-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.gui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import javax.swing.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.commands.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
-import jalview.util.GroupUrlLink;\r
-import jalview.util.GroupUrlLink.UrlStringTooLongException;\r
-import jalview.util.MessageManager;\r
-import jalview.util.UrlLink;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- * \r
- * @author $author$\r
- * @version $Revision: 1.118 $\r
- */\r
-public class PopupMenu extends JPopupMenu\r
-{\r
- JMenu groupMenu = new JMenu();\r
-\r
- JMenuItem groupName = new JMenuItem();\r
-\r
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
-\r
- protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
-\r
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
-\r
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();\r
-\r
- // protected JRadioButtonMenuItem covariationColour = new\r
- // JRadioButtonMenuItem();\r
-\r
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
-\r
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
-\r
- AlignmentPanel ap;\r
-\r
- JMenu sequenceMenu = new JMenu();\r
-\r
- JMenuItem sequenceName = new JMenuItem();\r
-\r
- JMenuItem sequenceDetails = new JMenuItem();\r
-\r
- JMenuItem sequenceSelDetails = new JMenuItem();\r
-\r
- SequenceI sequence;\r
- JMenuItem createGroupMenuItem = new JMenuItem();\r
- JMenuItem unGroupMenuItem = new JMenuItem();\r
-\r
- JMenuItem outline = new JMenuItem();\r
-\r
- JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
-\r
- JMenu colourMenu = new JMenu();\r
-\r
- JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
-\r
- JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
-\r
- JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
-\r
- JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();\r
-\r
- JMenu editMenu = new JMenu();\r
-\r
- JMenuItem cut = new JMenuItem();\r
-\r
- JMenuItem copy = new JMenuItem();\r
-\r
- JMenuItem upperCase = new JMenuItem();\r
-\r
- JMenuItem lowerCase = new JMenuItem();\r
-\r
- JMenuItem toggle = new JMenuItem();\r
-\r
- JMenu pdbMenu = new JMenu();\r
-\r
- JMenuItem pdbFromFile = new JMenuItem();\r
-\r
- JMenuItem enterPDB = new JMenuItem();\r
-\r
- JMenuItem discoverPDB = new JMenuItem();\r
-\r
- JMenu outputMenu = new JMenu();\r
-\r
- JMenuItem sequenceFeature = new JMenuItem();\r
-\r
- JMenuItem textColour = new JMenuItem();\r
-\r
- JMenu jMenu1 = new JMenu();\r
-\r
- JMenu structureMenu = new JMenu();\r
-\r
- JMenu viewStructureMenu = new JMenu();\r
-\r
- // JMenu colStructureMenu = new JMenu();\r
- JMenuItem editSequence = new JMenuItem();\r
-\r
- // JMenuItem annotationMenuItem = new JMenuItem();\r
-\r
- JMenu groupLinksMenu;\r
-\r
- /**\r
- * Creates a new PopupMenu object.\r
- * \r
- * @param ap\r
- * DOCUMENT ME!\r
- * @param seq\r
- * DOCUMENT ME!\r
- */\r
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
- {\r
- this(ap, seq, links, null);\r
- }\r
-\r
- /**\r
- * \r
- * @param ap\r
- * @param seq\r
- * @param links\r
- * @param groupLinks\r
- */\r
- public PopupMenu(final AlignmentPanel ap, final SequenceI seq,\r
- Vector links, Vector groupLinks)\r
- {\r
- // /////////////////////////////////////////////////////////\r
- // If this is activated from the sequence panel, the user may want to\r
- // edit or annotate a particular residue. Therefore display the residue menu\r
- //\r
- // If from the IDPanel, we must display the sequence menu\r
- // ////////////////////////////////////////////////////////\r
- this.ap = ap;\r
- sequence = seq;\r
-\r
- ButtonGroup colours = new ButtonGroup();\r
- colours.add(noColourmenuItem);\r
- colours.add(clustalColour);\r
- colours.add(zappoColour);\r
- colours.add(taylorColour);\r
- colours.add(hydrophobicityColour);\r
- colours.add(helixColour);\r
- colours.add(strandColour);\r
- colours.add(turnColour);\r
- colours.add(buriedColour);\r
- colours.add(abovePIDColour);\r
- colours.add(userDefinedColour);\r
- colours.add(PIDColour);\r
- colours.add(BLOSUM62Colour);\r
- colours.add(purinePyrimidineColour);\r
- // colours.add(covariationColour);\r
-\r
- for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
- {\r
- JMenuItem item = new JMenuItem(\r
- jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);\r
-\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputMenu.add(item);\r
- }\r
-\r
- try\r
- {\r
- jbInit();\r
- } catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- JMenuItem menuItem;\r
- if (seq != null)\r
- {\r
- sequenceMenu.setText(sequence.getName());\r
-\r
- if (seq.getDatasetSequence().getPDBId() != null\r
- && seq.getDatasetSequence().getPDBId().size() > 0)\r
- {\r
- java.util.Enumeration e = seq.getDatasetSequence().getPDBId()\r
- .elements();\r
-\r
- while (e.hasMoreElements())\r
- {\r
- final PDBEntry pdb = (PDBEntry) e.nextElement();\r
-\r
- menuItem = new JMenuItem();\r
- menuItem.setText(pdb.getId());\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- // TODO re JAL-860: optionally open dialog or provide a menu entry\r
- // allowing user to open just one structure per sequence\r
- new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]\r
- { pdb })[0], null, ap);\r
- // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);\r
- }\r
-\r
- });\r
- viewStructureMenu.add(menuItem);\r
-\r
- /*\r
- * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());\r
- * menuItem.addActionListener(new java.awt.event.ActionListener() {\r
- * public void actionPerformed(ActionEvent e) {\r
- * colourByStructure(pdb.getId()); } });\r
- * colStructureMenu.add(menuItem);\r
- */\r
- }\r
- }\r
- else\r
- {\r
- if (ap.av.getAlignment().isNucleotide() == false)\r
- {\r
- structureMenu.remove(viewStructureMenu);\r
- }\r
- // structureMenu.remove(colStructureMenu);\r
- }\r
-\r
- if (ap.av.getAlignment().isNucleotide() == true)\r
- {\r
- AlignmentAnnotation[] aa = ap.av.getAlignment()\r
- .getAlignmentAnnotation();\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if (aa[i].getRNAStruc() != null)\r
- {\r
- final String rnastruc = aa[i].getRNAStruc();\r
- final String structureLine = aa[i].label;\r
- menuItem = new JMenuItem();\r
- menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- new AppVarna(structureLine, seq, seq.getSequenceAsString(),\r
- rnastruc, seq.getName(), ap);\r
- }\r
- });\r
- viewStructureMenu.add(menuItem);\r
- }\r
- }\r
-\r
- // SequenceFeatures[] test = seq.getSequenceFeatures();\r
-\r
- if (seq.getAnnotation() != null)\r
- {\r
- AlignmentAnnotation seqAnno[] = seq.getAnnotation();\r
- for (int i = 0; i < seqAnno.length; i++)\r
- {\r
- if (seqAnno[i].getRNAStruc() != null)\r
- {\r
- final String rnastruc = seqAnno[i].getRNAStruc();\r
-\r
- // TODO: make rnastrucF a bit more nice\r
- menuItem = new JMenuItem();\r
- menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- // TODO: VARNA does'nt print gaps in the sequence\r
- new AppVarna(seq.getName() + " structure", seq, seq\r
- .getSequenceAsString(), rnastruc, seq.getName(),\r
- ap);\r
- }\r
- });\r
- viewStructureMenu.add(menuItem);\r
- }\r
- }\r
- }\r
-\r
- }\r
-\r
- menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hideSequences(false);\r
- }\r
- });\r
- add(menuItem);\r
-\r
- if (ap.av.getSelectionGroup() != null\r
- && ap.av.getSelectionGroup().getSize() > 1)\r
- {\r
- menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hideSequences(true);\r
- }\r
- });\r
- sequenceMenu.add(menuItem);\r
- }\r
-\r
- if (ap.av.hasHiddenRows())\r
- {\r
- final int index = ap.av.getAlignment().findIndex(seq);\r
-\r
- if (ap.av.adjustForHiddenSeqs(index)\r
- - ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
- {\r
- menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ap.av.showSequence(index);\r
- if (ap.overviewPanel != null)\r
- {\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- }\r
- });\r
- add(menuItem);\r
- }\r
- }\r
- }\r
- // for the case when no sequences are even visible\r
- if (ap.av.hasHiddenRows())\r
- {\r
- {\r
- menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ap.av.showAllHiddenSeqs();\r
- if (ap.overviewPanel != null)\r
- {\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- }\r
- });\r
-\r
- add(menuItem);\r
- }\r
-\r
- }\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;\r
-\r
- if (sg != null && sg.getSize() > 0)\r
- { \r
- groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));\r
- groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));\r
-\r
- if (sg.cs instanceof ZappoColourScheme)\r
- {\r
- zappoColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof TaylorColourScheme)\r
- {\r
- taylorColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof PIDColourScheme)\r
- {\r
- PIDColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof Blosum62ColourScheme)\r
- {\r
- BLOSUM62Colour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof UserColourScheme)\r
- {\r
- userDefinedColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof HydrophobicColourScheme)\r
- {\r
- hydrophobicityColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof HelixColourScheme)\r
- {\r
- helixColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof StrandColourScheme)\r
- {\r
- strandColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof TurnColourScheme)\r
- {\r
- turnColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof BuriedColourScheme)\r
- {\r
- buriedColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof ClustalxColourScheme)\r
- {\r
- clustalColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof PurinePyrimidineColourScheme)\r
- {\r
- purinePyrimidineColour.setSelected(true);\r
- }\r
- /*\r
- * else if (sg.cs instanceof CovariationColourScheme) {\r
- * covariationColour.setSelected(true); }\r
- */\r
- else\r
- {\r
- noColourmenuItem.setSelected(true);\r
- }\r
-\r
- if (sg.cs != null && sg.cs.conservationApplied())\r
- {\r
- conservationMenuItem.setSelected(true);\r
- }\r
- displayNonconserved.setSelected(sg.getShowNonconserved());\r
- showText.setSelected(sg.getDisplayText());\r
- showColourText.setSelected(sg.getColourText());\r
- showBoxes.setSelected(sg.getDisplayBoxes());\r
- // add any groupURLs to the groupURL submenu and make it visible\r
- if (groupLinks != null && groupLinks.size() > 0)\r
- {\r
- buildGroupURLMenu(sg, groupLinks);\r
- }\r
- // Add a 'show all structures' for the current selection\r
- Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();\r
- SequenceI sqass = null;\r
- for (SequenceI sq : ap.av.getSequenceSelection())\r
- {\r
- Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()\r
- .getPDBId();\r
- if (pes != null)\r
- {\r
- for (PDBEntry pe : pes)\r
- {\r
- pdbe.put(pe.getId(), pe);\r
- if (sqass == null)\r
- {\r
- sqass = sq;\r
- }\r
- }\r
- }\r
- }\r
- if (pdbe.size() > 0)\r
- {\r
- final PDBEntry[] pe = pdbe.values().toArray(\r
- new PDBEntry[pdbe.size()]);\r
- final JMenuItem gpdbview;\r
- if (pdbe.size() == 1)\r
- {\r
- structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));\r
- }\r
- else\r
- {\r
- structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));\r
- }\r
- gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));\r
- gpdbview.addActionListener(new ActionListener()\r
- {\r
-\r
- @Override\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- new AppJmol(ap, pe, ap.av.collateForPDB(pe));\r
- }\r
- });\r
- }\r
- }\r
- else\r
- {\r
- groupMenu.setVisible(false);\r
- editMenu.setVisible(false);\r
- }\r
-\r
- if (!isDefinedGroup)\r
- {\r
- createGroupMenuItem.setVisible(true);\r
- unGroupMenuItem.setVisible(false);\r
- jMenu1.setText(MessageManager.getString("action.edit_new_group"));\r
- } else {\r
- createGroupMenuItem.setVisible(false);\r
- unGroupMenuItem.setVisible(true);\r
- jMenu1.setText(MessageManager.getString("action.edit_group"));\r
- }\r
-\r
- if (seq == null)\r
- {\r
- sequenceMenu.setVisible(false);\r
- structureMenu.setVisible(false);\r
- }\r
-\r
- if (links != null && links.size() > 0)\r
- {\r
-\r
- JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));\r
- Vector linkset = new Vector();\r
- for (int i = 0; i < links.size(); i++)\r
- {\r
- String link = links.elementAt(i).toString();\r
- UrlLink urlLink = null;\r
- try\r
- {\r
- urlLink = new UrlLink(link);\r
- } catch (Exception foo)\r
- {\r
- jalview.bin.Cache.log.error("Exception for URLLink '" + link\r
- + "'", foo);\r
- continue;\r
- }\r
- ;\r
- if (!urlLink.isValid())\r
- {\r
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());\r
- continue;\r
- }\r
- final String label = urlLink.getLabel();\r
- if (seq != null && urlLink.isDynamic())\r
- {\r
-\r
- // collect matching db-refs\r
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(\r
- seq.getDBRef(), new String[]\r
- { urlLink.getTarget() });\r
- // collect id string too\r
- String id = seq.getName();\r
- String descr = seq.getDescription();\r
- if (descr != null && descr.length() < 1)\r
- {\r
- descr = null;\r
- }\r
-\r
- if (dbr != null)\r
- {\r
- for (int r = 0; r < dbr.length; r++)\r
- {\r
- if (id != null && dbr[r].getAccessionId().equals(id))\r
- {\r
- // suppress duplicate link creation for the bare sequence ID\r
- // string with this link\r
- id = null;\r
- }\r
- // create Bare ID link for this RUL\r
- String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),\r
- true);\r
- if (urls != null)\r
- {\r
- for (int u = 0; u < urls.length; u += 2)\r
- {\r
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
- {\r
- linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
- addshowLink(linkMenu, label + "|" + urls[u],\r
- urls[u + 1]);\r
- }\r
- }\r
- }\r
- }\r
- }\r
- if (id != null)\r
- {\r
- // create Bare ID link for this RUL\r
- String[] urls = urlLink.makeUrls(id, true);\r
- if (urls != null)\r
- {\r
- for (int u = 0; u < urls.length; u += 2)\r
- {\r
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
- {\r
- linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
- addshowLink(linkMenu, label, urls[u + 1]);\r
- }\r
- }\r
- }\r
- }\r
- // Create urls from description but only for URL links which are regex\r
- // links\r
- if (descr != null && urlLink.getRegexReplace() != null)\r
- {\r
- // create link for this URL from description where regex matches\r
- String[] urls = urlLink.makeUrls(descr, true);\r
- if (urls != null)\r
- {\r
- for (int u = 0; u < urls.length; u += 2)\r
- {\r
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
- {\r
- linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
- addshowLink(linkMenu, label, urls[u + 1]);\r
- }\r
- }\r
- }\r
- }\r
- }\r
- else\r
- {\r
- if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))\r
- {\r
- linkset.addElement(label + "|" + urlLink.getUrl_prefix());\r
- // Add a non-dynamic link\r
- addshowLink(linkMenu, label, urlLink.getUrl_prefix());\r
- }\r
- }\r
- }\r
- if (sequence != null)\r
- {\r
- sequenceMenu.add(linkMenu);\r
- }\r
- else\r
- {\r
- add(linkMenu);\r
- }\r
- }\r
- }\r
-\r
- private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)\r
- {\r
-\r
- // TODO: usability: thread off the generation of group url content so root\r
- // menu appears asap\r
- // sequence only URLs\r
- // ID/regex match URLs\r
- groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
- JMenu[] linkMenus = new JMenu[]\r
- { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),\r
- new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be\r
- // created.\r
- SequenceI[] seqs = ap.av.getSelectionAsNewSequence();\r
- String[][] idandseqs = GroupUrlLink.formStrings(seqs);\r
- Hashtable commonDbrefs = new Hashtable();\r
- for (int sq = 0; sq < seqs.length; sq++)\r
- {\r
-\r
- int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]\r
- .findPosition(sg.getEndRes());\r
- // just collect ids from dataset sequence\r
- // TODO: check if IDs collected from selecton group intersects with the\r
- // current selection, too\r
- SequenceI sqi = seqs[sq];\r
- while (sqi.getDatasetSequence() != null)\r
- {\r
- sqi = sqi.getDatasetSequence();\r
- }\r
- DBRefEntry[] dbr = sqi.getDBRef();\r
- if (dbr != null && dbr.length > 0)\r
- {\r
- for (int d = 0; d < dbr.length; d++)\r
- {\r
- String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();\r
- Object[] sarray = (Object[]) commonDbrefs.get(src);\r
- if (sarray == null)\r
- {\r
- sarray = new Object[2];\r
- sarray[0] = new int[]\r
- { 0 };\r
- sarray[1] = new String[seqs.length];\r
-\r
- commonDbrefs.put(src, sarray);\r
- }\r
-\r
- if (((String[]) sarray[1])[sq] == null)\r
- {\r
- if (!dbr[d].hasMap()\r
- || (dbr[d].getMap().locateMappedRange(start, end) != null))\r
- {\r
- ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();\r
- ((int[]) sarray[0])[0]++;\r
- }\r
- }\r
- }\r
- }\r
- }\r
- // now create group links for all distinct ID/sequence sets.\r
- boolean addMenu = false; // indicates if there are any group links to give\r
- // to user\r
- for (int i = 0; i < groupLinks.size(); i++)\r
- {\r
- String link = groupLinks.elementAt(i).toString();\r
- GroupUrlLink urlLink = null;\r
- try\r
- {\r
- urlLink = new GroupUrlLink(link);\r
- } catch (Exception foo)\r
- {\r
- jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link\r
- + "'", foo);\r
- continue;\r
- }\r
- ;\r
- if (!urlLink.isValid())\r
- {\r
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());\r
- continue;\r
- }\r
- final String label = urlLink.getLabel();\r
- boolean usingNames = false;\r
- // Now see which parts of the group apply for this URL\r
- String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());\r
- Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());\r
- String[] seqstr, ids; // input to makeUrl\r
- if (idset != null)\r
- {\r
- int numinput = ((int[]) idset[0])[0];\r
- String[] allids = ((String[]) idset[1]);\r
- seqstr = new String[numinput];\r
- ids = new String[numinput];\r
- for (int sq = 0, idcount = 0; sq < seqs.length; sq++)\r
- {\r
- if (allids[sq] != null)\r
- {\r
- ids[idcount] = allids[sq];\r
- seqstr[idcount++] = idandseqs[1][sq];\r
- }\r
- }\r
- }\r
- else\r
- {\r
- // just use the id/seq set\r
- seqstr = idandseqs[1];\r
- ids = idandseqs[0];\r
- usingNames = true;\r
- }\r
- // and try and make the groupURL!\r
-\r
- Object[] urlset = null;\r
- try\r
- {\r
- urlset = urlLink.makeUrlStubs(ids, seqstr,\r
- "FromJalview" + System.currentTimeMillis(), false);\r
- } catch (UrlStringTooLongException e)\r
- {\r
- }\r
- if (urlset != null)\r
- {\r
- int type = urlLink.getGroupURLType() & 3;\r
- // System.out.println(urlLink.getGroupURLType()\r
- // +" "+((String[])urlset[3])[0]);\r
- // first two bits ofurlLink type bitfield are sequenceids and sequences\r
- // TODO: FUTURE: ensure the groupURL menu structure can be generalised\r
- addshowLink(linkMenus[type], label\r
- + (((type & 1) == 1) ? ("("\r
- + (usingNames ? "Names" : ltarget) + ")") : ""),\r
- urlLink, urlset);\r
- addMenu = true;\r
- }\r
- }\r
- if (addMenu)\r
- {\r
- groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
- for (int m = 0; m < linkMenus.length; m++)\r
- {\r
- if (linkMenus[m] != null\r
- && linkMenus[m].getMenuComponentCount() > 0)\r
- {\r
- groupLinksMenu.add(linkMenus[m]);\r
- }\r
- }\r
-\r
- groupMenu.add(groupLinksMenu);\r
- }\r
- }\r
-\r
- /**\r
- * add a show URL menu item to the given linkMenu\r
- * \r
- * @param linkMenu\r
- * @param label\r
- * - menu label string\r
- * @param url\r
- * - url to open\r
- */\r
- private void addshowLink(JMenu linkMenu, String label, final String url)\r
- {\r
- JMenuItem item = new JMenuItem(label);\r
- item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- new Thread(new Runnable()\r
- {\r
-\r
- public void run()\r
- {\r
- showLink(url);\r
- }\r
-\r
- }).start();\r
- }\r
- });\r
-\r
- linkMenu.add(item);\r
- }\r
-\r
- /**\r
- * add a late bound groupURL item to the given linkMenu\r
- * \r
- * @param linkMenu\r
- * @param label\r
- * - menu label string\r
- * @param urlgenerator\r
- * GroupURLLink used to generate URL\r
- * @param urlstub\r
- * Object array returned from the makeUrlStubs function.\r
- */\r
- private void addshowLink(JMenu linkMenu, String label,\r
- final GroupUrlLink urlgenerator, final Object[] urlstub)\r
- {\r
- JMenuItem item = new JMenuItem(label);\r
- item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));\r
- // TODO: put in info about what is being sent.\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- new Thread(new Runnable()\r
- {\r
-\r
- public void run()\r
- {\r
- try\r
- {\r
- showLink(urlgenerator.constructFrom(urlstub));\r
- } catch (UrlStringTooLongException e)\r
- {\r
- }\r
- }\r
-\r
- }).start();\r
- }\r
- });\r
-\r
- linkMenu.add(item);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @throws Exception\r
- * DOCUMENT ME!\r
- */\r
- private void jbInit() throws Exception\r
- {\r
- groupMenu.setText(MessageManager.getString("label.group"));\r
- groupMenu.setText(MessageManager.getString("label.selection"));\r
- groupName.setText(MessageManager.getString("label.name"));\r
- groupName.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- groupName_actionPerformed();\r
- }\r
- });\r
- sequenceMenu.setText(MessageManager.getString("label.sequence"));\r
- sequenceName.setText(MessageManager.getString("label.edit_name_description"));\r
- sequenceName.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceName_actionPerformed();\r
- }\r
- });\r
- sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
- sequenceDetails.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceDetails_actionPerformed();\r
- }\r
- });\r
- sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
- sequenceSelDetails\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceSelectionDetails_actionPerformed();\r
- }\r
- });\r
- PIDColour.setFocusPainted(false);\r
- unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));\r
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- unGroupMenuItem_actionPerformed();\r
- }\r
- });\r
- createGroupMenuItem.setText(MessageManager.getString("action.create_group"));\r
- createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- createGroupMenuItem_actionPerformed();\r
- }\r
- });\r
-\r
- outline.setText(MessageManager.getString("action.border_colour"));\r
- outline.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outline_actionPerformed();\r
- }\r
- });\r
- nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));\r
- nucleotideMenuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideMenuItem_actionPerformed();\r
- }\r
- });\r
- colourMenu.setText(MessageManager.getString("label.group_colour"));\r
- showBoxes.setText(MessageManager.getString("action.boxes"));\r
- showBoxes.setState(true);\r
- showBoxes.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showBoxes_actionPerformed();\r
- }\r
- });\r
- showText.setText(MessageManager.getString("action.text"));\r
- showText.setState(true);\r
- showText.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showText_actionPerformed();\r
- }\r
- });\r
- showColourText.setText(MessageManager.getString("label.colour_text"));\r
- showColourText.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showColourText_actionPerformed();\r
- }\r
- });\r
- displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));\r
- displayNonconserved.setState(true);\r
- displayNonconserved.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showNonconserved_actionPerformed();\r
- }\r
- });\r
- editMenu.setText(MessageManager.getString("action.edit"));\r
- cut.setText(MessageManager.getString("action.cut"));\r
- cut.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cut_actionPerformed();\r
- }\r
- });\r
- upperCase.setText(MessageManager.getString("label.to_upper_case"));\r
- upperCase.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
- copy.setText(MessageManager.getString("action.copy"));\r
- copy.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed();\r
- }\r
- });\r
- lowerCase.setText(MessageManager.getString("label.to_lower_case"));\r
- lowerCase.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
- toggle.setText(MessageManager.getString("label.toggle_case"));\r
- toggle.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
- pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));\r
- pdbFromFile.setText(MessageManager.getString("label.from_file"));\r
- pdbFromFile.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pdbFromFile_actionPerformed();\r
- }\r
- });\r
- enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));\r
- enterPDB.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- enterPDB_actionPerformed();\r
- }\r
- });\r
- discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));\r
- discoverPDB.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- discoverPDB_actionPerformed();\r
- }\r
- });\r
- outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");\r
- sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));\r
- sequenceFeature.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceFeature_actionPerformed();\r
- }\r
- });\r
- textColour.setText(MessageManager.getString("label.text_colour"));\r
- textColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- textColour_actionPerformed();\r
- }\r
- });\r
- jMenu1.setText(MessageManager.getString("label.group"));\r
- structureMenu.setText(MessageManager.getString("label.structure"));\r
- viewStructureMenu.setText(MessageManager.getString("label.view_structure"));\r
- // colStructureMenu.setText("Colour By Structure");\r
- editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");\r
- editSequence.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- editSequence_actionPerformed(actionEvent);\r
- }\r
- });\r
-\r
- /*\r
- * annotationMenuItem.setText("By Annotation");\r
- * annotationMenuItem.addActionListener(new ActionListener() { public void\r
- * actionPerformed(ActionEvent actionEvent) {\r
- * annotationMenuItem_actionPerformed(actionEvent); } });\r
- */\r
- groupMenu.add(sequenceSelDetails);\r
- add(groupMenu);\r
- add(sequenceMenu);\r
- this.add(structureMenu);\r
- groupMenu.add(editMenu);\r
- groupMenu.add(outputMenu);\r
- groupMenu.add(sequenceFeature);\r
- groupMenu.add(createGroupMenuItem);\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(jMenu1);\r
- sequenceMenu.add(sequenceName);\r
- sequenceMenu.add(sequenceDetails);\r
- colourMenu.add(textColour);\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideMenuItem);\r
- if (ap.getAlignment().isNucleotide())\r
- {\r
- colourMenu.add(purinePyrimidineColour);\r
- }\r
- // colourMenu.add(covariationColour);\r
- colourMenu.add(userDefinedColour);\r
-\r
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
- {\r
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours\r
- .getUserColourSchemes().keys();\r
-\r
- while (userColours.hasMoreElements())\r
- {\r
- JMenuItem item = new JMenuItem(userColours.nextElement().toString());\r
- item.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- userDefinedColour_actionPerformed(evt);\r
- }\r
- });\r
- colourMenu.add(item);\r
- }\r
- }\r
-\r
- colourMenu.addSeparator();\r
- colourMenu.add(abovePIDColour);\r
- colourMenu.add(conservationMenuItem);\r
- // colourMenu.add(annotationMenuItem);\r
- editMenu.add(copy);\r
- editMenu.add(cut);\r
- editMenu.add(editSequence);\r
- editMenu.add(upperCase);\r
- editMenu.add(lowerCase);\r
- editMenu.add(toggle);\r
- pdbMenu.add(pdbFromFile);\r
- pdbMenu.add(enterPDB);\r
- pdbMenu.add(discoverPDB);\r
- jMenu1.add(groupName);\r
- jMenu1.add(colourMenu);\r
- jMenu1.add(showBoxes);\r
- jMenu1.add(showText);\r
- jMenu1.add(showColourText);\r
- jMenu1.add(outline);\r
- jMenu1.add(displayNonconserved);\r
- structureMenu.add(pdbMenu);\r
- structureMenu.add(viewStructureMenu);\r
- // structureMenu.add(colStructureMenu);\r
- noColourmenuItem.setText(MessageManager.getString("label.none"));\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed();\r
- }\r
- });\r
-\r
- clustalColour.setText(MessageManager.getString("label.clustalx_colours"));\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed();\r
- }\r
- });\r
- zappoColour.setText(MessageManager.getString("label.zappo"));\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed();\r
- }\r
- });\r
- taylorColour.setText(MessageManager.getString("label.taylor"));\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed();\r
- }\r
- });\r
- hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));\r
- hydrophobicityColour\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed();\r
- }\r
- });\r
- helixColour.setText(MessageManager.getString("label.helix_propensity"));\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed();\r
- }\r
- });\r
- strandColour.setText(MessageManager.getString("label.strand_propensity"));\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed();\r
- }\r
- });\r
- turnColour.setText(MessageManager.getString("label.turn_propensity"));\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed();\r
- }\r
- });\r
- buriedColour.setText(MessageManager.getString("label.buried_index"));\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed();\r
- }\r
- });\r
- abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));\r
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- abovePIDColour_actionPerformed();\r
- }\r
- });\r
- userDefinedColour.setText(MessageManager.getString("action.user_defined"));\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
- PIDColour.setText(MessageManager.getString("label.percentage_identity"));\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed();\r
- }\r
- });\r
- BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed();\r
- }\r
- });\r
- purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));\r
- purinePyrimidineColour\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- purinePyrimidineColour_actionPerformed();\r
- }\r
- });\r
- /*\r
- * covariationColour.addActionListener(new java.awt.event.ActionListener() {\r
- * public void actionPerformed(ActionEvent e) {\r
- * covariationColour_actionPerformed(); } });\r
- */\r
-\r
- conservationMenuItem.setText(MessageManager.getString("label.conservation"));\r
- conservationMenuItem\r
- .addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed();\r
- }\r
- });\r
- }\r
-\r
- protected void sequenceSelectionDetails_actionPerformed()\r
- {\r
- createSequenceDetailsReport(ap.av.getSequenceSelection());\r
- }\r
-\r
- protected void sequenceDetails_actionPerformed()\r
- {\r
- createSequenceDetailsReport(new SequenceI[]\r
- { sequence });\r
- }\r
-\r
- public void createSequenceDetailsReport(SequenceI[] sequences)\r
- {\r
- CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();\r
- StringBuffer contents = new StringBuffer();\r
- for (SequenceI seq : sequences)\r
- { \r
- contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})\r
- + "</h2></p><p>");\r
- new SequenceAnnotationReport(null)\r
- .createSequenceAnnotationReport(\r
- contents,\r
- seq,\r
- true,\r
- true,\r
- false,\r
- (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax\r
- : null);\r
- contents.append("</p>");\r
- }\r
- cap.setText("<html>" + contents.toString() + "</html>");\r
-\r
- 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")}))\r
- ,500, 400);\r
-\r
- }\r
-\r
- protected void showNonconserved_actionPerformed()\r
- {\r
- getGroup().setShowNonconserved(displayNonconserved.isSelected());\r
- refresh();\r
- }\r
-\r
- /**\r
- * call to refresh view after settings change\r
- */\r
- void refresh()\r
- {\r
- ap.updateAnnotation();\r
- ap.paintAlignment(true);\r
-\r
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void clustalColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void zappoColour_actionPerformed()\r
- {\r
- getGroup().cs = new ZappoColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void taylorColour_actionPerformed()\r
- {\r
- getGroup().cs = new TaylorColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void hydrophobicityColour_actionPerformed()\r
- {\r
- getGroup().cs = new HydrophobicColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void helixColour_actionPerformed()\r
- {\r
- getGroup().cs = new HelixColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void strandColour_actionPerformed()\r
- {\r
- getGroup().cs = new StrandColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void turnColour_actionPerformed()\r
- {\r
- getGroup().cs = new TurnColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void buriedColour_actionPerformed()\r
- {\r
- getGroup().cs = new BuriedColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void nucleotideMenuItem_actionPerformed()\r
- {\r
- getGroup().cs = new NucleotideColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void purinePyrimidineColour_actionPerformed()\r
- {\r
- getGroup().cs = new PurinePyrimidineColourScheme();\r
- refresh();\r
- }\r
-\r
- /*\r
- * protected void covariationColour_actionPerformed() { getGroup().cs = new\r
- * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }\r
- */\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void abovePIDColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg.cs == null)\r
- {\r
- return;\r
- }\r
-\r
- if (abovePIDColour.isSelected())\r
- {\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(ap.av.getHiddenRepSequences()),\r
- sg.getStartRes(), sg.getEndRes() + 1));\r
-\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()\r
- .getName());\r
-\r
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
-\r
- SliderPanel.showPIDSlider();\r
- }\r
- else\r
- // remove PIDColouring\r
- {\r
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- if (e.getSource().equals(userDefinedColour))\r
- {\r
- new UserDefinedColours(ap, sg);\r
- }\r
- else\r
- {\r
- UserColourScheme udc = (UserColourScheme) UserDefinedColours\r
- .getUserColourSchemes().get(e.getActionCommand());\r
-\r
- sg.cs = udc;\r
- }\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void PIDColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(ap.av.getHiddenRepSequences()),\r
- sg.getStartRes(), sg.getEndRes() + 1));\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void BLOSUM62Colour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- sg.cs = new Blosum62ColourScheme();\r
-\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(ap.av.getHiddenRepSequences()),\r
- sg.getStartRes(), sg.getEndRes() + 1));\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void noColourmenuItem_actionPerformed()\r
- {\r
- getGroup().cs = null;\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void conservationMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg.cs == null)\r
- {\r
- return;\r
- }\r
-\r
- if (conservationMenuItem.isSelected())\r
- {\r
- Conservation c = new Conservation(MessageManager.getString("label.group"),\r
- ResidueProperties.propHash, 3, sg.getSequences(ap.av\r
- .getHiddenRepSequences()), sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
-\r
- c.calculate();\r
- c.verdict(false, ap.av.getConsPercGaps());\r
-\r
- sg.cs.setConservation(c);\r
-\r
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
- SliderPanel.showConservationSlider();\r
- }\r
- else\r
- // remove ConservationColouring\r
- {\r
- sg.cs.setConservation(null);\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg == null)\r
- {\r
- return;\r
- }\r
-\r
- AnnotationColourGradient acg = new AnnotationColourGradient(\r
- sequence.getAnnotation()[0], null,\r
- AnnotationColourGradient.NO_THRESHOLD);\r
-\r
- acg.setPredefinedColours(true);\r
- sg.cs = acg;\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void groupName_actionPerformed()\r
- {\r
-\r
- SequenceGroup sg = getGroup();\r
- EditNameDialog dialog = new EditNameDialog(sg.getName(),\r
- sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ",\r
- MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),\r
- ap.alignFrame);\r
-\r
- if (!dialog.accept)\r
- {\r
- return;\r
- }\r
-\r
- sg.setName(dialog.getName());\r
- sg.setDescription(dialog.getDescription());\r
- refresh();\r
- }\r
-\r
- /**\r
- * Get selection group - adding it to the alignment if necessary.\r
- * \r
- * @return sequence group to operate on\r
- */\r
- SequenceGroup getGroup()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- // this method won't add a new group if it already exists\r
- if (sg != null)\r
- {\r
- ap.av.getAlignment().addGroup(sg);\r
- }\r
-\r
- return sg;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- void sequenceName_actionPerformed()\r
- {\r
- EditNameDialog dialog = new EditNameDialog(sequence.getName(),\r
- sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ",\r
- MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),\r
- ap.alignFrame);\r
-\r
- if (!dialog.accept)\r
- {\r
- return;\r
- }\r
-\r
- if (dialog.getName() != null)\r
- {\r
- if (dialog.getName().indexOf(" ") > -1)\r
- {\r
- JOptionPane.showMessageDialog(ap,\r
- MessageManager.getString("label.spaces_converted_to_backslashes"),\r
- MessageManager.getString("label.no_spaces_allowed_sequence_name"),\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
-\r
- sequence.setName(dialog.getName().replace(' ', '_'));\r
- ap.paintAlignment(false);\r
- }\r
-\r
- sequence.setDescription(dialog.getDescription());\r
-\r
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
- .getSequences());\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- void unGroupMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.getAlignment().deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- refresh();\r
- }\r
- void createGroupMenuItem_actionPerformed()\r
- {\r
- getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void outline_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),\r
- Color.BLUE);\r
-\r
- if (col != null)\r
- {\r
- sg.setOutlineColour(col);\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void showBoxes_actionPerformed()\r
- {\r
- getGroup().setDisplayBoxes(showBoxes.isSelected());\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void showText_actionPerformed()\r
- {\r
- getGroup().setDisplayText(showText.isSelected());\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void showColourText_actionPerformed()\r
- {\r
- getGroup().setColourText(showColourText.isSelected());\r
- refresh();\r
- }\r
-\r
- public void showLink(String url)\r
- {\r
- try\r
- {\r
- jalview.util.BrowserLauncher.openURL(url);\r
- } catch (Exception ex)\r
- {\r
- JOptionPane\r
- .showInternalMessageDialog(\r
- Desktop.desktop,\r
- MessageManager.getString("label.web_browser_not_found_unix"),\r
- MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);\r
-\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- void hideSequences(boolean representGroup)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg == null || sg.getSize() < 1)\r
- {\r
- ap.av.hideSequence(new SequenceI[]\r
- { sequence });\r
- return;\r
- }\r
-\r
- ap.av.setSelectionGroup(null);\r
-\r
- if (representGroup)\r
- {\r
- ap.av.hideRepSequences(sequence, sg);\r
-\r
- return;\r
- }\r
-\r
- int gsize = sg.getSize();\r
- SequenceI[] hseqs;\r
-\r
- hseqs = new SequenceI[gsize];\r
-\r
- int index = 0;\r
- for (int i = 0; i < gsize; i++)\r
- {\r
- hseqs[index++] = sg.getSequenceAt(i);\r
- }\r
-\r
- ap.av.hideSequence(hseqs);\r
- // refresh(); TODO: ? needed ?\r
- ap.av.sendSelection();\r
- }\r
-\r
- public void copy_actionPerformed()\r
- {\r
- ap.alignFrame.copy_actionPerformed(null);\r
- }\r
-\r
- public void cut_actionPerformed()\r
- {\r
- ap.alignFrame.cut_actionPerformed(null);\r
- }\r
-\r
- void changeCase(ActionEvent e)\r
- {\r
- Object source = e.getSource();\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if (sg != null)\r
- {\r
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
-\r
- String description;\r
- int caseChange;\r
-\r
- if (source == toggle)\r
- {\r
- description = MessageManager.getString("label.toggle_case");\r
- caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
- }\r
- else if (source == upperCase)\r
- {\r
- description = MessageManager.getString("label.to_upper_case");\r
- caseChange = ChangeCaseCommand.TO_UPPER;\r
- }\r
- else\r
- {\r
- description = MessageManager.getString("label.to_lower_case");\r
- caseChange = ChangeCaseCommand.TO_LOWER;\r
- }\r
-\r
- ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,\r
- sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),\r
- startEnd, caseChange);\r
-\r
- ap.alignFrame.addHistoryItem(caseCommand);\r
-\r
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
- .getSequences());\r
-\r
- }\r
- }\r
-\r
- public void outputText_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setForInput(null);\r
- Desktop.addInternalFrame(cap,\r
- MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
-\r
- String[] omitHidden = null;\r
-\r
- System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens\r
- // or we simply trust the user wants\r
- // wysiwig behaviour\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());\r
- omitHidden = ap.av.getViewAsString(true);\r
- Alignment oal = new Alignment(ap.av.getSequenceSelection());\r
- AlignmentAnnotation[] nala = ap.av.getAlignment()\r
- .getAlignmentAnnotation();\r
- if (nala != null)\r
- {\r
- for (int i = 0; i < nala.length; i++)\r
- {\r
- AlignmentAnnotation na = nala[i];\r
- oal.addAnnotation(na);\r
- }\r
- }\r
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
- oal, omitHidden, csel, sg));\r
- oal = null;\r
- }\r
-\r
- public void pdbFromFile_actionPerformed()\r
- {\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));\r
- chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));\r
-\r
- int value = chooser.showOpenDialog(null);\r
-\r
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,\r
- jalview.io.AppletFormatAdapter.FILE, sequence, true);\r
- }\r
-\r
- }\r
-\r
- public void enterPDB_actionPerformed()\r
- {\r
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);\r
-\r
- if (id != null && id.length() > 0)\r
- {\r
- PDBEntry entry = new PDBEntry();\r
- entry.setId(id.toUpperCase());\r
- sequence.getDatasetSequence().addPDBId(entry);\r
- }\r
- }\r
-\r
- public void discoverPDB_actionPerformed()\r
- {\r
-\r
- final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]\r
- { sequence }\r
- : ap.av.getSequenceSelection());\r
- Thread discpdb = new Thread(new Runnable()\r
- {\r
- public void run()\r
- {\r
-\r
- new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)\r
- .fetchDBRefs(false);\r
- }\r
-\r
- });\r
- discpdb.start();\r
- }\r
-\r
- public void sequenceFeature_actionPerformed()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg == null)\r
- {\r
- return;\r
- }\r
-\r
- int rsize = 0, gSize = sg.getSize();\r
- SequenceI[] rseqs, seqs = new SequenceI[gSize];\r
- SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];\r
-\r
- for (int i = 0; i < gSize; i++)\r
- {\r
- int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
- int end = sg.findEndRes(sg.getSequenceAt(i));\r
- if (start <= end)\r
- {\r
- seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();\r
- features[rsize] = new SequenceFeature(null, null, null, start, end,\r
- "Jalview");\r
- rsize++;\r
- }\r
- }\r
- rseqs = new SequenceI[rsize];\r
- tfeatures = new SequenceFeature[rsize];\r
- System.arraycopy(seqs, 0, rseqs, 0, rsize);\r
- System.arraycopy(features, 0, tfeatures, 0, rsize);\r
- features = tfeatures;\r
- seqs = rseqs;\r
- if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,\r
- features, true, ap))\r
- {\r
- ap.alignFrame.setShowSeqFeatures(true);\r
- ap.highlightSearchResults(null);\r
- }\r
- }\r
-\r
- public void textColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg != null)\r
- {\r
- new TextColourChooser().chooseColour(ap, sg);\r
- }\r
- }\r
-\r
- public void colourByStructure(String pdbid)\r
- {\r
- Annotation[] anots = ap.av.getStructureSelectionManager()\r
- .colourSequenceFromStructure(sequence, pdbid);\r
-\r
- AlignmentAnnotation an = new AlignmentAnnotation("Structure",\r
- "Coloured by " + pdbid, anots);\r
-\r
- ap.av.getAlignment().addAnnotation(an);\r
- an.createSequenceMapping(sequence, 0, true);\r
- // an.adjustForAlignment();\r
- ap.av.getAlignment().setAnnotationIndex(an, 0);\r
-\r
- ap.adjustAnnotationHeight();\r
-\r
- sequence.addAlignmentAnnotation(an);\r
-\r
- }\r
-\r
- public void editSequence_actionPerformed(ActionEvent actionEvent)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if (sg != null)\r
- {\r
- if (sequence == null)\r
- sequence = (Sequence) sg.getSequenceAt(0);\r
-\r
- EditNameDialog dialog = new EditNameDialog(\r
- sequence.getSequenceAsString(sg.getStartRes(),\r
- sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,\r
- MessageManager.getString("label.edit_sequence"), ap.alignFrame);\r
-\r
- if (dialog.accept)\r
- {\r
- EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),\r
- EditCommand.REPLACE, dialog.getName().replace(' ',\r
- ap.av.getGapCharacter()),\r
- sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),\r
- sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());\r
-\r
- ap.alignFrame.addHistoryItem(editCommand);\r
-\r
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
- .getSequences());\r
- }\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentAnnotationUtils;
+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.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+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();
+
+ // 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();
+
+ 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();
+
+ // JBPNote: Commented these out - Should add these services via the web
+ // services menu system.
+ // JMenuItem ContraFold = new JMenuItem();
+
+ // JMenuItem RNAFold = new JMenuItem();
+
+ JMenuItem enterPDB = new JMenuItem();
+
+ JMenuItem discoverPDB = new JMenuItem();
+
+ JMenu outputMenu = new JMenu();
+
+ JMenu seqShowAnnotationsMenu = new JMenu();
+
+ JMenu seqHideAnnotationsMenu = new JMenu();
+
+ JMenuItem seqAddReferenceAnnotations = new JMenuItem();
+
+ JMenu groupShowAnnotationsMenu = new JMenu();
+
+ JMenu groupHideAnnotationsMenu = new JMenu();
+
+ JMenuItem groupAddReferenceAnnotations = new JMenuItem();
+
+ 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;
+
+ 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);
+ // 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()
+ {
+ @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<SequenceI> selectedSequence = (seq == null ? Collections
+ .<SequenceI> emptyList() : Arrays.asList(seq));
+ buildAnnotationTypesMenus(seqShowAnnotationsMenu,
+ seqHideAnnotationsMenu, selectedSequence);
+ configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
+ selectedSequence);
+
+ /*
+ * And repeat for the current selection group (if there is one):
+ */
+ final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
+ .<SequenceI> 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("Unmark representative");
+ } else {
+ makeReferenceSeq.setText("Mark as representative");
+ }
+
+ 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 ActionListener()
+ {
+ @Override
+ 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 StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(pdb,
+ ap.av.collateForPDB(new PDBEntry[]
+ { pdb })[0], null, ap);
+ }
+ });
+ 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; aa != null && i < aa.length; i++)
+ {
+ if (aa[i].isValidStruc() && aa[i].sequenceRef == null)
+ {
+ final String rnastruc = aa[i].getRNAStruc();
+ final String structureLine = aa[i].label + " (alignment)";
+ menuItem = new JMenuItem();
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_structure_line", new String[]
+ { structureLine }));
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // // System.out.println("1:"+structureLine);
+ // System.out.println("1:sname" + seq.getName());
+ // System.out.println("2:seq" + seq);
+ //
+ // // System.out.println("3:"+seq.getSequenceAsString());
+ // System.out.println("3:strucseq" + rnastruc);
+ // // System.out.println("4:struc"+seq.getRNA());
+ // System.out.println("5:name" + seq.getName());
+ // System.out.println("6:ap" + ap);
+ new AppVarna(structureLine, seq, seq.getSequenceAsString(),
+ rnastruc, seq.getName(), ap);
+ // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
+ // seq.getName(), ap);
+ System.out.println("end");
+ }
+ });
+ viewStructureMenu.add(menuItem);
+ }
+ }
+
+ // SequenceFeatures[] test = seq.getSequenceFeatures();
+
+ if (seq.getAnnotation() != null)
+ {
+ AlignmentAnnotation seqAnno[] = seq.getAnnotation();
+ for (int i = 0; i < seqAnno.length; i++)
+ {
+ if (seqAnno[i].isValidStruc())
+ {
+ 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()
+ {
+ @Override
+ 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()
+ {
+ @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 String[]
+ { 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 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<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
+ SequenceI sqass = null;
+ for (SequenceI sq : ap.av.getSequenceSelection())
+ {
+ Vector<PDBEntry> pes = sq.getDatasetSequence().getPDBId();
+ if (pes != null && pes.size() > 0)
+ {
+ reppdb.put(pes.get(0).getId(), pes.get(0));
+ for (PDBEntry pe : pes)
+ {
+ pdbe.put(pe.getId(), pe);
+ if (sqass == null)
+ {
+ sqass = sq;
+ }
+ }
+ }
+ }
+ if (pdbe.size() > 0)
+ {
+ final PDBEntry[] pe = pdbe.values().toArray(
+ new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
+ new PDBEntry[reppdb.size()]);
+ final JMenuItem gpdbview, rpdbview;
+ if (pdbe.size() == 1)
+ {
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ .formatMessage("label.view_structure_for", new String[]
+ { sqass.getDisplayId(false) })));
+ }
+ else
+ {
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ .formatMessage("label.view_all_structures", new String[]
+ { new Integer(pdbe.size()).toString() })));
+ }
+ gpdbview.setToolTipText(MessageManager
+ .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
+ gpdbview.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pe, ap.av.collateForPDB(pe));
+ }
+ });
+ if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
+ {
+ structureMenu.add(rpdbview = new JMenuItem(MessageManager
+ .formatMessage(
+ "label.view_all_representative_structures",
+ new String[]
+ { new Integer(reppdb.size()).toString() })));
+ rpdbview.setToolTipText(MessageManager
+ .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
+ rpdbview.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pr, ap.av.collateForPDB(pr));
+ }
+ });
+ }
+ }
+ }
+ else
+ {
+ groupMenu.setVisible(false);
+ editMenu.setVisible(false);
+ }
+
+ if (!isDefinedGroup)
+ {
+ createGroupMenuItem.setVisible(true);
+ unGroupMenuItem.setVisible(false);
+ jMenu1.setText(MessageManager.getString("action.edit_new_group"));
+ }
+ else
+ {
+ createGroupMenuItem.setVisible(false);
+ unGroupMenuItem.setVisible(true);
+ jMenu1.setText(MessageManager.getString("action.edit_group"));
+ }
+
+ if (seq == null)
+ {
+ sequenceMenu.setVisible(false);
+ structureMenu.setVisible(false);
+ }
+
+ if (links != null && links.size() > 0)
+ {
+
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
+ Vector linkset = new Vector();
+ for (int i = 0; i < links.size(); i++)
+ {
+ String link = links.elementAt(i).toString();
+ UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(link);
+ } catch (Exception foo)
+ {
+ jalview.bin.Cache.log.error("Exception for URLLink '" + link
+ + "'", foo);
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
+ {
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ if (seq != null && urlLink.isDynamic())
+ {
+
+ // collect matching db-refs
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+ seq.getDBRef(), new String[]
+ { urlLink.getTarget() });
+ // collect id string too
+ String id = seq.getName();
+ String descr = seq.getDescription();
+ if (descr != null && descr.length() < 1)
+ {
+ descr = null;
+ }
+
+ if (dbr != null)
+ {
+ for (int r = 0; r < dbr.length; r++)
+ {
+ if (id != null && dbr[r].getAccessionId().equals(id))
+ {
+ // suppress duplicate link creation for the bare sequence ID
+ // string with this link
+ id = null;
+ }
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
+ true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+ {
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ addshowLink(linkMenu, label + "|" + urls[u],
+ urls[u + 1]);
+ }
+ }
+ }
+ }
+ }
+ if (id != null)
+ {
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(id, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+ {
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
+ }
+ }
+ }
+ // Create urls from description but only for URL links which are regex
+ // links
+ if (descr != null && urlLink.getRegexReplace() != null)
+ {
+ // create link for this URL from description where regex matches
+ String[] urls = urlLink.makeUrls(descr, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+ {
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
+ {
+ linkset.addElement(label + "|" + urlLink.getUrl_prefix());
+ // Add a non-dynamic link
+ addshowLink(linkMenu, label, urlLink.getUrl_prefix());
+ }
+ }
+ }
+ if (sequence != null)
+ {
+ sequenceMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+ }
+ }
+
+ /**
+ * 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.
+ * <p>
+ * 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.
+ * <p>
+ * IUPredWS (Long), IUPredWS (Short)
+ *
+ * @param seq
+ */
+ protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
+ List<SequenceI> forSequences)
+ {
+ showMenu.removeAll();
+ hideMenu.removeAll();
+
+ final List<String> 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<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
+ hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations),
+ forSequences);
+
+ for (String calcId : hiddenTypes.keySet())
+ {
+ for (List<String> 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<String> 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<SequenceI> getSequenceScope(SequenceI seq)
+ {
+ List<SequenceI> forSequences = null;
+ final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
+ if (selectionGroup != null && selectionGroup.getSize() > 0)
+ {
+ forSequences = selectionGroup.getSequences();
+ }
+ else
+ {
+ forSequences = seq == null ? Collections.<SequenceI> 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<SequenceI> forSequences, String calcId,
+ final List<String> types, final boolean allTypes,
+ final boolean actionIsShow)
+ {
+ String label = types.toString(); // [a, b, c]
+ label = label.substring(1, label.length() - 1);
+ final JMenuItem item = new JMenuItem(label);
+ item.setToolTipText(calcId);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showHideAnnotation_actionPerformed(types, forSequences, allTypes,
+ actionIsShow);
+ }
+ });
+ showOrHideMenu.add(item);
+ }
+
+ /**
+ * Action on selecting a list of annotation type (or the 'all types' values)
+ * to show or hide for the specified sequences.
+ *
+ * @param types
+ * @param forSequences
+ * @param anyType
+ * @param doShow
+ */
+ protected void showHideAnnotation_actionPerformed(
+ Collection<String> types, List<SequenceI> forSequences,
+ boolean anyType, boolean doShow)
+ {
+ for (AlignmentAnnotation aa : ap.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (anyType || types.contains(aa.label))
+ {
+ if ((aa.sequenceRef != null)
+ && forSequences.contains(aa.sequenceRef))
+ {
+ aa.visible = doShow;
+ }
+ }
+ }
+ refresh();
+ }
+
+ 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()
+ {
+ @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("label.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();
+ }
+ });
+ // RNAFold.setText("From RNA Fold with predict2D");
+ // RNAFold.addActionListener(new ActionListener()
+ // {
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // try {
+ // RNAFold_actionPerformed();
+ // } catch (Exception e1) {
+ // // TODO Auto-generated catch block
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
+ // ContraFold.setText("From Contra Fold with predict2D");
+ // ContraFold.addActionListener(new ActionListener()
+ // {
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // try {
+ // ContraFold_actionPerformed();
+ // } catch (Exception e1) {
+ // // TODO Auto-generated catch block
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
+ enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
+ enterPDB.addActionListener(new ActionListener()
+ {
+ @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"));
+ 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()
+ {
+ @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(structureMenu);
+ 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(RNAInteractionColour);
+ colourMenu.add(purinePyrimidineColour);
+ }
+ // colourMenu.add(covariationColour);
+ colourMenu.add(userDefinedColour);
+
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ .getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ JMenuItem item = new JMenuItem(userColours.nextElement().toString());
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ colourMenu.add(item);
+ }
+ }
+
+ colourMenu.addSeparator();
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(conservationMenuItem);
+ // colourMenu.add(annotationMenuItem);
+ editMenu.add(copy);
+ editMenu.add(cut);
+ editMenu.add(editSequence);
+ editMenu.add(upperCase);
+ editMenu.add(lowerCase);
+ editMenu.add(toggle);
+ pdbMenu.add(pdbFromFile);
+ // JBPNote: These shouldn't be added here - should appear in a generic
+ // 'apply web service to this sequence menu'
+ // pdbMenu.add(RNAFold);
+ // pdbMenu.add(ContraFold);
+ pdbMenu.add(enterPDB);
+ pdbMenu.add(discoverPDB);
+ jMenu1.add(groupName);
+ jMenu1.add(colourMenu);
+ jMenu1.add(showBoxes);
+ jMenu1.add(showText);
+ jMenu1.add(showColourText);
+ jMenu1.add(outline);
+ jMenu1.add(displayNonconserved);
+ structureMenu.add(pdbMenu);
+ structureMenu.add(viewStructureMenu);
+ // structureMenu.add(colStructureMenu);
+ noColourmenuItem.setText(MessageManager.getString("label.none"));
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ @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<SequenceI> forSequences)
+ {
+ menuItem.setText(MessageManager
+ .getString("label.add_reference_annotations"));
+ menuItem.setEnabled(false);
+ if (forSequences == null)
+ {
+ return;
+ }
+
+ /*
+ * Temporary store to hold distinct calcId / type pairs for the tooltip.
+ * Using TreeMap means calcIds are shown in alphabetical order.
+ */
+ Map<String, String> tipEntries = new TreeMap<String, String>();
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
+ /*
+ * For each sequence selected in the alignment, make a list of any
+ * annotations on the underlying dataset sequence which are not already on
+ * the alignment.
+ *
+ * Build a map of { alignmentSequence, <List of annotations to add> }
+ */
+ AlignmentI al = this.ap.av.getAlignment();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+ for (SequenceI seq : forSequences)
+ {
+ SequenceI dataset = seq.getDatasetSequence();
+ if (dataset == null)
+ {
+ continue;
+ }
+ AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
+ if (datasetAnnotations == null)
+ {
+ continue;
+ }
+ final List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation dsann : datasetAnnotations)
+ {
+ /*
+ * Find matching annotations on the alignment.
+ */
+ final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
+ .findAnnotations(seq, dsann.getCalcId(),
+ dsann.label);
+ if (!matchedAlignmentAnnotations.iterator().hasNext())
+ {
+ result.add(dsann);
+ tipEntries.put(dsann.getCalcId(), dsann.label);
+ }
+ }
+ /*
+ * Save any addable annotations for this sequence
+ */
+ if (!result.isEmpty())
+ {
+ candidates.put(seq, result);
+ }
+ }
+ if (!candidates.isEmpty())
+ {
+ /*
+ * 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("<br/>" + 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<SequenceI, List<AlignmentAnnotation>> candidates)
+ {
+ /*
+ * Add annotations at the top of the annotation, in the same order as their
+ * related sequences.
+ */
+ for (SequenceI seq : candidates.keySet())
+ {
+ for (AlignmentAnnotation ann : candidates.get(seq))
+ {
+ AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
+ int startRes = 0;
+ int endRes = ann.annotations.length;
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ if (selectionGroup != null)
+ {
+ startRes = selectionGroup.getStartRes();
+ endRes = selectionGroup.getEndRes();
+ }
+ copyAnn.restrict(startRes, endRes);
+
+ /*
+ * Add to the sequence (sets copyAnn.datasetSequence), unless the
+ * original annotation is already on the sequence.
+ */
+ if (!seq.hasAnnotation(ann))
+ {
+ seq.addAlignmentAnnotation(copyAnn);
+ }
+ // adjust for gaps
+ copyAnn.adjustForAlignment();
+ // add to the alignment and set visible
+ this.ap.getAlignment().addAnnotation(copyAnn);
+ copyAnn.visible = true;
+ }
+ }
+ 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("<p><h2>"
+ + MessageManager
+ .formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new String[]
+ { seq.getDisplayId(true) }) + "</h2></p><p>");
+ new SequenceAnnotationReport(null)
+ .createSequenceAnnotationReport(
+ contents,
+ seq,
+ true,
+ true,
+ false,
+ (ap.getSeqPanel().seqCanvas.fr != null) ? ap
+ .getSeqPanel().seqCanvas.fr
+ .getMinMax()
+ : null);
+ contents.append("</p>");
+ }
+ cap.setText("<html>" + contents.toString() + "</html>");
+
+ 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();
+ }
+
+ /**
+ * 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;
+
+ 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
+
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+ ap.av, 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 String[]
+ { sequence.getDisplayId(false) }));
+ chooser.setToolTipText(MessageManager.formatMessage(
+ "label.load_pdb_file_associate_with_sequence", new String[]
+ { 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);
+ }
+
+ }
+
+ // JBNote: commented out - these won't be instantiated here...!
+ // public void RNAFold_actionPerformed() throws Exception
+ // {
+ // Predict2D P2D = new Predict2D();
+ // P2D.getStructure2DFromRNAFold("toto");
+ // }
+ //
+ // public void ContraFold_actionPerformed() throws Exception
+ // {
+ // Predict2D P2D = new Predict2D();
+ // P2D.getStructure2DFromContraFold("toto");
+ // }
+ public void enterPDB_actionPerformed()
+ {
+ String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ MessageManager.getString("label.enter_pdb_id"),
+ MessageManager.getString("label.enter_pdb_id"),
+ JOptionPane.QUESTION_MESSAGE);
+
+ if (id != null && id.length() > 0)
+ {
+ PDBEntry entry = new PDBEntry();
+ entry.setId(id.toUpperCase());
+ sequence.getDatasetSequence().addPDBId(entry);
+ }
+ }
+
+ public void discoverPDB_actionPerformed()
+ {
+
+ final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
+ { sequence }
+ : ap.av.getSequenceSelection());
+ Thread discpdb = new Thread(new Runnable()
+ {
+ @Override
+ 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.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());
+ }
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff