/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.appletgui; import jalview.schemes.*; import jalview.datamodel.*; import jalview.analysis.*; import jalview.io.*; import java.awt.*; import java.awt.event.*; import java.util.*; import java.io.InputStreamReader; import java.io.BufferedReader; import java.net.URL; public class AlignFrame extends Frame implements ActionListener, ItemListener, KeyListener, MouseListener { public AlignmentPanel alignPanel; public AlignViewport viewport; int NEW_WINDOW_WIDTH = 700; int NEW_WINDOW_HEIGHT = 500; jalview.bin.JalviewLite applet; public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded) { try{ jbInit(); }catch(Exception ex) { ex.printStackTrace(); } this.applet = applet; viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); annotationPanelMenuItem.setState(viewport.showAnnotation); seqLimits.setState(viewport.showJVSuffix); if(applet!=null) { String param = applet.getParameter("sortBy"); if (param != null) { if (param.equalsIgnoreCase("Id")) sortIDMenuItem_actionPerformed(); else if (param.equalsIgnoreCase("Pairwise Identity")) sortPairwiseMenuItem_actionPerformed(); } param = applet.getParameter("wrap"); if (param != null) { if (param.equalsIgnoreCase("true")) { wrapMenuItem.setState(true); wrapMenuItem_actionPerformed(); } } try { param = applet.getParameter("windowWidth"); if (param != null) { int width = Integer.parseInt(param); NEW_WINDOW_WIDTH = width; } param = applet.getParameter("windowHeight"); if (param != null) { int height = Integer.parseInt(param); NEW_WINDOW_HEIGHT = height; } } catch (Exception ex) {} } //Some JVMS send keyevents to Top frame or lowest panel, //Havent worked out why yet. So add to both this frame and seqCanvas for now this.addKeyListener(this); alignPanel.seqPanel.seqCanvas.addKeyListener(this); alignPanel.idPanel.idCanvas.addKeyListener(this); viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() { public void propertyChange(java.beans.PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) { alignmentChanged(); } } }); if(embedded) { setEmbedded(); } else { add(alignPanel, BorderLayout.CENTER); jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); } alignPanel.validate(); alignPanel.repaint(); } public AlignViewport getAlignViewport() { return viewport; } public SeqCanvas getSeqcanvas() { return alignPanel.seqPanel.seqCanvas; } /** * DOCUMENT ME! * * @param String DOCUMENT ME! */ public void parseFeaturesFile(String file, String type) { Hashtable featureLinks = new Hashtable(); boolean featuresFile = false; try{ featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment, alignPanel.seqPanel.seqCanvas. getFeatureRenderer().featureColours, featureLinks, true); } catch(Exception ex) { ex.printStackTrace(); } if(featuresFile) { if(featureLinks.size()>0) alignPanel.seqPanel.seqCanvas .getFeatureRenderer().featureLinks = featureLinks; viewport.showSequenceFeatures = true; sequenceFeatures.setState(true); alignPanel.repaint(); } } public void keyPressed(KeyEvent evt) { if (viewport.cursorMode && evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) { alignPanel.seqPanel.numberPressed(evt.getKeyChar()); } switch (evt.getKeyCode()) { case 27: // escape key deselectAllSequenceMenuItem_actionPerformed(); break; case KeyEvent.VK_X: if (evt.isControlDown() || evt.isMetaDown()) { cut_actionPerformed(); } break; case KeyEvent.VK_C: if (viewport.cursorMode && !evt.isControlDown()) { alignPanel.seqPanel.setCursorColumn(); } if (evt.isControlDown() || evt.isMetaDown()) { copy_actionPerformed(); } break; case KeyEvent.VK_V: if (evt.isControlDown() || evt.isMetaDown()) { paste(true); } break; case KeyEvent.VK_A: if (evt.isControlDown() || evt.isMetaDown()) { selectAllSequenceMenuItem_actionPerformed(); } break; case KeyEvent.VK_DOWN: if(viewport.cursorMode) { alignPanel.seqPanel.moveCursor(0,1); } else moveSelectedSequences(false); break; case KeyEvent.VK_UP: if (viewport.cursorMode) { alignPanel.seqPanel.moveCursor(0,-1); } else moveSelectedSequences(true); break; case KeyEvent.VK_LEFT: if(viewport.cursorMode) { alignPanel.seqPanel.moveCursor(-1,0); } break; case KeyEvent.VK_RIGHT: if (viewport.cursorMode) { alignPanel.seqPanel.moveCursor(1,0); } break; case KeyEvent.VK_SPACE: if(viewport.cursorMode) { alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()); } break; case KeyEvent.VK_DELETE: case KeyEvent.VK_BACK_SPACE: if(viewport.cursorMode) { alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()); } else { cut_actionPerformed(); alignPanel.seqPanel.seqCanvas.repaint(); } break; case KeyEvent.VK_S: if(viewport.cursorMode) { alignPanel.seqPanel.setCursorRow(); } break; case KeyEvent.VK_P: if(viewport.cursorMode) { alignPanel.seqPanel.setCursorPosition(); } break; case KeyEvent.VK_ENTER: case KeyEvent.VK_COMMA: if(viewport.cursorMode) { alignPanel.seqPanel.setCursorRowAndColumn(); } break; case KeyEvent.VK_Q: if(viewport.cursorMode) { alignPanel.seqPanel.setSelectionAreaAtCursor(true); } break; case KeyEvent.VK_M: if(viewport.cursorMode) { alignPanel.seqPanel.setSelectionAreaAtCursor(false); } break; case KeyEvent.VK_F2: viewport.cursorMode = ! viewport.cursorMode; statusBar.setText("Keyboard editing mode is "+ (viewport.cursorMode ? "on" : "off")); if(viewport.cursorMode) { alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; } alignPanel.seqPanel.seqCanvas.repaint(); break; case KeyEvent.VK_F: if (evt.isControlDown()) { findMenuItem_actionPerformed(); } break; } } public void keyReleased(KeyEvent evt) {} public void keyTyped(KeyEvent evt) {} public void itemStateChanged(ItemEvent evt) { if(evt.getSource()==colourTextMenuItem) colourTextMenuItem_actionPerformed(); else if(evt.getSource()==wrapMenuItem) wrapMenuItem_actionPerformed(); else if(evt.getSource()==scaleAbove) scaleAbove_actionPerformed(); else if(evt.getSource()==scaleLeft) scaleLeft_actionPerformed(); else if(evt.getSource()==scaleRight) scaleRight_actionPerformed(); else if(evt.getSource()==seqLimits) seqLimits_itemStateChanged(); else if(evt.getSource()==viewBoxesMenuItem) viewBoxesMenuItem_actionPerformed(); else if(evt.getSource()==viewTextMenuItem) viewTextMenuItem_actionPerformed(); else if(evt.getSource()==renderGapsMenuItem) renderGapsMenuItem_actionPerformed(); else if(evt.getSource()==annotationPanelMenuItem) annotationPanelMenuItem_actionPerformed(); else if(evt.getSource()==sequenceFeatures) { viewport.showSequenceFeatures(sequenceFeatures.getState()); alignPanel.seqPanel.seqCanvas.repaint(); } else if(evt.getSource()==conservationMenuItem) conservationMenuItem_actionPerformed(); else if(evt.getSource()==abovePIDThreshold) abovePIDThreshold_actionPerformed(); else if(evt.getSource()==applyToAllGroups) applyToAllGroups_actionPerformed(); else if(evt.getSource()==autoCalculate) viewport.autocalculateConsensus = autoCalculate.getState(); } public void actionPerformed(ActionEvent evt) { if(evt.getSource()==inputText) inputText_actionPerformed(); else if(evt.getSource()==loadTree) loadTree_actionPerformed(); else if(evt.getSource()==loadApplication) launchFullApplication(); else if(evt.getSource()==closeMenuItem) closeMenuItem_actionPerformed(); else if(evt.getSource()==copy) copy_actionPerformed(); else if(evt.getSource()==undoMenuItem) undoMenuItem_actionPerformed(); else if(evt.getSource()==redoMenuItem) redoMenuItem_actionPerformed(); else if(evt.getSource()==inputText) inputText_actionPerformed(); else if(evt.getSource()==closeMenuItem) closeMenuItem_actionPerformed(); else if(evt.getSource()==undoMenuItem) undoMenuItem_actionPerformed(); else if(evt.getSource()==redoMenuItem) redoMenuItem_actionPerformed(); else if(evt.getSource()==copy) copy_actionPerformed(); else if(evt.getSource()==pasteNew) pasteNew_actionPerformed(); else if(evt.getSource()==pasteThis) pasteThis_actionPerformed(); else if(evt.getSource()==cut) cut_actionPerformed(); else if(evt.getSource()==delete) delete_actionPerformed(); else if(evt.getSource()==deleteGroups) deleteGroups_actionPerformed(); else if(evt.getSource()==selectAllSequenceMenuItem) selectAllSequenceMenuItem_actionPerformed(); else if(evt.getSource()==deselectAllSequenceMenuItem) deselectAllSequenceMenuItem_actionPerformed(); else if(evt.getSource()==invertSequenceMenuItem) invertSequenceMenuItem_actionPerformed(); else if(evt.getSource()==remove2LeftMenuItem) remove2LeftMenuItem_actionPerformed(); else if(evt.getSource()==remove2RightMenuItem) remove2RightMenuItem_actionPerformed(); else if(evt.getSource()==removeGappedColumnMenuItem) removeGappedColumnMenuItem_actionPerformed(); else if(evt.getSource()==removeAllGapsMenuItem) removeAllGapsMenuItem_actionPerformed(); else if(evt.getSource()==findMenuItem) findMenuItem_actionPerformed(); else if(evt.getSource()==font) font_actionPerformed(); else if(evt.getSource()==featureSettings) featureSettings_actionPerformed(); else if(evt.getSource()==overviewMenuItem) overviewMenuItem_actionPerformed(); else if(evt.getSource()==noColourmenuItem) noColourmenuItem_actionPerformed(); else if(evt.getSource()==clustalColour) clustalColour_actionPerformed(); else if(evt.getSource()==zappoColour) zappoColour_actionPerformed(); else if(evt.getSource()==taylorColour) taylorColour_actionPerformed(); else if(evt.getSource()==hydrophobicityColour) hydrophobicityColour_actionPerformed(); else if(evt.getSource()==helixColour) helixColour_actionPerformed(); else if(evt.getSource()==strandColour) strandColour_actionPerformed(); else if(evt.getSource()==turnColour) turnColour_actionPerformed(); else if(evt.getSource()==buriedColour) buriedColour_actionPerformed(); else if(evt.getSource()==nucleotideColour) nucleotideColour_actionPerformed(); else if(evt.getSource()==modifyPID) modifyPID_actionPerformed(); else if(evt.getSource()==modifyConservation) modifyConservation_actionPerformed(); else if(evt.getSource()==userDefinedColour) userDefinedColour_actionPerformed(); else if(evt.getSource()==PIDColour) PIDColour_actionPerformed(); else if(evt.getSource()==BLOSUM62Colour) BLOSUM62Colour_actionPerformed(); else if(evt.getSource()==annotationColour) new AnnotationColourChooser(viewport, alignPanel); else if(evt.getSource()==sortPairwiseMenuItem) sortPairwiseMenuItem_actionPerformed(); else if(evt.getSource()==sortIDMenuItem) sortIDMenuItem_actionPerformed(); else if(evt.getSource()==sortGroupMenuItem) sortGroupMenuItem_actionPerformed(); else if(evt.getSource()==removeRedundancyMenuItem) removeRedundancyMenuItem_actionPerformed(); else if(evt.getSource()==pairwiseAlignmentMenuItem) pairwiseAlignmentMenuItem_actionPerformed(); else if(evt.getSource()==PCAMenuItem) PCAMenuItem_actionPerformed(); else if(evt.getSource()==averageDistanceTreeMenuItem) averageDistanceTreeMenuItem_actionPerformed(); else if(evt.getSource()==neighbourTreeMenuItem) neighbourTreeMenuItem_actionPerformed(); else if(evt.getSource()==njTreeBlosumMenuItem) njTreeBlosumMenuItem_actionPerformed(); else if(evt.getSource()==avDistanceTreeBlosumMenuItem) avTreeBlosumMenuItem_actionPerformed(); else if(evt.getSource()==documentation) documentation_actionPerformed(); else if(evt.getSource()==about) about_actionPerformed(); } public void inputText_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); } protected void outputText_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Alignment output - " + e.getActionCommand(), 600, 500); cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences(), viewport.showJVSuffix)); } void launchFullApplication() { StringBuffer url = new StringBuffer("http://bug.compbio.dundee.ac.uk:8080/Jalview/jalview?"); url.append("open="+ appendProtocol( applet.getParameter("file") ) ); if(applet.getParameter("features")!=null) { url.append( "&features=" ); url.append( appendProtocol( applet.getParameter("features") ) ); } if(applet.getParameter("defaultColour")!=null) { url.append("&colour=" + removeWhiteSpace(applet.getParameter("defaultColour")) ); } if(applet.getParameter("userDefinedColour")!=null) { url.append( "&colour=" + removeWhiteSpace( applet.getParameter("userDefinedColour") ) ); } showURL(url.toString(), "FULL_APP"); } String removeWhiteSpace(String colour) { StringBuffer sb = new StringBuffer(); for (int i = 0; i < colour.length(); i++) { if (Character.isWhitespace(colour.charAt(i))) sb.append("%20"); else sb.append(colour.charAt(i)); } return sb.toString(); } String appendProtocol(String url) { try{ new URL(url); }catch(java.net.MalformedURLException ex) { url = applet.getCodeBase()+url; } return url; } public void closeMenuItem_actionPerformed() { PaintRefresher.components.remove(viewport.alignment); if(PaintRefresher.components.size()==0 && applet==null) System.exit(0); this.dispose(); } Stack historyList = new Stack(); Stack redoList = new Stack(); void updateEditMenuBar() { if (historyList.size() > 0) { undoMenuItem.setEnabled(true); HistoryItem hi = (HistoryItem) historyList.peek(); undoMenuItem.setLabel("Undo " + hi.getDescription()); } else { undoMenuItem.setEnabled(false); undoMenuItem.setLabel("Undo"); } if (redoList.size() > 0) { redoMenuItem.setEnabled(true); HistoryItem hi = (HistoryItem) redoList.peek(); redoMenuItem.setLabel("Redo " + hi.getDescription()); } else { redoMenuItem.setEnabled(false); redoMenuItem.setLabel("Redo"); } } public void addHistoryItem(HistoryItem hi) { historyList.push(hi); updateEditMenuBar(); } protected void undoMenuItem_actionPerformed() { HistoryItem hi = (HistoryItem) historyList.pop(); redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE)); restoreHistoryItem(hi); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } protected void redoMenuItem_actionPerformed() { HistoryItem hi = (HistoryItem) redoList.pop(); restoreHistoryItem(hi); updateEditMenuBar(); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } // used by undo and redo void restoreHistoryItem(HistoryItem hi) { hi.restore(); updateEditMenuBar(); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } public void moveSelectedSequences(boolean up) { SequenceGroup sg = viewport.getSelectionGroup(); if (sg == null) { return; } if (up) { for (int i = 1; i < viewport.alignment.getHeight(); i++) { SequenceI seq = viewport.alignment.getSequenceAt(i); if (!sg.getSequences(false).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); if (sg.getSequences(false).contains(temp)) { continue; } viewport.alignment.getSequences().setElementAt(temp, i); viewport.alignment.getSequences().setElementAt(seq, i - 1); } } else { for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) { SequenceI seq = viewport.alignment.getSequenceAt(i); if (!sg.getSequences(true).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); if (sg.getSequences(true).contains(temp)) { continue; } viewport.alignment.getSequences().setElementAt(temp, i); viewport.alignment.getSequences().setElementAt(seq, i + 1); } } alignPanel.repaint(); } StringBuffer copiedSequences; protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) { return; } SequenceGroup sg = viewport.getSelectionGroup(); copiedSequences = new StringBuffer(); Hashtable orderedSeqs = new Hashtable(); for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.alignment.findIndex(seq); orderedSeqs.put(index + "", seq); } int index = 0, startRes, endRes; char ch; for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = null; while (seq == null) { if (orderedSeqs.containsKey(index + "")) { seq = (SequenceI) orderedSeqs.get(index + ""); index++; break; } else { index++; } } //FIND START RES //Returns residue following index if gap startRes = seq.findPosition(sg.getStartRes()); //FIND END RES //Need to find the residue preceeding index if gap endRes = 0; for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++) { ch = seq.getCharAt(j); if (!jalview.util.Comparison.isGap( (ch))) { endRes++; } } if(endRes>0) { endRes += seq.getStart() -1; } copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes + "\t" + seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1) + "\n"); } } protected void pasteNew_actionPerformed() { paste(true); } protected void pasteThis_actionPerformed() { addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE)); paste(false); } void paste(boolean newAlignment) { try { if (copiedSequences == null) { return; } StringTokenizer st = new StringTokenizer(copiedSequences.toString()); Vector seqs = new Vector(); while (st.hasMoreElements()) { String name = st.nextToken(); int start = Integer.parseInt(st.nextToken()); int end = Integer.parseInt(st.nextToken()); Sequence sequence = new Sequence(name, st.nextToken(), start, end); if (!newAlignment) { viewport.alignment.addSequence(sequence); } else { seqs.addElement(sequence); } } if (newAlignment) { SequenceI[] newSeqs = new SequenceI[seqs.size()]; for (int i = 0; i < seqs.size(); i++) { newSeqs[i] = (SequenceI) seqs.elementAt(i); } String newtitle = new String("Copied sequences"); if (getTitle().startsWith("Copied sequences")) { newtitle = getTitle(); } else { newtitle = newtitle.concat("- from " + getTitle()); } AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle, false); jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); } else { viewport.setEndSeq(viewport.alignment.getHeight()); viewport.alignment.getWidth(); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } catch (Exception ex) {} // could be anything being pasted in here } protected void cut_actionPerformed() { copy_actionPerformed(); delete_actionPerformed(); } protected void delete_actionPerformed() { addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE)); if (viewport.getSelectionGroup() == null) { return; } SequenceGroup sg = viewport.getSelectionGroup(); boolean allSequences = false; if(sg.getSize(false)==viewport.alignment.getHeight()) allSequences = true; for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.getAlignment().findIndex(seq); seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); // If the cut affects all sequences, remove highlighted columns if (allSequences) { viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); } if (seq.getSequence().length() < 1) { viewport.getAlignment().deleteSequence(seq); } else { viewport.getAlignment().getSequences().setElementAt(seq, index); } } viewport.setSelectionGroup(null); viewport.alignment.deleteGroup(sg); viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height); if (viewport.getAlignment().getHeight() < 1) { try { this.setVisible(false); } catch (Exception ex) {} } viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } protected void deleteGroups_actionPerformed() { viewport.alignment.deleteAllGroups(); viewport.setSelectionGroup(null); alignPanel.repaint(); } public void selectAllSequenceMenuItem_actionPerformed() { SequenceGroup sg = new SequenceGroup(); for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } sg.setEndRes(viewport.alignment.getWidth()-1); viewport.setSelectionGroup(sg); alignPanel.repaint(); PaintRefresher.Refresh(null, viewport.alignment); } public void deselectAllSequenceMenuItem_actionPerformed() { if(viewport.cursorMode) { alignPanel.seqPanel.keyboardNo1=null; alignPanel.seqPanel.keyboardNo2=null; } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); alignPanel.repaint(); PaintRefresher.Refresh(null, viewport.alignment); } public void invertSequenceMenuItem_actionPerformed() { SequenceGroup sg = viewport.getSelectionGroup(); for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); } PaintRefresher.Refresh(null, viewport.alignment); } public void remove2LeftMenuItem_actionPerformed() { ColumnSelection colSel = viewport.getColumnSelection(); if (colSel.size() > 0) { addHistoryItem(new HistoryItem("Remove Left", viewport.alignment, HistoryItem.HIDE)); int min = colSel.getMin(); viewport.getAlignment().trimLeft(min); colSel.compensateForEdit(0, min); if (viewport.getSelectionGroup() != null) { viewport.getSelectionGroup().adjustForRemoveLeft(min); } Vector groups = viewport.alignment.getGroups(); for (int i = 0; i < groups.size(); i++) { SequenceGroup sg = (SequenceGroup) groups.elementAt(i); if (!sg.adjustForRemoveLeft(min)) { viewport.alignment.deleteGroup(sg); } } viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } public void remove2RightMenuItem_actionPerformed() { ColumnSelection colSel = viewport.getColumnSelection(); if (colSel.size() > 0) { addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, HistoryItem.HIDE)); int max = colSel.getMax(); viewport.getAlignment().trimRight(max); if (viewport.getSelectionGroup() != null) { viewport.getSelectionGroup().adjustForRemoveRight(max); } Vector groups = viewport.alignment.getGroups(); for (int i = 0; i < groups.size(); i++) { SequenceGroup sg = (SequenceGroup) groups.elementAt(i); if (!sg.adjustForRemoveRight(max)) { viewport.alignment.deleteGroup(sg); } } viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } public void removeGappedColumnMenuItem_actionPerformed() { addHistoryItem(new HistoryItem("Remove Gapped Columns", viewport.alignment, HistoryItem.HIDE)); //This is to maintain viewport position on first residue //of first sequence SequenceI seq = viewport.alignment.getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); viewport.getAlignment().removeGaps(); viewport.setStartRes(seq.findIndex(startRes)-1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } public void removeAllGapsMenuItem_actionPerformed() { addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, HistoryItem.HIDE)); //This is to maintain viewport position on first residue //of first sequence SequenceI seq = viewport.alignment.getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); SequenceI current; int jSize; Vector seqs=null; int start=0, end = viewport.alignment.getWidth(); if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSequences(false) != null && viewport.getSelectionGroup().getSize(false)>0) { seqs = viewport.getSelectionGroup().getSequences(true); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes()+1; } else seqs = viewport.alignment.getSequences(); for (int i = 0; i < seqs.size(); i++) { current = (SequenceI) seqs.elementAt(i); jSize = current.getLength(); // Removing a range is much quicker than removing gaps // one by one for long sequences int j = start; int rangeStart=-1, rangeEnd=-1; do { if (jalview.util.Comparison.isGap(current.getCharAt(j))) { if(rangeStart==-1) { rangeStart = j; rangeEnd = j+1; } else { rangeEnd++; } j++; } else { if(rangeStart>-1) { current.deleteChars(rangeStart, rangeEnd); j-=rangeEnd-rangeStart; jSize-=rangeEnd-rangeStart; rangeStart = -1; rangeEnd = -1; } else j++; } } while (j < end && j < jSize); if(rangeStart>-1) { current.deleteChars(rangeStart, rangeEnd); } } viewport.setStartRes(seq.findIndex(startRes)-1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } public void alignmentChanged() { viewport.alignment.padGaps(); if(viewport.autocalculateConsensus) { viewport.updateConsensus(); viewport.updateConservation(); } resetAllColourSchemes(); if(alignPanel.overviewPanel!=null) alignPanel.overviewPanel.updateOverviewImage(); viewport.alignment.adjustSequenceAnnotations(); alignPanel.repaint(); } void resetAllColourSchemes() { ColourSchemeI cs = viewport.globalColourScheme; if(cs!=null) { if (cs instanceof ClustalxColourScheme) { ( (ClustalxColourScheme) viewport.getGlobalColourScheme()). resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth()); } cs.setConsensus(viewport.vconsensus); if (cs.conservationApplied()) { Alignment al = (Alignment) viewport.alignment; Conservation c = new Conservation("All", ResidueProperties.propHash, 3, al.getSequences(), 0, al.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); cs.setConservation(c); } } int s, sSize = viewport.alignment.getGroups().size(); for(s=0; s 1) { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500); } } public void PCAMenuItem_actionPerformed() { //are the sequences aligned? if (!viewport.alignment.isAligned()) { SequenceI current; int Width = viewport.getAlignment().getWidth(); for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { current = viewport.getAlignment().getSequenceAt(i); if (current.getLength() < Width) { current.insertCharAt(Width - 1, viewport.getGapCharacter()); } } alignPanel.repaint(); } if ( (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize(false) < 4 && viewport.getSelectionGroup().getSize(false) > 0) || viewport.getAlignment().getHeight() < 4) { return; } try { new PCAPanel(viewport); } catch (java.lang.OutOfMemoryError ex) { } } public void averageDistanceTreeMenuItem_actionPerformed() { NewTreePanel("AV", "PID", "Average distance tree using PID"); } public void neighbourTreeMenuItem_actionPerformed() { NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); } protected void njTreeBlosumMenuItem_actionPerformed() { NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); } protected void avTreeBlosumMenuItem_actionPerformed() { NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID"); } void NewTreePanel(String type, String pwType, String title) { //are the sequences aligned? if (!viewport.alignment.isAligned()) { SequenceI current; int Width = viewport.getAlignment().getWidth(); for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { current = viewport.getAlignment().getSequenceAt(i); if (current.getLength() < Width) { current.insertCharAt(Width - 1, viewport.getGapCharacter()); } } alignPanel.repaint(); } final TreePanel tp; if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize(false) > 3) { tp = new TreePanel(viewport, viewport.getSelectionGroup().getSequences(false), type, pwType, 0, viewport.alignment.getWidth()); } else { tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), type, pwType, 0, viewport.alignment.getWidth()); } addTreeMenuItem(tp, title); jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); } void loadTree_actionPerformed() { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); cap.setText("Paste your Newick tree file here."); cap.treeImport = true; Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300); } public void loadTree(jalview.io.NewickFile tree, String treeFile) { TreePanel tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), tree, "From File - ", treeFile); jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); addTreeMenuItem(tp, treeFile); } void addTreeMenuItem(final TreePanel treePanel, String title) { final MenuItem item = new MenuItem(title); sortByTreeMenu.add(item); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent evt) { addHistoryItem(new HistoryItem("Sort", viewport.alignment, HistoryItem.SORT)); AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); alignPanel.repaint(); } }); treePanel.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent e) { sortByTreeMenu.remove(item); }; }); } protected void documentation_actionPerformed() { showURL("http://www.jalview.org/help.html", "HELP"); } protected void about_actionPerformed() { class AboutPanel extends Canvas { String version; public AboutPanel(String version) { this.version = version; } public void paint(Graphics g) { g.setColor(Color.white); g.fillRect(0, 0, getSize().width, getSize().height); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); FontMetrics fm = g.getFontMetrics(); int fh = fm.getHeight(); int y = 5, x = 7; g.setColor(Color.black); g.setFont(new Font("Helvetica", Font.BOLD, 14)); g.drawString("Jalview - Release "+version, 200, y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.", x, y += fh * 2); g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.", x, y += fh); g.drawString( "For any issues relating to Jalview, email help@jalview.org", x, y += fh); g.drawString("If you use JalView, please cite:", x, y += fh + 8); g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", x, y += fh); g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh); } } String version = "test"; java.net.URL url = getClass().getResource("/.build_properties"); if (url != null) { try { BufferedReader reader = new BufferedReader(new InputStreamReader( url.openStream())); String line; while ( (line = reader.readLine()) != null) { if (line.indexOf("VERSION") > -1) { version = line.substring(line.indexOf("=") + 1); } } } catch (Exception ex) { ex.printStackTrace(); } } Frame frame = new Frame(); frame.add(new AboutPanel(version)); jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); } public void showURL(String url, String target) { if (applet == null) { System.out.println("Not running as applet - no browser available."); } else { try { System.out.println("Show url: "+url); applet.getAppletContext().showDocument(new java.net.URL(url), target); } catch (Exception ex) { ex.printStackTrace(); } } } ////////////////////////////////////////////////////////////////////////////////// //JBuilder Graphics here protected MenuBar alignFrameMenuBar = new MenuBar(); protected Menu fileMenu = new Menu("File"); protected MenuItem loadApplication = new MenuItem("View in Full Application"); protected MenuItem loadTree = new MenuItem("Load Associated Tree"); protected MenuItem closeMenuItem = new MenuItem("Close"); protected Menu editMenu = new Menu("Edit"); protected Menu viewMenu = new Menu("View"); protected Menu colourMenu = new Menu("Colour"); protected Menu calculateMenu = new Menu("Calculate"); protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); protected MenuItem remove2LeftMenuItem = new MenuItem(); protected MenuItem remove2RightMenuItem = new MenuItem(); protected MenuItem removeGappedColumnMenuItem = new MenuItem(); protected MenuItem removeAllGapsMenuItem = new MenuItem(); protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); protected MenuItem sortPairwiseMenuItem = new MenuItem(); protected MenuItem sortIDMenuItem = new MenuItem(); protected MenuItem sortGroupMenuItem = new MenuItem(); protected MenuItem removeRedundancyMenuItem = new MenuItem(); protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); protected MenuItem PCAMenuItem = new MenuItem(); protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); protected MenuItem neighbourTreeMenuItem = new MenuItem(); BorderLayout borderLayout1 = new BorderLayout(); public Label statusBar = new Label(); protected Menu outputTextboxMenu = new Menu(); protected MenuItem clustalColour = new MenuItem(); protected MenuItem zappoColour = new MenuItem(); protected MenuItem taylorColour = new MenuItem(); protected MenuItem hydrophobicityColour = new MenuItem(); protected MenuItem helixColour = new MenuItem(); protected MenuItem strandColour = new MenuItem(); protected MenuItem turnColour = new MenuItem(); protected MenuItem buriedColour = new MenuItem(); protected MenuItem userDefinedColour = new MenuItem(); protected MenuItem PIDColour = new MenuItem(); protected MenuItem BLOSUM62Colour = new MenuItem(); MenuItem njTreeBlosumMenuItem = new MenuItem(); MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); MenuItem overviewMenuItem = new MenuItem(); protected MenuItem undoMenuItem = new MenuItem(); protected MenuItem redoMenuItem = new MenuItem(); protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); MenuItem noColourmenuItem = new MenuItem(); protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); MenuItem findMenuItem = new MenuItem(); Menu searchMenu = new Menu(); protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); protected MenuItem nucleotideColour = new MenuItem(); MenuItem deleteGroups = new MenuItem(); MenuItem delete = new MenuItem(); MenuItem copy = new MenuItem(); MenuItem cut = new MenuItem(); Menu pasteMenu = new Menu(); MenuItem pasteNew = new MenuItem(); MenuItem pasteThis = new MenuItem(); protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); protected MenuItem font = new MenuItem(); protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); MenuItem modifyPID = new MenuItem(); MenuItem modifyConservation = new MenuItem(); protected CheckboxMenuItem autoCalculate = new CheckboxMenuItem("Autocalculate Consensus", true); protected Menu sortByTreeMenu = new Menu(); Menu sort = new Menu(); Menu calculate = new Menu(); MenuItem inputText = new MenuItem(); Menu helpMenu = new Menu(); MenuItem documentation = new MenuItem(); MenuItem about = new MenuItem(); protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); Panel embeddedMenu; Label embeddedEdit; Label embeddedSearch; Label embeddedView; Label embeddedColour; Label embeddedFile; Label embeddedHelp; Label embeddedCalculate; FlowLayout flowLayout1; private void jbInit() throws Exception { setMenuBar(alignFrameMenuBar); MenuItem item; // dynamically fill save as menu with available formats for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++) { item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats. elementAt( i)); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); } }); outputTextboxMenu.add(item); } closeMenuItem.addActionListener(this); loadApplication.addActionListener(this); loadTree.addActionListener(this); selectAllSequenceMenuItem.addActionListener(this); deselectAllSequenceMenuItem.addActionListener(this); invertSequenceMenuItem.addActionListener(this); remove2LeftMenuItem.setLabel("Remove Left"); remove2LeftMenuItem.addActionListener(this); remove2RightMenuItem.setLabel("Remove Right"); remove2RightMenuItem.addActionListener(this); removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); removeGappedColumnMenuItem.addActionListener(this); removeAllGapsMenuItem.setLabel("Remove All Gaps"); removeAllGapsMenuItem.addActionListener(this); viewBoxesMenuItem.setLabel("Boxes"); viewBoxesMenuItem.setState(true); viewBoxesMenuItem.addItemListener(this); viewTextMenuItem.setLabel("Text"); viewTextMenuItem.setState(true); viewTextMenuItem.addItemListener(this); sortPairwiseMenuItem.setLabel("by Pairwise Identity"); sortPairwiseMenuItem.addActionListener(this); sortIDMenuItem.setLabel("by ID"); sortIDMenuItem.addActionListener(this); sortGroupMenuItem.setLabel("by Group"); sortGroupMenuItem.addActionListener(this); removeRedundancyMenuItem.setLabel("Remove Redundancy..."); removeRedundancyMenuItem.addActionListener(this); pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); pairwiseAlignmentMenuItem.addActionListener(this); PCAMenuItem.setLabel("Principal Component Analysis"); PCAMenuItem.addActionListener(this); averageDistanceTreeMenuItem.setLabel( "Average Distance Using % Identity"); averageDistanceTreeMenuItem.addActionListener(this); neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); neighbourTreeMenuItem.addActionListener(this); alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setBackground(Color.white); statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); statusBar.setText("Status bar"); outputTextboxMenu.setLabel("Output to Textbox"); clustalColour.setLabel("Clustalx"); clustalColour.addActionListener(this); zappoColour.setLabel("Zappo"); zappoColour.addActionListener(this); taylorColour.setLabel("Taylor"); taylorColour.addActionListener(this); hydrophobicityColour.setLabel("Hydrophobicity"); hydrophobicityColour.addActionListener(this); helixColour.setLabel("Helix Propensity"); helixColour.addActionListener(this); strandColour.setLabel("Strand Propensity"); strandColour.addActionListener(this); turnColour.setLabel("Turn Propensity"); turnColour.addActionListener(this); buriedColour.setLabel("Buried Index"); buriedColour.addActionListener(this); userDefinedColour.setLabel("User Defined..."); userDefinedColour.addActionListener(this); PIDColour.setLabel("Percentage Identity"); PIDColour.addActionListener(this); BLOSUM62Colour.setLabel("BLOSUM62 Score"); BLOSUM62Colour.addActionListener(this); avDistanceTreeBlosumMenuItem.setLabel( "Average Distance Using BLOSUM62"); avDistanceTreeBlosumMenuItem.addActionListener(this); njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); njTreeBlosumMenuItem.addActionListener(this); annotationPanelMenuItem.setLabel("Show Annotations"); annotationPanelMenuItem.addItemListener(this); colourTextMenuItem.setLabel("Colour Text"); colourTextMenuItem.addItemListener(this); overviewMenuItem.setLabel("Overview Window"); overviewMenuItem.addActionListener(this); undoMenuItem.setEnabled(false); undoMenuItem.setLabel("Undo"); undoMenuItem.addActionListener(this); redoMenuItem.setEnabled(false); redoMenuItem.setLabel("Redo"); redoMenuItem.addActionListener(this); conservationMenuItem.setLabel("by Conservation"); conservationMenuItem.addItemListener(this); noColourmenuItem.setLabel("None"); noColourmenuItem.addActionListener(this); wrapMenuItem.setLabel("Wrap"); wrapMenuItem.addItemListener(this); renderGapsMenuItem.setLabel("Show Gaps"); renderGapsMenuItem.setState(true); renderGapsMenuItem.addItemListener(this); findMenuItem.setLabel("Find..."); findMenuItem.addActionListener(this); searchMenu.setLabel("Search"); abovePIDThreshold.setLabel("Above Identity Threshold"); abovePIDThreshold.addItemListener(this); nucleotideColour.setLabel("Nucleotide"); nucleotideColour.addActionListener(this); deleteGroups.setLabel("Undefine Groups"); deleteGroups.addActionListener(this); copy.setLabel("Copy"); copy.addActionListener(this); cut.setLabel("Cut"); cut.addActionListener(this); delete.setLabel("Delete"); delete.addActionListener(this); pasteMenu.setLabel("Paste"); pasteNew.setLabel("To New Alignment"); pasteNew.addActionListener(this); pasteThis.setLabel("Add To This Alignment"); pasteThis.addActionListener(this); applyToAllGroups.setLabel("Apply Colour To All Groups"); applyToAllGroups.setState(true); applyToAllGroups.addItemListener(this); font.setLabel("Font..."); font.addActionListener(this); scaleAbove.setLabel("Scale Above"); scaleAbove.setState(true); scaleAbove.setEnabled(false); scaleAbove.addItemListener(this); scaleLeft.setEnabled(false); scaleLeft.setState(true); scaleLeft.setLabel("Scale Left"); scaleLeft.addItemListener(this); scaleRight.setEnabled(false); scaleRight.setState(true); scaleRight.setLabel("Scale Right"); scaleRight.addItemListener(this); modifyPID.setLabel("Modify Identity Threshold..."); modifyPID.addActionListener(this); modifyConservation.setLabel("Modify Conservation Threshold..."); modifyConservation.addActionListener(this); sortByTreeMenu.setLabel("By Tree Order"); sort.setLabel("Sort"); calculate.setLabel("Calculate Tree"); autoCalculate.addItemListener(this); inputText.setLabel("Input from textbox"); inputText.addActionListener(this); helpMenu.setLabel("Help"); documentation.setLabel("Documentation"); documentation.addActionListener(this); about.setLabel("About..."); about.addActionListener(this); seqLimits.setState(true); seqLimits.setLabel("Show Sequence Limits"); seqLimits.addItemListener(this); featureSettings.setLabel("Feature Settings..."); featureSettings.addActionListener(this); sequenceFeatures.setLabel("Sequence Features"); sequenceFeatures.addItemListener(this); sequenceFeatures.setState(false); annotationColour.setLabel("by Annotation..."); annotationColour.addActionListener(this); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(searchMenu); alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(colourMenu); alignFrameMenuBar.add(calculateMenu); alignFrameMenuBar.add(helpMenu); fileMenu.add(inputText); fileMenu.add(outputTextboxMenu); // fileMenu.add(loadApplication); fileMenu.addSeparator(); fileMenu.add(loadTree); fileMenu.add(closeMenuItem); editMenu.add(undoMenuItem); editMenu.add(redoMenuItem); editMenu.add(cut); editMenu.add(copy); editMenu.add(pasteMenu); editMenu.add(delete); editMenu.addSeparator(); editMenu.add(selectAllSequenceMenuItem); editMenu.add(deselectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); editMenu.add(deleteGroups); editMenu.addSeparator(); editMenu.add(remove2LeftMenuItem); editMenu.add(remove2RightMenuItem); editMenu.add(removeGappedColumnMenuItem); editMenu.add(removeAllGapsMenuItem); editMenu.add(removeRedundancyMenuItem); searchMenu.add(findMenuItem); viewMenu.add(font); viewMenu.addSeparator(); viewMenu.add(seqLimits); viewMenu.addSeparator(); viewMenu.add(wrapMenuItem); viewMenu.add(scaleAbove); viewMenu.add(scaleLeft); viewMenu.add(scaleRight); viewMenu.addSeparator(); viewMenu.add(viewBoxesMenuItem); viewMenu.add(viewTextMenuItem); viewMenu.add(colourTextMenuItem); viewMenu.add(renderGapsMenuItem); viewMenu.add(annotationPanelMenuItem); viewMenu.addSeparator(); viewMenu.add(sequenceFeatures); viewMenu.add(featureSettings); viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); colourMenu.add(applyToAllGroups); colourMenu.addSeparator(); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); colourMenu.add(PIDColour); colourMenu.add(zappoColour); colourMenu.add(taylorColour); colourMenu.add(hydrophobicityColour); colourMenu.add(helixColour); colourMenu.add(strandColour); colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); colourMenu.add(modifyConservation); colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); colourMenu.add(annotationColour); calculateMenu.add(sort); calculateMenu.add(calculate); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); calculateMenu.add(autoCalculate); this.add(statusBar, BorderLayout.SOUTH); pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); sort.add(sortIDMenuItem); sort.add(sortByTreeMenu); sort.add(sortGroupMenuItem); sort.add(sortPairwiseMenuItem); calculate.add(averageDistanceTreeMenuItem); calculate.add(neighbourTreeMenuItem); calculate.add(avDistanceTreeBlosumMenuItem); calculate.add(njTreeBlosumMenuItem); helpMenu.add(documentation); helpMenu.add(about); } public void setEmbedded() { embeddedMenu = new Panel(); embeddedEdit = new Label(); embeddedSearch = new Label(); embeddedView = new Label(); embeddedColour = new Label(); embeddedFile = new Label(); embeddedHelp = new Label(); embeddedCalculate = new Label(); flowLayout1 = new FlowLayout(); embeddedMenu.setBackground(Color.lightGray); embeddedMenu.setLayout(flowLayout1); embeddedEdit.setText("Edit"); embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); embeddedSearch.setText("Search"); embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); embeddedView.setText("View"); embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); embeddedColour.setText("Colour"); embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); embeddedFile.setText("File"); embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); embeddedHelp.setText("Help"); embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); embeddedCalculate.setText("Calculate"); embeddedMenu.add(embeddedFile); embeddedMenu.add(embeddedEdit); embeddedMenu.add(embeddedSearch); embeddedMenu.add(embeddedView); embeddedMenu.add(embeddedColour); embeddedMenu.add(embeddedCalculate); embeddedMenu.add(embeddedHelp); flowLayout1.setAlignment(FlowLayout.LEFT); flowLayout1.setHgap(2); flowLayout1.setVgap(0); embeddedFile.addMouseListener(this); embeddedEdit.addMouseListener(this); embeddedSearch.addMouseListener(this); embeddedView.addMouseListener(this); embeddedColour.addMouseListener(this); embeddedCalculate.addMouseListener(this); embeddedHelp.addMouseListener(this); // setVisible(false); fileMenu.remove(closeMenuItem); fileMenu.remove(3); // Seperator applet.setLayout(new BorderLayout()); applet.add(embeddedMenu, BorderLayout.NORTH); applet.add(statusBar, BorderLayout.SOUTH); // applet.validate(); alignPanel.setSize(applet.size().width, applet.size().height - embeddedMenu.HEIGHT - statusBar.HEIGHT); applet.add(alignPanel, BorderLayout.CENTER); applet.validate(); } PopupMenu filePopup, editPopup, searchPopup, viewPopup, colourPopup, calculatePopup, helpPopup; MenuItem featureSettings = new MenuItem(); CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); MenuItem annotationColour = new MenuItem(); public void mousePressed(MouseEvent evt) { PopupMenu popup = null; Label source = (Label)evt.getSource(); if(source==embeddedFile) { popup = filePopup = genPopupMenu(filePopup, fileMenu); } else if(source==embeddedEdit) { popup = editPopup = genPopupMenu(editPopup, editMenu); } else if(source==embeddedSearch) { popup = searchPopup = genPopupMenu(searchPopup, searchMenu); } else if(source==embeddedView) { popup = viewPopup = genPopupMenu(viewPopup, viewMenu); } else if(source==embeddedColour) { popup = colourPopup = genPopupMenu(colourPopup, colourMenu); } else if(source==embeddedCalculate) { popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu); } else if(source==embeddedHelp) { popup = helpPopup = genPopupMenu(helpPopup, helpMenu); } embeddedMenu.add(popup); popup.show(embeddedMenu, source.getBounds().x, source.getBounds().y + source.getBounds().getSize().height); } PopupMenu genPopupMenu(PopupMenu popup, Menu original) { if(popup!=null) { return popup; } popup = new PopupMenu(); int m, mSize = original.getItemCount(); for(m=0; m