2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.appletgui;
24 import java.awt.event.*;
26 import jalview.analysis.*;
27 import jalview.api.SequenceStructureBinding;
28 import jalview.bin.JalviewLite;
29 import jalview.commands.*;
30 import jalview.datamodel.*;
32 import jalview.schemes.*;
33 import jalview.structure.StructureSelectionManager;
35 public class AlignFrame extends EmbmenuFrame implements ActionListener,
36 ItemListener, KeyListener
38 public AlignmentPanel alignPanel;
40 public AlignViewport viewport;
42 int DEFAULT_WIDTH = 700;
44 int DEFAULT_HEIGHT = 500;
46 String jalviewServletURL;
48 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
49 String title, boolean embedded)
54 jalviewServletURL = applet.getParameter("APPLICATION_URL");
60 } catch (Exception ex)
65 viewport = new AlignViewport(al, applet);
66 alignPanel = new AlignmentPanel(this, viewport);
68 viewport.updateConservation(alignPanel);
69 viewport.updateConsensus(alignPanel);
71 annotationPanelMenuItem.setState(viewport.showAnnotation);
72 displayNonconservedMenuItem.setState(viewport.getShowunconserved());
73 followMouseOverFlag.setState(viewport.getFollowHighlight());
74 showGroupConsensus.setState(viewport.showGroupConsensus);
75 showGroupConservation.setState(viewport.showGroupConservation);
76 showConsensusHistogram.setState(viewport.showConsensusHistogram);
77 showSequenceLogo.setState(viewport.showSequenceLogo);
79 seqLimits.setState(viewport.showJVSuffix);
83 String param = applet.getParameter("sortBy");
86 if (param.equalsIgnoreCase("Id"))
88 sortIDMenuItem_actionPerformed();
90 else if (param.equalsIgnoreCase("Pairwise Identity"))
92 sortPairwiseMenuItem_actionPerformed();
94 else if (param.equalsIgnoreCase("Length"))
96 sortLengthMenuItem_actionPerformed();
100 param = applet.getParameter("wrap");
103 if (param.equalsIgnoreCase("true"))
105 wrapMenuItem.setState(true);
106 wrapMenuItem_actionPerformed();
109 param = applet.getParameter("centrecolumnlabels");
112 centreColumnLabelFlag.setState(true);
113 centreColumnLabelFlag_stateChanged();
117 param = applet.getParameter("windowWidth");
120 int width = Integer.parseInt(param);
121 DEFAULT_WIDTH = width;
123 param = applet.getParameter("windowHeight");
126 int height = Integer.parseInt(param);
127 DEFAULT_HEIGHT = height;
129 } catch (Exception ex)
135 // Some JVMS send keyevents to Top frame or lowest panel,
136 // Havent worked out why yet. So add to both this frame and seqCanvas for
138 this.addKeyListener(this);
139 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
140 alignPanel.idPanel.idCanvas.addKeyListener(this);
141 alignPanel.scalePanel.addKeyListener(this);
142 alignPanel.annotationPanel.addKeyListener(this);
143 alignPanel.annotationPanelHolder.addKeyListener(this);
144 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
145 alignPanel.alabels.addKeyListener(this);
146 createAlignFrameWindow(embedded, title);
147 alignPanel.validate();
148 alignPanel.paintAlignment(true);
151 public AlignViewport getAlignViewport()
156 public SeqCanvas getSeqcanvas()
158 return alignPanel.seqPanel.seqCanvas;
168 public void parseFeaturesFile(String file, String type)
170 Hashtable featureLinks = new Hashtable();
171 boolean featuresFile = false;
174 featuresFile = new jalview.io.FeaturesFile(file, type)
175 .parse(viewport.alignment,
176 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
177 featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
178 } catch (Exception ex)
180 ex.printStackTrace();
185 if (featureLinks.size() > 0)
187 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
189 viewport.showSequenceFeatures = true;
190 sequenceFeatures.setState(true);
191 if (viewport.featureSettings != null)
193 viewport.featureSettings.refreshTable();
195 alignPanel.paintAlignment(true);
200 public void keyPressed(KeyEvent evt)
202 if (viewport.cursorMode
203 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
204 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
205 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
206 && Character.isDigit(evt.getKeyChar()))
207 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
209 switch (evt.getKeyCode())
211 case 27: // escape key
212 deselectAllSequenceMenuItem_actionPerformed();
215 if (evt.isControlDown() || evt.isMetaDown())
217 cut_actionPerformed();
221 if (viewport.cursorMode && !evt.isControlDown())
223 alignPanel.seqPanel.setCursorColumn();
225 if (evt.isControlDown() || evt.isMetaDown())
227 copy_actionPerformed();
231 if (evt.isControlDown())
233 paste(evt.isShiftDown());
237 if (evt.isControlDown() || evt.isMetaDown())
239 selectAllSequenceMenuItem_actionPerformed();
242 case KeyEvent.VK_DOWN:
243 if (viewport.cursorMode)
245 alignPanel.seqPanel.moveCursor(0, 1);
249 moveSelectedSequences(false);
254 if (viewport.cursorMode)
256 alignPanel.seqPanel.moveCursor(0, -1);
260 moveSelectedSequences(true);
264 case KeyEvent.VK_LEFT:
265 if (evt.isAltDown() || !viewport.cursorMode)
266 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
268 alignPanel.seqPanel.moveCursor(-1, 0);
271 case KeyEvent.VK_RIGHT:
272 if (evt.isAltDown() || !viewport.cursorMode)
273 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
275 alignPanel.seqPanel.moveCursor(1, 0);
278 case KeyEvent.VK_SPACE:
279 if (viewport.cursorMode)
281 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
282 || evt.isShiftDown() || evt.isAltDown());
286 case KeyEvent.VK_DELETE:
287 case KeyEvent.VK_BACK_SPACE:
288 if (viewport.cursorMode)
290 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
291 || evt.isShiftDown() || evt.isAltDown());
295 cut_actionPerformed();
296 alignPanel.seqPanel.seqCanvas.repaint();
301 if (viewport.cursorMode)
303 alignPanel.seqPanel.setCursorRow();
307 if (viewport.cursorMode)
309 alignPanel.seqPanel.setCursorPosition();
313 case KeyEvent.VK_ENTER:
314 case KeyEvent.VK_COMMA:
315 if (viewport.cursorMode)
317 alignPanel.seqPanel.setCursorRowAndColumn();
322 if (viewport.cursorMode)
324 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
328 if (viewport.cursorMode)
330 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
335 viewport.cursorMode = !viewport.cursorMode;
336 statusBar.setText("Keyboard editing mode is "
337 + (viewport.cursorMode ? "on" : "off"));
338 if (viewport.cursorMode)
340 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
341 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
346 if (evt.isControlDown())
348 findMenuItem_actionPerformed();
354 boolean toggleSeqs = !evt.isControlDown();
355 boolean toggleCols = !evt.isShiftDown();
356 toggleHiddenRegions(toggleSeqs, toggleCols);
360 case KeyEvent.VK_PAGE_UP:
361 if (viewport.wrapAlignment)
363 alignPanel.scrollUp(true);
367 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
368 - viewport.endSeq + viewport.startSeq);
372 case KeyEvent.VK_PAGE_DOWN:
373 if (viewport.wrapAlignment)
375 alignPanel.scrollUp(false);
379 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
380 + viewport.endSeq - viewport.startSeq);
385 if (evt.isControlDown())
387 undoMenuItem_actionPerformed();
392 if (evt.isControlDown())
394 redoMenuItem_actionPerformed();
399 if (evt.isControlDown())
406 if (evt.isControlDown())
408 trimAlignment(false);
413 if (evt.isControlDown())
415 if (evt.isShiftDown())
417 this.removeAllGapsMenuItem_actionPerformed();
421 removeGappedColumnMenuItem_actionPerformed();
426 if (evt.isControlDown())
430 invertColSel_actionPerformed();
434 invertSequenceMenuItem_actionPerformed();
440 if (evt.isControlDown())
442 this.deleteGroups_actionPerformed();
447 if (evt.isControlDown())
454 alignPanel.paintAlignment(true);
458 * called by key handler and the hide all/show all menu items
463 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
465 boolean hide = false;
466 SequenceGroup sg = viewport.getSelectionGroup();
467 if (!toggleSeqs && !toggleCols)
469 // Hide everything by the current selection - this is a hack - we do the
470 // invert and then hide
471 // first check that there will be visible columns after the invert.
472 if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
473 .getSelected().size() > 0)
474 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
477 // now invert the sequence set, if required - empty selection implies
478 // that no hiding is required.
481 invertSequenceMenuItem_actionPerformed();
482 sg = viewport.getSelectionGroup();
486 viewport.expandColSelection(sg, true);
487 // finally invert the column selection and get the new sequence
488 // selection and indicate it should be hidden.
489 invertColSel_actionPerformed();
496 if (sg != null && sg.getSize() != viewport.alignment.getHeight())
499 viewport.hideAllSelectedSeqs();
501 else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
503 viewport.showAllHiddenSeqs();
509 if (viewport.colSel.getSelected().size() > 0)
511 viewport.hideSelectedColumns();
514 viewport.selectionGroup = sg;
519 viewport.showAllHiddenColumns();
524 public void keyReleased(KeyEvent evt)
528 public void keyTyped(KeyEvent evt)
532 public void itemStateChanged(ItemEvent evt)
534 if (evt.getSource() == displayNonconservedMenuItem)
536 displayNonconservedMenuItem_actionPerformed();
538 else if (evt.getSource() == colourTextMenuItem)
540 colourTextMenuItem_actionPerformed();
542 else if (evt.getSource() == wrapMenuItem)
544 wrapMenuItem_actionPerformed();
546 else if (evt.getSource() == scaleAbove)
548 viewport.setScaleAboveWrapped(scaleAbove.getState());
550 else if (evt.getSource() == scaleLeft)
552 viewport.setScaleLeftWrapped(scaleLeft.getState());
554 else if (evt.getSource() == scaleRight)
556 viewport.setScaleRightWrapped(scaleRight.getState());
558 else if (evt.getSource() == seqLimits)
560 seqLimits_itemStateChanged();
562 else if (evt.getSource() == viewBoxesMenuItem)
564 viewport.setShowBoxes(viewBoxesMenuItem.getState());
566 else if (evt.getSource() == viewTextMenuItem)
568 viewport.setShowText(viewTextMenuItem.getState());
570 else if (evt.getSource() == renderGapsMenuItem)
572 viewport.setRenderGaps(renderGapsMenuItem.getState());
574 else if (evt.getSource() == annotationPanelMenuItem)
576 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
577 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
579 else if (evt.getSource() == sequenceFeatures)
581 viewport.showSequenceFeatures(sequenceFeatures.getState());
582 alignPanel.seqPanel.seqCanvas.repaint();
584 else if (evt.getSource() == conservationMenuItem)
586 conservationMenuItem_actionPerformed();
588 else if (evt.getSource() == abovePIDThreshold)
590 abovePIDThreshold_actionPerformed();
592 else if (evt.getSource() == applyToAllGroups)
594 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
596 else if (evt.getSource() == autoCalculate)
598 viewport.autocalculateConsensus = autoCalculate.getState();
600 else if (evt.getSource() == this.centreColumnLabelFlag)
602 centreColumnLabelFlag_stateChanged();
604 else if (evt.getSource() == this.followMouseOverFlag)
606 mouseOverFlag_stateChanged();
608 else if (evt.getSource() == showGroupConsensus)
610 showGroupConsensus_actionPerformed();
612 else if (evt.getSource() == showGroupConservation)
614 showGroupConservation_actionPerformed();
616 else if (evt.getSource() == showSequenceLogo)
618 showSequenceLogo_actionPerformed();
620 else if (evt.getSource() == showConsensusHistogram)
622 showConsensusHistogram_actionPerformed();
624 else if (evt.getSource() == applyAutoAnnotationSettings)
626 applyAutoAnnotationSettings_actionPerformed();
628 alignPanel.paintAlignment(true);
631 private void mouseOverFlag_stateChanged()
633 viewport.followHighlight = followMouseOverFlag.getState();
634 // TODO: could kick the scrollTo mechanism to reset view for current
638 private void centreColumnLabelFlag_stateChanged()
640 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
641 this.alignPanel.annotationPanel.repaint();
644 public void actionPerformed(ActionEvent evt)
646 Object source = evt.getSource();
648 if (source == inputText)
650 inputText_actionPerformed();
652 else if (source == loadTree)
654 loadTree_actionPerformed();
656 else if (source == loadApplication)
658 launchFullApplication();
660 else if (source == loadAnnotations)
664 else if (source == outputAnnotations)
666 outputAnnotations(true);
668 else if (source == outputFeatures)
670 outputFeatures(true, "Jalview");
672 else if (source == closeMenuItem)
674 closeMenuItem_actionPerformed();
676 else if (source == copy)
678 copy_actionPerformed();
680 else if (source == undoMenuItem)
682 undoMenuItem_actionPerformed();
684 else if (source == redoMenuItem)
686 redoMenuItem_actionPerformed();
688 else if (source == inputText)
690 inputText_actionPerformed();
692 else if (source == closeMenuItem)
694 closeMenuItem_actionPerformed();
696 else if (source == undoMenuItem)
698 undoMenuItem_actionPerformed();
700 else if (source == redoMenuItem)
702 redoMenuItem_actionPerformed();
704 else if (source == copy)
706 copy_actionPerformed();
708 else if (source == pasteNew)
710 pasteNew_actionPerformed();
712 else if (source == pasteThis)
714 pasteThis_actionPerformed();
716 else if (source == cut)
718 cut_actionPerformed();
720 else if (source == delete)
722 delete_actionPerformed();
724 else if (source == grpsFromSelection)
726 makeGrpsFromSelection_actionPerformed();
728 else if (source == deleteGroups)
730 deleteGroups_actionPerformed();
732 else if (source == selectAllSequenceMenuItem)
734 selectAllSequenceMenuItem_actionPerformed();
736 else if (source == deselectAllSequenceMenuItem)
738 deselectAllSequenceMenuItem_actionPerformed();
740 else if (source == invertSequenceMenuItem)
742 invertSequenceMenuItem_actionPerformed();
744 else if (source == invertColSel)
746 viewport.invertColumnSelection();
747 alignPanel.paintAlignment(true);
749 else if (source == remove2LeftMenuItem)
753 else if (source == remove2RightMenuItem)
755 trimAlignment(false);
757 else if (source == removeGappedColumnMenuItem)
759 removeGappedColumnMenuItem_actionPerformed();
761 else if (source == removeAllGapsMenuItem)
763 removeAllGapsMenuItem_actionPerformed();
765 else if (source == findMenuItem)
767 findMenuItem_actionPerformed();
769 else if (source == font)
771 new FontChooser(alignPanel);
773 else if (source == newView)
777 else if (source == showColumns)
779 viewport.showAllHiddenColumns();
780 alignPanel.paintAlignment(true);
782 else if (source == showSeqs)
784 viewport.showAllHiddenSeqs();
785 alignPanel.paintAlignment(true);
787 else if (source == hideColumns)
789 viewport.hideSelectedColumns();
790 alignPanel.paintAlignment(true);
792 else if (source == hideSequences
793 && viewport.getSelectionGroup() != null)
795 viewport.hideAllSelectedSeqs();
796 alignPanel.paintAlignment(true);
798 else if (source == hideAllButSelection)
800 toggleHiddenRegions(false, false);
801 alignPanel.paintAlignment(true);
803 else if (source == hideAllSelection)
805 SequenceGroup sg = viewport.getSelectionGroup();
806 viewport.expandColSelection(sg, false);
807 viewport.hideAllSelectedSeqs();
808 viewport.hideSelectedColumns();
809 alignPanel.paintAlignment(true);
811 else if (source == showAllHidden)
813 viewport.showAllHiddenColumns();
814 viewport.showAllHiddenSeqs();
815 alignPanel.paintAlignment(true);
817 else if (source == showGroupConsensus)
819 showGroupConsensus_actionPerformed();
821 else if (source == showGroupConservation)
823 showGroupConservation_actionPerformed();
825 else if (source == showSequenceLogo)
827 showSequenceLogo_actionPerformed();
829 else if (source == showConsensusHistogram)
831 showConsensusHistogram_actionPerformed();
833 else if (source == applyAutoAnnotationSettings)
835 applyAutoAnnotationSettings_actionPerformed();
837 else if (source == featureSettings)
839 new FeatureSettings(alignPanel);
841 else if (source == alProperties)
843 StringBuffer contents = new jalview.io.AlignmentProperties(
844 viewport.alignment).formatAsString();
845 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
846 cap.setText(contents.toString());
847 Frame frame = new Frame();
849 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
850 + getTitle(), 400, 250);
852 else if (source == overviewMenuItem)
854 overviewMenuItem_actionPerformed();
856 else if (source == noColourmenuItem)
860 else if (source == clustalColour)
862 abovePIDThreshold.setState(false);
863 changeColour(new ClustalxColourScheme(
864 viewport.alignment.getSequences(),
865 viewport.alignment.getWidth()));
867 else if (source == zappoColour)
869 changeColour(new ZappoColourScheme());
871 else if (source == taylorColour)
873 changeColour(new TaylorColourScheme());
875 else if (source == hydrophobicityColour)
877 changeColour(new HydrophobicColourScheme());
879 else if (source == helixColour)
881 changeColour(new HelixColourScheme());
883 else if (source == strandColour)
885 changeColour(new StrandColourScheme());
887 else if (source == turnColour)
889 changeColour(new TurnColourScheme());
891 else if (source == buriedColour)
893 changeColour(new BuriedColourScheme());
895 else if (source == nucleotideColour)
897 changeColour(new NucleotideColourScheme());
899 else if (source == modifyPID)
901 modifyPID_actionPerformed();
903 else if (source == modifyConservation)
905 modifyConservation_actionPerformed();
907 else if (source == userDefinedColour)
909 new UserDefinedColours(alignPanel, null);
911 else if (source == PIDColour)
913 changeColour(new PIDColourScheme());
915 else if (source == BLOSUM62Colour)
917 changeColour(new Blosum62ColourScheme());
919 else if (source == annotationColour)
921 new AnnotationColourChooser(viewport, alignPanel);
923 else if (source == sortPairwiseMenuItem)
925 sortPairwiseMenuItem_actionPerformed();
927 else if (source == sortIDMenuItem)
929 sortIDMenuItem_actionPerformed();
931 else if (source == sortLengthMenuItem)
933 sortLengthMenuItem_actionPerformed();
935 else if (source == sortGroupMenuItem)
937 sortGroupMenuItem_actionPerformed();
939 else if (source == removeRedundancyMenuItem)
941 removeRedundancyMenuItem_actionPerformed();
943 else if (source == pairwiseAlignmentMenuItem)
945 pairwiseAlignmentMenuItem_actionPerformed();
947 else if (source == PCAMenuItem)
949 PCAMenuItem_actionPerformed();
951 else if (source == averageDistanceTreeMenuItem)
953 averageDistanceTreeMenuItem_actionPerformed();
955 else if (source == neighbourTreeMenuItem)
957 neighbourTreeMenuItem_actionPerformed();
959 else if (source == njTreeBlosumMenuItem)
961 njTreeBlosumMenuItem_actionPerformed();
963 else if (source == avDistanceTreeBlosumMenuItem)
965 avTreeBlosumMenuItem_actionPerformed();
967 else if (source == documentation)
969 documentation_actionPerformed();
971 else if (source == about)
973 about_actionPerformed();
978 public void inputText_actionPerformed()
980 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
981 Frame frame = new Frame();
983 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
986 protected void outputText_actionPerformed(ActionEvent e)
988 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
989 Frame frame = new Frame();
991 jalview.bin.JalviewLite.addFrame(frame,
992 "Alignment output - " + e.getActionCommand(), 600, 500);
993 cap.setText(new AppletFormatAdapter().formatSequences(
994 e.getActionCommand(), viewport.getAlignment(),
995 viewport.showJVSuffix));
998 public void loadAnnotations()
1000 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1001 cap.setText("Paste your features / annotations file here.");
1002 cap.setAnnotationImport();
1003 Frame frame = new Frame();
1005 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
1009 public String outputAnnotations(boolean displayTextbox)
1011 String annotation = new AnnotationFile().printAnnotations(
1012 viewport.showAnnotation ? viewport.alignment
1013 .getAlignmentAnnotation() : null, viewport.alignment
1015 ((Alignment) viewport.alignment).alignmentProperties);
1019 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1020 Frame frame = new Frame();
1022 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
1023 cap.setText(annotation);
1029 private Hashtable getDisplayedFeatureCols()
1031 if (alignPanel.getFeatureRenderer() != null)
1033 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1034 Hashtable fcols = new Hashtable();
1035 Enumeration en = viewport.featuresDisplayed.keys();
1036 while (en.hasMoreElements())
1038 Object col = en.nextElement();
1039 fcols.put(col, fr.featureColours.get(col));
1046 public String outputFeatures(boolean displayTextbox, String format)
1049 if (format.equalsIgnoreCase("Jalview"))
1051 features = new FeaturesFile().printJalviewFormat(
1052 viewport.alignment.getSequencesArray(),
1053 getDisplayedFeatureCols());
1057 features = new FeaturesFile().printGFFFormat(
1058 viewport.alignment.getSequencesArray(),
1059 getDisplayedFeatureCols());
1064 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1065 Frame frame = new Frame();
1067 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
1069 cap.setText(features);
1075 void launchFullApplication()
1077 StringBuffer url = new StringBuffer(jalviewServletURL);
1080 + appendProtocol(viewport.applet.getParameter("file")));
1082 if (viewport.applet.getParameter("features") != null)
1084 url.append("&features=");
1085 url.append(appendProtocol(viewport.applet.getParameter("features")));
1088 if (viewport.applet.getParameter("annotations") != null)
1090 url.append("&annotations=");
1091 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1094 if (viewport.applet.getParameter("jnetfile") != null)
1096 url.append("&annotations=");
1097 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1100 if (viewport.applet.getParameter("defaultColour") != null)
1102 url.append("&colour="
1103 + removeWhiteSpace(viewport.applet
1104 .getParameter("defaultColour")));
1107 if (viewport.applet.getParameter("userDefinedColour") != null)
1109 url.append("&colour="
1110 + removeWhiteSpace(viewport.applet
1111 .getParameter("userDefinedColour")));
1113 if (viewport.applet.getParameter("tree") != null)
1116 + appendProtocol(viewport.applet.getParameter("tree")));
1118 if (viewport.applet.getParameter("treeFile") != null)
1121 + appendProtocol(viewport.applet.getParameter("treeFile")));
1124 showURL(url.toString(), "FULL_APP");
1127 String removeWhiteSpace(String colour)
1129 StringBuffer sb = new StringBuffer();
1130 for (int i = 0; i < colour.length(); i++)
1132 if (Character.isWhitespace(colour.charAt(i)))
1138 sb.append(colour.charAt(i));
1142 return sb.toString();
1145 String appendProtocol(String url)
1150 url = URLEncoder.encode(url);
1153 * When we finally deprecate 1.1 compatibility, we can start to use
1154 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1155 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1156 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1157 * ex.printStackTrace(); }
1159 catch (java.net.MalformedURLException ex)
1161 url = viewport.applet.getCodeBase() + url;
1166 public void closeMenuItem_actionPerformed()
1168 PaintRefresher.RemoveComponent(alignPanel);
1169 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1170 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1172 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1183 void updateEditMenuBar()
1186 if (viewport.historyList.size() > 0)
1188 undoMenuItem.setEnabled(true);
1189 CommandI command = (CommandI) viewport.historyList.peek();
1190 undoMenuItem.setLabel("Undo " + command.getDescription());
1194 undoMenuItem.setEnabled(false);
1195 undoMenuItem.setLabel("Undo");
1198 if (viewport.redoList.size() > 0)
1200 redoMenuItem.setEnabled(true);
1202 CommandI command = (CommandI) viewport.redoList.peek();
1203 redoMenuItem.setLabel("Redo " + command.getDescription());
1207 redoMenuItem.setEnabled(false);
1208 redoMenuItem.setLabel("Redo");
1212 public void addHistoryItem(CommandI command)
1214 if (command.getSize() > 0)
1216 viewport.historyList.push(command);
1217 viewport.redoList.removeAllElements();
1218 updateEditMenuBar();
1219 viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1229 protected void undoMenuItem_actionPerformed()
1231 if (viewport.historyList.size() < 1)
1236 CommandI command = (CommandI) viewport.historyList.pop();
1237 viewport.redoList.push(command);
1238 command.undoCommand(null);
1240 AlignViewport originalSource = getOriginatingSource(command);
1242 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1243 updateEditMenuBar();
1244 originalSource.firePropertyChange("alignment", null,
1245 originalSource.alignment.getSequences());
1254 protected void redoMenuItem_actionPerformed()
1256 if (viewport.redoList.size() < 1)
1261 CommandI command = (CommandI) viewport.redoList.pop();
1262 viewport.historyList.push(command);
1263 command.doCommand(null);
1265 AlignViewport originalSource = getOriginatingSource(command);
1266 originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
1268 updateEditMenuBar();
1269 originalSource.firePropertyChange("alignment", null,
1270 originalSource.alignment.getSequences());
1273 AlignViewport getOriginatingSource(CommandI command)
1275 AlignViewport originalSource = null;
1276 // For sequence removal and addition, we need to fire
1277 // the property change event FROM the viewport where the
1278 // original alignment was altered
1279 AlignmentI al = null;
1280 if (command instanceof EditCommand)
1282 EditCommand editCommand = (EditCommand) command;
1283 al = editCommand.getAlignment();
1284 Vector comps = (Vector) PaintRefresher.components.get(viewport
1285 .getSequenceSetId());
1286 for (int i = 0; i < comps.size(); i++)
1288 if (comps.elementAt(i) instanceof AlignmentPanel)
1290 if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
1292 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1299 if (originalSource == null)
1301 // The original view is closed, we must validate
1302 // the current view against the closed view first
1305 PaintRefresher.validateSequences(al, viewport.alignment);
1308 originalSource = viewport;
1311 return originalSource;
1314 public void moveSelectedSequences(boolean up)
1316 SequenceGroup sg = viewport.getSelectionGroup();
1324 for (int i = 1; i < viewport.alignment.getHeight(); i++)
1326 SequenceI seq = viewport.alignment.getSequenceAt(i);
1327 if (!sg.getSequences(null).contains(seq))
1332 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
1333 if (sg.getSequences(null).contains(temp))
1338 viewport.alignment.getSequences().setElementAt(temp, i);
1339 viewport.alignment.getSequences().setElementAt(seq, i - 1);
1344 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
1346 SequenceI seq = viewport.alignment.getSequenceAt(i);
1347 if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
1352 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
1353 if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
1358 viewport.alignment.getSequences().setElementAt(temp, i);
1359 viewport.alignment.getSequences().setElementAt(seq, i + 1);
1363 alignPanel.paintAlignment(true);
1366 synchronized void slideSequences(boolean right, int size)
1368 Vector sg = new Vector();
1369 if (viewport.cursorMode)
1371 sg.addElement(viewport.alignment
1372 .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1374 else if (viewport.getSelectionGroup() != null
1375 && viewport.getSelectionGroup().getSize() != viewport.alignment
1378 sg = viewport.getSelectionGroup().getSequences(
1379 viewport.hiddenRepSequences);
1387 Vector invertGroup = new Vector();
1389 for (int i = 0; i < viewport.alignment.getHeight(); i++)
1391 if (!sg.contains(viewport.alignment.getSequenceAt(i)))
1392 invertGroup.addElement(viewport.alignment.getSequenceAt(i));
1395 SequenceI[] seqs1 = new SequenceI[sg.size()];
1396 for (int i = 0; i < sg.size(); i++)
1397 seqs1[i] = (SequenceI) sg.elementAt(i);
1399 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1400 for (int i = 0; i < invertGroup.size(); i++)
1401 seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1403 SlideSequencesCommand ssc;
1405 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1406 size, viewport.getGapCharacter());
1408 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1409 size, viewport.getGapCharacter());
1411 int groupAdjustment = 0;
1412 if (ssc.getGapsInsertedBegin() && right)
1414 if (viewport.cursorMode)
1415 alignPanel.seqPanel.moveCursor(size, 0);
1417 groupAdjustment = size;
1419 else if (!ssc.getGapsInsertedBegin() && !right)
1421 if (viewport.cursorMode)
1422 alignPanel.seqPanel.moveCursor(-size, 0);
1424 groupAdjustment = -size;
1427 if (groupAdjustment != 0)
1429 viewport.getSelectionGroup().setStartRes(
1430 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1431 viewport.getSelectionGroup().setEndRes(
1432 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1435 boolean appendHistoryItem = false;
1436 if (viewport.historyList != null && viewport.historyList.size() > 0
1437 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1439 appendHistoryItem = ssc
1440 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1444 if (!appendHistoryItem)
1445 addHistoryItem(ssc);
1450 static StringBuffer copiedSequences;
1452 static Vector copiedHiddenColumns;
1454 protected void copy_actionPerformed()
1456 if (viewport.getSelectionGroup() == null)
1461 SequenceGroup sg = viewport.getSelectionGroup();
1462 copiedSequences = new StringBuffer();
1463 Hashtable orderedSeqs = new Hashtable();
1464 for (int i = 0; i < sg.getSize(); i++)
1466 SequenceI seq = sg.getSequenceAt(i);
1467 int index = viewport.alignment.findIndex(seq);
1468 orderedSeqs.put(index + "", seq);
1471 int index = 0, startRes, endRes;
1474 if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
1476 copiedHiddenColumns = new Vector();
1477 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1478 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1481 int[] region = (int[]) viewport.getColumnSelection()
1482 .getHiddenColumns().elementAt(i);
1484 copiedHiddenColumns.addElement(new int[]
1485 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1490 copiedHiddenColumns = null;
1493 for (int i = 0; i < sg.getSize(); i++)
1495 SequenceI seq = null;
1499 if (orderedSeqs.containsKey(index + ""))
1501 seq = (SequenceI) orderedSeqs.get(index + "");
1513 // Returns residue following index if gap
1514 startRes = seq.findPosition(sg.getStartRes());
1517 // Need to find the residue preceeding index if gap
1520 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1522 ch = seq.getCharAt(j);
1523 if (!jalview.util.Comparison.isGap((ch)))
1531 endRes += seq.getStart() - 1;
1534 copiedSequences.append(seq.getName()
1540 + seq.getSequenceAsString(sg.getStartRes(),
1541 sg.getEndRes() + 1) + "\n");
1546 protected void pasteNew_actionPerformed()
1551 protected void pasteThis_actionPerformed()
1556 void paste(boolean newAlignment)
1561 if (copiedSequences == null)
1566 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1567 Vector seqs = new Vector();
1568 while (st.hasMoreElements())
1570 String name = st.nextToken();
1571 int start = Integer.parseInt(st.nextToken());
1572 int end = Integer.parseInt(st.nextToken());
1573 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1575 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1576 for (int i = 0; i < seqs.size(); i++)
1578 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1583 String newtitle = new String("Copied sequences");
1584 if (getTitle().startsWith("Copied sequences"))
1586 newtitle = getTitle();
1590 newtitle = newtitle.concat("- from " + getTitle());
1592 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1593 viewport.applet, newtitle, false);
1594 if (copiedHiddenColumns != null)
1596 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1598 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1599 af.viewport.hideColumns(region[0], region[1]);
1603 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1608 addSequences(newSeqs);
1611 } catch (Exception ex)
1613 } // could be anything being pasted in here
1617 void addSequences(SequenceI[] seqs)
1619 for (int i = 0; i < seqs.length; i++)
1621 viewport.alignment.addSequence(seqs[i]);
1625 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1626 seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
1628 viewport.setEndSeq(viewport.alignment.getHeight());
1629 viewport.alignment.getWidth();
1630 viewport.firePropertyChange("alignment", null,
1631 viewport.alignment.getSequences());
1635 protected void cut_actionPerformed()
1637 copy_actionPerformed();
1638 delete_actionPerformed();
1641 protected void delete_actionPerformed()
1644 SequenceGroup sg = viewport.getSelectionGroup();
1650 Vector seqs = new Vector();
1652 for (int i = 0; i < sg.getSize(); i++)
1654 seq = sg.getSequenceAt(i);
1655 seqs.addElement(seq);
1658 // If the cut affects all sequences, remove highlighted columns
1659 if (sg.getSize() == viewport.alignment.getHeight())
1661 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1662 sg.getEndRes() + 1);
1665 SequenceI[] cut = new SequenceI[seqs.size()];
1666 for (int i = 0; i < seqs.size(); i++)
1668 cut[i] = (SequenceI) seqs.elementAt(i);
1672 * //ADD HISTORY ITEM
1674 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1675 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1676 viewport.alignment));
1678 viewport.setSelectionGroup(null);
1679 viewport.alignment.deleteGroup(sg);
1681 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1684 if (viewport.getAlignment().getHeight() < 1)
1686 this.setVisible(false);
1688 viewport.sendSelection();
1692 * group consensus toggled
1695 protected void showGroupConsensus_actionPerformed()
1697 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1698 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1703 * group conservation toggled.
1705 protected void showGroupConservation_actionPerformed()
1707 viewport.setShowGroupConservation(showGroupConservation.getState());
1708 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1715 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1716 * .event.ActionEvent)
1718 protected void showConsensusHistogram_actionPerformed()
1720 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1721 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1727 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1728 * .event.ActionEvent)
1730 protected void showSequenceLogo_actionPerformed()
1732 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1733 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1736 protected void applyAutoAnnotationSettings_actionPerformed()
1738 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1741 protected void makeGrpsFromSelection_actionPerformed()
1743 if (viewport.getSelectionGroup() != null)
1745 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
1746 viewport.getSequenceSelection(),
1747 viewport.getAlignmentView(true).getSequenceStrings(
1748 viewport.getGapCharacter()),
1749 viewport.alignment.getGroups());
1750 viewport.alignment.deleteAllGroups();
1751 viewport.sequenceColours = null;
1752 viewport.setSelectionGroup(null);
1753 // set view properties for each group
1754 for (int g = 0; g < gps.length; g++)
1756 // gps[g].setShowunconserved(viewport.getShowUnconserved());
1757 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
1758 viewport.alignment.addGroup(gps[g]);
1759 Color col = new Color((int) (Math.random() * 255),
1760 (int) (Math.random() * 255), (int) (Math.random() * 255));
1761 col = col.brighter();
1762 for (Enumeration sq = gps[g].getSequences(null).elements(); sq
1763 .hasMoreElements(); viewport.setSequenceColour(
1764 (SequenceI) sq.nextElement(), col))
1767 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1768 alignPanel.updateAnnotation();
1769 alignPanel.paintAlignment(true);
1773 protected void deleteGroups_actionPerformed()
1775 viewport.alignment.deleteAllGroups();
1776 viewport.sequenceColours = null;
1777 viewport.setSelectionGroup(null);
1779 alignPanel.paintAlignment(true);
1782 public void selectAllSequenceMenuItem_actionPerformed()
1784 SequenceGroup sg = new SequenceGroup();
1785 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1787 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1789 sg.setEndRes(viewport.alignment.getWidth() - 1);
1790 viewport.setSelectionGroup(sg);
1791 alignPanel.paintAlignment(true);
1792 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1793 viewport.sendSelection();
1796 public void deselectAllSequenceMenuItem_actionPerformed()
1798 if (viewport.cursorMode)
1800 alignPanel.seqPanel.keyboardNo1 = null;
1801 alignPanel.seqPanel.keyboardNo2 = null;
1803 viewport.setSelectionGroup(null);
1804 viewport.getColumnSelection().clear();
1805 viewport.setSelectionGroup(null);
1806 alignPanel.idPanel.idCanvas.searchResults = null;
1807 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1808 alignPanel.paintAlignment(true);
1809 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1810 viewport.sendSelection();
1813 public void invertSequenceMenuItem_actionPerformed()
1815 SequenceGroup sg = viewport.getSelectionGroup();
1816 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1818 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1821 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1822 viewport.sendSelection();
1825 public void invertColSel_actionPerformed()
1827 viewport.invertColumnSelection();
1828 alignPanel.paintAlignment(true);
1829 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1830 viewport.sendSelection();
1833 void trimAlignment(boolean trimLeft)
1835 ColumnSelection colSel = viewport.getColumnSelection();
1838 if (colSel.size() > 0)
1842 column = colSel.getMin();
1846 column = colSel.getMax();
1850 if (viewport.getSelectionGroup() != null)
1852 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1853 viewport.hiddenRepSequences);
1857 seqs = viewport.alignment.getSequencesArray();
1860 TrimRegionCommand trimRegion;
1863 trimRegion = new TrimRegionCommand("Remove Left",
1864 TrimRegionCommand.TRIM_LEFT, seqs, column,
1865 viewport.alignment, viewport.colSel,
1866 viewport.selectionGroup);
1867 viewport.setStartRes(0);
1871 trimRegion = new TrimRegionCommand("Remove Right",
1872 TrimRegionCommand.TRIM_RIGHT, seqs, column,
1873 viewport.alignment, viewport.colSel,
1874 viewport.selectionGroup);
1877 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
1879 addHistoryItem(trimRegion);
1881 Vector groups = viewport.alignment.getGroups();
1883 for (int i = 0; i < groups.size(); i++)
1885 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
1887 if ((trimLeft && !sg.adjustForRemoveLeft(column))
1888 || (!trimLeft && !sg.adjustForRemoveRight(column)))
1890 viewport.alignment.deleteGroup(sg);
1894 viewport.firePropertyChange("alignment", null, viewport
1895 .getAlignment().getSequences());
1899 public void removeGappedColumnMenuItem_actionPerformed()
1901 int start = 0, end = viewport.alignment.getWidth() - 1;
1904 if (viewport.getSelectionGroup() != null)
1906 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1907 viewport.hiddenRepSequences);
1908 start = viewport.getSelectionGroup().getStartRes();
1909 end = viewport.getSelectionGroup().getEndRes();
1913 seqs = viewport.alignment.getSequencesArray();
1916 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
1917 "Remove Gapped Columns", seqs, start, end, viewport.alignment);
1919 addHistoryItem(removeGapCols);
1921 statusBar.setText("Removed " + removeGapCols.getSize()
1922 + " empty columns.");
1924 // This is to maintain viewport position on first residue
1925 // of first sequence
1926 SequenceI seq = viewport.alignment.getSequenceAt(0);
1927 int startRes = seq.findPosition(viewport.startRes);
1928 // ShiftList shifts;
1929 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
1930 // edit.alColumnChanges=shifts.getInverse();
1931 // if (viewport.hasHiddenColumns)
1932 // viewport.getColumnSelection().compensateForEdits(shifts);
1933 viewport.setStartRes(seq.findIndex(startRes) - 1);
1934 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1939 public void removeAllGapsMenuItem_actionPerformed()
1941 int start = 0, end = viewport.alignment.getWidth() - 1;
1944 if (viewport.getSelectionGroup() != null)
1946 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1947 viewport.hiddenRepSequences);
1948 start = viewport.getSelectionGroup().getStartRes();
1949 end = viewport.getSelectionGroup().getEndRes();
1953 seqs = viewport.alignment.getSequencesArray();
1956 // This is to maintain viewport position on first residue
1957 // of first sequence
1958 SequenceI seq = viewport.alignment.getSequenceAt(0);
1959 int startRes = seq.findPosition(viewport.startRes);
1961 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
1962 viewport.alignment));
1964 viewport.setStartRes(seq.findIndex(startRes) - 1);
1966 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1971 public void findMenuItem_actionPerformed()
1973 new Finder(alignPanel);
1977 * create a new view derived from the current view
1980 * @return frame for the new view
1982 public AlignFrame newView(String viewtitle)
1985 if (viewport.hasHiddenRows)
1987 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
1988 .getFullAlignment().getSequencesArray());
1992 newal = new Alignment(viewport.alignment.getSequencesArray());
1995 if (viewport.alignment.getAlignmentAnnotation() != null)
1997 for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
1999 if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
2001 newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
2006 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2008 newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
2009 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2010 PaintRefresher.Register(newaf.alignPanel,
2011 newaf.alignPanel.av.getSequenceSetId());
2013 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2014 newaf.alignPanel.av.getSequenceSetId());
2015 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2016 newaf.alignPanel.av.getSequenceSetId());
2018 Vector comps = (Vector) PaintRefresher.components.get(viewport
2019 .getSequenceSetId());
2021 for (int i = 0; i < comps.size(); i++)
2023 if (comps.elementAt(i) instanceof AlignmentPanel)
2029 String title = new String(this.getTitle());
2030 if (viewtitle != null)
2032 title = viewtitle + " ( " + title + ")";
2036 if (title.indexOf("(View") > -1)
2038 title = title.substring(0, title.indexOf("(View"));
2040 title += "(View " + viewSize + ")";
2043 newaf.setTitle(title.toString());
2045 newaf.viewport.historyList = viewport.historyList;
2046 newaf.viewport.redoList = viewport.redoList;
2052 * @return list of feature groups on the view
2054 public String[] getFeatureGroups()
2056 FeatureRenderer fr = null;
2057 if (alignPanel != null
2058 && (fr = alignPanel.getFeatureRenderer()) != null)
2060 return fr.getGroups();
2066 * get sequence feature groups that are hidden or shown
2072 public String[] getFeatureGroupsOfState(boolean visible)
2074 FeatureRenderer fr = null;
2075 if (alignPanel != null
2076 && (fr = alignPanel.getFeatureRenderer()) != null)
2078 return fr.getGroups(visible);
2084 * Change the display state for the given feature groups
2087 * list of group strings
2089 * visible or invisible
2091 public void setFeatureGroupState(String[] groups, boolean state)
2093 FeatureRenderer fr = null;
2094 this.sequenceFeatures.setState(true);
2095 viewport.showSequenceFeatures(true);
2096 if (alignPanel != null
2097 && (fr = alignPanel.getFeatureRenderer()) != null)
2099 fr.setGroupState(groups, state);
2100 alignPanel.seqPanel.seqCanvas.repaint();
2101 if (alignPanel.overviewPanel != null)
2103 alignPanel.overviewPanel.updateOverviewImage();
2108 public void seqLimits_itemStateChanged()
2110 viewport.setShowJVSuffix(seqLimits.getState());
2111 alignPanel.fontChanged();
2112 alignPanel.paintAlignment(true);
2115 protected void colourTextMenuItem_actionPerformed()
2117 viewport.setColourText(colourTextMenuItem.getState());
2118 alignPanel.paintAlignment(true);
2121 protected void displayNonconservedMenuItem_actionPerformed()
2123 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2124 alignPanel.paintAlignment(true);
2127 protected void wrapMenuItem_actionPerformed()
2129 viewport.setWrapAlignment(wrapMenuItem.getState());
2130 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2131 scaleAbove.setEnabled(wrapMenuItem.getState());
2132 scaleLeft.setEnabled(wrapMenuItem.getState());
2133 scaleRight.setEnabled(wrapMenuItem.getState());
2134 alignPanel.paintAlignment(true);
2137 public void overviewMenuItem_actionPerformed()
2139 if (alignPanel.overviewPanel != null)
2144 Frame frame = new Frame();
2145 OverviewPanel overview = new OverviewPanel(alignPanel);
2146 frame.add(overview);
2147 // +50 must allow for applet frame window
2148 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
2149 overview.getPreferredSize().width,
2150 overview.getPreferredSize().height + 50);
2153 frame.addWindowListener(new WindowAdapter()
2155 public void windowClosing(WindowEvent e)
2157 alignPanel.setOverviewPanel(null);
2161 alignPanel.setOverviewPanel(overview);
2165 void changeColour(ColourSchemeI cs)
2171 if (viewport.getAbovePIDThreshold())
2173 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2176 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2178 viewport.setGlobalColourScheme(cs);
2182 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2185 if (viewport.getConservationSelected())
2188 Alignment al = (Alignment) viewport.alignment;
2189 Conservation c = new Conservation("All",
2190 ResidueProperties.propHash, 3, al.getSequences(), 0,
2194 c.verdict(false, viewport.ConsPercGaps);
2196 cs.setConservation(c);
2198 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2204 cs.setConservation(null);
2207 cs.setConsensus(viewport.hconsensus);
2210 viewport.setGlobalColourScheme(cs);
2212 if (viewport.getColourAppliesToAllGroups())
2214 Vector groups = viewport.alignment.getGroups();
2215 for (int i = 0; i < groups.size(); i++)
2217 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
2224 if (cs instanceof ClustalxColourScheme)
2226 sg.cs = new ClustalxColourScheme(
2227 sg.getSequences(viewport.hiddenRepSequences),
2234 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
2235 } catch (Exception ex)
2237 ex.printStackTrace();
2242 if (viewport.getAbovePIDThreshold()
2243 || cs instanceof PIDColourScheme
2244 || cs instanceof Blosum62ColourScheme)
2246 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2247 sg.cs.setConsensus(AAFrequency.calculate(
2248 sg.getSequences(viewport.hiddenRepSequences), 0,
2253 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2256 if (viewport.getConservationSelected())
2258 Conservation c = new Conservation("Group",
2259 ResidueProperties.propHash, 3,
2260 sg.getSequences(viewport.hiddenRepSequences), 0,
2261 viewport.alignment.getWidth() - 1);
2263 c.verdict(false, viewport.ConsPercGaps);
2264 sg.cs.setConservation(c);
2268 sg.cs.setConservation(null);
2269 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2275 if (alignPanel.getOverviewPanel() != null)
2277 alignPanel.getOverviewPanel().updateOverviewImage();
2280 jalview.structure.StructureSelectionManager
2281 .getStructureSelectionManager().sequenceColoursChanged(
2284 alignPanel.paintAlignment(true);
2287 protected void modifyPID_actionPerformed()
2289 if (viewport.getAbovePIDThreshold()
2290 && viewport.globalColourScheme != null)
2292 SliderPanel.setPIDSliderSource(alignPanel,
2293 viewport.getGlobalColourScheme(), "Background");
2294 SliderPanel.showPIDSlider();
2298 protected void modifyConservation_actionPerformed()
2300 if (viewport.getConservationSelected()
2301 && viewport.globalColourScheme != null)
2303 SliderPanel.setConservationSlider(alignPanel,
2304 viewport.globalColourScheme, "Background");
2305 SliderPanel.showConservationSlider();
2309 protected void conservationMenuItem_actionPerformed()
2311 viewport.setConservationSelected(conservationMenuItem.getState());
2313 viewport.setAbovePIDThreshold(false);
2314 abovePIDThreshold.setState(false);
2316 changeColour(viewport.getGlobalColourScheme());
2318 modifyConservation_actionPerformed();
2321 public void abovePIDThreshold_actionPerformed()
2323 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2325 conservationMenuItem.setState(false);
2326 viewport.setConservationSelected(false);
2328 changeColour(viewport.getGlobalColourScheme());
2330 modifyPID_actionPerformed();
2333 public void sortPairwiseMenuItem_actionPerformed()
2335 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2336 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2337 .getAlignment().getSequenceAt(0), null);
2339 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2340 viewport.alignment));
2341 alignPanel.paintAlignment(true);
2344 public void sortIDMenuItem_actionPerformed()
2346 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2347 AlignmentSorter.sortByID(viewport.getAlignment());
2348 addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
2349 alignPanel.paintAlignment(true);
2352 public void sortLengthMenuItem_actionPerformed()
2354 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2355 AlignmentSorter.sortByLength(viewport.getAlignment());
2356 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2357 viewport.alignment));
2358 alignPanel.paintAlignment(true);
2361 public void sortGroupMenuItem_actionPerformed()
2363 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2364 AlignmentSorter.sortByGroup(viewport.getAlignment());
2365 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2366 viewport.alignment));
2367 alignPanel.paintAlignment(true);
2371 public void removeRedundancyMenuItem_actionPerformed()
2373 new RedundancyPanel(alignPanel);
2376 public void pairwiseAlignmentMenuItem_actionPerformed()
2378 if (viewport.getSelectionGroup() != null
2379 && viewport.getSelectionGroup().getSize() > 1)
2381 Frame frame = new Frame();
2382 frame.add(new PairwiseAlignPanel(alignPanel));
2383 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
2388 public void PCAMenuItem_actionPerformed()
2390 // are the sequences aligned?
2391 if (!viewport.alignment.isAligned(false))
2394 int Width = viewport.getAlignment().getWidth();
2396 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2398 current = viewport.getAlignment().getSequenceAt(i);
2400 if (current.getLength() < Width)
2402 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2405 alignPanel.paintAlignment(true);
2408 if ((viewport.getSelectionGroup() != null
2409 && viewport.getSelectionGroup().getSize() < 4 && viewport
2410 .getSelectionGroup().getSize() > 0)
2411 || viewport.getAlignment().getHeight() < 4)
2418 new PCAPanel(viewport);
2419 } catch (java.lang.OutOfMemoryError ex)
2425 public void averageDistanceTreeMenuItem_actionPerformed()
2427 NewTreePanel("AV", "PID", "Average distance tree using PID");
2430 public void neighbourTreeMenuItem_actionPerformed()
2432 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2435 protected void njTreeBlosumMenuItem_actionPerformed()
2437 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2440 protected void avTreeBlosumMenuItem_actionPerformed()
2442 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2445 void NewTreePanel(String type, String pwType, String title)
2447 // are the sequences aligned?
2448 if (!viewport.alignment.isAligned(false))
2451 int Width = viewport.getAlignment().getWidth();
2453 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2455 current = viewport.getAlignment().getSequenceAt(i);
2457 if (current.getLength() < Width)
2459 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2462 alignPanel.paintAlignment(true);
2466 if ((viewport.getSelectionGroup() != null && viewport
2467 .getSelectionGroup().getSize() > 1)
2468 || (viewport.getSelectionGroup() == null && viewport.alignment
2471 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2473 addTreeMenuItem(tp, title);
2475 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2479 void loadTree_actionPerformed()
2481 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2482 cap.setText("Paste your Newick tree file here.");
2483 cap.setTreeImport();
2484 Frame frame = new Frame();
2486 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
2489 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2491 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
2492 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2493 addTreeMenuItem(tp, treeFile);
2497 * sort the alignment using the given treePanel
2500 * tree used to sort view
2502 * string used for undo event name
2504 public void sortByTree(TreePanel treePanel, String title)
2506 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2508 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2509 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2510 // HistoryItem.SORT));
2511 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
2512 viewport.alignment));
2513 alignPanel.paintAlignment(true);
2517 * Do any automatic reordering of the alignment and add the necessary bits to
2518 * the menu structure for the new tree
2523 protected void addTreeMenuItem(final TreePanel treePanel,
2526 final MenuItem item = new MenuItem(title);
2527 sortByTreeMenu.add(item);
2528 item.addActionListener(new java.awt.event.ActionListener()
2530 public void actionPerformed(ActionEvent evt)
2532 sortByTree(treePanel, title); // treePanel.getTitle());
2536 treePanel.addWindowListener(new WindowAdapter()
2538 public void windowOpened(WindowEvent e)
2540 if (viewport.sortByTree)
2542 sortByTree(treePanel, title);
2544 super.windowOpened(e);
2547 public void windowClosing(WindowEvent e)
2549 sortByTreeMenu.remove(item);
2553 public boolean sortBy(AlignmentOrder alorder, String undoname)
2555 SequenceI[] oldOrder = viewport.getAlignment()
2556 .getSequencesArray();
2557 if (viewport.applet.debug)
2559 System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
2561 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2564 addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
2566 alignPanel.paintAlignment(true);
2569 protected void documentation_actionPerformed()
2571 showURL("http://www.jalview.org/help.html", "HELP");
2574 protected void about_actionPerformed()
2577 class AboutPanel extends Canvas
2583 public AboutPanel(String version, String builddate)
2585 this.version = version;
2586 this.builddate = builddate;
2589 public void paint(Graphics g)
2591 g.setColor(Color.white);
2592 g.fillRect(0, 0, getSize().width, getSize().height);
2593 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2594 FontMetrics fm = g.getFontMetrics();
2595 int fh = fm.getHeight();
2597 g.setColor(Color.black);
2598 // TODO: update this text for each release or centrally store it for
2599 // lite and application
2600 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2601 g.drawString("JalviewLite - Release " + version, x, y += fh);
2602 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2603 g.drawString("Build date: " + builddate, x, y += fh);
2604 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2606 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
2608 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
2610 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
2613 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
2615 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
2617 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
2620 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
2622 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
2627 Frame frame = new Frame();
2628 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2630 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
2634 public void showURL(String url, String target)
2636 if (viewport.applet == null)
2638 System.out.println("Not running as applet - no browser available.");
2644 if (url.indexOf(":") == -1)
2646 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
2648 if (url.indexOf("/") == 0)
2650 String codebase = viewport.applet.getCodeBase().toString();
2651 url = codebase.substring(0, codebase.length()
2652 - viewport.applet.getCodeBase().getFile().length())
2657 url = viewport.applet.getCodeBase() + url;
2659 System.out.println("Show url (prepended codebase): " + url);
2663 System.out.println("Show url: " + url);
2665 if (url.indexOf("javascript:") == 0)
2667 // no target for the javascript context
2668 viewport.applet.getAppletContext().showDocument(
2669 new java.net.URL(url));
2673 viewport.applet.getAppletContext().showDocument(
2674 new java.net.URL(url), target);
2676 } catch (Exception ex)
2678 ex.printStackTrace();
2683 // ////////////////////////////////////////////////////////////////////////////////
2684 // JBuilder Graphics here
2686 MenuBar alignFrameMenuBar = new MenuBar();
2688 Menu fileMenu = new Menu("File");
2690 MenuItem loadApplication = new MenuItem("View in Full Application");
2692 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
2694 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
2696 MenuItem outputFeatures = new MenuItem("Export Features ...");
2698 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
2700 MenuItem closeMenuItem = new MenuItem("Close");
2702 Menu editMenu = new Menu("Edit");
2704 Menu viewMenu = new Menu("View");
2706 Menu colourMenu = new Menu("Colour");
2708 Menu calculateMenu = new Menu("Calculate");
2710 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
2712 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
2714 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
2716 MenuItem remove2LeftMenuItem = new MenuItem();
2718 MenuItem remove2RightMenuItem = new MenuItem();
2720 MenuItem removeGappedColumnMenuItem = new MenuItem();
2722 MenuItem removeAllGapsMenuItem = new MenuItem();
2724 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2726 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2728 MenuItem sortPairwiseMenuItem = new MenuItem();
2730 MenuItem sortIDMenuItem = new MenuItem();
2732 MenuItem sortLengthMenuItem = new MenuItem();
2734 MenuItem sortGroupMenuItem = new MenuItem();
2736 MenuItem removeRedundancyMenuItem = new MenuItem();
2738 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2740 MenuItem PCAMenuItem = new MenuItem();
2742 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2744 MenuItem neighbourTreeMenuItem = new MenuItem();
2746 BorderLayout borderLayout1 = new BorderLayout();
2748 public Label statusBar = new Label();
2750 Menu outputTextboxMenu = new Menu();
2752 MenuItem clustalColour = new MenuItem();
2754 MenuItem zappoColour = new MenuItem();
2756 MenuItem taylorColour = new MenuItem();
2758 MenuItem hydrophobicityColour = new MenuItem();
2760 MenuItem helixColour = new MenuItem();
2762 MenuItem strandColour = new MenuItem();
2764 MenuItem turnColour = new MenuItem();
2766 MenuItem buriedColour = new MenuItem();
2768 MenuItem userDefinedColour = new MenuItem();
2770 MenuItem PIDColour = new MenuItem();
2772 MenuItem BLOSUM62Colour = new MenuItem();
2774 MenuItem njTreeBlosumMenuItem = new MenuItem();
2776 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2778 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2780 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2782 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2784 MenuItem alProperties = new MenuItem("Alignment Properties...");
2786 MenuItem overviewMenuItem = new MenuItem();
2788 MenuItem undoMenuItem = new MenuItem();
2790 MenuItem redoMenuItem = new MenuItem();
2792 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2794 MenuItem noColourmenuItem = new MenuItem();
2796 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2798 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2800 MenuItem findMenuItem = new MenuItem();
2802 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2804 MenuItem nucleotideColour = new MenuItem();
2806 MenuItem deleteGroups = new MenuItem();
2808 MenuItem grpsFromSelection = new MenuItem();
2810 MenuItem delete = new MenuItem();
2812 MenuItem copy = new MenuItem();
2814 MenuItem cut = new MenuItem();
2816 Menu pasteMenu = new Menu();
2818 MenuItem pasteNew = new MenuItem();
2820 MenuItem pasteThis = new MenuItem();
2822 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2824 MenuItem font = new MenuItem();
2826 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2828 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2830 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2832 MenuItem modifyPID = new MenuItem();
2834 MenuItem modifyConservation = new MenuItem();
2836 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2837 "Autocalculate Consensus", true);
2839 Menu sortByTreeMenu = new Menu();
2841 Menu sort = new Menu();
2843 Menu calculate = new Menu();
2845 MenuItem inputText = new MenuItem();
2847 Menu helpMenu = new Menu();
2849 MenuItem documentation = new MenuItem();
2851 MenuItem about = new MenuItem();
2853 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2855 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2857 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2858 Menu autoAnnMenu=new Menu();
2859 CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
2860 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2861 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2862 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2863 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2865 private void jbInit() throws Exception
2868 setMenuBar(alignFrameMenuBar);
2872 // dynamically fill save as menu with available formats
2873 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2876 item = new MenuItem(
2877 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2879 item.addActionListener(new java.awt.event.ActionListener()
2881 public void actionPerformed(ActionEvent e)
2883 outputText_actionPerformed(e);
2887 outputTextboxMenu.add(item);
2889 closeMenuItem.addActionListener(this);
2890 loadApplication.addActionListener(this);
2892 loadTree.addActionListener(this);
2893 loadAnnotations.addActionListener(this);
2894 outputFeatures.addActionListener(this);
2895 outputAnnotations.addActionListener(this);
2896 selectAllSequenceMenuItem.addActionListener(this);
2897 deselectAllSequenceMenuItem.addActionListener(this);
2898 invertSequenceMenuItem.addActionListener(this);
2899 remove2LeftMenuItem.setLabel("Remove Left");
2900 remove2LeftMenuItem.addActionListener(this);
2901 remove2RightMenuItem.setLabel("Remove Right");
2902 remove2RightMenuItem.addActionListener(this);
2903 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2904 removeGappedColumnMenuItem.addActionListener(this);
2905 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2906 removeAllGapsMenuItem.addActionListener(this);
2907 viewBoxesMenuItem.setLabel("Boxes");
2908 viewBoxesMenuItem.setState(true);
2909 viewBoxesMenuItem.addItemListener(this);
2910 viewTextMenuItem.setLabel("Text");
2911 viewTextMenuItem.setState(true);
2912 viewTextMenuItem.addItemListener(this);
2913 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2914 sortPairwiseMenuItem.addActionListener(this);
2915 sortIDMenuItem.setLabel("by ID");
2916 sortIDMenuItem.addActionListener(this);
2917 sortLengthMenuItem.setLabel("by Length");
2918 sortLengthMenuItem.addActionListener(this);
2919 sortGroupMenuItem.setLabel("by Group");
2920 sortGroupMenuItem.addActionListener(this);
2921 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2922 removeRedundancyMenuItem.addActionListener(this);
2923 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
2924 pairwiseAlignmentMenuItem.addActionListener(this);
2925 PCAMenuItem.setLabel("Principal Component Analysis");
2926 PCAMenuItem.addActionListener(this);
2927 averageDistanceTreeMenuItem
2928 .setLabel("Average Distance Using % Identity");
2929 averageDistanceTreeMenuItem.addActionListener(this);
2930 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
2931 neighbourTreeMenuItem.addActionListener(this);
2932 statusBar.setBackground(Color.white);
2933 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2934 statusBar.setText("Status bar");
2935 outputTextboxMenu.setLabel("Output to Textbox");
2936 clustalColour.setLabel("Clustalx");
2938 clustalColour.addActionListener(this);
2939 zappoColour.setLabel("Zappo");
2940 zappoColour.addActionListener(this);
2941 taylorColour.setLabel("Taylor");
2942 taylorColour.addActionListener(this);
2943 hydrophobicityColour.setLabel("Hydrophobicity");
2944 hydrophobicityColour.addActionListener(this);
2945 helixColour.setLabel("Helix Propensity");
2946 helixColour.addActionListener(this);
2947 strandColour.setLabel("Strand Propensity");
2948 strandColour.addActionListener(this);
2949 turnColour.setLabel("Turn Propensity");
2950 turnColour.addActionListener(this);
2951 buriedColour.setLabel("Buried Index");
2952 buriedColour.addActionListener(this);
2953 userDefinedColour.setLabel("User Defined...");
2954 userDefinedColour.addActionListener(this);
2955 PIDColour.setLabel("Percentage Identity");
2956 PIDColour.addActionListener(this);
2957 BLOSUM62Colour.setLabel("BLOSUM62 Score");
2958 BLOSUM62Colour.addActionListener(this);
2959 avDistanceTreeBlosumMenuItem
2960 .setLabel("Average Distance Using BLOSUM62");
2961 avDistanceTreeBlosumMenuItem.addActionListener(this);
2962 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
2963 njTreeBlosumMenuItem.addActionListener(this);
2964 annotationPanelMenuItem.setLabel("Show Annotations");
2965 annotationPanelMenuItem.addItemListener(this);
2966 colourTextMenuItem.setLabel("Colour Text");
2967 colourTextMenuItem.addItemListener(this);
2968 displayNonconservedMenuItem.setLabel("Show nonconserved");
2969 displayNonconservedMenuItem.addItemListener(this);
2970 alProperties.addActionListener(this);
2971 overviewMenuItem.setLabel("Overview Window");
2972 overviewMenuItem.addActionListener(this);
2973 undoMenuItem.setEnabled(false);
2974 undoMenuItem.setLabel("Undo");
2975 undoMenuItem.addActionListener(this);
2976 redoMenuItem.setEnabled(false);
2977 redoMenuItem.setLabel("Redo");
2978 redoMenuItem.addActionListener(this);
2979 conservationMenuItem.setLabel("by Conservation");
2980 conservationMenuItem.addItemListener(this);
2981 noColourmenuItem.setLabel("None");
2982 noColourmenuItem.addActionListener(this);
2983 wrapMenuItem.setLabel("Wrap");
2984 wrapMenuItem.addItemListener(this);
2985 renderGapsMenuItem.setLabel("Show Gaps");
2986 renderGapsMenuItem.setState(true);
2987 renderGapsMenuItem.addItemListener(this);
2988 findMenuItem.setLabel("Find...");
2989 findMenuItem.addActionListener(this);
2990 abovePIDThreshold.setLabel("Above Identity Threshold");
2991 abovePIDThreshold.addItemListener(this);
2992 nucleotideColour.setLabel("Nucleotide");
2993 nucleotideColour.addActionListener(this);
2994 deleteGroups.setLabel("Undefine Groups");
2995 deleteGroups.addActionListener(this);
2996 grpsFromSelection.setLabel("Make Groups for selection");
2997 grpsFromSelection.addActionListener(this);
2998 copy.setLabel("Copy");
2999 copy.addActionListener(this);
3000 cut.setLabel("Cut");
3001 cut.addActionListener(this);
3002 delete.setLabel("Delete");
3003 delete.addActionListener(this);
3004 pasteMenu.setLabel("Paste");
3005 pasteNew.setLabel("To New Alignment");
3006 pasteNew.addActionListener(this);
3007 pasteThis.setLabel("Add To This Alignment");
3008 pasteThis.addActionListener(this);
3009 applyToAllGroups.setLabel("Apply Colour To All Groups");
3010 applyToAllGroups.setState(true);
3011 applyToAllGroups.addItemListener(this);
3012 font.setLabel("Font...");
3013 font.addActionListener(this);
3014 scaleAbove.setLabel("Scale Above");
3015 scaleAbove.setState(true);
3016 scaleAbove.setEnabled(false);
3017 scaleAbove.addItemListener(this);
3018 scaleLeft.setEnabled(false);
3019 scaleLeft.setState(true);
3020 scaleLeft.setLabel("Scale Left");
3021 scaleLeft.addItemListener(this);
3022 scaleRight.setEnabled(false);
3023 scaleRight.setState(true);
3024 scaleRight.setLabel("Scale Right");
3025 scaleRight.addItemListener(this);
3026 modifyPID.setLabel("Modify Identity Threshold...");
3027 modifyPID.addActionListener(this);
3028 modifyConservation.setLabel("Modify Conservation Threshold...");
3029 modifyConservation.addActionListener(this);
3030 sortByTreeMenu.setLabel("By Tree Order");
3031 sort.setLabel("Sort");
3032 calculate.setLabel("Calculate Tree");
3033 autoCalculate.addItemListener(this);
3034 inputText.setLabel("Input from textbox");
3035 inputText.addActionListener(this);
3036 centreColumnLabelFlag.setLabel("Centre column labels");
3037 centreColumnLabelFlag.addItemListener(this);
3038 followMouseOverFlag.setLabel("Automatic Scrolling");
3039 followMouseOverFlag.addItemListener(this);
3040 helpMenu.setLabel("Help");
3041 documentation.setLabel("Documentation");
3042 documentation.addActionListener(this);
3044 about.setLabel("About...");
3045 about.addActionListener(this);
3046 seqLimits.setState(true);
3047 seqLimits.setLabel("Show Sequence Limits");
3048 seqLimits.addItemListener(this);
3049 featureSettings.setLabel("Feature Settings...");
3050 featureSettings.addActionListener(this);
3051 sequenceFeatures.setLabel("Sequence Features");
3052 sequenceFeatures.addItemListener(this);
3053 sequenceFeatures.setState(false);
3054 annotationColour.setLabel("by Annotation...");
3055 annotationColour.addActionListener(this);
3056 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
3057 invertColSel.setLabel("Invert Column Selection");
3058 menu1.setLabel("Show");
3059 showColumns.setLabel("All Columns ");
3060 showSeqs.setLabel("All Sequences");
3061 menu2.setLabel("Hide");
3062 hideColumns.setLabel("Selected Columns");
3063 hideSequences.setLabel("Selected Sequences");
3064 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
3065 hideAllSelection.setLabel("Selected Region");
3066 showAllHidden.setLabel("All Sequences and Columns");
3067 showGroupConsensus.setLabel("Group Consensus");
3068 showGroupConservation.setLabel("Group Conservation");
3069 showConsensusHistogram.setLabel("Show Consensus Histogram");
3070 showSequenceLogo.setLabel("Show Consensus Logo");
3071 applyAutoAnnotationSettings.setLabel("Apply to all groups");
3072 applyAutoAnnotationSettings.setState(true);
3073 autoAnnMenu.setLabel("Autocalculated Annotation");
3075 invertColSel.addActionListener(this);
3076 showColumns.addActionListener(this);
3077 showSeqs.addActionListener(this);
3078 hideColumns.addActionListener(this);
3079 hideSequences.addActionListener(this);
3080 hideAllButSelection.addActionListener(this);
3081 hideAllSelection.addActionListener(this);
3082 showAllHidden.addActionListener(this);
3083 showGroupConsensus.addItemListener(this);
3084 showGroupConservation.addItemListener(this);
3085 showConsensusHistogram.addItemListener(this);
3086 showSequenceLogo.addItemListener(this);
3087 applyAutoAnnotationSettings.addItemListener(this);
3088 formatMenu.setLabel("Format");
3089 selectMenu.setLabel("Select");
3090 newView.setLabel("New View");
3091 newView.addActionListener(this);
3092 alignFrameMenuBar.add(fileMenu);
3093 alignFrameMenuBar.add(editMenu);
3094 alignFrameMenuBar.add(selectMenu);
3095 alignFrameMenuBar.add(viewMenu);
3096 alignFrameMenuBar.add(formatMenu);
3097 alignFrameMenuBar.add(colourMenu);
3098 alignFrameMenuBar.add(calculateMenu);
3099 alignFrameMenuBar.add(helpMenu);
3101 fileMenu.add(inputText);
3102 fileMenu.add(loadTree);
3103 fileMenu.add(loadAnnotations);
3105 fileMenu.addSeparator();
3106 fileMenu.add(outputTextboxMenu);
3107 fileMenu.add(outputFeatures);
3108 fileMenu.add(outputAnnotations);
3110 if (jalviewServletURL != null)
3112 fileMenu.add(loadApplication);
3115 fileMenu.addSeparator();
3116 fileMenu.add(closeMenuItem);
3118 editMenu.add(undoMenuItem);
3119 editMenu.add(redoMenuItem);
3122 editMenu.add(pasteMenu);
3123 editMenu.add(delete);
3124 editMenu.addSeparator();
3125 editMenu.add(remove2LeftMenuItem);
3126 editMenu.add(remove2RightMenuItem);
3127 editMenu.add(removeGappedColumnMenuItem);
3128 editMenu.add(removeAllGapsMenuItem);
3129 editMenu.add(removeRedundancyMenuItem);
3130 viewMenu.add(newView);
3131 viewMenu.addSeparator();
3132 viewMenu.add(menu1);
3133 viewMenu.add(menu2);
3134 viewMenu.addSeparator();
3135 viewMenu.add(followMouseOverFlag);
3136 viewMenu.add(annotationPanelMenuItem);
3137 autoAnnMenu.add(applyAutoAnnotationSettings);
3138 autoAnnMenu.add(showConsensusHistogram);
3139 autoAnnMenu.add(showSequenceLogo);
3140 autoAnnMenu.addSeparator();
3141 autoAnnMenu.add(showGroupConservation);
3142 autoAnnMenu.add(showGroupConsensus);
3143 viewMenu.add(autoAnnMenu);
3144 viewMenu.addSeparator();
3145 viewMenu.add(sequenceFeatures);
3146 viewMenu.add(featureSettings);
3147 viewMenu.addSeparator();
3148 viewMenu.add(alProperties);
3149 viewMenu.addSeparator();
3150 viewMenu.add(overviewMenuItem);
3151 colourMenu.add(applyToAllGroups);
3152 colourMenu.addSeparator();
3153 colourMenu.add(noColourmenuItem);
3154 colourMenu.add(clustalColour);
3155 colourMenu.add(BLOSUM62Colour);
3156 colourMenu.add(PIDColour);
3157 colourMenu.add(zappoColour);
3158 colourMenu.add(taylorColour);
3159 colourMenu.add(hydrophobicityColour);
3160 colourMenu.add(helixColour);
3161 colourMenu.add(strandColour);
3162 colourMenu.add(turnColour);
3163 colourMenu.add(buriedColour);
3164 colourMenu.add(nucleotideColour);
3165 colourMenu.add(userDefinedColour);
3166 colourMenu.addSeparator();
3167 colourMenu.add(conservationMenuItem);
3168 colourMenu.add(modifyConservation);
3169 colourMenu.add(abovePIDThreshold);
3170 colourMenu.add(modifyPID);
3171 colourMenu.add(annotationColour);
3172 calculateMenu.add(sort);
3173 calculateMenu.add(calculate);
3174 calculateMenu.addSeparator();
3175 calculateMenu.add(pairwiseAlignmentMenuItem);
3176 calculateMenu.add(PCAMenuItem);
3177 calculateMenu.add(autoCalculate);
3178 this.add(statusBar, BorderLayout.SOUTH);
3179 pasteMenu.add(pasteNew);
3180 pasteMenu.add(pasteThis);
3181 sort.add(sortIDMenuItem);
3182 sort.add(sortLengthMenuItem);
3183 sort.add(sortByTreeMenu);
3184 sort.add(sortGroupMenuItem);
3185 sort.add(sortPairwiseMenuItem);
3186 calculate.add(averageDistanceTreeMenuItem);
3187 calculate.add(neighbourTreeMenuItem);
3188 calculate.add(avDistanceTreeBlosumMenuItem);
3189 calculate.add(njTreeBlosumMenuItem);
3190 helpMenu.add(documentation);
3191 helpMenu.add(about);
3192 menu1.add(showColumns);
3193 menu1.add(showSeqs);
3194 menu1.add(showAllHidden);
3195 menu2.add(hideColumns);
3196 menu2.add(hideSequences);
3197 menu2.add(hideAllSelection);
3198 menu2.add(hideAllButSelection);
3199 formatMenu.add(font);
3200 formatMenu.add(seqLimits);
3201 formatMenu.add(wrapMenuItem);
3202 formatMenu.add(scaleAbove);
3203 formatMenu.add(scaleLeft);
3204 formatMenu.add(scaleRight);
3205 formatMenu.add(viewBoxesMenuItem);
3206 formatMenu.add(viewTextMenuItem);
3207 formatMenu.add(colourTextMenuItem);
3208 formatMenu.add(displayNonconservedMenuItem);
3209 formatMenu.add(renderGapsMenuItem);
3210 formatMenu.add(centreColumnLabelFlag);
3211 selectMenu.add(findMenuItem);
3212 selectMenu.addSeparator();
3213 selectMenu.add(selectAllSequenceMenuItem);
3214 selectMenu.add(deselectAllSequenceMenuItem);
3215 selectMenu.add(invertSequenceMenuItem);
3216 selectMenu.add(invertColSel);
3217 selectMenu.add(grpsFromSelection);
3218 selectMenu.add(deleteGroups);
3222 MenuItem featureSettings = new MenuItem();
3224 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3226 MenuItem annotationColour = new MenuItem();
3228 MenuItem invertColSel = new MenuItem();
3230 Menu menu1 = new Menu();
3232 MenuItem showColumns = new MenuItem();
3234 MenuItem showSeqs = new MenuItem();
3236 Menu menu2 = new Menu();
3238 MenuItem hideColumns = new MenuItem();
3240 MenuItem hideSequences = new MenuItem();
3242 MenuItem hideAllButSelection = new MenuItem();
3244 MenuItem hideAllSelection = new MenuItem();
3246 MenuItem showAllHidden = new MenuItem();
3248 Menu formatMenu = new Menu();
3250 Menu selectMenu = new Menu();
3252 MenuItem newView = new MenuItem();
3255 * Attach the alignFrame panels after embedding menus, if necessary. This used
3256 * to be called setEmbedded, but is now creates the dropdown menus in a
3257 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3259 * @param reallyEmbedded
3260 * true to attach the view to the applet area on the page rather than
3263 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3268 // Explicly build the embedded menu panel for the on-page applet
3270 // view cannot be closed if its actually on the page
3271 fileMenu.remove(closeMenuItem);
3272 fileMenu.remove(3); // Remove Seperator
3273 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3274 Font.PLAIN, 10, false); // use our own fonts.
3275 // and actually add the components to the applet area
3276 viewport.applet.setLayout(new BorderLayout());
3277 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3278 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3279 alignPanel.setSize(viewport.applet.getSize().width,
3280 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3281 - statusBar.HEIGHT);
3282 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3283 final AlignFrame me = this;
3284 viewport.applet.addFocusListener(new FocusListener()
3288 public void focusLost(FocusEvent e)
3290 if (me.viewport.applet.currentAlignFrame==me) {
3291 me.viewport.applet.currentAlignFrame = null;
3295 public void focusGained(FocusEvent e)
3297 me.viewport.applet.currentAlignFrame = me;
3300 viewport.applet.validate();
3305 // test and embed menu bar if necessary.
3307 if (embedMenuIfNeeded(alignPanel))
3309 // adjust for status bar height too
3310 alignPanel.setSize(getSize().width, getSize().height
3311 - statusBar.HEIGHT);
3313 add(statusBar, BorderLayout.SOUTH);
3314 add(alignPanel, BorderLayout.CENTER);
3315 // and register with the applet so it can pass external API calls to us
3316 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3322 * create a new binding between structures in an existing jmol viewer instance
3323 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3324 * this does not open a new Jmol window, or modify the display of the
3325 * structures in the original jmol window. Note This method doesn't work
3326 * without an additional javascript library to exchange messages between the
3327 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3330 * JmolViewer instance
3331 * @param sequenceIds
3332 * - sequence Ids to search for associations
3334 public SequenceStructureBinding addStructureViewInstance(
3335 Object jmolviewer, String[] sequenceIds)
3337 org.jmol.api.JmolViewer viewer = null;
3340 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3341 } catch (ClassCastException ex)
3343 System.err.println("Unsupported viewer object :"
3344 + jmolviewer.getClass());
3348 System.err.println("Can't use this object as a structure viewer:"
3349 + jmolviewer.getClass());
3352 SequenceI[] seqs = null;
3353 if (sequenceIds == null || sequenceIds.length == 0)
3355 seqs = viewport.getAlignment().getSequencesArray();
3359 Vector sqi = new Vector();
3360 AlignmentI al = viewport.getAlignment();
3361 for (int sid = 0; sid < sequenceIds.length; sid++)
3363 SequenceI sq = al.findName(sequenceIds[sid]);
3371 seqs = new SequenceI[sqi.size()];
3372 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3374 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3383 // TODO: search for a jmv that involves viewer
3385 { // create a new viewer/jalview binding.
3386 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});
3392 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3395 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3396 boolean needtoadd = false;
3397 if (toaddpdb != null)
3399 Vector pdbe = toaddpdb.getPDBId();
3400 PDBEntry pdbentry = null;
3401 if (pdbe != null && pdbe.size() > 0)
3403 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3405 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3406 if (!pdbentry.getId().equals(pdbEntryString)
3407 && !pdbentry.getFile().equals(pdbFile))
3417 if (pdbentry == null)
3419 pdbentry = new PDBEntry();
3420 pdbentry.setId(pdbEntryString);
3421 pdbentry.setFile(pdbFile);
3422 needtoadd = true; // add this new entry to sequence.
3424 // resolve data source
3425 // TODO: this code should be a refactored to an io package
3426 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3427 if (protocol == null)
3433 // make a note of the access mode and add
3434 if (pdbentry.getProperty() == null)
3436 pdbentry.setProperty(new Hashtable());
3438 pdbentry.getProperty().put("protocol", protocol);
3439 toaddpdb.addPDBId(pdbentry);
3445 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3449 Vector sequences = new Vector();
3450 for (int i = 0; i < seqs.length; i++)
3452 if (seqs[i] != null)
3454 sequences.addElement(new Object[]
3455 { seqs[i], (chains != null) ? chains[i] : null });
3458 seqs = new SequenceI[sequences.size()];
3459 chains = new String[sequences.size()];
3460 for (int i = 0, isize = sequences.size(); i < isize; i++)
3462 Object[] oj = (Object[]) sequences.elementAt(i);
3464 seqs[i] = (SequenceI) oj[0];
3465 chains[i] = (String) oj[1];
3473 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3474 SequenceI[] seqs, String[] chains, String protocol)
3476 // Scrub any null sequences from the array
3477 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3478 seqs = (SequenceI[]) sqch[0];
3479 chains = (String[]) sqch[1];
3480 if (seqs == null || seqs.length == 0)
3483 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3485 if (protocol == null || protocol.trim().length() == 0
3486 || protocol.equals("null"))
3488 protocol = (String) pdb.getProperty().get("protocol");
3489 if (protocol == null)
3491 System.err.println("Couldn't work out protocol to open structure: "
3496 if (applet.useXtrnalSviewer)
3498 // register the association(s) and quit, don't create any windows.
3499 StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol);
3502 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3504 // can only do alignments with Jmol
3505 // find the last jmol window assigned to this alignment
3506 jalview.appletgui.AppletJmol ajm = null, tajm;
3507 Vector jmols = applet
3508 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3509 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3511 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3512 if (tajm.ap.alignFrame == this)
3521 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3522 // try and add the pdb structure
3527 // otherwise, create a new window
3528 if (applet.jmolAvailable)
3530 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3532 applet.lastFrameX += 40;
3533 applet.lastFrameY += 40;
3537 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3542 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3543 SequenceI[][] seqs, String[][] chains, String[] protocols)
3545 // TODO Auto-generated method stub
3546 System.err.println("Aligned Structure View: Not yet implemented.");
3550 * modify the current selection, providing the user has not made a selection already.
3551 * @param sel - sequences from this alignment
3552 * @param csel - columns to be selected on the alignment
3554 public void select(SequenceGroup sel, ColumnSelection csel)
3556 alignPanel.seqPanel.selection(sel, csel, null);