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);
72 seqLimits.setState(viewport.showJVSuffix);
76 String param = applet.getParameter("sortBy");
79 if (param.equalsIgnoreCase("Id"))
81 sortIDMenuItem_actionPerformed();
83 else if (param.equalsIgnoreCase("Pairwise Identity"))
85 sortPairwiseMenuItem_actionPerformed();
89 param = applet.getParameter("wrap");
92 if (param.equalsIgnoreCase("true"))
94 wrapMenuItem.setState(true);
95 wrapMenuItem_actionPerformed();
98 param = applet.getParameter("centrecolumnlabels");
101 centreColumnLabelFlag.setState(true);
102 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() == colourTextMenuItem)
482 colourTextMenuItem_actionPerformed();
484 else if (evt.getSource() == wrapMenuItem)
486 wrapMenuItem_actionPerformed();
488 else if (evt.getSource() == scaleAbove)
490 viewport.setScaleAboveWrapped(scaleAbove.getState());
492 else if (evt.getSource() == scaleLeft)
494 viewport.setScaleLeftWrapped(scaleLeft.getState());
496 else if (evt.getSource() == scaleRight)
498 viewport.setScaleRightWrapped(scaleRight.getState());
500 else if (evt.getSource() == seqLimits)
502 seqLimits_itemStateChanged();
504 else if (evt.getSource() == viewBoxesMenuItem)
506 viewport.setShowBoxes(viewBoxesMenuItem.getState());
508 else if (evt.getSource() == viewTextMenuItem)
510 viewport.setShowText(viewTextMenuItem.getState());
512 else if (evt.getSource() == renderGapsMenuItem)
514 viewport.setRenderGaps(renderGapsMenuItem.getState());
516 else if (evt.getSource() == annotationPanelMenuItem)
518 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
519 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
521 else if (evt.getSource() == sequenceFeatures)
523 viewport.showSequenceFeatures(sequenceFeatures.getState());
524 alignPanel.seqPanel.seqCanvas.repaint();
526 else if (evt.getSource() == conservationMenuItem)
528 conservationMenuItem_actionPerformed();
530 else if (evt.getSource() == abovePIDThreshold)
532 abovePIDThreshold_actionPerformed();
534 else if (evt.getSource() == applyToAllGroups)
536 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
538 else if (evt.getSource() == autoCalculate)
540 viewport.autocalculateConsensus = autoCalculate.getState();
542 else if (evt.getSource() == this.centreColumnLabelFlag)
544 centreColumnLabelFlag_stateChanged();
547 alignPanel.paintAlignment(true);
550 private void centreColumnLabelFlag_stateChanged()
552 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
553 this.alignPanel.annotationPanel.repaint();
556 public void actionPerformed(ActionEvent evt)
558 Object source = evt.getSource();
560 if (source == inputText)
562 inputText_actionPerformed();
564 else if (source == loadTree)
566 loadTree_actionPerformed();
568 else if (source == loadApplication)
570 launchFullApplication();
572 else if (source == loadAnnotations)
576 else if (source == outputAnnotations)
578 outputAnnotations(true);
580 else if (source == outputFeatures)
582 outputFeatures(true, "Jalview");
584 else if (source == closeMenuItem)
586 closeMenuItem_actionPerformed();
588 else if (source == copy)
590 copy_actionPerformed();
592 else if (source == undoMenuItem)
594 undoMenuItem_actionPerformed();
596 else if (source == redoMenuItem)
598 redoMenuItem_actionPerformed();
600 else if (source == inputText)
602 inputText_actionPerformed();
604 else if (source == closeMenuItem)
606 closeMenuItem_actionPerformed();
608 else if (source == undoMenuItem)
610 undoMenuItem_actionPerformed();
612 else if (source == redoMenuItem)
614 redoMenuItem_actionPerformed();
616 else if (source == copy)
618 copy_actionPerformed();
620 else if (source == pasteNew)
622 pasteNew_actionPerformed();
624 else if (source == pasteThis)
626 pasteThis_actionPerformed();
628 else if (source == cut)
630 cut_actionPerformed();
632 else if (source == delete)
634 delete_actionPerformed();
636 else if (source == deleteGroups)
638 deleteGroups_actionPerformed();
640 else if (source == selectAllSequenceMenuItem)
642 selectAllSequenceMenuItem_actionPerformed();
644 else if (source == deselectAllSequenceMenuItem)
646 deselectAllSequenceMenuItem_actionPerformed();
648 else if (source == invertSequenceMenuItem)
650 invertSequenceMenuItem_actionPerformed();
652 else if (source == invertColSel)
654 viewport.invertColumnSelection();
655 alignPanel.paintAlignment(true);
657 else if (source == remove2LeftMenuItem)
661 else if (source == remove2RightMenuItem)
663 trimAlignment(false);
665 else if (source == removeGappedColumnMenuItem)
667 removeGappedColumnMenuItem_actionPerformed();
669 else if (source == removeAllGapsMenuItem)
671 removeAllGapsMenuItem_actionPerformed();
673 else if (source == findMenuItem)
675 findMenuItem_actionPerformed();
677 else if (source == font)
679 new FontChooser(alignPanel);
681 else if (source == newView)
685 else if (source == showColumns)
687 viewport.showAllHiddenColumns();
688 alignPanel.paintAlignment(true);
690 else if (source == showSeqs)
692 viewport.showAllHiddenSeqs();
694 else if (source == hideColumns)
696 viewport.hideSelectedColumns();
697 alignPanel.paintAlignment(true);
699 else if (source == hideSequences
700 && viewport.getSelectionGroup() != null)
702 viewport.hideAllSelectedSeqs();
704 else if (source == featureSettings)
706 new FeatureSettings(alignPanel);
708 else if (source == alProperties)
710 StringBuffer contents = new StringBuffer();
713 int min = Integer.MAX_VALUE, max = 0;
714 for (int i = 0; i < viewport.alignment.getHeight(); i++)
716 int size = viewport.alignment.getSequenceAt(i).getEnd()
717 - viewport.alignment.getSequenceAt(i).getStart();
724 avg = avg / (float) viewport.alignment.getHeight();
726 contents.append("\nSequences: " + viewport.alignment.getHeight());
727 contents.append("\nMinimum Sequence Length: " + min);
728 contents.append("\nMaximum Sequence Length: " + max);
729 contents.append("\nAverage Length: " + (int) avg);
731 if (((Alignment) viewport.alignment).alignmentProperties != null)
733 Hashtable props = ((Alignment) viewport.alignment).alignmentProperties;
734 Enumeration en = props.keys();
735 while (en.hasMoreElements())
737 String key = en.nextElement().toString();
738 contents.append("\n" + key + "\t" + props.get(key));
742 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
743 cap.setText(contents.toString());
744 Frame frame = new Frame();
746 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
747 + getTitle(), 400, 250);
749 else if (source == overviewMenuItem)
751 overviewMenuItem_actionPerformed();
753 else if (source == noColourmenuItem)
757 else if (source == clustalColour)
759 abovePIDThreshold.setState(false);
760 changeColour(new ClustalxColourScheme(viewport.alignment
761 .getSequences(), viewport.alignment.getWidth()));
763 else if (source == zappoColour)
765 changeColour(new ZappoColourScheme());
767 else if (source == taylorColour)
769 changeColour(new TaylorColourScheme());
771 else if (source == hydrophobicityColour)
773 changeColour(new HydrophobicColourScheme());
775 else if (source == helixColour)
777 changeColour(new HelixColourScheme());
779 else if (source == strandColour)
781 changeColour(new StrandColourScheme());
783 else if (source == turnColour)
785 changeColour(new TurnColourScheme());
787 else if (source == buriedColour)
789 changeColour(new BuriedColourScheme());
791 else if (source == nucleotideColour)
793 changeColour(new NucleotideColourScheme());
795 else if (source == modifyPID)
797 modifyPID_actionPerformed();
799 else if (source == modifyConservation)
801 modifyConservation_actionPerformed();
803 else if (source == userDefinedColour)
805 new UserDefinedColours(alignPanel, null);
807 else if (source == PIDColour)
809 changeColour(new PIDColourScheme());
811 else if (source == BLOSUM62Colour)
813 changeColour(new Blosum62ColourScheme());
815 else if (source == annotationColour)
817 new AnnotationColourChooser(viewport, alignPanel);
819 else if (source == sortPairwiseMenuItem)
821 sortPairwiseMenuItem_actionPerformed();
823 else if (source == sortIDMenuItem)
825 sortIDMenuItem_actionPerformed();
827 else if (source == sortGroupMenuItem)
829 sortGroupMenuItem_actionPerformed();
831 else if (source == removeRedundancyMenuItem)
833 removeRedundancyMenuItem_actionPerformed();
835 else if (source == pairwiseAlignmentMenuItem)
837 pairwiseAlignmentMenuItem_actionPerformed();
839 else if (source == PCAMenuItem)
841 PCAMenuItem_actionPerformed();
843 else if (source == averageDistanceTreeMenuItem)
845 averageDistanceTreeMenuItem_actionPerformed();
847 else if (source == neighbourTreeMenuItem)
849 neighbourTreeMenuItem_actionPerformed();
851 else if (source == njTreeBlosumMenuItem)
853 njTreeBlosumMenuItem_actionPerformed();
855 else if (source == avDistanceTreeBlosumMenuItem)
857 avTreeBlosumMenuItem_actionPerformed();
859 else if (source == documentation)
861 documentation_actionPerformed();
863 else if (source == about)
865 about_actionPerformed();
870 public void inputText_actionPerformed()
872 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
873 Frame frame = new Frame();
875 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
878 protected void outputText_actionPerformed(ActionEvent e)
880 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
881 Frame frame = new Frame();
883 jalview.bin.JalviewLite.addFrame(frame, "Alignment output - "
884 + e.getActionCommand(), 600, 500);
885 cap.setText(new AppletFormatAdapter().formatSequences(e
886 .getActionCommand(), viewport.getAlignment(),
887 viewport.showJVSuffix));
890 public void loadAnnotations()
892 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
893 cap.setText("Paste your features / annotations file here.");
894 cap.setAnnotationImport();
895 Frame frame = new Frame();
897 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
901 public String outputAnnotations(boolean displayTextbox)
903 String annotation = new AnnotationFile().printAnnotations(
904 viewport.showAnnotation ? viewport.alignment
905 .getAlignmentAnnotation() : null, viewport.alignment
907 ((Alignment) viewport.alignment).alignmentProperties);
911 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
912 Frame frame = new Frame();
914 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
915 cap.setText(annotation);
921 public String outputFeatures(boolean displayTextbox, String format)
924 if (format.equalsIgnoreCase("Jalview"))
926 features = new FeaturesFile().printJalviewFormat(viewport.alignment
927 .getSequencesArray(), viewport.featuresDisplayed);
931 features = new FeaturesFile().printGFFFormat(viewport.alignment
932 .getSequencesArray(), viewport.featuresDisplayed);
937 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
938 Frame frame = new Frame();
940 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
942 cap.setText(features);
948 void launchFullApplication()
950 StringBuffer url = new StringBuffer(jalviewServletURL);
953 + appendProtocol(viewport.applet.getParameter("file")));
955 if (viewport.applet.getParameter("features") != null)
957 url.append("&features=");
958 url.append(appendProtocol(viewport.applet.getParameter("features")));
961 if (viewport.applet.getParameter("annotations") != null)
963 url.append("&annotations=");
965 .append(appendProtocol(viewport.applet
966 .getParameter("annotations")));
969 if (viewport.applet.getParameter("jnetfile") != null)
971 url.append("&annotations=");
972 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
975 if (viewport.applet.getParameter("defaultColour") != null)
977 url.append("&colour="
978 + removeWhiteSpace(viewport.applet
979 .getParameter("defaultColour")));
982 if (viewport.applet.getParameter("userDefinedColour") != null)
984 url.append("&colour="
985 + removeWhiteSpace(viewport.applet
986 .getParameter("userDefinedColour")));
988 if (viewport.applet.getParameter("tree") != null)
991 + appendProtocol(viewport.applet.getParameter("tree")));
993 if (viewport.applet.getParameter("treeFile") != null)
996 + appendProtocol(viewport.applet.getParameter("treeFile")));
999 showURL(url.toString(), "FULL_APP");
1002 String removeWhiteSpace(String colour)
1004 StringBuffer sb = new StringBuffer();
1005 for (int i = 0; i < colour.length(); i++)
1007 if (Character.isWhitespace(colour.charAt(i)))
1013 sb.append(colour.charAt(i));
1017 return sb.toString();
1020 String appendProtocol(String url)
1025 url = URLEncoder.encode(url);
1028 * When we finally deprecate 1.1 compatibility, we can start to use
1029 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1030 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1031 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1032 * ex.printStackTrace(); }
1034 catch (java.net.MalformedURLException ex)
1036 url = viewport.applet.getCodeBase() + url;
1041 public void closeMenuItem_actionPerformed()
1043 PaintRefresher.RemoveComponent(alignPanel);
1044 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1045 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1047 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1058 void updateEditMenuBar()
1061 if (viewport.historyList.size() > 0)
1063 undoMenuItem.setEnabled(true);
1064 CommandI command = (CommandI) viewport.historyList.peek();
1065 undoMenuItem.setLabel("Undo " + command.getDescription());
1069 undoMenuItem.setEnabled(false);
1070 undoMenuItem.setLabel("Undo");
1073 if (viewport.redoList.size() > 0)
1075 redoMenuItem.setEnabled(true);
1077 CommandI command = (CommandI) viewport.redoList.peek();
1078 redoMenuItem.setLabel("Redo " + command.getDescription());
1082 redoMenuItem.setEnabled(false);
1083 redoMenuItem.setLabel("Redo");
1087 public void addHistoryItem(CommandI command)
1089 if (command.getSize() > 0)
1091 viewport.historyList.push(command);
1092 viewport.redoList.removeAllElements();
1093 updateEditMenuBar();
1094 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1104 protected void undoMenuItem_actionPerformed()
1106 if (viewport.historyList.size() < 1)
1111 CommandI command = (CommandI) viewport.historyList.pop();
1112 viewport.redoList.push(command);
1113 command.undoCommand(null);
1115 AlignViewport originalSource = getOriginatingSource(command);
1117 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1118 updateEditMenuBar();
1119 originalSource.firePropertyChange("alignment", null,
1120 originalSource.alignment.getSequences());
1129 protected void redoMenuItem_actionPerformed()
1131 if (viewport.redoList.size() < 1)
1136 CommandI command = (CommandI) viewport.redoList.pop();
1137 viewport.historyList.push(command);
1138 command.doCommand(null);
1140 AlignViewport originalSource = getOriginatingSource(command);
1141 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1143 updateEditMenuBar();
1144 originalSource.firePropertyChange("alignment", null,
1145 originalSource.alignment.getSequences());
1148 AlignViewport getOriginatingSource(CommandI command)
1150 AlignViewport originalSource = null;
1151 // For sequence removal and addition, we need to fire
1152 // the property change event FROM the viewport where the
1153 // original alignment was altered
1154 AlignmentI al = null;
1155 if (command instanceof EditCommand)
1157 EditCommand editCommand = (EditCommand) command;
1158 al = editCommand.getAlignment();
1159 Vector comps = (Vector) PaintRefresher.components.get(viewport
1160 .getSequenceSetId());
1161 for (int i = 0; i < comps.size(); i++)
1163 if (comps.elementAt(i) instanceof AlignmentPanel)
1165 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1167 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1174 if (originalSource == null)
1176 // The original view is closed, we must validate
1177 // the current view against the closed view first
1180 PaintRefresher.validateSequences(al, viewport.alignment);
1183 originalSource = viewport;
1186 return originalSource;
1189 public void moveSelectedSequences(boolean up)
1191 SequenceGroup sg = viewport.getSelectionGroup();
1199 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1201 SequenceI seq = viewport.alignment.getSequenceAt(i);
1202 if (!sg.getSequences(null).contains(seq))
1207 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1208 if (sg.getSequences(null).contains(temp))
1213 viewport.alignment.getSequences().setElementAt(temp, i);
1214 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1219 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1221 SequenceI seq = viewport.alignment.getSequenceAt(i);
1222 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
1227 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1228 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
1233 viewport.alignment.getSequences().setElementAt(temp, i);
1234 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1238 alignPanel.paintAlignment(true);
1241 synchronized void slideSequences(boolean right, int size)
1243 Vector sg = new Vector();
1244 if (viewport.cursorMode)
1246 sg.addElement(viewport.alignment
1247 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1249 else if (viewport.getSelectionGroup() != null
1250 && viewport.getSelectionGroup().getSize() != viewport.alignment
1253 sg = viewport.getSelectionGroup().getSequences(
1254 viewport.hiddenRepSequences);
1262 Vector invertGroup = new Vector();
1264 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1266 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1267 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
1270 SequenceI[] seqs1 = new SequenceI[sg.size()];
1271 for (int i = 0; i < sg.size(); i++)
1272 seqs1[i] = (SequenceI) sg.elementAt(i);
1274 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1275 for (int i = 0; i < invertGroup.size(); i++)
1276 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1278 SlideSequencesCommand ssc;
1280 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1281 size, viewport.getGapCharacter());
1283 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1284 size, viewport.getGapCharacter());
1286 int groupAdjustment = 0;
1287 if (ssc.getGapsInsertedBegin() && right)
1289 if (viewport.cursorMode)
1290 alignPanel.seqPanel.moveCursor(size, 0);
1292 groupAdjustment = size;
1294 else if (!ssc.getGapsInsertedBegin() && !right)
1296 if (viewport.cursorMode)
1297 alignPanel.seqPanel.moveCursor(-size, 0);
1299 groupAdjustment = -size;
1302 if (groupAdjustment != 0)
1304 viewport.getSelectionGroup().setStartRes(
1305 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1306 viewport.getSelectionGroup().setEndRes(
1307 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1310 boolean appendHistoryItem = false;
1311 if (viewport.historyList != null && viewport.historyList.size() > 0
1312 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1314 appendHistoryItem = ssc
1315 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1319 if (!appendHistoryItem)
1320 addHistoryItem(ssc);
1325 static StringBuffer copiedSequences;
1327 static Vector copiedHiddenColumns;
1329 protected void copy_actionPerformed()
1331 if (viewport.getSelectionGroup() == null)
1336 SequenceGroup sg = viewport.getSelectionGroup();
1337 copiedSequences = new StringBuffer();
1338 Hashtable orderedSeqs = new Hashtable();
1339 for (int i = 0; i < sg.getSize(); i++)
1341 SequenceI seq = sg.getSequenceAt(i);
1342 int index = viewport.alignment.findIndex(seq);
1343 orderedSeqs.put(index + "", seq);
1346 int index = 0, startRes, endRes;
1349 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
1351 copiedHiddenColumns = new Vector();
1352 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1353 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1356 int[] region = (int[]) viewport.getColumnSelection()
1357 .getHiddenColumns().elementAt(i);
1359 copiedHiddenColumns.addElement(new int[]
1360 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1365 copiedHiddenColumns = null;
1368 for (int i = 0; i < sg.getSize(); i++)
1370 SequenceI seq = null;
1374 if (orderedSeqs.containsKey(index + ""))
1376 seq = (SequenceI) orderedSeqs.get(index + "");
1388 // Returns residue following index if gap
1389 startRes = seq.findPosition(sg.getStartRes());
1392 // Need to find the residue preceeding index if gap
1395 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1397 ch = seq.getCharAt(j);
1398 if (!jalview.util.Comparison.isGap((ch)))
1406 endRes += seq.getStart() - 1;
1409 copiedSequences.append(seq.getName()
1415 + seq.getSequenceAsString(sg.getStartRes(),
1416 sg.getEndRes() + 1) + "\n");
1421 protected void pasteNew_actionPerformed()
1426 protected void pasteThis_actionPerformed()
1431 void paste(boolean newAlignment)
1436 if (copiedSequences == null)
1441 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1442 Vector seqs = new Vector();
1443 while (st.hasMoreElements())
1445 String name = st.nextToken();
1446 int start = Integer.parseInt(st.nextToken());
1447 int end = Integer.parseInt(st.nextToken());
1448 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1450 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1451 for (int i = 0; i < seqs.size(); i++)
1453 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1458 String newtitle = new String("Copied sequences");
1459 if (getTitle().startsWith("Copied sequences"))
1461 newtitle = getTitle();
1465 newtitle = newtitle.concat("- from " + getTitle());
1467 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1468 viewport.applet, newtitle, false);
1469 if (copiedHiddenColumns != null)
1471 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1473 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1474 af.viewport.hideColumns(region[0], region[1]);
1478 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1483 addSequences(newSeqs);
1486 } catch (Exception ex)
1488 } // could be anything being pasted in here
1492 void addSequences(SequenceI[] seqs)
1494 for (int i = 0; i < seqs.length; i++)
1496 viewport.alignment.addSequence(seqs[i]);
1500 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1501 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
1503 viewport.setEndSeq(viewport.alignment.getHeight());
1504 viewport.alignment.getWidth();
1505 viewport.firePropertyChange("alignment", null, viewport.alignment
1510 protected void cut_actionPerformed()
1512 copy_actionPerformed();
1513 delete_actionPerformed();
1516 protected void delete_actionPerformed()
1519 SequenceGroup sg = viewport.getSelectionGroup();
1525 Vector seqs = new Vector();
1527 for (int i = 0; i < sg.getSize(); i++)
1529 seq = sg.getSequenceAt(i);
1530 seqs.addElement(seq);
1533 // If the cut affects all sequences, remove highlighted columns
1534 if (sg.getSize() == viewport.alignment.getHeight())
1536 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1537 sg.getEndRes() + 1);
1540 SequenceI[] cut = new SequenceI[seqs.size()];
1541 for (int i = 0; i < seqs.size(); i++)
1543 cut[i] = (SequenceI) seqs.elementAt(i);
1547 * //ADD HISTORY ITEM
1549 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1550 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1551 viewport.alignment));
1553 viewport.setSelectionGroup(null);
1554 viewport.alignment.deleteGroup(sg);
1556 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1559 if (viewport.getAlignment().getHeight() < 1)
1561 this.setVisible(false);
1565 protected void deleteGroups_actionPerformed()
1567 viewport.alignment.deleteAllGroups();
1568 viewport.sequenceColours = null;
1569 viewport.setSelectionGroup(null);
1571 alignPanel.paintAlignment(true);
1574 public void selectAllSequenceMenuItem_actionPerformed()
1576 SequenceGroup sg = new SequenceGroup();
1577 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1579 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1581 sg.setEndRes(viewport.alignment.getWidth() - 1);
1582 viewport.setSelectionGroup(sg);
1583 alignPanel.paintAlignment(true);
1584 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1587 public void deselectAllSequenceMenuItem_actionPerformed()
1589 if (viewport.cursorMode)
1591 alignPanel.seqPanel.keyboardNo1 = null;
1592 alignPanel.seqPanel.keyboardNo2 = null;
1594 viewport.setSelectionGroup(null);
1595 viewport.getColumnSelection().clear();
1596 viewport.setSelectionGroup(null);
1597 alignPanel.idPanel.idCanvas.searchResults = null;
1598 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1599 alignPanel.paintAlignment(true);
1600 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1603 public void invertSequenceMenuItem_actionPerformed()
1605 SequenceGroup sg = viewport.getSelectionGroup();
1606 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1608 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1611 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1614 void trimAlignment(boolean trimLeft)
1616 ColumnSelection colSel = viewport.getColumnSelection();
1619 if (colSel.size() > 0)
1623 column = colSel.getMin();
1627 column = colSel.getMax();
1631 if (viewport.getSelectionGroup() != null)
1633 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1634 viewport.hiddenRepSequences);
1638 seqs = viewport.alignment.getSequencesArray();
1641 TrimRegionCommand trimRegion;
1644 trimRegion = new TrimRegionCommand("Remove Left",
1645 TrimRegionCommand.TRIM_LEFT, seqs, column,
1646 viewport.alignment, viewport.colSel,
1647 viewport.selectionGroup);
1648 viewport.setStartRes(0);
1652 trimRegion = new TrimRegionCommand("Remove Right",
1653 TrimRegionCommand.TRIM_RIGHT, seqs, column,
1654 viewport.alignment, viewport.colSel,
1655 viewport.selectionGroup);
1658 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
1660 addHistoryItem(trimRegion);
1662 Vector groups = viewport.alignment.getGroups();
1664 for (int i = 0; i < groups.size(); i++)
1666 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1668 if ((trimLeft && !sg.adjustForRemoveLeft(column))
1669 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1671 viewport.alignment.deleteGroup(sg);
1675 viewport.firePropertyChange("alignment", null, viewport
1676 .getAlignment().getSequences());
1680 public void removeGappedColumnMenuItem_actionPerformed()
1682 int start = 0, end = viewport.alignment.getWidth() - 1;
1685 if (viewport.getSelectionGroup() != null)
1687 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1688 viewport.hiddenRepSequences);
1689 start = viewport.getSelectionGroup().getStartRes();
1690 end = viewport.getSelectionGroup().getEndRes();
1694 seqs = viewport.alignment.getSequencesArray();
1697 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
1698 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
1700 addHistoryItem(removeGapCols);
1702 statusBar.setText("Removed " + removeGapCols.getSize()
1703 + " empty columns.");
1705 // This is to maintain viewport position on first residue
1706 // of first sequence
1707 SequenceI seq = viewport.alignment.getSequenceAt(0);
1708 int startRes = seq.findPosition(viewport.startRes);
1709 // ShiftList shifts;
1710 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1711 // edit.alColumnChanges=shifts.getInverse();
1712 // if (viewport.hasHiddenColumns)
1713 // viewport.getColumnSelection().compensateForEdits(shifts);
1714 viewport.setStartRes(seq.findIndex(startRes) - 1);
1715 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1720 public void removeAllGapsMenuItem_actionPerformed()
1722 int start = 0, end = viewport.alignment.getWidth() - 1;
1725 if (viewport.getSelectionGroup() != null)
1727 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1728 viewport.hiddenRepSequences);
1729 start = viewport.getSelectionGroup().getStartRes();
1730 end = viewport.getSelectionGroup().getEndRes();
1734 seqs = viewport.alignment.getSequencesArray();
1737 // This is to maintain viewport position on first residue
1738 // of first sequence
1739 SequenceI seq = viewport.alignment.getSequenceAt(0);
1740 int startRes = seq.findPosition(viewport.startRes);
1742 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
1743 viewport.alignment));
1745 viewport.setStartRes(seq.findIndex(startRes) - 1);
1747 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1752 public void findMenuItem_actionPerformed()
1754 new Finder(alignPanel);
1758 * create a new view derived from the current view
1761 * @return frame for the new view
1763 public AlignFrame newView(String viewtitle)
1766 if (viewport.hasHiddenRows)
1768 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
1769 .getFullAlignment().getSequencesArray());
1773 newal = new Alignment(viewport.alignment.getSequencesArray());
1776 if (viewport.alignment.getAlignmentAnnotation() != null)
1778 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
1780 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
1783 .addAnnotation(viewport.alignment
1784 .getAlignmentAnnotation()[i]);
1789 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
1791 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
1792 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
1793 PaintRefresher.Register(newaf.alignPanel, newaf.alignPanel.av
1794 .getSequenceSetId());
1796 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
1797 newaf.alignPanel.av.getSequenceSetId());
1798 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
1799 newaf.alignPanel.av.getSequenceSetId());
1801 Vector comps = (Vector) PaintRefresher.components.get(viewport
1802 .getSequenceSetId());
1804 for (int i = 0; i < comps.size(); i++)
1806 if (comps.elementAt(i) instanceof AlignmentPanel)
1812 String title = new String(this.getTitle());
1813 if (viewtitle != null)
1815 title = viewtitle + " ( " + title + ")";
1819 if (title.indexOf("(View") > -1)
1821 title = title.substring(0, title.indexOf("(View"));
1823 title += "(View " + viewSize + ")";
1826 newaf.setTitle(title.toString());
1828 newaf.viewport.historyList = viewport.historyList;
1829 newaf.viewport.redoList = viewport.redoList;
1835 * @return list of feature groups on the view
1837 public String[] getFeatureGroups()
1839 FeatureRenderer fr = null;
1840 if (alignPanel != null
1841 && (fr = alignPanel.getFeatureRenderer()) != null)
1843 return fr.getGroups();
1849 * get sequence feature groups that are hidden or shown
1855 public String[] getFeatureGroupsOfState(boolean visible)
1857 FeatureRenderer fr = null;
1858 if (alignPanel != null
1859 && (fr = alignPanel.getFeatureRenderer()) != null)
1861 return fr.getGroups(visible);
1867 * Change the display state for the given feature groups
1870 * list of group strings
1872 * visible or invisible
1874 public void setFeatureGroupState(String[] groups, boolean state)
1876 FeatureRenderer fr = null;
1877 this.sequenceFeatures.setState(true);
1878 viewport.showSequenceFeatures(true);
1879 if (alignPanel != null
1880 && (fr = alignPanel.getFeatureRenderer()) != null)
1882 fr.setGroupState(groups, state);
1883 alignPanel.seqPanel.seqCanvas.repaint();
1884 if (alignPanel.overviewPanel != null)
1886 alignPanel.overviewPanel.updateOverviewImage();
1891 public void seqLimits_itemStateChanged()
1893 viewport.setShowJVSuffix(seqLimits.getState());
1894 alignPanel.fontChanged();
1895 alignPanel.paintAlignment(true);
1898 protected void colourTextMenuItem_actionPerformed()
1900 viewport.setColourText(colourTextMenuItem.getState());
1901 alignPanel.paintAlignment(true);
1904 protected void wrapMenuItem_actionPerformed()
1906 viewport.setWrapAlignment(wrapMenuItem.getState());
1907 alignPanel.setWrapAlignment(wrapMenuItem.getState());
1908 scaleAbove.setEnabled(wrapMenuItem.getState());
1909 scaleLeft.setEnabled(wrapMenuItem.getState());
1910 scaleRight.setEnabled(wrapMenuItem.getState());
1911 alignPanel.paintAlignment(true);
1914 public void overviewMenuItem_actionPerformed()
1916 if (alignPanel.overviewPanel != null)
1921 Frame frame = new Frame();
1922 OverviewPanel overview = new OverviewPanel(alignPanel);
1923 frame.add(overview);
1924 // +50 must allow for applet frame window
1925 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
1926 overview.getPreferredSize().width,
1927 overview.getPreferredSize().height + 50);
1930 frame.addWindowListener(new WindowAdapter()
1932 public void windowClosing(WindowEvent e)
1934 alignPanel.setOverviewPanel(null);
1938 alignPanel.setOverviewPanel(overview);
1942 void changeColour(ColourSchemeI cs)
1948 if (viewport.getAbovePIDThreshold())
1950 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
1953 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
1955 viewport.setGlobalColourScheme(cs);
1959 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
1962 if (viewport.getConservationSelected())
1965 Alignment al = (Alignment) viewport.alignment;
1966 Conservation c = new Conservation("All",
1967 ResidueProperties.propHash, 3, al.getSequences(), 0, al
1971 c.verdict(false, viewport.ConsPercGaps);
1973 cs.setConservation(c);
1975 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
1981 cs.setConservation(null);
1984 cs.setConsensus(viewport.hconsensus);
1987 viewport.setGlobalColourScheme(cs);
1989 if (viewport.getColourAppliesToAllGroups())
1991 Vector groups = viewport.alignment.getGroups();
1992 for (int i = 0; i < groups.size(); i++)
1994 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2001 if (cs instanceof ClustalxColourScheme)
2003 sg.cs = new ClustalxColourScheme(sg
2004 .getSequences(viewport.hiddenRepSequences), sg.getWidth());
2010 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2011 } catch (Exception ex)
2013 ex.printStackTrace();
2018 if (viewport.getAbovePIDThreshold()
2019 || cs instanceof PIDColourScheme
2020 || cs instanceof Blosum62ColourScheme)
2022 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2023 sg.cs.setConsensus(AAFrequency.calculate(sg
2024 .getSequences(viewport.hiddenRepSequences), 0, sg
2029 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2032 if (viewport.getConservationSelected())
2034 Conservation c = new Conservation("Group",
2035 ResidueProperties.propHash, 3, sg
2036 .getSequences(viewport.hiddenRepSequences), 0,
2037 viewport.alignment.getWidth() - 1);
2039 c.verdict(false, viewport.ConsPercGaps);
2040 sg.cs.setConservation(c);
2044 sg.cs.setConservation(null);
2045 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2051 if (alignPanel.getOverviewPanel() != null)
2053 alignPanel.getOverviewPanel().updateOverviewImage();
2056 jalview.structure.StructureSelectionManager
2057 .getStructureSelectionManager().sequenceColoursChanged(
2060 alignPanel.paintAlignment(true);
2063 protected void modifyPID_actionPerformed()
2065 if (viewport.getAbovePIDThreshold()
2066 && viewport.globalColourScheme != null)
2068 SliderPanel.setPIDSliderSource(alignPanel, viewport
2069 .getGlobalColourScheme(), "Background");
2070 SliderPanel.showPIDSlider();
2074 protected void modifyConservation_actionPerformed()
2076 if (viewport.getConservationSelected()
2077 && viewport.globalColourScheme != null)
2079 SliderPanel.setConservationSlider(alignPanel,
2080 viewport.globalColourScheme, "Background");
2081 SliderPanel.showConservationSlider();
2085 protected void conservationMenuItem_actionPerformed()
2087 viewport.setConservationSelected(conservationMenuItem.getState());
2089 viewport.setAbovePIDThreshold(false);
2090 abovePIDThreshold.setState(false);
2092 changeColour(viewport.getGlobalColourScheme());
2094 modifyConservation_actionPerformed();
2097 public void abovePIDThreshold_actionPerformed()
2099 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2101 conservationMenuItem.setState(false);
2102 viewport.setConservationSelected(false);
2104 changeColour(viewport.getGlobalColourScheme());
2106 modifyPID_actionPerformed();
2109 public void sortPairwiseMenuItem_actionPerformed()
2111 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2112 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2113 .getAlignment().getSequenceAt(0), null);
2114 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2115 viewport.alignment));
2116 alignPanel.paintAlignment(true);
2119 public void sortIDMenuItem_actionPerformed()
2121 // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
2122 // HistoryItem.SORT));
2123 AlignmentSorter.sortByID(viewport.getAlignment());
2124 alignPanel.paintAlignment(true);
2127 public void sortGroupMenuItem_actionPerformed()
2129 // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
2130 // HistoryItem.SORT));
2131 AlignmentSorter.sortByGroup(viewport.getAlignment());
2132 alignPanel.paintAlignment(true);
2136 public void removeRedundancyMenuItem_actionPerformed()
2138 new RedundancyPanel(alignPanel);
2141 public void pairwiseAlignmentMenuItem_actionPerformed()
2143 if (viewport.getSelectionGroup() != null
2144 && viewport.getSelectionGroup().getSize() > 1)
2146 Frame frame = new Frame();
2147 frame.add(new PairwiseAlignPanel(alignPanel));
2148 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
2153 public void PCAMenuItem_actionPerformed()
2155 // are the sequences aligned?
2156 if (!viewport.alignment.isAligned())
2159 int Width = viewport.getAlignment().getWidth();
2161 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2163 current = viewport.getAlignment().getSequenceAt(i);
2165 if (current.getLength() < Width)
2167 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2170 alignPanel.paintAlignment(true);
2173 if ((viewport.getSelectionGroup() != null
2174 && viewport.getSelectionGroup().getSize() < 4 && viewport
2175 .getSelectionGroup().getSize() > 0)
2176 || viewport.getAlignment().getHeight() < 4)
2183 new PCAPanel(viewport);
2184 } catch (java.lang.OutOfMemoryError ex)
2190 public void averageDistanceTreeMenuItem_actionPerformed()
2192 NewTreePanel("AV", "PID", "Average distance tree using PID");
2195 public void neighbourTreeMenuItem_actionPerformed()
2197 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2200 protected void njTreeBlosumMenuItem_actionPerformed()
2202 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2205 protected void avTreeBlosumMenuItem_actionPerformed()
2207 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2210 void NewTreePanel(String type, String pwType, String title)
2212 // are the sequences aligned?
2213 if (!viewport.alignment.isAligned())
2216 int Width = viewport.getAlignment().getWidth();
2218 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2220 current = viewport.getAlignment().getSequenceAt(i);
2222 if (current.getLength() < Width)
2224 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2227 alignPanel.paintAlignment(true);
2231 if ((viewport.getSelectionGroup() != null && viewport
2232 .getSelectionGroup().getSize() > 1)
2233 || (viewport.getSelectionGroup() == null && viewport.alignment
2236 final TreePanel tp = new TreePanel(viewport, type, pwType);
2238 addTreeMenuItem(tp, title);
2240 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2244 void loadTree_actionPerformed()
2246 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2247 cap.setText("Paste your Newick tree file here.");
2248 cap.setTreeImport();
2249 Frame frame = new Frame();
2251 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
2254 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2256 TreePanel tp = new TreePanel(viewport, treeFile, "From File - ", tree);
2257 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2258 addTreeMenuItem(tp, treeFile);
2261 void addTreeMenuItem(final TreePanel treePanel, String title)
2263 final MenuItem item = new MenuItem(title);
2264 sortByTreeMenu.add(item);
2265 item.addActionListener(new java.awt.event.ActionListener()
2267 public void actionPerformed(ActionEvent evt)
2269 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2270 // HistoryItem.SORT));
2271 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel
2273 alignPanel.paintAlignment(true);
2277 treePanel.addWindowListener(new WindowAdapter()
2279 public void windowClosing(WindowEvent e)
2281 sortByTreeMenu.remove(item);
2286 protected void documentation_actionPerformed()
2288 showURL("http://www.jalview.org/help.html", "HELP");
2291 protected void about_actionPerformed()
2294 class AboutPanel extends Canvas
2298 public AboutPanel(String version)
2300 this.version = version;
2303 public void paint(Graphics g)
2305 g.setColor(Color.white);
2306 g.fillRect(0, 0, getSize().width, getSize().height);
2307 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2308 FontMetrics fm = g.getFontMetrics();
2309 int fh = fm.getHeight();
2311 g.setColor(Color.black);
2312 // TODO: update this text for each release or centrally store it for
2313 // lite and application
2314 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2315 g.drawString("JalviewLite - Release " + version, x, y += fh);
2316 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2319 "Authors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,",
2321 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
2324 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
2328 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
2330 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
2333 "\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
2335 g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
2339 String version = "test";
2340 java.net.URL url = getClass().getResource("/.build_properties");
2345 BufferedReader reader = new BufferedReader(new InputStreamReader(
2348 while ((line = reader.readLine()) != null)
2350 if (line.indexOf("VERSION") > -1)
2352 version = line.substring(line.indexOf("=") + 1);
2355 } catch (Exception ex)
2357 ex.printStackTrace();
2361 Frame frame = new Frame();
2362 frame.add(new AboutPanel(version));
2363 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
2367 public void showURL(String url, String target)
2369 if (viewport.applet == null)
2371 System.out.println("Not running as applet - no browser available.");
2377 if (url.indexOf(":")==-1)
2379 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to form valid URL
2380 if (url.indexOf("/")==0)
2382 String codebase = viewport.applet.getCodeBase().toString();
2383 url = codebase.substring(0,codebase.length()-viewport.applet.getCodeBase().getFile().length())+url;
2385 url = viewport.applet.getCodeBase()+url;
2387 System.out.println("Show url (prepended codebase): " + url);
2389 System.out.println("Show url: " + url);
2391 viewport.applet.getAppletContext().showDocument(
2392 new java.net.URL(url), target);
2393 } catch (Exception ex)
2395 ex.printStackTrace();
2400 // ////////////////////////////////////////////////////////////////////////////////
2401 // JBuilder Graphics here
2403 MenuBar alignFrameMenuBar = new MenuBar();
2405 Menu fileMenu = new Menu("File");
2407 MenuItem loadApplication = new MenuItem("View in Full Application");
2409 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
2411 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
2413 MenuItem outputFeatures = new MenuItem("Export Features ...");
2415 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
2417 MenuItem closeMenuItem = new MenuItem("Close");
2419 Menu editMenu = new Menu("Edit");
2421 Menu viewMenu = new Menu("View");
2423 Menu colourMenu = new Menu("Colour");
2425 Menu calculateMenu = new Menu("Calculate");
2427 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
2429 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
2431 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
2433 MenuItem remove2LeftMenuItem = new MenuItem();
2435 MenuItem remove2RightMenuItem = new MenuItem();
2437 MenuItem removeGappedColumnMenuItem = new MenuItem();
2439 MenuItem removeAllGapsMenuItem = new MenuItem();
2441 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2443 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2445 MenuItem sortPairwiseMenuItem = new MenuItem();
2447 MenuItem sortIDMenuItem = new MenuItem();
2449 MenuItem sortGroupMenuItem = new MenuItem();
2451 MenuItem removeRedundancyMenuItem = new MenuItem();
2453 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2455 MenuItem PCAMenuItem = new MenuItem();
2457 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2459 MenuItem neighbourTreeMenuItem = new MenuItem();
2461 BorderLayout borderLayout1 = new BorderLayout();
2463 public Label statusBar = new Label();
2465 Menu outputTextboxMenu = new Menu();
2467 MenuItem clustalColour = new MenuItem();
2469 MenuItem zappoColour = new MenuItem();
2471 MenuItem taylorColour = new MenuItem();
2473 MenuItem hydrophobicityColour = new MenuItem();
2475 MenuItem helixColour = new MenuItem();
2477 MenuItem strandColour = new MenuItem();
2479 MenuItem turnColour = new MenuItem();
2481 MenuItem buriedColour = new MenuItem();
2483 MenuItem userDefinedColour = new MenuItem();
2485 MenuItem PIDColour = new MenuItem();
2487 MenuItem BLOSUM62Colour = new MenuItem();
2489 MenuItem njTreeBlosumMenuItem = new MenuItem();
2491 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2493 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2495 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2497 MenuItem alProperties = new MenuItem("Alignment Properties...");
2499 MenuItem overviewMenuItem = new MenuItem();
2501 MenuItem undoMenuItem = new MenuItem();
2503 MenuItem redoMenuItem = new MenuItem();
2505 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2507 MenuItem noColourmenuItem = new MenuItem();
2509 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2511 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2513 MenuItem findMenuItem = new MenuItem();
2515 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2517 MenuItem nucleotideColour = new MenuItem();
2519 MenuItem deleteGroups = new MenuItem();
2521 MenuItem delete = new MenuItem();
2523 MenuItem copy = new MenuItem();
2525 MenuItem cut = new MenuItem();
2527 Menu pasteMenu = new Menu();
2529 MenuItem pasteNew = new MenuItem();
2531 MenuItem pasteThis = new MenuItem();
2533 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2535 MenuItem font = new MenuItem();
2537 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2539 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2541 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2543 MenuItem modifyPID = new MenuItem();
2545 MenuItem modifyConservation = new MenuItem();
2547 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2548 "Autocalculate Consensus", true);
2550 Menu sortByTreeMenu = new Menu();
2552 Menu sort = new Menu();
2554 Menu calculate = new Menu();
2556 MenuItem inputText = new MenuItem();
2558 Menu helpMenu = new Menu();
2560 MenuItem documentation = new MenuItem();
2562 MenuItem about = new MenuItem();
2564 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2566 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2568 private void jbInit() throws Exception
2571 setMenuBar(alignFrameMenuBar);
2575 // dynamically fill save as menu with available formats
2576 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2579 item = new MenuItem(
2580 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2582 item.addActionListener(new java.awt.event.ActionListener()
2584 public void actionPerformed(ActionEvent e)
2586 outputText_actionPerformed(e);
2590 outputTextboxMenu.add(item);
2592 closeMenuItem.addActionListener(this);
2593 loadApplication.addActionListener(this);
2595 loadTree.addActionListener(this);
2596 loadAnnotations.addActionListener(this);
2597 outputFeatures.addActionListener(this);
2598 outputAnnotations.addActionListener(this);
2599 selectAllSequenceMenuItem.addActionListener(this);
2600 deselectAllSequenceMenuItem.addActionListener(this);
2601 invertSequenceMenuItem.addActionListener(this);
2602 remove2LeftMenuItem.setLabel("Remove Left");
2603 remove2LeftMenuItem.addActionListener(this);
2604 remove2RightMenuItem.setLabel("Remove Right");
2605 remove2RightMenuItem.addActionListener(this);
2606 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2607 removeGappedColumnMenuItem.addActionListener(this);
2608 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2609 removeAllGapsMenuItem.addActionListener(this);
2610 viewBoxesMenuItem.setLabel("Boxes");
2611 viewBoxesMenuItem.setState(true);
2612 viewBoxesMenuItem.addItemListener(this);
2613 viewTextMenuItem.setLabel("Text");
2614 viewTextMenuItem.setState(true);
2615 viewTextMenuItem.addItemListener(this);
2616 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2617 sortPairwiseMenuItem.addActionListener(this);
2618 sortIDMenuItem.setLabel("by ID");
2619 sortIDMenuItem.addActionListener(this);
2620 sortGroupMenuItem.setLabel("by Group");
2621 sortGroupMenuItem.addActionListener(this);
2622 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2623 removeRedundancyMenuItem.addActionListener(this);
2624 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
2625 pairwiseAlignmentMenuItem.addActionListener(this);
2626 PCAMenuItem.setLabel("Principal Component Analysis");
2627 PCAMenuItem.addActionListener(this);
2628 averageDistanceTreeMenuItem
2629 .setLabel("Average Distance Using % Identity");
2630 averageDistanceTreeMenuItem.addActionListener(this);
2631 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
2632 neighbourTreeMenuItem.addActionListener(this);
2633 statusBar.setBackground(Color.white);
2634 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2635 statusBar.setText("Status bar");
2636 outputTextboxMenu.setLabel("Output to Textbox");
2637 clustalColour.setLabel("Clustalx");
2639 clustalColour.addActionListener(this);
2640 zappoColour.setLabel("Zappo");
2641 zappoColour.addActionListener(this);
2642 taylorColour.setLabel("Taylor");
2643 taylorColour.addActionListener(this);
2644 hydrophobicityColour.setLabel("Hydrophobicity");
2645 hydrophobicityColour.addActionListener(this);
2646 helixColour.setLabel("Helix Propensity");
2647 helixColour.addActionListener(this);
2648 strandColour.setLabel("Strand Propensity");
2649 strandColour.addActionListener(this);
2650 turnColour.setLabel("Turn Propensity");
2651 turnColour.addActionListener(this);
2652 buriedColour.setLabel("Buried Index");
2653 buriedColour.addActionListener(this);
2654 userDefinedColour.setLabel("User Defined...");
2655 userDefinedColour.addActionListener(this);
2656 PIDColour.setLabel("Percentage Identity");
2657 PIDColour.addActionListener(this);
2658 BLOSUM62Colour.setLabel("BLOSUM62 Score");
2659 BLOSUM62Colour.addActionListener(this);
2660 avDistanceTreeBlosumMenuItem
2661 .setLabel("Average Distance Using BLOSUM62");
2662 avDistanceTreeBlosumMenuItem.addActionListener(this);
2663 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
2664 njTreeBlosumMenuItem.addActionListener(this);
2665 annotationPanelMenuItem.setLabel("Show Annotations");
2666 annotationPanelMenuItem.addItemListener(this);
2667 colourTextMenuItem.setLabel("Colour Text");
2668 colourTextMenuItem.addItemListener(this);
2669 alProperties.addActionListener(this);
2670 overviewMenuItem.setLabel("Overview Window");
2671 overviewMenuItem.addActionListener(this);
2672 undoMenuItem.setEnabled(false);
2673 undoMenuItem.setLabel("Undo");
2674 undoMenuItem.addActionListener(this);
2675 redoMenuItem.setEnabled(false);
2676 redoMenuItem.setLabel("Redo");
2677 redoMenuItem.addActionListener(this);
2678 conservationMenuItem.setLabel("by Conservation");
2679 conservationMenuItem.addItemListener(this);
2680 noColourmenuItem.setLabel("None");
2681 noColourmenuItem.addActionListener(this);
2682 wrapMenuItem.setLabel("Wrap");
2683 wrapMenuItem.addItemListener(this);
2684 renderGapsMenuItem.setLabel("Show Gaps");
2685 renderGapsMenuItem.setState(true);
2686 renderGapsMenuItem.addItemListener(this);
2687 findMenuItem.setLabel("Find...");
2688 findMenuItem.addActionListener(this);
2689 abovePIDThreshold.setLabel("Above Identity Threshold");
2690 abovePIDThreshold.addItemListener(this);
2691 nucleotideColour.setLabel("Nucleotide");
2692 nucleotideColour.addActionListener(this);
2693 deleteGroups.setLabel("Undefine Groups");
2694 deleteGroups.addActionListener(this);
2695 copy.setLabel("Copy");
2696 copy.addActionListener(this);
2697 cut.setLabel("Cut");
2698 cut.addActionListener(this);
2699 delete.setLabel("Delete");
2700 delete.addActionListener(this);
2701 pasteMenu.setLabel("Paste");
2702 pasteNew.setLabel("To New Alignment");
2703 pasteNew.addActionListener(this);
2704 pasteThis.setLabel("Add To This Alignment");
2705 pasteThis.addActionListener(this);
2706 applyToAllGroups.setLabel("Apply Colour To All Groups");
2707 applyToAllGroups.setState(true);
2708 applyToAllGroups.addItemListener(this);
2709 font.setLabel("Font...");
2710 font.addActionListener(this);
2711 scaleAbove.setLabel("Scale Above");
2712 scaleAbove.setState(true);
2713 scaleAbove.setEnabled(false);
2714 scaleAbove.addItemListener(this);
2715 scaleLeft.setEnabled(false);
2716 scaleLeft.setState(true);
2717 scaleLeft.setLabel("Scale Left");
2718 scaleLeft.addItemListener(this);
2719 scaleRight.setEnabled(false);
2720 scaleRight.setState(true);
2721 scaleRight.setLabel("Scale Right");
2722 scaleRight.addItemListener(this);
2723 modifyPID.setLabel("Modify Identity Threshold...");
2724 modifyPID.addActionListener(this);
2725 modifyConservation.setLabel("Modify Conservation Threshold...");
2726 modifyConservation.addActionListener(this);
2727 sortByTreeMenu.setLabel("By Tree Order");
2728 sort.setLabel("Sort");
2729 calculate.setLabel("Calculate Tree");
2730 autoCalculate.addItemListener(this);
2731 inputText.setLabel("Input from textbox");
2732 inputText.addActionListener(this);
2733 centreColumnLabelFlag.setLabel("Centre column labels");
2734 centreColumnLabelFlag.addItemListener(this);
2736 helpMenu.setLabel("Help");
2737 documentation.setLabel("Documentation");
2738 documentation.addActionListener(this);
2740 about.setLabel("About...");
2741 about.addActionListener(this);
2742 seqLimits.setState(true);
2743 seqLimits.setLabel("Show Sequence Limits");
2744 seqLimits.addItemListener(this);
2745 featureSettings.setLabel("Feature Settings...");
2746 featureSettings.addActionListener(this);
2747 sequenceFeatures.setLabel("Sequence Features");
2748 sequenceFeatures.addItemListener(this);
2749 sequenceFeatures.setState(false);
2750 annotationColour.setLabel("by Annotation...");
2751 annotationColour.addActionListener(this);
2752 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
2753 invertColSel.setLabel("Invert Column Selection");
2754 menu1.setLabel("Show");
2755 showColumns.setLabel("All Columns ");
2756 showSeqs.setLabel("All Sequences");
2757 menu2.setLabel("Hide");
2758 hideColumns.setLabel("Selected Columns");
2759 hideSequences.setLabel("Selected Sequences");
2760 invertColSel.addActionListener(this);
2761 showColumns.addActionListener(this);
2762 showSeqs.addActionListener(this);
2763 hideColumns.addActionListener(this);
2764 hideSequences.addActionListener(this);
2765 formatMenu.setLabel("Format");
2766 selectMenu.setLabel("Select");
2767 newView.setLabel("New View");
2768 newView.addActionListener(this);
2769 alignFrameMenuBar.add(fileMenu);
2770 alignFrameMenuBar.add(editMenu);
2771 alignFrameMenuBar.add(selectMenu);
2772 alignFrameMenuBar.add(viewMenu);
2773 alignFrameMenuBar.add(formatMenu);
2774 alignFrameMenuBar.add(colourMenu);
2775 alignFrameMenuBar.add(calculateMenu);
2776 alignFrameMenuBar.add(helpMenu);
2778 fileMenu.add(inputText);
2779 fileMenu.add(loadTree);
2780 fileMenu.add(loadAnnotations);
2782 fileMenu.addSeparator();
2783 fileMenu.add(outputTextboxMenu);
2784 fileMenu.add(outputFeatures);
2785 fileMenu.add(outputAnnotations);
2787 if (jalviewServletURL != null)
2789 fileMenu.add(loadApplication);
2792 fileMenu.addSeparator();
2793 fileMenu.add(closeMenuItem);
2795 editMenu.add(undoMenuItem);
2796 editMenu.add(redoMenuItem);
2799 editMenu.add(pasteMenu);
2800 editMenu.add(delete);
2801 editMenu.addSeparator();
2802 editMenu.add(remove2LeftMenuItem);
2803 editMenu.add(remove2RightMenuItem);
2804 editMenu.add(removeGappedColumnMenuItem);
2805 editMenu.add(removeAllGapsMenuItem);
2806 editMenu.add(removeRedundancyMenuItem);
2807 viewMenu.add(newView);
2808 viewMenu.addSeparator();
2809 viewMenu.add(menu1);
2810 viewMenu.add(menu2);
2811 viewMenu.addSeparator();
2812 viewMenu.add(annotationPanelMenuItem);
2813 viewMenu.addSeparator();
2814 viewMenu.add(sequenceFeatures);
2815 viewMenu.add(featureSettings);
2816 viewMenu.addSeparator();
2817 viewMenu.add(alProperties);
2818 viewMenu.addSeparator();
2819 viewMenu.add(overviewMenuItem);
2820 colourMenu.add(applyToAllGroups);
2821 colourMenu.addSeparator();
2822 colourMenu.add(noColourmenuItem);
2823 colourMenu.add(clustalColour);
2824 colourMenu.add(BLOSUM62Colour);
2825 colourMenu.add(PIDColour);
2826 colourMenu.add(zappoColour);
2827 colourMenu.add(taylorColour);
2828 colourMenu.add(hydrophobicityColour);
2829 colourMenu.add(helixColour);
2830 colourMenu.add(strandColour);
2831 colourMenu.add(turnColour);
2832 colourMenu.add(buriedColour);
2833 colourMenu.add(nucleotideColour);
2834 colourMenu.add(userDefinedColour);
2835 colourMenu.addSeparator();
2836 colourMenu.add(conservationMenuItem);
2837 colourMenu.add(modifyConservation);
2838 colourMenu.add(abovePIDThreshold);
2839 colourMenu.add(modifyPID);
2840 colourMenu.add(annotationColour);
2841 calculateMenu.add(sort);
2842 calculateMenu.add(calculate);
2843 calculateMenu.addSeparator();
2844 calculateMenu.add(pairwiseAlignmentMenuItem);
2845 calculateMenu.add(PCAMenuItem);
2846 calculateMenu.add(autoCalculate);
2847 this.add(statusBar, BorderLayout.SOUTH);
2848 pasteMenu.add(pasteNew);
2849 pasteMenu.add(pasteThis);
2850 sort.add(sortIDMenuItem);
2851 sort.add(sortByTreeMenu);
2852 sort.add(sortGroupMenuItem);
2853 sort.add(sortPairwiseMenuItem);
2854 calculate.add(averageDistanceTreeMenuItem);
2855 calculate.add(neighbourTreeMenuItem);
2856 calculate.add(avDistanceTreeBlosumMenuItem);
2857 calculate.add(njTreeBlosumMenuItem);
2858 helpMenu.add(documentation);
2859 helpMenu.add(about);
2860 menu1.add(showColumns);
2861 menu1.add(showSeqs);
2862 menu2.add(hideColumns);
2863 menu2.add(hideSequences);
2864 formatMenu.add(font);
2865 formatMenu.add(seqLimits);
2866 formatMenu.add(wrapMenuItem);
2867 formatMenu.add(scaleAbove);
2868 formatMenu.add(scaleLeft);
2869 formatMenu.add(scaleRight);
2870 formatMenu.add(viewBoxesMenuItem);
2871 formatMenu.add(viewTextMenuItem);
2872 formatMenu.add(colourTextMenuItem);
2873 formatMenu.add(renderGapsMenuItem);
2874 formatMenu.add(centreColumnLabelFlag);
2875 selectMenu.add(findMenuItem);
2876 selectMenu.addSeparator();
2877 selectMenu.add(selectAllSequenceMenuItem);
2878 selectMenu.add(deselectAllSequenceMenuItem);
2879 selectMenu.add(invertSequenceMenuItem);
2880 selectMenu.add(invertColSel);
2881 selectMenu.add(deleteGroups);
2884 MenuItem featureSettings = new MenuItem();
2886 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
2888 MenuItem annotationColour = new MenuItem();
2890 MenuItem invertColSel = new MenuItem();
2892 Menu menu1 = new Menu();
2894 MenuItem showColumns = new MenuItem();
2896 MenuItem showSeqs = new MenuItem();
2898 Menu menu2 = new Menu();
2900 MenuItem hideColumns = new MenuItem();
2902 MenuItem hideSequences = new MenuItem();
2904 Menu formatMenu = new Menu();
2906 Menu selectMenu = new Menu();
2908 MenuItem newView = new MenuItem();
2911 * Attach the alignFrame panels after embedding menus, if necessary. This used
2912 * to be called setEmbedded, but is now creates the dropdown menus in a
2913 * platform independent manner to avoid OSX/Mac menu appendage daftness.
2915 * @param reallyEmbedded
2916 * true to attach the view to the applet area on the page
2917 * rather than in a new window
2919 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
2924 // Explicly build the embedded menu panel for the on-page applet
2926 // view cannot be closed if its actually on the page
2927 fileMenu.remove(closeMenuItem);
2928 fileMenu.remove(3); // Remove Seperator
2929 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
2930 Font.PLAIN, 10, false); // use our own fonts.
2931 // and actually add the components to the applet area
2932 viewport.applet.setLayout(new BorderLayout());
2933 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
2934 viewport.applet.add(statusBar, BorderLayout.SOUTH);
2935 alignPanel.setSize(viewport.applet.getSize().width, viewport.applet
2937 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
2938 viewport.applet.add(alignPanel, BorderLayout.CENTER);
2939 viewport.applet.validate();
2944 // test and embed menu bar if necessary.
2946 if (embedMenuIfNeeded(alignPanel))
2948 // adjust for status bar height too
2949 alignPanel.setSize(getSize().width, getSize().height
2950 - statusBar.HEIGHT);
2952 add(statusBar, BorderLayout.SOUTH);
2953 add(alignPanel, BorderLayout.CENTER);
2954 // and register with the applet so it can pass external API calls to us
2955 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,