/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2007 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 java.util.*; import java.awt.*; import java.awt.event.*; import jalview.analysis.*; import jalview.commands.*; import jalview.datamodel.*; import jalview.schemes.*; import jalview.io.AppletFormatAdapter; public class APopupMenu extends java.awt.PopupMenu implements ActionListener, ItemListener { Menu groupMenu = new Menu(); MenuItem editGroupName = new MenuItem(); 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 CheckboxMenuItem abovePIDColour = new CheckboxMenuItem(); protected MenuItem userDefinedColour = new MenuItem(); protected MenuItem PIDColour = new MenuItem(); protected MenuItem BLOSUM62Colour = new MenuItem(); MenuItem noColourmenuItem = new MenuItem(); protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); final AlignmentPanel ap; MenuItem unGroupMenuItem = new MenuItem(); MenuItem nucleotideMenuItem = new MenuItem(); Menu colourMenu = new Menu(); CheckboxMenuItem showBoxes = new CheckboxMenuItem(); CheckboxMenuItem showText = new CheckboxMenuItem(); CheckboxMenuItem showColourText = new CheckboxMenuItem(); Menu editMenu = new Menu("Edit"); MenuItem copy = new MenuItem("Copy (Jalview Only)"); MenuItem cut = new MenuItem("Cut (Jalview Only)"); MenuItem toUpper = new MenuItem("To Upper Case"); MenuItem toLower = new MenuItem("To Lower Case"); MenuItem toggleCase = new MenuItem("Toggle Case"); Menu outputmenu = new Menu(); Menu seqMenu = new Menu(); MenuItem pdb = new MenuItem(); MenuItem hideSeqs = new MenuItem(); MenuItem repGroup = new MenuItem(); MenuItem sequenceName = new MenuItem("Edit Name/Description"); MenuItem sequenceFeature = new MenuItem("Create Sequence Feature"); MenuItem editSequence = new MenuItem("Edit Sequence"); Sequence seq; MenuItem revealAll = new MenuItem(); Menu menu1 = new Menu(); public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) { /////////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to // edit or annotate a particular residue. Therefore display the residue menu // // If from the IDPanel, we must display the sequence menu ////////////////////////////////////////////////////////// this.ap = apanel; this.seq = seq; try { jbInit(); } catch (Exception e) { e.printStackTrace(); } for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) { MenuItem item = new MenuItem(jalview.io.AppletFormatAdapter. WRITEABLE_FORMATS[i]); item.addActionListener(this); outputmenu.add(item); } SequenceGroup sg = ap.av.getSelectionGroup(); if (sg != null && sg.getSize() > 0) { editGroupName.setLabel(sg.getName()); showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); if (!ap.av.alignment.getGroups().contains(sg)) { groupMenu.remove(unGroupMenuItem); } } else { remove(hideSeqs); remove(groupMenu); } if (links != null) { Menu linkMenu = new Menu("Link"); MenuItem item; String link; for (int i = 0; i < links.size(); i++) { link = links.elementAt(i).toString(); final String target = link.substring(0, link.indexOf("|")); item = new MenuItem(target); final String url; if (link.indexOf("$SEQUENCE_ID$") > -1) { String id = seq.getName(); if (id.indexOf("|") > -1) { id = id.substring(id.lastIndexOf("|") + 1); } url = link.substring(link.indexOf("|") + 1, link.indexOf("$SEQUENCE_ID$")) + id + link.substring(link.indexOf("$SEQUENCE_ID$") + 13); } else { url = link.substring(link.lastIndexOf("|") + 1); } item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { ap.alignFrame.showURL(url, target); } }); linkMenu.add(item); } if (seq != null) { seqMenu.add(linkMenu); } else { add(linkMenu); } } if (seq != null) { seqMenu.setLabel(seq.getName()); repGroup.setLabel("Represent Group with " + seq.getName()); } else { remove(seqMenu); } if (!ap.av.hasHiddenRows) { remove(revealAll); } } public void itemStateChanged(ItemEvent evt) { if (evt.getSource() == abovePIDColour) { abovePIDColour_itemStateChanged(); } else if (evt.getSource() == showColourText) { showColourText_itemStateChanged(); } else if (evt.getSource() == showText) { showText_itemStateChanged(); } else if (evt.getSource() == showBoxes) { showBoxes_itemStateChanged(); } } public void actionPerformed(ActionEvent evt) { Object source = evt.getSource(); if (source == clustalColour) { clustalColour_actionPerformed(); } else if (source == zappoColour) { zappoColour_actionPerformed(); } else if (source == taylorColour) { taylorColour_actionPerformed(); } else if (source == hydrophobicityColour) { hydrophobicityColour_actionPerformed(); } else if (source == helixColour) { helixColour_actionPerformed(); } else if (source == strandColour) { strandColour_actionPerformed(); } else if (source == turnColour) { turnColour_actionPerformed(); } else if (source == buriedColour) { buriedColour_actionPerformed(); } else if (source == nucleotideMenuItem) { nucleotideMenuItem_actionPerformed(); } else if (source == userDefinedColour) { userDefinedColour_actionPerformed(); } else if (source == PIDColour) { PIDColour_actionPerformed(); } else if (source == BLOSUM62Colour) { BLOSUM62Colour_actionPerformed(); } else if (source == noColourmenuItem) { noColourmenuItem_actionPerformed(); } else if (source == conservationMenuItem) { conservationMenuItem_itemStateChanged(); } else if (source == unGroupMenuItem) { unGroupMenuItem_actionPerformed(); } else if (source == sequenceName) { editName(); } else if (source == pdb) { addPDB(); } else if (source == hideSeqs) { hideSequences(false); } else if (source == repGroup) { hideSequences(true); } else if (source == revealAll) { ap.av.showAllHiddenSeqs(); } else if (source == editGroupName) { EditNameDialog dialog = new EditNameDialog( getGroup().getName(), getGroup().getDescription(), " Group Name", "Group Description", ap.alignFrame, "Edit Group Name / Description", 500,100, true); if (dialog.accept) { getGroup().setName(dialog.getName().replace(' ', '_')); getGroup().setDescription(dialog.getDescription()); } } else if (source == copy) { ap.alignFrame.copy_actionPerformed(); } else if (source == cut) { ap.alignFrame.cut_actionPerformed(); } else if(source == editSequence) { SequenceGroup sg = ap.av.getSelectionGroup(); if(sg!=null) { if (seq == null) seq = (Sequence) sg.getSequenceAt(0); EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString( sg.getStartRes(), sg.getEndRes() + 1), null, "Edit Sequence ", null, ap.alignFrame, "Edit Sequence", 500, 100, true); if (dialog.accept) { EditCommand editCommand = new EditCommand( "Edit Sequences", EditCommand.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.hiddenRepSequences), sg.getStartRes(), sg.getEndRes()+1, ap.av.alignment ); ap.alignFrame.addHistoryItem(editCommand); ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences()); } } } else if (source == toUpper || source == toLower || source == toggleCase) { SequenceGroup sg = ap.av.getSelectionGroup(); Vector regions = new Vector(); if (sg != null) { int start = sg.getStartRes(); int end = sg.getEndRes() + 1; do { if (ap.av.hasHiddenColumns) { if (start == 0) { start = ap.av.colSel.adjustForHiddenColumns(start); } end = ap.av.colSel.getHiddenBoundaryRight(start); if (start == end) { end = sg.getEndRes() + 1; } if (end > sg.getEndRes()) { end = sg.getEndRes() + 1; } } regions.addElement(new int[] {start, end}); if (ap.av.hasHiddenColumns) { start = ap.av.colSel.adjustForHiddenColumns(end); start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; } } while (end < sg.getEndRes()); int[][] startEnd = new int[regions.size()][2]; for (int i = 0; i < regions.size(); i++) { startEnd[i] = (int[]) regions.elementAt(i); } String description; int caseChange; if (source == toggleCase) { description = "Toggle Case"; caseChange = ChangeCaseCommand.TOGGLE_CASE; } else if (source == toUpper) { description = "To Upper Case"; caseChange = ChangeCaseCommand.TO_UPPER; } else { description = "To Lower Case"; caseChange = ChangeCaseCommand.TO_LOWER; } ChangeCaseCommand caseCommand = new ChangeCaseCommand( description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, caseChange ); ap.alignFrame.addHistoryItem(caseCommand); ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences()); } } else if(source == sequenceFeature) { SequenceGroup sg = ap.av.getSelectionGroup(); if (sg == null) { return; } int gSize = sg.getSize(); SequenceI[] seqs = new SequenceI[gSize]; SequenceFeature[] features = new SequenceFeature[gSize]; for (int i = 0; i < gSize; i++) { seqs[i] = sg.getSequenceAt(i); int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); features[i] = new SequenceFeature(null, null, null, start, end, "Jalview"); } if (ap.seqPanel.seqCanvas.getFeatureRenderer() .amendFeatures(seqs, features, true, ap)) { ap.alignFrame.sequenceFeatures.setState(true); ap.av.showSequenceFeatures(true); ap.highlightSearchResults(null); } } else { outputText(evt); } } void outputText(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Selection output - " + e.getActionCommand(), 600, 500); cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( e.getActionCommand(), new Alignment(ap.av.getSelectionAsNewSequence()), ap.av.showJVSuffix)); } void editName() { EditNameDialog dialog = new EditNameDialog( seq.getName(), seq.getDescription(), " Sequence Name", "Sequence Description", ap.alignFrame, "Edit Sequence Name / Description", 500,100, true); if (dialog.accept) { seq.setName(dialog.getName()); seq.setDescription(dialog.getDescription()); ap.paintAlignment(false); } } void addPDB() { if(seq.getPDBId()!=null) { PDBEntry entry = (PDBEntry)seq.getPDBId().firstElement(); if ( ap.av.applet.jmolAvailable ) new jalview.appletgui.AppletJmol(entry, new Sequence[]{seq}, null, ap, AppletFormatAdapter.URL); else new MCview.AppletPDBViewer(entry, new Sequence[]{seq}, null, ap, AppletFormatAdapter.URL); } else { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); cap.setText("Paste your PDB file here."); cap.setPDBImport(seq); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300); } } private void jbInit() throws Exception { groupMenu.setLabel("Group"); groupMenu.setLabel("Selection"); sequenceFeature.addActionListener(this); editGroupName.addActionListener(this); unGroupMenuItem.setLabel("Remove Group"); unGroupMenuItem.addActionListener(this); nucleotideMenuItem.setLabel("Nucleotide"); nucleotideMenuItem.addActionListener(this); conservationMenuItem.addItemListener(this); abovePIDColour.addItemListener(this); colourMenu.setLabel("Group Colour"); showBoxes.setLabel("Boxes"); showBoxes.setState(true); showBoxes.addItemListener(this); sequenceName.addActionListener(this); showText.setLabel("Text"); showText.addItemListener(this); showColourText.setLabel("Colour Text"); showColourText.addItemListener(this); outputmenu.setLabel("Output to Textbox..."); seqMenu.setLabel("Sequence"); pdb.setLabel("View PDB Structure"); hideSeqs.setLabel("Hide Sequences"); repGroup.setLabel("Represent Group with"); revealAll.setLabel("Reveal All"); menu1.setLabel("Group"); add(groupMenu); this.add(seqMenu); this.add(hideSeqs); this.add(revealAll); groupMenu.add(editGroupName); groupMenu.add(editMenu); groupMenu.add(outputmenu); groupMenu.add(sequenceFeature); groupMenu.add(menu1); 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(nucleotideMenuItem); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(abovePIDColour); colourMenu.add(conservationMenuItem); noColourmenuItem.setLabel("None"); noColourmenuItem.addActionListener(this); clustalColour.setLabel("Clustalx colours"); 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); abovePIDColour.setLabel("Above % Identity"); userDefinedColour.setLabel("User Defined"); userDefinedColour.addActionListener(this); PIDColour.setLabel("Percentage Identity"); PIDColour.addActionListener(this); BLOSUM62Colour.setLabel("BLOSUM62"); BLOSUM62Colour.addActionListener(this); conservationMenuItem.setLabel("Conservation"); editMenu.add(copy); copy.addActionListener(this); editMenu.add(cut); cut.addActionListener(this); editMenu.add(editSequence); editSequence.addActionListener(this); editMenu.add(toUpper); toUpper.addActionListener(this); editMenu.add(toLower); toLower.addActionListener(this); editMenu.add(toggleCase); seqMenu.add(sequenceName); seqMenu.add(pdb); seqMenu.add(repGroup); menu1.add(unGroupMenuItem); menu1.add(colourMenu); menu1.add(showBoxes); menu1.add(showText); menu1.add(showColourText); toggleCase.addActionListener(this); pdb.addActionListener(this); hideSeqs.addActionListener(this); repGroup.addActionListener(this); revealAll.addActionListener(this); } void refresh() { ap.paintAlignment(true); } protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences), ap.av.alignment.getWidth()); refresh(); } protected void zappoColour_actionPerformed() { getGroup().cs = new ZappoColourScheme(); refresh(); } protected void taylorColour_actionPerformed() { getGroup().cs = new TaylorColourScheme(); refresh(); } protected void hydrophobicityColour_actionPerformed() { getGroup().cs = new HydrophobicColourScheme(); refresh(); } protected void helixColour_actionPerformed() { getGroup().cs = new HelixColourScheme(); refresh(); } protected void strandColour_actionPerformed() { getGroup().cs = new StrandColourScheme(); refresh(); } protected void turnColour_actionPerformed() { getGroup().cs = new TurnColourScheme(); refresh(); } protected void buriedColour_actionPerformed() { getGroup().cs = new BuriedColourScheme(); refresh(); } public void nucleotideMenuItem_actionPerformed() { getGroup().cs = new NucleotideColourScheme(); refresh(); } protected void abovePIDColour_itemStateChanged() { SequenceGroup sg = getGroup(); if (sg.cs == null) { return; } if (abovePIDColour.getState()) { sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av. hiddenRepSequences), 0, ap.av.alignment.getWidth())); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); SliderPanel.showPIDSlider(); } else // remove PIDColouring { sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); } refresh(); } protected void userDefinedColour_actionPerformed() { new UserDefinedColours(ap, getGroup()); } protected void PIDColour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av. hiddenRepSequences), 0, ap.av.alignment.getWidth())); refresh(); } protected void BLOSUM62Colour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new Blosum62ColourScheme(); sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av. hiddenRepSequences), 0, ap.av.alignment.getWidth())); refresh(); } protected void noColourmenuItem_actionPerformed() { getGroup().cs = null; refresh(); } protected void conservationMenuItem_itemStateChanged() { SequenceGroup sg = getGroup(); if (sg.cs == null) { return; } if (conservationMenuItem.getState()) { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, sg.getSequences(ap.av. hiddenRepSequences), 0, ap.av.alignment.getWidth()); c.calculate(); c.verdict(false, ap.av.ConsPercGaps); sg.cs.setConservation(c); SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); SliderPanel.showConservationSlider(); } else // remove ConservationColouring { sg.cs.setConservation(null); } refresh(); } SequenceGroup getGroup() { SequenceGroup sg = ap.av.getSelectionGroup(); // this method won't add a new group if it already exists if (sg != null) { ap.av.alignment.addGroup(sg); } return sg; } void unGroupMenuItem_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); ap.av.alignment.deleteGroup(sg); ap.av.setSelectionGroup(null); ap.paintAlignment(true); } public void showColourText_itemStateChanged() { getGroup().setColourText(showColourText.getState()); refresh(); } public void showText_itemStateChanged() { getGroup().setDisplayText(showText.getState()); refresh(); } public void showBoxes_itemStateChanged() { getGroup().setDisplayBoxes(showBoxes.getState()); refresh(); } void hideSequences(boolean representGroup) { SequenceGroup sg = ap.av.getSelectionGroup(); if (sg == null || sg.getSize() < 1) { ap.av.hideSequence(new SequenceI[] {seq}); return; } ap.av.setSelectionGroup(null); if (representGroup) { ap.av.hideRepSequences(seq, sg); return; } int gsize = sg.getSize(); SequenceI[] hseqs; hseqs = new SequenceI[gsize]; int index = 0; for (int i = 0; i < gsize; i++) { hseqs[index++] = sg.getSequenceAt(i); } ap.av.hideSequence(hseqs); } }