/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview 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 3 * of the License, or (at your option) any later version. * * Jalview 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 Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.util.*; import java.awt.*; import java.awt.event.*; import javax.swing.*; import jalview.analysis.*; import jalview.commands.*; import jalview.datamodel.*; import jalview.io.*; import jalview.schemes.*; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; import jalview.util.UrlLink; /** * DOCUMENT ME! * * @author $author$ * @version $Revision: 1.118 $ */ public class PopupMenu extends JPopupMenu { JMenu groupMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); // protected JRadioButtonMenuItem covariationColour = new // JRadioButtonMenuItem(); JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); AlignmentPanel ap; JMenu sequenceMenu = new JMenu(); JMenuItem sequenceName = new JMenuItem(); JMenuItem sequenceDetails = new JMenuItem(); JMenuItem sequenceSelDetails = new JMenuItem(); SequenceI sequence; JMenuItem createGroupMenuItem = new JMenuItem(); JMenuItem unGroupMenuItem = new JMenuItem(); JMenuItem outline = new JMenuItem(); JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); JMenu colourMenu = new JMenu(); JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); JCheckBoxMenuItem showText = new JCheckBoxMenuItem(); JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem(); JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem(); JMenu editMenu = new JMenu(); JMenuItem cut = new JMenuItem(); JMenuItem copy = new JMenuItem(); JMenuItem upperCase = new JMenuItem(); JMenuItem lowerCase = new JMenuItem(); JMenuItem toggle = new JMenuItem(); JMenu pdbMenu = new JMenu(); JMenuItem pdbFromFile = new JMenuItem(); // JBPNote: Commented these out - Should add these services via the web // services menu system. // JMenuItem ContraFold = new JMenuItem(); // JMenuItem RNAFold = new JMenuItem(); JMenuItem enterPDB = new JMenuItem(); JMenuItem discoverPDB = new JMenuItem(); JMenu outputMenu = new JMenu(); JMenuItem sequenceFeature = new JMenuItem(); JMenuItem textColour = new JMenuItem(); JMenu jMenu1 = new JMenu(); JMenu structureMenu = new JMenu(); JMenu viewStructureMenu = new JMenu(); // JMenu colStructureMenu = new JMenu(); JMenuItem editSequence = new JMenuItem(); // JMenuItem annotationMenuItem = new JMenuItem(); JMenu groupLinksMenu; /** * Creates a new PopupMenu object. * * @param ap * DOCUMENT ME! * @param seq * DOCUMENT ME! */ public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) { this(ap, seq, links, null); } /** * * @param ap * @param seq * @param links * @param groupLinks */ public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links, Vector groupLinks) { // ///////////////////////////////////////////////////////// // 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 = ap; sequence = seq; ButtonGroup colours = new ButtonGroup(); colours.add(noColourmenuItem); colours.add(clustalColour); colours.add(zappoColour); colours.add(taylorColour); colours.add(hydrophobicityColour); colours.add(helixColour); colours.add(strandColour); colours.add(turnColour); colours.add(buriedColour); colours.add(abovePIDColour); colours.add(userDefinedColour); colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(purinePyrimidineColour); colours.add(RNAInteractionColour); // colours.add(covariationColour); for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); } }); outputMenu.add(item); } try { jbInit(); } catch (Exception e) { e.printStackTrace(); } JMenuItem menuItem; if (seq != null) { sequenceMenu.setText(sequence.getName()); if (seq.getDatasetSequence().getPDBId() != null && seq.getDatasetSequence().getPDBId().size() > 0) { java.util.Enumeration e = seq.getDatasetSequence().getPDBId() .elements(); while (e.hasMoreElements()) { final PDBEntry pdb = (PDBEntry) e.nextElement(); menuItem = new JMenuItem(); menuItem.setText(pdb.getId()); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { // TODO re JAL-860: optionally open dialog or provide a menu entry // allowing user to open just one structure per sequence new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap); // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE); } }); viewStructureMenu.add(menuItem); /* * menuItem = new JMenuItem(); menuItem.setText(pdb.getId()); * menuItem.addActionListener(new java.awt.event.ActionListener() { * public void actionPerformed(ActionEvent e) { * colourByStructure(pdb.getId()); } }); * colStructureMenu.add(menuItem); */ } } else { if (ap.av.getAlignment().isNucleotide() == false) { structureMenu.remove(viewStructureMenu); } // structureMenu.remove(colStructureMenu); } if (ap.av.getAlignment().isNucleotide() == true) { AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); for (int i = 0; i < aa.length; i++) { if (aa[i].getRNAStruc() != null) { final String rnastruc = aa[i].getRNAStruc(); final String structureLine = aa[i].label; menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( "label.2d_rna_structure_line", new String[] { structureLine })); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { // System.out.println("1:"+structureLine); System.out.println("1:sname" + seq.getName()); System.out.println("2:seq" + seq); // System.out.println("3:"+seq.getSequenceAsString()); System.out.println("3:strucseq" + rnastruc); // System.out.println("4:struc"+seq.getRNA()); System.out.println("5:name" + seq.getName()); System.out.println("6:ap" + ap); new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq.getName(), ap); // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), // seq.getName(), ap); System.out.println("end"); } }); viewStructureMenu.add(menuItem); } } // SequenceFeatures[] test = seq.getSequenceFeatures(); if (seq.getAnnotation() != null) { AlignmentAnnotation seqAnno[] = seq.getAnnotation(); for (int i = 0; i < seqAnno.length; i++) { if (seqAnno[i].getRNAStruc() != null) { final String rnastruc = seqAnno[i].getRNAStruc(); // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( "label.2d_rna_sequence_name", new String[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { // TODO: VARNA does'nt print gaps in the sequence new AppVarna(seq.getName() + " structure", seq, seq .getSequenceAsString(), rnastruc, seq.getName(), ap); } }); viewStructureMenu.add(menuItem); } } } } menuItem = new JMenuItem( MessageManager.getString("action.hide_sequences")); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { hideSequences(false); } }); add(menuItem); if (ap.av.getSelectionGroup() != null && ap.av.getSelectionGroup().getSize() > 1) { menuItem = new JMenuItem(MessageManager.formatMessage( "label.represent_group_with", new String[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { hideSequences(true); } }); sequenceMenu.add(menuItem); } if (ap.av.hasHiddenRows()) { final int index = ap.av.getAlignment().findIndex(seq); if (ap.av.adjustForHiddenSeqs(index) - ap.av.adjustForHiddenSeqs(index - 1) > 1) { menuItem = new JMenuItem( MessageManager.getString("action.reveal_sequences")); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { ap.av.showSequence(index); if (ap.overviewPanel != null) { ap.overviewPanel.updateOverviewImage(); } } }); add(menuItem); } } } // for the case when no sequences are even visible if (ap.av.hasHiddenRows()) { { menuItem = new JMenuItem( MessageManager.getString("action.reveal_all")); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { ap.av.showAllHiddenSeqs(); if (ap.overviewPanel != null) { ap.overviewPanel.updateOverviewImage(); } } }); add(menuItem); } } SequenceGroup sg = ap.av.getSelectionGroup(); boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment() .getGroups().contains(sg) : false; if (sg != null && sg.getSize() > 0) { groupName.setText(MessageManager.formatMessage("label.name_param", new String[] { sg.getName() })); groupName.setText(MessageManager .getString("label.edit_name_and_description_current_group")); if (sg.cs instanceof ZappoColourScheme) { zappoColour.setSelected(true); } else if (sg.cs instanceof TaylorColourScheme) { taylorColour.setSelected(true); } else if (sg.cs instanceof PIDColourScheme) { PIDColour.setSelected(true); } else if (sg.cs instanceof Blosum62ColourScheme) { BLOSUM62Colour.setSelected(true); } else if (sg.cs instanceof UserColourScheme) { userDefinedColour.setSelected(true); } else if (sg.cs instanceof HydrophobicColourScheme) { hydrophobicityColour.setSelected(true); } else if (sg.cs instanceof HelixColourScheme) { helixColour.setSelected(true); } else if (sg.cs instanceof StrandColourScheme) { strandColour.setSelected(true); } else if (sg.cs instanceof TurnColourScheme) { turnColour.setSelected(true); } else if (sg.cs instanceof BuriedColourScheme) { buriedColour.setSelected(true); } else if (sg.cs instanceof ClustalxColourScheme) { clustalColour.setSelected(true); } else if (sg.cs instanceof PurinePyrimidineColourScheme) { purinePyrimidineColour.setSelected(true); } /* * else if (sg.cs instanceof CovariationColourScheme) { * covariationColour.setSelected(true); } */ else { noColourmenuItem.setSelected(true); } if (sg.cs != null && sg.cs.conservationApplied()) { conservationMenuItem.setSelected(true); } displayNonconserved.setSelected(sg.getShowNonconserved()); showText.setSelected(sg.getDisplayText()); showColourText.setSelected(sg.getColourText()); showBoxes.setSelected(sg.getDisplayBoxes()); // add any groupURLs to the groupURL submenu and make it visible if (groupLinks != null && groupLinks.size() > 0) { buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection Hashtable pdbe = new Hashtable(), reppdb = new Hashtable(); SequenceI sqass = null; for (SequenceI sq : ap.av.getSequenceSelection()) { Vector pes = (Vector) sq.getDatasetSequence() .getPDBId(); if (pes != null && pes.size()>0) { reppdb.put(pes.get(0).getId(), pes.get(0)); for (PDBEntry pe : pes) { pdbe.put(pe.getId(), pe); if (sqass == null) { sqass = sq; } } } } if (pdbe.size() > 0) { final PDBEntry[] pe = pdbe.values().toArray( new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray( new PDBEntry[reppdb.size()]); final JMenuItem gpdbview, rpdbview; if (pdbe.size() == 1) { structureMenu.add(gpdbview = new JMenuItem(MessageManager .formatMessage("label.view_structure_for", new String[] { sqass.getDisplayId(false) }))); } else { structureMenu.add(gpdbview = new JMenuItem(MessageManager .formatMessage("label.view_all_structures", new String[] { new Integer(pdbe.size()).toString() }))); } gpdbview.setToolTipText(MessageManager .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment")); gpdbview.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { new AppJmol(ap, pe, ap.av.collateForPDB(pe)); } }); if (reppdb.size() > 1 && reppdb.size() < pdbe.size()) { structureMenu.add(rpdbview = new JMenuItem(MessageManager .formatMessage( "label.view_all_representative_structures", new String[] { new Integer(reppdb.size()).toString() }))); rpdbview.setToolTipText(MessageManager .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment")); rpdbview.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { new AppJmol(ap, pr, ap.av.collateForPDB(pr)); } }); } } } else { groupMenu.setVisible(false); editMenu.setVisible(false); } if (!isDefinedGroup) { createGroupMenuItem.setVisible(true); unGroupMenuItem.setVisible(false); jMenu1.setText(MessageManager.getString("action.edit_new_group")); } else { createGroupMenuItem.setVisible(false); unGroupMenuItem.setVisible(true); jMenu1.setText(MessageManager.getString("action.edit_group")); } if (seq == null) { sequenceMenu.setVisible(false); structureMenu.setVisible(false); } if (links != null && links.size() > 0) { JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); Vector linkset = new Vector(); for (int i = 0; i < links.size(); i++) { String link = links.elementAt(i).toString(); UrlLink urlLink = null; try { urlLink = new UrlLink(link); } catch (Exception foo) { jalview.bin.Cache.log.error("Exception for URLLink '" + link + "'", foo); continue; } ; if (!urlLink.isValid()) { jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); continue; } final String label = urlLink.getLabel(); if (seq != null && urlLink.isDynamic()) { // collect matching db-refs DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( seq.getDBRef(), new String[] { urlLink.getTarget() }); // collect id string too String id = seq.getName(); String descr = seq.getDescription(); if (descr != null && descr.length() < 1) { descr = null; } if (dbr != null) { for (int r = 0; r < dbr.length; r++) { if (id != null && dbr[r].getAccessionId().equals(id)) { // suppress duplicate link creation for the bare sequence ID // string with this link id = null; } // create Bare ID link for this RUL String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true); if (urls != null) { for (int u = 0; u < urls.length; u += 2) { if (!linkset.contains(urls[u] + "|" + urls[u + 1])) { linkset.addElement(urls[u] + "|" + urls[u + 1]); addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]); } } } } } if (id != null) { // create Bare ID link for this RUL String[] urls = urlLink.makeUrls(id, true); if (urls != null) { for (int u = 0; u < urls.length; u += 2) { if (!linkset.contains(urls[u] + "|" + urls[u + 1])) { linkset.addElement(urls[u] + "|" + urls[u + 1]); addshowLink(linkMenu, label, urls[u + 1]); } } } } // Create urls from description but only for URL links which are regex // links if (descr != null && urlLink.getRegexReplace() != null) { // create link for this URL from description where regex matches String[] urls = urlLink.makeUrls(descr, true); if (urls != null) { for (int u = 0; u < urls.length; u += 2) { if (!linkset.contains(urls[u] + "|" + urls[u + 1])) { linkset.addElement(urls[u] + "|" + urls[u + 1]); addshowLink(linkMenu, label, urls[u + 1]); } } } } } else { if (!linkset.contains(label + "|" + urlLink.getUrl_prefix())) { linkset.addElement(label + "|" + urlLink.getUrl_prefix()); // Add a non-dynamic link addshowLink(linkMenu, label, urlLink.getUrl_prefix()); } } } if (sequence != null) { sequenceMenu.add(linkMenu); } else { add(linkMenu); } } } private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks) { // TODO: usability: thread off the generation of group url content so root // menu appears asap // sequence only URLs // ID/regex match URLs groupLinksMenu = new JMenu( MessageManager.getString("action.group_link")); JMenu[] linkMenus = new JMenu[] { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")), new JMenu(MessageManager.getString("action.ids_sequences")) }; // three // types // of url // that // might // be // created. SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); String[][] idandseqs = GroupUrlLink.formStrings(seqs); Hashtable commonDbrefs = new Hashtable(); for (int sq = 0; sq < seqs.length; sq++) { int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq] .findPosition(sg.getEndRes()); // just collect ids from dataset sequence // TODO: check if IDs collected from selecton group intersects with the // current selection, too SequenceI sqi = seqs[sq]; while (sqi.getDatasetSequence() != null) { sqi = sqi.getDatasetSequence(); } DBRefEntry[] dbr = sqi.getDBRef(); if (dbr != null && dbr.length > 0) { for (int d = 0; d < dbr.length; d++) { String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(); Object[] sarray = (Object[]) commonDbrefs.get(src); if (sarray == null) { sarray = new Object[2]; sarray[0] = new int[] { 0 }; sarray[1] = new String[seqs.length]; commonDbrefs.put(src, sarray); } if (((String[]) sarray[1])[sq] == null) { if (!dbr[d].hasMap() || (dbr[d].getMap().locateMappedRange(start, end) != null)) { ((String[]) sarray[1])[sq] = dbr[d].getAccessionId(); ((int[]) sarray[0])[0]++; } } } } } // now create group links for all distinct ID/sequence sets. boolean addMenu = false; // indicates if there are any group links to give // to user for (int i = 0; i < groupLinks.size(); i++) { String link = groupLinks.elementAt(i).toString(); GroupUrlLink urlLink = null; try { urlLink = new GroupUrlLink(link); } catch (Exception foo) { jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link + "'", foo); continue; } ; if (!urlLink.isValid()) { jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); continue; } final String label = urlLink.getLabel(); boolean usingNames = false; // Now see which parts of the group apply for this URL String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget()); Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase()); String[] seqstr, ids; // input to makeUrl if (idset != null) { int numinput = ((int[]) idset[0])[0]; String[] allids = ((String[]) idset[1]); seqstr = new String[numinput]; ids = new String[numinput]; for (int sq = 0, idcount = 0; sq < seqs.length; sq++) { if (allids[sq] != null) { ids[idcount] = allids[sq]; seqstr[idcount++] = idandseqs[1][sq]; } } } else { // just use the id/seq set seqstr = idandseqs[1]; ids = idandseqs[0]; usingNames = true; } // and try and make the groupURL! Object[] urlset = null; try { urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview" + System.currentTimeMillis(), false); } catch (UrlStringTooLongException e) { } if (urlset != null) { int type = urlLink.getGroupURLType() & 3; // System.out.println(urlLink.getGroupURLType() // +" "+((String[])urlset[3])[0]); // first two bits ofurlLink type bitfield are sequenceids and sequences // TODO: FUTURE: ensure the groupURL menu structure can be generalised addshowLink(linkMenus[type], label + (((type & 1) == 1) ? ("(" + (usingNames ? "Names" : ltarget) + ")") : ""), urlLink, urlset); addMenu = true; } } if (addMenu) { groupLinksMenu = new JMenu( MessageManager.getString("action.group_link")); for (int m = 0; m < linkMenus.length; m++) { if (linkMenus[m] != null && linkMenus[m].getMenuComponentCount() > 0) { groupLinksMenu.add(linkMenus[m]); } } groupMenu.add(groupLinksMenu); } } /** * add a show URL menu item to the given linkMenu * * @param linkMenu * @param label * - menu label string * @param url * - url to open */ private void addshowLink(JMenu linkMenu, String label, final String url) { JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( "label.open_url_param", new String[] { url })); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { public void run() { showLink(url); } }).start(); } }); linkMenu.add(item); } /** * add a late bound groupURL item to the given linkMenu * * @param linkMenu * @param label * - menu label string * @param urlgenerator * GroupURLLink used to generate URL * @param urlstub * Object array returned from the makeUrlStubs function. */ private void addshowLink(JMenu linkMenu, String label, final GroupUrlLink urlgenerator, final Object[] urlstub) { JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( "label.open_url_seqs_param", new Object[] { urlgenerator.getUrl_prefix(), urlgenerator.getNumberInvolved(urlstub) })); // TODO: put in info about what is being sent. item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { public void run() { try { showLink(urlgenerator.constructFrom(urlstub)); } catch (UrlStringTooLongException e) { } } }).start(); } }); linkMenu.add(item); } /** * DOCUMENT ME! * * @throws Exception * DOCUMENT ME! */ private void jbInit() throws Exception { groupMenu.setText(MessageManager.getString("label.group")); groupMenu.setText(MessageManager.getString("label.selection")); groupName.setText(MessageManager.getString("label.name")); groupName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { groupName_actionPerformed(); } }); sequenceMenu.setText(MessageManager.getString("label.sequence")); sequenceName.setText(MessageManager .getString("label.edit_name_description")); sequenceName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { sequenceName_actionPerformed(); } }); sequenceDetails.setText(MessageManager .getString("label.sequence_details") + "..."); sequenceDetails.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { sequenceDetails_actionPerformed(); } }); sequenceSelDetails.setText(MessageManager .getString("label.sequence_details") + "..."); sequenceSelDetails .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { sequenceSelectionDetails_actionPerformed(); } }); PIDColour.setFocusPainted(false); unGroupMenuItem .setText(MessageManager.getString("action.remove_group")); unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { unGroupMenuItem_actionPerformed(); } }); createGroupMenuItem.setText(MessageManager .getString("action.create_group")); createGroupMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { createGroupMenuItem_actionPerformed(); } }); outline.setText(MessageManager.getString("action.border_colour")); outline.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { outline_actionPerformed(); } }); nucleotideMenuItem .setText(MessageManager.getString("label.nucleotide")); nucleotideMenuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { nucleotideMenuItem_actionPerformed(); } }); colourMenu.setText(MessageManager.getString("label.group_colour")); showBoxes.setText(MessageManager.getString("action.boxes")); showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showBoxes_actionPerformed(); } }); showText.setText(MessageManager.getString("action.text")); showText.setState(true); showText.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showText_actionPerformed(); } }); showColourText.setText(MessageManager.getString("label.colour_text")); showColourText.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showColourText_actionPerformed(); } }); displayNonconserved.setText(MessageManager .getString("label.show_non_conversed")); displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showNonconserved_actionPerformed(); } }); editMenu.setText(MessageManager.getString("action.edit")); cut.setText(MessageManager.getString("action.cut")); cut.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { cut_actionPerformed(); } }); upperCase.setText(MessageManager.getString("label.to_upper_case")); upperCase.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { changeCase(e); } }); copy.setText(MessageManager.getString("action.copy")); copy.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { copy_actionPerformed(); } }); lowerCase.setText(MessageManager.getString("label.to_lower_case")); lowerCase.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { changeCase(e); } }); toggle.setText(MessageManager.getString("label.toggle_case")); toggle.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { changeCase(e); } }); pdbMenu.setText(MessageManager .getString("label.associate_structure_with_sequence")); pdbFromFile.setText(MessageManager.getString("label.from_file")); pdbFromFile.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { pdbFromFile_actionPerformed(); } }); // RNAFold.setText("From RNA Fold with predict2D"); // RNAFold.addActionListener(new ActionListener() // { // public void actionPerformed(ActionEvent e) // { // try { // RNAFold_actionPerformed(); // } catch (Exception e1) { // // TODO Auto-generated catch block // e1.printStackTrace(); // } // } // }); // ContraFold.setText("From Contra Fold with predict2D"); // ContraFold.addActionListener(new ActionListener() // { // public void actionPerformed(ActionEvent e) // { // try { // ContraFold_actionPerformed(); // } catch (Exception e1) { // // TODO Auto-generated catch block // e1.printStackTrace(); // } // } // }); enterPDB.setText(MessageManager.getString("label.enter_pdb_id")); enterPDB.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { enterPDB_actionPerformed(); } }); discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids")); discoverPDB.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { discoverPDB_actionPerformed(); } }); outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "..."); sequenceFeature.setText(MessageManager .getString("label.create_sequence_feature")); sequenceFeature.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { sequenceFeature_actionPerformed(); } }); textColour.setText(MessageManager.getString("label.text_colour")); textColour.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { textColour_actionPerformed(); } }); jMenu1.setText(MessageManager.getString("label.group")); structureMenu.setText(MessageManager.getString("label.structure")); viewStructureMenu.setText(MessageManager .getString("label.view_structure")); // colStructureMenu.setText("Colour By Structure"); editSequence.setText(MessageManager.getString("label.edit_sequence") + "..."); editSequence.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) { editSequence_actionPerformed(actionEvent); } }); /* * annotationMenuItem.setText("By Annotation"); * annotationMenuItem.addActionListener(new ActionListener() { public void * actionPerformed(ActionEvent actionEvent) { * annotationMenuItem_actionPerformed(actionEvent); } }); */ groupMenu.add(sequenceSelDetails); add(groupMenu); add(sequenceMenu); this.add(structureMenu); groupMenu.add(editMenu); groupMenu.add(outputMenu); groupMenu.add(sequenceFeature); groupMenu.add(createGroupMenuItem); groupMenu.add(unGroupMenuItem); groupMenu.add(jMenu1); sequenceMenu.add(sequenceName); sequenceMenu.add(sequenceDetails); colourMenu.add(textColour); 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); if (ap.getAlignment().isNucleotide()) { // JBPNote - commented since the colourscheme isn't functional // colourMenu.add(RNAInteractionColour); colourMenu.add(purinePyrimidineColour); } // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) { java.util.Enumeration userColours = jalview.gui.UserDefinedColours .getUserColourSchemes().keys(); while (userColours.hasMoreElements()) { JMenuItem item = new JMenuItem(userColours.nextElement().toString()); item.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); } }); colourMenu.add(item); } } colourMenu.addSeparator(); colourMenu.add(abovePIDColour); colourMenu.add(conservationMenuItem); // colourMenu.add(annotationMenuItem); editMenu.add(copy); editMenu.add(cut); editMenu.add(editSequence); editMenu.add(upperCase); editMenu.add(lowerCase); editMenu.add(toggle); pdbMenu.add(pdbFromFile); // JBPNote: These shouldn't be added here - should appear in a generic // 'apply web service to this sequence menu' // pdbMenu.add(RNAFold); // pdbMenu.add(ContraFold); pdbMenu.add(enterPDB); pdbMenu.add(discoverPDB); jMenu1.add(groupName); jMenu1.add(colourMenu); jMenu1.add(showBoxes); jMenu1.add(showText); jMenu1.add(showColourText); jMenu1.add(outline); jMenu1.add(displayNonconserved); structureMenu.add(pdbMenu); structureMenu.add(viewStructureMenu); // structureMenu.add(colStructureMenu); noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { noColourmenuItem_actionPerformed(); } }); clustalColour.setText(MessageManager .getString("label.clustalx_colours")); clustalColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { clustalColour_actionPerformed(); } }); zappoColour.setText(MessageManager.getString("label.zappo")); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { zappoColour_actionPerformed(); } }); taylorColour.setText(MessageManager.getString("label.taylor")); taylorColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { taylorColour_actionPerformed(); } }); hydrophobicityColour.setText(MessageManager .getString("label.hydrophobicity")); hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { hydrophobicityColour_actionPerformed(); } }); helixColour.setText(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { helixColour_actionPerformed(); } }); strandColour.setText(MessageManager .getString("label.strand_propensity")); strandColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { strandColour_actionPerformed(); } }); turnColour.setText(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { turnColour_actionPerformed(); } }); buriedColour.setText(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { buriedColour_actionPerformed(); } }); abovePIDColour.setText(MessageManager .getString("label.above_identity_percentage")); abovePIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { abovePIDColour_actionPerformed(); } }); userDefinedColour.setText(MessageManager .getString("action.user_defined")); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { userDefinedColour_actionPerformed(e); } }); PIDColour .setText(MessageManager.getString("label.percentage_identity")); PIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { PIDColour_actionPerformed(); } }); BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { BLOSUM62Colour_actionPerformed(); } }); purinePyrimidineColour.setText(MessageManager .getString("label.purine_pyrimidine")); purinePyrimidineColour .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { purinePyrimidineColour_actionPerformed(); } }); /* * covariationColour.addActionListener(new java.awt.event.ActionListener() { * public void actionPerformed(ActionEvent e) { * covariationColour_actionPerformed(); } }); */ conservationMenuItem.setText(MessageManager .getString("label.conservation")); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { conservationMenuItem_actionPerformed(); } }); } protected void sequenceSelectionDetails_actionPerformed() { createSequenceDetailsReport(ap.av.getSequenceSelection()); } protected void sequenceDetails_actionPerformed() { createSequenceDetailsReport(new SequenceI[] { sequence }); } public void createSequenceDetailsReport(SequenceI[] sequences) { CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); StringBuffer contents = new StringBuffer(); for (SequenceI seq : sequences) { contents.append("

" + MessageManager .formatMessage( "label.create_sequence_details_report_annotation_for", new String[] { seq.getDisplayId(true) }) + "

"); new SequenceAnnotationReport(null) .createSequenceAnnotationReport( contents, seq, true, true, false, (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax : null); contents.append("

"); } cap.setText("" + contents.toString() + ""); Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage( "label.sequece_details_for", (sequences.length == 1 ? new String[] { sequences[0].getDisplayId(true) } : new String[] { MessageManager.getString("label.selection") })), 500, 400); } protected void showNonconserved_actionPerformed() { getGroup().setShowNonconserved(displayNonconserved.isSelected()); refresh(); } /** * call to refresh view after settings change */ void refresh() { ap.updateAnnotation(); ap.paintAlignment(true); PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void zappoColour_actionPerformed() { getGroup().cs = new ZappoColourScheme(); refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void taylorColour_actionPerformed() { getGroup().cs = new TaylorColourScheme(); refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void hydrophobicityColour_actionPerformed() { getGroup().cs = new HydrophobicColourScheme(); refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void helixColour_actionPerformed() { getGroup().cs = new HelixColourScheme(); refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void strandColour_actionPerformed() { getGroup().cs = new StrandColourScheme(); refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void turnColour_actionPerformed() { getGroup().cs = new TurnColourScheme(); refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void buriedColour_actionPerformed() { getGroup().cs = new BuriedColourScheme(); refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void nucleotideMenuItem_actionPerformed() { getGroup().cs = new NucleotideColourScheme(); refresh(); } protected void purinePyrimidineColour_actionPerformed() { getGroup().cs = new PurinePyrimidineColourScheme(); refresh(); } /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } */ /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void abovePIDColour_actionPerformed() { SequenceGroup sg = getGroup(); if (sg.cs == null) { return; } if (abovePIDColour.isSelected()) { sg.cs.setConsensus(AAFrequency.calculate( sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); 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(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void userDefinedColour_actionPerformed(ActionEvent e) { SequenceGroup sg = getGroup(); if (e.getSource().equals(userDefinedColour)) { new UserDefinedColours(ap, sg); } else { UserColourScheme udc = (UserColourScheme) UserDefinedColours .getUserColourSchemes().get(e.getActionCommand()); sg.cs = udc; } refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void PIDColour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void BLOSUM62Colour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new Blosum62ColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void noColourmenuItem_actionPerformed() { getGroup().cs = null; refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void conservationMenuItem_actionPerformed() { SequenceGroup sg = getGroup(); if (sg.cs == null) { return; } if (conservationMenuItem.isSelected()) { // JBPNote: Conservation name shouldn't be i18n translated Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, sg.getSequences(ap.av .getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); c.verdict(false, ap.av.getConsPercGaps()); sg.cs.setConservation(c); SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); SliderPanel.showConservationSlider(); } else // remove ConservationColouring { sg.cs.setConservation(null); } refresh(); } public void annotationMenuItem_actionPerformed(ActionEvent actionEvent) { SequenceGroup sg = getGroup(); if (sg == null) { return; } AnnotationColourGradient acg = new AnnotationColourGradient( sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD); acg.setPredefinedColours(true); sg.cs = acg; refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void groupName_actionPerformed() { SequenceGroup sg = getGroup(); EditNameDialog dialog = new EditNameDialog(sg.getName(), sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ", MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"), ap.alignFrame); if (!dialog.accept) { return; } sg.setName(dialog.getName()); sg.setDescription(dialog.getDescription()); refresh(); } /** * Get selection group - adding it to the alignment if necessary. * * @return sequence group to operate on */ SequenceGroup getGroup() { SequenceGroup sg = ap.av.getSelectionGroup(); // this method won't add a new group if it already exists if (sg != null) { ap.av.getAlignment().addGroup(sg); } return sg; } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ void sequenceName_actionPerformed() { EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ", MessageManager.getString("label.sequence_description") + " ", MessageManager .getString("label.edit_sequence_name_description"), ap.alignFrame); if (!dialog.accept) { return; } if (dialog.getName() != null) { if (dialog.getName().indexOf(" ") > -1) { JOptionPane .showMessageDialog( ap, MessageManager .getString("label.spaces_converted_to_backslashes"), MessageManager .getString("label.no_spaces_allowed_sequence_name"), JOptionPane.WARNING_MESSAGE); } sequence.setName(dialog.getName().replace(' ', '_')); ap.paintAlignment(false); } sequence.setDescription(dialog.getDescription()); ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() .getSequences()); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ void unGroupMenuItem_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); ap.av.getAlignment().deleteGroup(sg); ap.av.setSelectionGroup(null); refresh(); } void createGroupMenuItem_actionPerformed() { getGroup(); // implicitly creates group - note - should apply defaults / use // standard alignment window logic for this refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ protected void outline_actionPerformed() { SequenceGroup sg = getGroup(); Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"), Color.BLUE); if (col != null) { sg.setOutlineColour(col); } refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void showBoxes_actionPerformed() { getGroup().setDisplayBoxes(showBoxes.isSelected()); refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void showText_actionPerformed() { getGroup().setDisplayText(showText.isSelected()); refresh(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void showColourText_actionPerformed() { getGroup().setColourText(showColourText.isSelected()); refresh(); } public void showLink(String url) { try { jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } } void hideSequences(boolean representGroup) { SequenceGroup sg = ap.av.getSelectionGroup(); if (sg == null || sg.getSize() < 1) { ap.av.hideSequence(new SequenceI[] { sequence }); return; } ap.av.setSelectionGroup(null); if (representGroup) { ap.av.hideRepSequences(sequence, 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); // refresh(); TODO: ? needed ? ap.av.sendSelection(); } public void copy_actionPerformed() { ap.alignFrame.copy_actionPerformed(null); } public void cut_actionPerformed() { ap.alignFrame.cut_actionPerformed(null); } void changeCase(ActionEvent e) { Object source = e.getSource(); SequenceGroup sg = ap.av.getSelectionGroup(); if (sg != null) { int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(), sg.getEndRes() + 1); String description; int caseChange; if (source == toggle) { description = MessageManager.getString("label.toggle_case"); caseChange = ChangeCaseCommand.TOGGLE_CASE; } else if (source == upperCase) { description = MessageManager.getString("label.to_upper_case"); caseChange = ChangeCaseCommand.TO_UPPER; } else { description = MessageManager.getString("label.to_lower_case"); caseChange = ChangeCaseCommand.TO_LOWER; } ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() .getSequences()); } } public void outputText_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); Desktop.addInternalFrame(cap, MessageManager.formatMessage( "label.alignment_output_command", new String[] { e.getActionCommand() }), 600, 500); String[] omitHidden = null; System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens // or we simply trust the user wants // wysiwig behaviour SequenceGroup sg = ap.av.getSelectionGroup(); ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); omitHidden = ap.av.getViewAsString(true); Alignment oal = new Alignment(ap.av.getSequenceSelection()); AlignmentAnnotation[] nala = ap.av.getAlignment() .getAlignmentAnnotation(); if (nala != null) { for (int i = 0; i < nala.length; i++) { AlignmentAnnotation na = nala[i]; oal.addAnnotation(na); } } cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), oal, omitHidden, csel, sg)); oal = null; } public void pdbFromFile_actionPerformed() { jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle(MessageManager.formatMessage( "label.select_pdb_file_for", new String[] { sequence.getDisplayId(false) })); chooser.setToolTipText(MessageManager.formatMessage( "label.load_pdb_file_associate_with_sequence", new String[] { new Integer(sequence.getDisplayId(false)).toString() })); int value = chooser.showOpenDialog(null); if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true); } } // JBNote: commented out - these won't be instantiated here...! // public void RNAFold_actionPerformed() throws Exception // { // Predict2D P2D = new Predict2D(); // P2D.getStructure2DFromRNAFold("toto"); // } // // public void ContraFold_actionPerformed() throws Exception // { // Predict2D P2D = new Predict2D(); // P2D.getStructure2DFromContraFold("toto"); // } public void enterPDB_actionPerformed() { String id = JOptionPane.showInternalInputDialog(Desktop.desktop, MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE); if (id != null && id.length() > 0) { PDBEntry entry = new PDBEntry(); entry.setId(id.toUpperCase()); sequence.getDatasetSequence().addPDBId(entry); } } public void discoverPDB_actionPerformed() { final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] { sequence } : ap.av.getSequenceSelection()); Thread discpdb = new Thread(new Runnable() { public void run() { new jalview.ws.DBRefFetcher(sequences, ap.alignFrame) .fetchDBRefs(false); } }); discpdb.start(); } public void sequenceFeature_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); if (sg == null) { return; } int rsize = 0, gSize = sg.getSize(); SequenceI[] rseqs, seqs = new SequenceI[gSize]; SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; for (int i = 0; i < gSize; i++) { int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); if (start <= end) { seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); features[rsize] = new SequenceFeature(null, null, null, start, end, "Jalview"); rsize++; } } rseqs = new SequenceI[rsize]; tfeatures = new SequenceFeature[rsize]; System.arraycopy(seqs, 0, rseqs, 0, rsize); System.arraycopy(features, 0, tfeatures, 0, rsize); features = tfeatures; seqs = rseqs; if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, true, ap)) { ap.alignFrame.setShowSeqFeatures(true); ap.highlightSearchResults(null); } } public void textColour_actionPerformed() { SequenceGroup sg = getGroup(); if (sg != null) { new TextColourChooser().chooseColour(ap, sg); } } public void colourByStructure(String pdbid) { Annotation[] anots = ap.av.getStructureSelectionManager() .colourSequenceFromStructure(sequence, pdbid); AlignmentAnnotation an = new AlignmentAnnotation("Structure", "Coloured by " + pdbid, anots); ap.av.getAlignment().addAnnotation(an); an.createSequenceMapping(sequence, 0, true); // an.adjustForAlignment(); ap.av.getAlignment().setAnnotationIndex(an, 0); ap.adjustAnnotationHeight(); sequence.addAlignmentAnnotation(an); } public void editSequence_actionPerformed(ActionEvent actionEvent) { SequenceGroup sg = ap.av.getSelectionGroup(); if (sg != null) { if (sequence == null) sequence = (Sequence) sg.getSequenceAt(0); EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null, MessageManager.getString("label.edit_sequence"), ap.alignFrame); if (dialog.accept) { EditCommand editCommand = new EditCommand( MessageManager.getString("label.edit_sequences"), EditCommand.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand); ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() .getSequences()); } } } }