMenuItem.addActionListener(this);
2655 statusBar.setBackground(Color.white);
2656 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2657 statusBar.setText("Status bar");
2658 outputTextboxMenu.setLabel("Output to Textbox");
2659 clustalColour.setLabel("Clustalx");
2661 clustalColour.addActionListener(this);
2662 zappoColour.setLabel("Zappo");
2663 zappoColour.addActionListener(this);
2664 taylorColour.setLabel("Taylor");
2665 taylorColour.addActionListener(this);
2666 hydrophobicityColour.setLabel("Hydrophobicity");
2667 hydrophobicityColour.addActionListener(this);
2668 helixColour.setLabel("Helix Propensity");
2669 helixColour.addActionListener(this);
2670 strandColour.setLabel("Strand Propensity");
2671 strandColour.addActionListener(this);
2672 turnColour.setLabel("Turn Propensity");
2673 turnColour.addActionListener(this);
2674 buriedColour.setLabel("Buried Index");
2675 buriedColour.addActionListener(this);
2676 userDefinedColour.setLabel("User Defined...");
2677 userDefinedColour.addActionListener(this);
2678 PIDColour.setLabel("Percentage Identity");
2679 PIDColour.addActionListener(this);
2680 BLOSUM62Colour.setLabel("BLOSUM62 Score");
2681 BLOSUM62Colour.addActionListener(this);
2682 avDistanceTreeBlosumMenuItem
2683 .setLabel("Average Distance Using BLOSUM62");
2684 avDistanceTreeBlosumMenuItem.addActionListener(this);
2685 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
2686 njTreeBlosumMenuItem.addActionListener(this);
2687 annotationPanelMenuItem.setLabel("Show Annotations");
2688 annotationPanelMenuItem.addItemListener(this);
2689 colourTextMenuItem.setLabel("Colour Text");
2690 colourTextMenuItem.addItemListener(this);
2691 displayNonconservedMenuItem.setLabel("Show non-conserved");
2692 displayNonconservedMenuItem.addItemListener(this);
2693 alProperties.addActionListener(this);
2694 overviewMenuItem.setLabel("Overview Window");
2695 overviewMenuItem.addActionListener(this);
2696 undoMenuItem.setEnabled(false);
2697 undoMenuItem.setLabel("Undo");
2698 undoMenuItem.addActionListener(this);
2699 redoMenuItem.setEnabled(false);
2700 redoMenuItem.setLabel("Redo");
2701 redoMenuItem.addActionListener(this);
2702 conservationMenuItem.setLabel("by Conservation");
2703 conservationMenuItem.addItemListener(this);
2704 noColourmenuItem.setLabel("None");
2705 noColourmenuItem.addActionListener(this);
2706 wrapMenuItem.setLabel("Wrap");
2707 wrapMenuItem.addItemListener(this);
2708 renderGapsMenuItem.setLabel("Show Gaps");
2709 renderGapsMenuItem.setState(true);
2710 renderGapsMenuItem.addItemListener(this);
2711 findMenuItem.setLabel("Find...");
2712 findMenuItem.addActionListener(this);
2713 abovePIDThreshold.setLabel("Above Identity Threshold");
2714 abovePIDThreshold.addItemListener(this);
2715 nucleotideColour.setLabel("Nucleotide");
2716 nucleotideColour.addActionListener(this);
2717 deleteGroups.setLabel("Undefine Groups");
2718 deleteGroups.addActionListener(this);
2719 copy.setLabel("Copy");
2720 copy.addActionListener(this);
2721 cut.setLabel("Cut");
2722 cut.addActionListener(this);
2723 delete.setLabel("Delete");
2724 delete.addActionListener(this);
2725 pasteMenu.setLabel("Paste");
2726 pasteNew.setLabel("To New Alignment");
2727 pasteNew.addActionListener(this);
2728 pasteThis.setLabel("Add To This Alignment");
2729 pasteThis.addActionListener(this);
2730 applyToAllGroups.setLabel("Apply Colour To All Groups");
2731 applyToAllGroups.setState(true);
2732 applyToAllGroups.addItemListener(this);
2733 font.setLabel("Font...");
2734 font.addActionListener(this);
2735 scaleAbove.setLabel("Scale Above");
2736 scaleAbove.setState(true);
2737 scaleAbove.setEnabled(false);
2738 scaleAbove.addItemListener(this);
2739 scaleLeft.setEnabled(false);
2740 scaleLeft.setState(true);
2741 scaleLeft.setLabel("Scale Left");
2742 scaleLeft.addItemListener(this);
2743 scaleRight.setEnabled(false);
2744 scaleRight.setState(true);
2745 scaleRight.setLabel("Scale Right");
2746 scaleRight.addItemListener(this);
2747 modifyPID.setLabel("Modify Identity Threshold...");
2748 modifyPID.addActionListener(this);
2749 modifyConservation.setLabel("Modify Conservation Threshold...");
2750 modifyConservation.addActionListener(this);
2751 sortByTreeMenu.setLabel("By Tree Order");
2752 sort.setLabel("Sort");
2753 calculate.setLabel("Calculate Tree");
2754 autoCalculate.addItemListener(this);
2755 inputText.setLabel("Input from textbox");
2756 inputText.addActionListener(this);
2757 centreColumnLabelFlag.setLabel("Centre column labels");
2758 centreColumnLabelFlag.addItemListener(this);
2759 followMouseOverFlag.setLabel("Automatic Scrolling");
2760 followMouseOverFlag.addItemListener(this);
2761 helpMenu.setLabel("Help");
2762 documentation.setLabel("Documentation");
2763 documentation.addActionListener(this);
2765 about.setLabel("About...");
2766 about.addActionListener(this);
2767 seqLimits.setState(true);
2768 seqLimits.setLabel("Show Sequence Limits");
2769 seqLimits.addItemListener(this);
2770 featureSettings.setLabel("Feature Settings...");
2771 featureSettings.addActionListener(this);
2772 sequenceFeatures.setLabel("Sequence Features");
2773 sequenceFeatures.addItemListener(this);
2774 sequenceFeatures.setState(false);
2775 annotationColour.setLabel("by Annotation...");
2776 annotationColour.addActionListener(this);
2777 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
2778 invertColSel.setLabel("Invert Column Selection");
2779 menu1.setLabel("Show");
2780 showColumns.setLabel("All Columns ");
2781 showSeqs.setLabel("All Sequences");
2782 menu2.setLabel("Hide");
2783 hideColumns.setLabel("Selected Columns");
2784 hideSequences.setLabel("Selected Sequences");
2785 invertColSel.addActionListener(this);
2786 showColumns.addActionListener(this);
2787 showSeqs.addActionListener(this);
2788 hideColumns.addActionListener(this);
2789 hideSequences.addActionListener(this);
2790 formatMenu.setLabel("Format");
2791 selectMenu.setLabel("Select");
2792 newView.setLabel("New View");
2793 newView.addActionListener(this);
2794 alignFrameMenuBar.add(fileMenu);
2795 alignFrameMenuBar.add(editMenu);
2796 alignFrameMenuBar.add(selectMenu);
2797 alignFrameMenuBar.add(viewMenu);
2798 alignFrameMenuBar.add(formatMenu);
2799 alignFrameMenuBar.add(colourMenu);
2800 alignFrameMenuBar.add(calculateMenu);
2801 alignFrameMenuBar.add(helpMenu);
2803 fileMenu.add(inputText);
2804 fileMenu.add(loadTree);
2805 fileMenu.add(loadAnnotations);
2807 fileMenu.addSeparator();
2808 fileMenu.add(outputTextboxMenu);
2809 fileMenu.add(outputFeatures);
2810 fileMenu.add(outputAnnotations);
2812 if (jalviewServletURL != null)
2814 fileMenu.add(loadApplication);
2817 fileMenu.addSeparator();
2818 fileMenu.add(closeMenuItem);
2820 editMenu.add(undoMenuItem);
2821 editMenu.add(redoMenuItem);
2824 editMenu.add(pasteMenu);
2825 editMenu.add(delete);
2826 editMenu.addSeparator();
2827 editMenu.add(remove2LeftMenuItem);
2828 editMenu.add(remove2RightMenuItem);
2829 editMenu.add(removeGappedColumnMenuItem);
2830 editMenu.add(removeAllGapsMenuItem);
2831 editMenu.add(removeRedundancyMenuItem);
2832 viewMenu.add(newView);
2833 viewMenu.addSeparator();
2834 viewMenu.add(menu1);
2835 viewMenu.add(menu2);
2836 viewMenu.addSeparator();
2837 viewMenu.add(followMouseOverFlag);
2838 viewMenu.add(annotationPanelMenuItem);
2839 viewMenu.addSeparator();
2840 viewMenu.add(sequenceFeatures);
2841 viewMenu.add(featureSettings);
2842 viewMenu.addSeparator();
2843 viewMenu.add(alProperties);
2844 viewMenu.addSeparator();
2845 viewMenu.add(overviewMenuItem);
2846 colourMenu.add(applyToAllGroups);
2847 colourMenu.addSeparator();
2848 colourMenu.add(noColourmenuItem);
2849 colourMenu.add(clustalColour);
2850 colourMenu.add(BLOSUM62Colour);
2851 colourMenu.add(PIDColour);
2852 colourMenu.add(zappoColour);
2853 colourMenu.add(taylorColour);
2854 colourMenu.add(hydrophobicityColour);
2855 colourMenu.add(helixColour);
2856 colourMenu.add(strandColour);
2857 colourMenu.add(turnColour);
2858 colourMenu.add(buriedColour);
2859 colourMenu.add(nucleotideColour);
2860 colourMenu.add(userDefinedColour);
2861 colourMenu.addSeparator();
2862 colourMenu.add(conservationMenuItem);
2863 colourMenu.add(modifyConservation);
2864 colourMenu.add(abovePIDThreshold);
2865 colourMenu.add(modifyPID);
2866 colourMenu.add(annotationColour);
2867 calculateMenu.add(sort);
2868 calculateMenu.add(calculate);
2869 calculateMenu.addSeparator();
2870 calculateMenu.add(pairwiseAlignmentMenuItem);
2871 calculateMenu.add(PCAMenuItem);
2872 calculateMenu.add(autoCalculate);
2873 this.add(statusBar, BorderLayout.SOUTH);
2874 pasteMenu.add(pasteNew);
2875 pasteMenu.add(pasteThis);
2876 sort.add(sortIDMenuItem);
2877 sort.add(sortByTreeMenu);
2878 sort.add(sortGroupMenuItem);
2879 sort.add(sortPairwiseMenuItem);
2880 calculate.add(averageDistanceTreeMenuItem);
2881 calculate.add(neighbourTreeMenuItem);
2882 calculate.add(avDistanceTreeBlosumMenuItem);
2883 calculate.add(njTreeBlosumMenuItem);
2884 helpMenu.add(documentation);
2885 helpMenu.add(about);
2886 menu1.add(showColumns);
2887 menu1.add(showSeqs);
2888 menu2.add(hideColumns);
2889 menu2.add(hideSequences);
2890 formatMenu.add(font);
2891 formatMenu.add(seqLimits);
2892 formatMenu.add(wrapMenuItem);
2893 formatMenu.add(scaleAbove);
2894 formatMenu.add(scaleLeft);
2895 formatMenu.add(scaleRight);
2896 formatMenu.add(viewBoxesMenuItem);
2897 formatMenu.add(viewTextMenuItem);
2898 formatMenu.add(colourTextMenuItem);
2899 formatMenu.add(displayNonconservedMenuItem);
2900 formatMenu.add(renderGapsMenuItem);
2901 formatMenu.add(centreColumnLabelFlag);
2902 selectMenu.add(findMenuItem);
2903 selectMenu.addSeparator();
2904 selectMenu.add(selectAllSequenceMenuItem);
2905 selectMenu.add(deselectAllSequenceMenuItem);
2906 selectMenu.add(invertSequenceMenuItem);
2907 selectMenu.add(invertColSel);
2908 selectMenu.add(deleteGroups);
2911 MenuItem featureSettings = new MenuItem();
2913 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
2915 MenuItem annotationColour = new MenuItem();
2917 MenuItem invertColSel = new MenuItem();
2919 Menu menu1 = new Menu();
2921 MenuItem showColumns = new MenuItem();
2923 MenuItem showSeqs = new MenuItem();
2925 Menu menu2 = new Menu();
2927 MenuItem hideColumns = new MenuItem();
2929 MenuItem hideSequences = new MenuItem();
2931 Menu formatMenu = new Menu();
2933 Menu selectMenu = new Menu();
2935 MenuItem newView = new MenuItem();
2938 * Attach the alignFrame panels after embedding menus, if necessary. This used
2939 * to be called setEmbedded, but is now creates the dropdown menus in a
2940 * platform independent manner to avoid OSX/Mac menu appendage daftness.
2942 * @param reallyEmbedded
2943 * true to attach the view to the applet area on the page
2944 * rather than in a new window
2946 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
2951 // Explicly build the embedded menu panel for the on-page applet
2953 // view cannot be closed if its actually on the page
2954 fileMenu.remove(closeMenuItem);
2955 fileMenu.remove(3); // Remove Seperator
2956 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
2957 Font.PLAIN, 10, false); // use our own fonts.
2958 // and actually add the components to the applet area
2959 viewport.applet.setLayout(new BorderLayout());
2960 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
2961 viewport.applet.add(statusBar, BorderLayout.SOUTH);
2962 alignPanel.setSize(viewport.applet.getSize().width, viewport.applet
2964 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
2965 viewport.applet.add(alignPanel, BorderLayout.CENTER);
2966 viewport.applet.validate();
2971 // test and embed menu bar if necessary.
2973 if (embedMenuIfNeeded(alignPanel))
2975 // adjust for status bar height too
2976 alignPanel.setSize(getSize().width, getSize().height
2977 - statusBar.HEIGHT);
2979 add(statusBar, BorderLayout.SOUTH);
2980 add(alignPanel, BorderLayout.CENTER);
2981 // and register with the applet so it can pass external API calls to us
2982 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,