X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=e86b2c5c69e4b0ea838cfa9d1d043346f7441143;hb=7f8ddabd82dcf91860e0a8dc972cfd1ab6c59fc5;hp=a7f070dedc9433befb0a1a4aa50377bc00baf39b;hpb=4cea7a0328724b90a6a7c16ae8c926e0cc12cedd;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index a7f070d..e86b2c5 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,2079 +1,2568 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle - * - * 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 . - */ -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 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(); - - 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(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) - { - new AppVarna(structureLine, seq, seq.getSequenceAsString(), - rnastruc, seq.getName(), ap); - } - }); - 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(); - SequenceI sqass = null; - for (SequenceI sq : ap.av.getSequenceSelection()) - { - Vector pes = (Vector) sq.getDatasetSequence() - .getPDBId(); - if (pes != null) - { - 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()]); - final JMenuItem gpdbview; - 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)); - } - }); - } - } - 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(); - } - }); - 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()) - { - 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); - 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()) - { - Conservation c = new Conservation(MessageManager.getString("label.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); - } - - } - - 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()); - } - } - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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 jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentAnnotationUtils; +import jalview.analysis.AlignmentUtils; +import jalview.analysis.Conservation; +import jalview.commands.ChangeCaseCommand; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.FormatAdapter; +import jalview.io.SequenceAnnotationReport; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.UserColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.util.GroupUrlLink; +import jalview.util.GroupUrlLink.UrlStringTooLongException; +import jalview.util.MessageManager; +import jalview.util.UrlLink; + +import java.awt.Color; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.Arrays; +import java.util.Collections; +import java.util.Hashtable; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPopupMenu; +import javax.swing.JRadioButtonMenuItem; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision: 1.118 $ + */ +public class PopupMenu extends JPopupMenu +{ + private static final String ALL_ANNOTATIONS = "All"; + + private static final String COMMA = ","; + + 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(); + + 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(); + + JMenuItem makeReferenceSeq = new JMenuItem(); + + JMenuItem chooseAnnotations = 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(); + + JMenuItem enterPDB = new JMenuItem(); + + JMenuItem discoverPDB = new JMenuItem(); + + JMenu outputMenu = new JMenu(); + + JMenu seqShowAnnotationsMenu = new JMenu(); + + JMenu seqHideAnnotationsMenu = new JMenu(); + + JMenuItem seqAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); + + JMenu groupShowAnnotationsMenu = new JMenu(); + + JMenu groupHideAnnotationsMenu = new JMenu(); + + JMenuItem groupAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); + + JMenuItem sequenceFeature = new JMenuItem(); + + JMenuItem textColour = new JMenuItem(); + + JMenu jMenu1 = new JMenu(); + + JMenuItem pdbStructureDialog = new JMenuItem(); + + JMenu rnaStructureMenu = new JMenu(); + + JMenuItem editSequence = new JMenuItem(); + + JMenu groupLinksMenu; + + JMenuItem hideInsertions = new JMenuItem(); + + /** + * 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); + + 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() + { + @Override + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + outputMenu.add(item); + } + + /* + * Build menus for annotation types that may be shown or hidden, and for + * 'reference annotations' that may be added to the alignment. First for the + * currently selected sequence (if there is one): + */ + final List selectedSequence = (seq == null ? Collections + . emptyList() : Arrays.asList(seq)); + buildAnnotationTypesMenus(seqShowAnnotationsMenu, + seqHideAnnotationsMenu, selectedSequence); + configureReferenceAnnotationsMenu(seqAddReferenceAnnotations, + selectedSequence); + + /* + * And repeat for the current selection group (if there is one): + */ + final List selectedGroup = (ap.av.getSelectionGroup() == null ? Collections + . emptyList() : ap.av.getSelectionGroup() + .getSequences()); + buildAnnotationTypesMenus(groupShowAnnotationsMenu, + groupHideAnnotationsMenu, selectedGroup); + configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, + selectedGroup); + + try + { + jbInit(); + } catch (Exception e) + { + e.printStackTrace(); + } + + JMenuItem menuItem; + if (seq != null) + { + sequenceMenu.setText(sequence.getName()); + if (seq == ap.av.getAlignment().getSeqrep()) + { + makeReferenceSeq.setText(MessageManager + .getString("action.unmark_as_reference")); + } + else + { + makeReferenceSeq.setText(MessageManager + .getString("action.set_as_reference")); + } + + if (!ap.av.getAlignment().isNucleotide()) + { + remove(rnaStructureMenu); + } + else + { + int origCount = rnaStructureMenu.getItemCount(); + /* + * add menu items to 2D-render any alignment or sequence secondary + * structure annotation + */ + AlignmentAnnotation[] aas = ap.av.getAlignment() + .getAlignmentAnnotation(); + if (aas != null) + { + for (final AlignmentAnnotation aa : aas) + { + if (aa.isValidStruc() && aa.sequenceRef == null) + { + /* + * valid alignment RNA secondary structure annotation + */ + menuItem = new JMenuItem(); + menuItem.setText(MessageManager.formatMessage( + "label.2d_rna_structure_line", + new Object[] { aa.label })); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + new AppVarna(seq, aa, ap); + } + }); + rnaStructureMenu.add(menuItem); + } + } + } + + if (seq.getAnnotation() != null) + { + AlignmentAnnotation seqAnns[] = seq.getAnnotation(); + for (final AlignmentAnnotation aa : seqAnns) + { + if (aa.isValidStruc()) + { + /* + * valid sequence RNA secondary structure annotation + */ + // TODO: make rnastrucF a bit more nice + menuItem = new JMenuItem(); + menuItem.setText(MessageManager.formatMessage( + "label.2d_rna_sequence_name", + new Object[] { seq.getName() })); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: VARNA does'nt print gaps in the sequence + new AppVarna(seq, aa, ap); + } + }); + rnaStructureMenu.add(menuItem); + } + } + } + if (rnaStructureMenu.getItemCount() == origCount) + { + remove(rnaStructureMenu); + } + } + + menuItem = new JMenuItem( + MessageManager.getString("action.hide_sequences")); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + @Override + 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 Object[] { seq.getName() })); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + @Override + 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() + { + @Override + 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() + { + @Override + 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 Object[] { 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 = sq.getDatasetSequence().getAllPDBEntries(); + 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; + } + } + 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); + pdbStructureDialog.setVisible(false); + rnaStructureMenu.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.getDBRefs(), 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); + } + } + } + + /** + * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus. + * "All" is added first, followed by a separator. Then add any annotation + * types associated with the current selection. Separate menus are built for + * the selected sequence group (if any), and the selected sequence. + *

+ * Some annotation rows are always rendered together - these can be identified + * by a common graphGroup property > -1. Only one of each group will be marked + * as visible (to avoid duplication of the display). For such groups we add a + * composite type name, e.g. + *

+ * IUPredWS (Long), IUPredWS (Short) + * + * @param seq + */ + protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu, + List forSequences) + { + showMenu.removeAll(); + hideMenu.removeAll(); + + final List all = Arrays.asList(ALL_ANNOTATIONS); + addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true); + addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true, + false); + showMenu.addSeparator(); + hideMenu.addSeparator(); + + final AlignmentAnnotation[] annotations = ap.getAlignment() + .getAlignmentAnnotation(); + + /* + * Find shown/hidden annotations types, distinguished by source (calcId), + * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in + * the insertion order, which is the order of the annotations on the + * alignment. + */ + Map>> shownTypes = new LinkedHashMap>>(); + Map>> hiddenTypes = new LinkedHashMap>>(); + AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes, + AlignmentAnnotationUtils.asList(annotations), forSequences); + + for (String calcId : hiddenTypes.keySet()) + { + for (List type : hiddenTypes.get(calcId)) + { + addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type, + false, true); + } + } + // grey out 'show annotations' if none are hidden + showMenu.setEnabled(!hiddenTypes.isEmpty()); + + for (String calcId : shownTypes.keySet()) + { + for (List type : shownTypes.get(calcId)) + { + addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type, + false, false); + } + } + // grey out 'hide annotations' if none are shown + hideMenu.setEnabled(!shownTypes.isEmpty()); + } + + /** + * Returns a list of sequences - either the current selection group (if there + * is one), else the specified single sequence. + * + * @param seq + * @return + */ + protected List getSequenceScope(SequenceI seq) + { + List forSequences = null; + final SequenceGroup selectionGroup = ap.av.getSelectionGroup(); + if (selectionGroup != null && selectionGroup.getSize() > 0) + { + forSequences = selectionGroup.getSequences(); + } + else + { + forSequences = seq == null ? Collections. emptyList() + : Arrays.asList(seq); + } + return forSequences; + } + + /** + * Add one annotation type to the 'Show Annotations' or 'Hide Annotations' + * menus. + * + * @param showOrHideMenu + * the menu to add to + * @param forSequences + * the sequences whose annotations may be shown or hidden + * @param calcId + * @param types + * the label to add + * @param allTypes + * if true this is a special label meaning 'All' + * @param actionIsShow + * if true, the select menu item action is to show the annotation + * type, else hide + */ + protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu, + final List forSequences, String calcId, + final List types, final boolean allTypes, + final boolean actionIsShow) + { + String label = types.toString(); // [a, b, c] + label = label.substring(1, label.length() - 1); // a, b, c + final JMenuItem item = new JMenuItem(label); + item.setToolTipText(calcId); + item.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), + types, forSequences, allTypes, actionIsShow); + refresh(); + } + }); + showOrHideMenu.add(item); + } + + 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.getDBRefs(); + 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; + // 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 Object[] { url })); + item.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + @Override + 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() + { + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + @Override + 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() + { + @Override + 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() + { + @Override + public void actionPerformed(ActionEvent e) + { + sequenceName_actionPerformed(); + } + }); + chooseAnnotations.setText(MessageManager + .getString("action.choose_annotations")); + chooseAnnotations.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + chooseAnnotations_actionPerformed(e); + } + }); + sequenceDetails.setText(MessageManager + .getString("label.sequence_details")); + sequenceDetails.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sequenceDetails_actionPerformed(); + } + }); + sequenceSelDetails.setText(MessageManager + .getString("label.sequence_details")); + sequenceSelDetails + .addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sequenceSelectionDetails_actionPerformed(); + } + }); + PIDColour.setFocusPainted(false); + unGroupMenuItem + .setText(MessageManager.getString("action.remove_group")); + unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + unGroupMenuItem_actionPerformed(); + } + }); + createGroupMenuItem.setText(MessageManager + .getString("action.create_group")); + createGroupMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + createGroupMenuItem_actionPerformed(); + } + }); + + outline.setText(MessageManager.getString("action.border_colour")); + outline.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + outline_actionPerformed(); + } + }); + nucleotideMenuItem + .setText(MessageManager.getString("label.nucleotide")); + nucleotideMenuItem.addActionListener(new ActionListener() + { + @Override + 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() + { + @Override + public void actionPerformed(ActionEvent e) + { + showBoxes_actionPerformed(); + } + }); + showText.setText(MessageManager.getString("action.text")); + showText.setState(true); + showText.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showText_actionPerformed(); + } + }); + showColourText.setText(MessageManager.getString("label.colour_text")); + showColourText.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showColourText_actionPerformed(); + } + }); + displayNonconserved.setText(MessageManager + .getString("label.show_non_conversed")); + displayNonconserved.setState(true); + displayNonconserved.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showNonconserved_actionPerformed(); + } + }); + editMenu.setText(MessageManager.getString("action.edit")); + cut.setText(MessageManager.getString("action.cut")); + cut.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + cut_actionPerformed(); + } + }); + upperCase.setText(MessageManager.getString("label.to_upper_case")); + upperCase.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + changeCase(e); + } + }); + copy.setText(MessageManager.getString("action.copy")); + copy.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + copy_actionPerformed(); + } + }); + lowerCase.setText(MessageManager.getString("label.to_lower_case")); + lowerCase.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + changeCase(e); + } + }); + toggle.setText(MessageManager.getString("label.toggle_case")); + toggle.addActionListener(new ActionListener() + { + @Override + 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() + { + @Override + public void actionPerformed(ActionEvent e) + { + pdbFromFile_actionPerformed(); + } + }); + + enterPDB.setText(MessageManager.getString("label.enter_pdb_id")); + enterPDB.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + enterPDB_actionPerformed(); + } + }); + discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids")); + discoverPDB.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + discoverPDB_actionPerformed(); + } + }); + outputMenu.setText(MessageManager.getString("label.out_to_textbox") + + "..."); + seqShowAnnotationsMenu.setText(MessageManager + .getString("label.show_annotations")); + seqHideAnnotationsMenu.setText(MessageManager + .getString("label.hide_annotations")); + groupShowAnnotationsMenu.setText(MessageManager + .getString("label.show_annotations")); + groupHideAnnotationsMenu.setText(MessageManager + .getString("label.hide_annotations")); + sequenceFeature.setText(MessageManager + .getString("label.create_sequence_feature")); + sequenceFeature.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sequenceFeature_actionPerformed(); + } + }); + textColour.setText(MessageManager.getString("label.text_colour")); + textColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + textColour_actionPerformed(); + } + }); + jMenu1.setText(MessageManager.getString("label.group")); + pdbStructureDialog.setText(MessageManager + .getString("label.show_pdbstruct_dialog")); + pdbStructureDialog.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + SequenceI[] selectedSeqs = new SequenceI[] { sequence }; + if (ap.av.getSelectionGroup() != null) + { + selectedSeqs = ap.av.getSequenceSelection(); + } + new StructureChooser(selectedSeqs, sequence, ap); + } + }); + + rnaStructureMenu.setText(MessageManager + .getString("label.view_rna_structure")); + + // colStructureMenu.setText("Colour By Structure"); + editSequence.setText(MessageManager.getString("label.edit_sequence") + + "..."); + editSequence.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + editSequence_actionPerformed(actionEvent); + } + }); + makeReferenceSeq.setText(MessageManager + .getString("label.mark_as_representative")); + makeReferenceSeq.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent actionEvent) + { + makeReferenceSeq_actionPerformed(actionEvent); + + } + }); + hideInsertions.setText(MessageManager + .getString("label.hide_insertions")); + hideInsertions.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + hideInsertions_actionPerformed(e); + } + }); + /* + * annotationMenuItem.setText("By Annotation"); + * annotationMenuItem.addActionListener(new ActionListener() { public void + * actionPerformed(ActionEvent actionEvent) { + * annotationMenuItem_actionPerformed(actionEvent); } }); + */ + groupMenu.add(sequenceSelDetails); + add(groupMenu); + add(sequenceMenu); + add(rnaStructureMenu); + add(pdbStructureDialog); + if (sequence != null) + { + add(hideInsertions); + } + // annotations configuration panel suppressed for now + // groupMenu.add(chooseAnnotations); + + /* + * Add show/hide annotations to the Sequence menu, and to the Selection menu + * (if a selection group is in force). + */ + sequenceMenu.add(seqShowAnnotationsMenu); + sequenceMenu.add(seqHideAnnotationsMenu); + sequenceMenu.add(seqAddReferenceAnnotations); + groupMenu.add(groupShowAnnotationsMenu); + groupMenu.add(groupHideAnnotationsMenu); + groupMenu.add(groupAddReferenceAnnotations); + groupMenu.add(editMenu); + groupMenu.add(outputMenu); + groupMenu.add(sequenceFeature); + groupMenu.add(createGroupMenuItem); + groupMenu.add(unGroupMenuItem); + groupMenu.add(jMenu1); + sequenceMenu.add(sequenceName); + sequenceMenu.add(sequenceDetails); + sequenceMenu.add(makeReferenceSeq); + 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(purinePyrimidineColour); + } + 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() + { + @Override + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + colourMenu.add(item); + } + } + + colourMenu.addSeparator(); + colourMenu.add(abovePIDColour); + colourMenu.add(conservationMenuItem); + 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); + noColourmenuItem.setText(MessageManager.getString("label.none")); + noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + noColourmenuItem_actionPerformed(); + } + }); + + clustalColour.setText(MessageManager + .getString("label.clustalx_colours")); + clustalColour.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + clustalColour_actionPerformed(); + } + }); + zappoColour.setText(MessageManager.getString("label.zappo")); + zappoColour.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + zappoColour_actionPerformed(); + } + }); + taylorColour.setText(MessageManager.getString("label.taylor")); + taylorColour.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + taylorColour_actionPerformed(); + } + }); + hydrophobicityColour.setText(MessageManager + .getString("label.hydrophobicity")); + hydrophobicityColour + .addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hydrophobicityColour_actionPerformed(); + } + }); + helixColour.setText(MessageManager.getString("label.helix_propensity")); + helixColour.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + helixColour_actionPerformed(); + } + }); + strandColour.setText(MessageManager + .getString("label.strand_propensity")); + strandColour.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + strandColour_actionPerformed(); + } + }); + turnColour.setText(MessageManager.getString("label.turn_propensity")); + turnColour.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + turnColour_actionPerformed(); + } + }); + buriedColour.setText(MessageManager.getString("label.buried_index")); + buriedColour.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + buriedColour_actionPerformed(); + } + }); + abovePIDColour.setText(MessageManager + .getString("label.above_identity_percentage")); + abovePIDColour.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + abovePIDColour_actionPerformed(); + } + }); + userDefinedColour.setText(MessageManager + .getString("action.user_defined")); + userDefinedColour.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + userDefinedColour_actionPerformed(e); + } + }); + PIDColour + .setText(MessageManager.getString("label.percentage_identity")); + PIDColour.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + PIDColour_actionPerformed(); + } + }); + BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); + BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + BLOSUM62Colour_actionPerformed(); + } + }); + purinePyrimidineColour.setText(MessageManager + .getString("label.purine_pyrimidine")); + purinePyrimidineColour + .addActionListener(new java.awt.event.ActionListener() + { + @Override + 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() + { + @Override + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(); + } + }); + } + + /** + * Check for any annotations on the underlying dataset sequences (for the + * current selection group) which are not 'on the alignment'.If any are found, + * enable the option to add them to the alignment. The criteria for 'on the + * alignment' is finding an alignment annotation on the alignment, matched on + * calcId, label and sequenceRef. + * + * A tooltip is also constructed that displays the source (calcId) and type + * (label) of the annotations that can be added. + * + * @param menuItem + * @param forSequences + */ + protected void configureReferenceAnnotationsMenu(JMenuItem menuItem, + List forSequences) + { + menuItem.setEnabled(false); + + /* + * Temporary store to hold distinct calcId / type pairs for the tooltip. + * Using TreeMap means calcIds are shown in alphabetical order. + */ + Map tipEntries = new TreeMap(); + final Map> candidates = new LinkedHashMap>(); + AlignmentI al = this.ap.av.getAlignment(); + AlignmentUtils.findAddableReferenceAnnotations(forSequences, + tipEntries, candidates, al); + if (!candidates.isEmpty()) + { + StringBuilder tooltip = new StringBuilder(64); + tooltip.append(MessageManager.getString("label.add_annotations_for")); + + /* + * Found annotations that could be added. Enable the menu item, and + * configure its tooltip and action. + */ + menuItem.setEnabled(true); + for (String calcId : tipEntries.keySet()) + { + tooltip.append("
" + calcId + "/" + tipEntries.get(calcId)); + } + String tooltipText = JvSwingUtils.wrapTooltip(true, + tooltip.toString()); + menuItem.setToolTipText(tooltipText); + + menuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + addReferenceAnnotations_actionPerformed(candidates); + } + }); + } + } + + /** + * Add annotations to the sequences and to the alignment. + * + * @param candidates + * a map whose keys are sequences on the alignment, and values a list + * of annotations to add to each sequence + */ + protected void addReferenceAnnotations_actionPerformed( + Map> candidates) + { + final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup(); + final AlignmentI alignment = this.ap.getAlignment(); + AlignmentUtils.addReferenceAnnotations(candidates, alignment, + selectionGroup); + refresh(); + } + + protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent) + { + if (!ap.av.getAlignment().hasSeqrep()) + { + // initialise the display flags so the user sees something happen + ap.av.setDisplayReferenceSeq(true); + ap.av.setColourByReferenceSeq(true); + ap.av.getAlignment().setSeqrep(sequence); + } + else + { + if (ap.av.getAlignment().getSeqrep() == sequence) + { + ap.av.getAlignment().setSeqrep(null); + } + else + { + ap.av.getAlignment().setSeqrep(sequence); + } + } + refresh(); + } + + protected void hideInsertions_actionPerformed(ActionEvent actionEvent) + { + if (sequence != null) + { + ColumnSelection cs = ap.av.getColumnSelection(); + if (cs == null) + { + cs = new ColumnSelection(); + } + cs.hideInsertionsFor(sequence); + ap.av.setColumnSelection(cs); + } + refresh(); + } + + 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 Object[] { seq.getDisplayId(true) }) + + "

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

"); + } + cap.setText("" + contents.toString() + ""); + + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.sequence_details_for", + (sequences.length == 1 ? new Object[] { sequences[0] + .getDisplayId(true) } : new Object[] { 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.isIgnoreGapsConsensus()); + + SliderPanel.showPIDSlider(); + } + else + // remove PIDColouring + { + sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); + } + + 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(); + } + + /** + * Open a panel where the user can choose which types of sequence annotation + * to show or hide. + * + * @param e + */ + protected void chooseAnnotations_actionPerformed(ActionEvent e) + { + // todo correct way to guard against opening a duplicate panel? + new AnnotationChooser(ap); + } + + /** + * 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 = sg.getSequences().toArray(new SequenceI[gsize]); + + 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) + { + List 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 Object[] { 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 + + cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(), + ap, true)); + } + + 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 Object[] { sequence.getDisplayId(false) })); + chooser.setToolTipText(MessageManager.formatMessage( + "label.load_pdb_file_associate_with_sequence", + new Object[] { sequence.getDisplayId(false) })); + + 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, + Desktop.instance); + } + + } + + 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() + { + @Override + public void run() + { + boolean isNuclueotide = ap.alignFrame.getViewport().getAlignment() + .isNucleotide(); + + new jalview.ws.DBRefFetcher(sequences, ap.alignFrame, null, + ap.alignFrame.featureSettings, isNuclueotide) + .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.getSeqPanel().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 = 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"), + Action.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()); + } + } + } + +}