-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program 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 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-\r
-import MCview.*;\r
-import jalview.analysis.*;\r
-import jalview.commands.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class PopupMenu\r
- extends JPopupMenu\r
-{\r
- JMenu groupMenu = new JMenu();\r
- JMenuItem groupName = new JMenuItem();\r
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem hydrophobicityColour = new\r
- JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
- protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
- AlignmentPanel ap;\r
- JMenu sequenceMenu = new JMenu();\r
- JMenuItem sequenceName = new JMenuItem();\r
- Sequence sequence;\r
- JMenuItem unGroupMenuItem = new JMenuItem();\r
- JMenuItem outline = new JMenuItem();\r
- JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
- JMenu colourMenu = new JMenu();\r
- JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
- JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
- JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
- JMenu editMenu = new JMenu();\r
- JMenuItem cut = new JMenuItem();\r
- JMenuItem copy = new JMenuItem();\r
- JMenuItem upperCase = new JMenuItem();\r
- JMenuItem lowerCase = new JMenuItem();\r
- JMenuItem toggle = new JMenuItem();\r
- JMenu pdbMenu = new JMenu();\r
- JMenuItem pdbFromFile = new JMenuItem();\r
- JMenuItem enterPDB = new JMenuItem();\r
- JMenuItem discoverPDB = new JMenuItem();\r
- JMenu outputMenu = new JMenu();\r
- JMenuItem sequenceFeature = new JMenuItem();\r
- JMenuItem textColour = new JMenuItem();\r
- JMenu jMenu1 = new JMenu();\r
- JMenu structureMenu = new JMenu();\r
- JMenu viewStructureMenu = new JMenu();\r
- // JMenu colStructureMenu = new JMenu();\r
- JMenuItem editSequence = new JMenuItem();\r
- // JMenuItem annotationMenuItem = new JMenuItem();\r
-\r
- /**\r
- * Creates a new PopupMenu object.\r
- *\r
- * @param ap DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- */\r
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\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
-\r
- for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
- {\r
- JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[\r
- 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
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- if (seq != null)\r
- {\r
- sequenceMenu.setText(sequence.getName());\r
-\r
- JMenuItem menuItem;\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
- Vector seqs = new Vector();\r
- for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
- {\r
- Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();\r
- if(pdbs==null)\r
- continue;\r
-\r
- for(int p=0; p<pdbs.size(); p++)\r
- {\r
- PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);\r
- if(p1.getId().equals(pdb.getId()))\r
- {\r
- if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))\r
- seqs.addElement(ap.av.alignment.getSequenceAt(i));\r
-\r
- continue;\r
- }\r
- }\r
- }\r
-\r
- SequenceI [] seqs2 = new SequenceI[seqs.size()];\r
- seqs.toArray(seqs2);\r
-\r
- new AppJMol(pdb, seqs2, null, ap);\r
- }\r
- });\r
- viewStructureMenu.add(menuItem);\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
- colourByStructure(pdb.getId());\r
- }\r
- });\r
- colStructureMenu.add(menuItem);*/\r
- }\r
- }\r
- else\r
- {\r
- structureMenu.remove(viewStructureMenu);\r
- // structureMenu.remove(colStructureMenu);\r
- }\r
-\r
- menuItem = new JMenuItem("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("Represent Group with " + 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.alignment.findIndex(seq);\r
-\r
- if (ap.av.adjustForHiddenSeqs(index) -\r
- ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
- {\r
- menuItem = new JMenuItem("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
- menuItem = new JMenuItem("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
-\r
- if (sg != null)\r
- {\r
- groupName.setText(sg.getName());\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\r
- {\r
- noColourmenuItem.setSelected(true);\r
- }\r
-\r
- if (sg.cs != null && sg.cs.conservationApplied())\r
- {\r
- conservationMenuItem.setSelected(true);\r
- }\r
-\r
- showText.setSelected(sg.getDisplayText());\r
- showColourText.setSelected(sg.getColourText());\r
- showBoxes.setSelected(sg.getDisplayBoxes());\r
- }\r
- else\r
- {\r
- groupMenu.setVisible(false);\r
- editMenu.setVisible(false);\r
- }\r
-\r
- if (!ap.av.alignment.getGroups().contains(sg))\r
- {\r
- unGroupMenuItem.setVisible(false);\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
- JMenu linkMenu = new JMenu("Link");\r
- JMenuItem item;\r
- for (int i = 0; i < links.size(); i++)\r
- {\r
- String link = links.elementAt(i).toString();\r
- final String label = link.substring(0, link.indexOf("|"));\r
- item = new JMenuItem(label);\r
- final String url;\r
-\r
- if (link.indexOf("$SEQUENCE_ID$") > -1)\r
- {\r
- String id = seq.getName();\r
- if (id.indexOf("|") > -1)\r
- {\r
- id = id.substring(id.lastIndexOf("|") + 1);\r
- }\r
-\r
- url = link.substring(link.indexOf("|") + 1,\r
- link.indexOf("$SEQUENCE_ID$"))\r
- + id +\r
- link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
- }\r
- else\r
- {\r
- url = link.substring(link.lastIndexOf("|") + 1);\r
- }\r
-\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showLink(url);\r
- }\r
- });\r
-\r
- linkMenu.add(item);\r
- }\r
- if (sequence != null)\r
- {\r
- sequenceMenu.add(linkMenu);\r
- }\r
- else\r
- {\r
- add(linkMenu);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @throws Exception DOCUMENT ME!\r
- */\r
- private void jbInit()\r
- throws Exception\r
- {\r
- groupMenu.setText("Group");\r
- groupMenu.setText("Selection");\r
- groupName.setText("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("Sequence");\r
- sequenceName.setText("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
- PIDColour.setFocusPainted(false);\r
- unGroupMenuItem.setText("Remove Group");\r
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- unGroupMenuItem_actionPerformed();\r
- }\r
- });\r
-\r
- outline.setText("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("Nucleotide");\r
- nucleotideMenuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideMenuItem_actionPerformed();\r
- }\r
- });\r
- colourMenu.setText("Group Colour");\r
- showBoxes.setText("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("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("Colour Text");\r
- showColourText.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showColourText_actionPerformed();\r
- }\r
- });\r
- editMenu.setText("Edit");\r
- cut.setText("Cut");\r
- cut.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cut_actionPerformed();\r
- }\r
- });\r
- upperCase.setText("To Upper Case");\r
- upperCase.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
- copy.setText("Copy");\r
- copy.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed();\r
- }\r
- });\r
- lowerCase.setText("To Lower Case");\r
- lowerCase.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
- toggle.setText("Toggle Case");\r
- toggle.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
- pdbMenu.setText("Associate Structure with Sequence");\r
- pdbFromFile.setText("From File");\r
- pdbFromFile.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pdbFromFile_actionPerformed();\r
- }\r
- });\r
- enterPDB.setText("Enter PDB Id");\r
- enterPDB.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- enterPDB_actionPerformed();\r
- }\r
- });\r
- discoverPDB.setText("Discover PDB ids");\r
- discoverPDB.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- discoverPDB_actionPerformed();\r
- }\r
- });\r
- outputMenu.setText("Output to Textbox...");\r
- sequenceFeature.setText("Create Sequence Feature");\r
- sequenceFeature.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceFeature_actionPerformed();\r
- }\r
- });\r
- textColour.setText("Text Colour");\r
- textColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- textColour_actionPerformed();\r
- }\r
- });\r
- jMenu1.setText("Group");\r
- structureMenu.setText("Structure");\r
- viewStructureMenu.setText("View Structure");\r
- // colStructureMenu.setText("Colour By Structure");\r
- editSequence.setText("Edit Sequence...");\r
- editSequence.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- editSequence_actionPerformed(actionEvent);\r
- }\r
- });\r
- /* annotationMenuItem.setText("By Annotation");\r
- annotationMenuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- annotationMenuItem_actionPerformed(actionEvent);\r
- }\r
- });*/\r
-\r
- add(groupMenu);\r
-\r
- add(sequenceMenu);\r
- this.add(structureMenu);\r
- groupMenu.add(editMenu);\r
- groupMenu.add(outputMenu);\r
- groupMenu.add(sequenceFeature);\r
- groupMenu.add(jMenu1);\r
- sequenceMenu.add(sequenceName);\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
- 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.\r
- 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(unGroupMenuItem);\r
- jMenu1.add(colourMenu);\r
- jMenu1.add(showBoxes);\r
- jMenu1.add(showText);\r
- jMenu1.add(showColourText);\r
- jMenu1.add(outline);\r
- structureMenu.add(pdbMenu);\r
- structureMenu.add(viewStructureMenu);\r
- // structureMenu.add(colStructureMenu);\r
- noColourmenuItem.setText("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("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("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("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("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed();\r
- }\r
- });\r
- helixColour.setText("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("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("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("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("Above % Identity");\r
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- abovePIDColour_actionPerformed();\r
- }\r
- });\r
- userDefinedColour.setText("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("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("BLOSUM62");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed();\r
- }\r
- });\r
- conservationMenuItem.setText("Conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed();\r
- }\r
- });\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- void refresh()\r
- {\r
- ap.paintAlignment(true);\r
-\r
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void clustalColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
- ap.av.alignment.getWidth());\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e 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 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 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 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 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 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 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 DOCUMENT ME!\r
- */\r
- public void nucleotideMenuItem_actionPerformed()\r
- {\r
- getGroup().cs = new NucleotideColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e 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.hiddenRepSequences), sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
-\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
- getGroup().getName());\r
-\r
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
-\r
- SliderPanel.showPIDSlider();\r
- }\r
- else // 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 DOCUMENT ME!\r
- */\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- if (e.getActionCommand().equals("User Defined..."))\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 DOCUMENT ME!\r
- */\r
- protected void PIDColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
- hiddenRepSequences),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e 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(sg.getSequences(ap.av.\r
- hiddenRepSequences),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e 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 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("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(ap.av.\r
- hiddenRepSequences),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
-\r
- c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
-\r
- sg.cs.setConservation(c);\r
-\r
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
- SliderPanel.showConservationSlider();\r
- }\r
- else // 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, AnnotationColourGradient.NO_THRESHOLD);\r
-\r
- acg.predefinedColours = true;\r
- sg.cs = acg;\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void groupName_actionPerformed()\r
- {\r
-\r
- SequenceGroup sg = getGroup();\r
- EditNameDialog dialog = new EditNameDialog(sg.getName(),\r
- sg.getDescription(),\r
- " Group Name ",\r
- "Group Description ",\r
- "Edit Group Name/Description");\r
-\r
- if (!dialog.accept)\r
- {\r
- return;\r
- }\r
-\r
- sg.setName(dialog.getName());\r
- sg.setDescription(dialog.getDescription());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\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.alignment.addGroup(sg);\r
- }\r
-\r
- return sg;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- void sequenceName_actionPerformed()\r
- {\r
- EditNameDialog dialog = new EditNameDialog(sequence.getName(),\r
- sequence.getDescription(),\r
- " Sequence Name ",\r
- "Sequence Description ",\r
- "Edit Sequence Name/Description");\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
- "Spaces have been converted to \"_\"",\r
- "No spaces allowed in 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,\r
- ap.av.getAlignment().getSequences());\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- void unGroupMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void outline_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- Color col = JColorChooser.showDialog(this, "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 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 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 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
- }\r
- catch (Exception ex)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Unixers: Couldn't find default web browser."\r
- +\r
- "\nAdd the full path to your browser in Preferences.",\r
- "Web browser not found",\r
- 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
- }\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(\r
- sg.getStartRes(), sg.getEndRes() + 1);\r
-\r
- String description;\r
- int caseChange;\r
-\r
- if (source == toggle)\r
- {\r
- description = "Toggle Case";\r
- caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
- }\r
- else if (source == upperCase)\r
- {\r
- description = "To Upper Case";\r
- caseChange = ChangeCaseCommand.TO_UPPER;\r
- }\r
- else\r
- {\r
- description = "To Lower Case";\r
- caseChange = ChangeCaseCommand.TO_LOWER;\r
- }\r
-\r
- ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
- description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
- startEnd, caseChange\r
- );\r
-\r
- ap.alignFrame.addHistoryItem(caseCommand);\r
-\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().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
- "Alignment output - " + e.getActionCommand(), 600,\r
- 500);\r
-\r
- String[] omitHidden = null;\r
-\r
- if (ap.av.hasHiddenColumns)\r
- {\r
- System.out.println("PROMPT USER HERE");\r
- omitHidden = ap.av.getViewAsString(true);\r
- }\r
-\r
- cap.setText(new FormatAdapter().formatSequences(\r
- e.getActionCommand(),\r
- ap.av.getSelectionAsNewSequence(),\r
- omitHidden));\r
- }\r
-\r
- public void pdbFromFile_actionPerformed()\r
- {\r
- jalview.io.JalviewFileChooser chooser\r
- = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
- getProperty(\r
- "LAST_DIRECTORY"));\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Select a PDB file");\r
- chooser.setToolTipText("Load a PDB file");\r
-\r
- int value = chooser.showOpenDialog(null);\r
-\r
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- PDBEntry entry = new PDBEntry();\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- try\r
- {\r
- MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
- jalview.io.AppletFormatAdapter.FILE);\r
-\r
- if (pdbfile.id == null)\r
- {\r
- String reply = JOptionPane.showInternalInputDialog(\r
- Desktop.desktop,\r
- "Couldn't find a PDB id in the file supplied."\r
- + "Please enter an Id to identify this structure.",\r
- "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
- if (reply == null)\r
- {\r
- return;\r
- }\r
-\r
- entry.setId(reply);\r
- }\r
- else\r
- {\r
- entry.setId(pdbfile.id);\r
- }\r
- }\r
- catch (java.io.IOException ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- entry.setFile(choice);\r
- sequence.getDatasetSequence().addPDBId(entry);\r
- }\r
-\r
- }\r
-\r
- public void enterPDB_actionPerformed()\r
- {\r
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
-\r
- if (id != null && id.length() > 0)\r
- {\r
- PDBEntry entry = new PDBEntry();\r
- entry.setId(id);\r
- sequence.getDatasetSequence()\r
- .addPDBId(entry);\r
- }\r
- }\r
-\r
- public void discoverPDB_actionPerformed()\r
- {\r
- SequenceI[] sequences =\r
- ap.av.selectionGroup == null ?\r
- new Sequence[]{sequence}\r
- : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);\r
-\r
- new jalview.io.DBRefFetcher(sequences,\r
- ap.alignFrame).fetchDBRefs(false);\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 gSize = sg.getSize();\r
- SequenceI[] seqs = new SequenceI[gSize];\r
- SequenceFeature[] features = new SequenceFeature[gSize];\r
-\r
- for (int i = 0; i < gSize; i++)\r
- {\r
- seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
- int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
- int end = sg.findEndRes(sg.getSequenceAt(i));\r
- features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");\r
- }\r
-\r
- if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
- .amendFeatures(seqs, features, true, ap))\r
- {\r
- ap.alignFrame.showSeqFeatures.setSelected(true);\r
- ap.av.setShowSequenceFeatures(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 = jalview.structure.StructureSelectionManager.getStructureSelectionManager()\r
- .colourSequenceFromStructure(sequence, pdbid);\r
-\r
- AlignmentAnnotation an = new AlignmentAnnotation(\r
- "Structure", "Coloured by "+pdbid, anots);\r
-\r
- ap.av.alignment.addAnnotation(an);\r
- an.createSequenceMapping(sequence, 0, true);\r
- //an.adjustForAlignment();\r
- ap.av.alignment.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(\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1),\r
- null,\r
- "Edit Sequence ",\r
- null,\r
- "Edit Sequence");\r
-\r
- if (dialog.accept)\r
- {\r
- EditCommand editCommand = new EditCommand(\r
- "Edit Sequences", EditCommand.REPLACE,\r
- dialog.getName().replace(' ', ap.av.getGapCharacter()),\r
- sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
- sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment\r
- );\r
-\r
- ap.alignFrame.addHistoryItem(editCommand);\r
-\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
- }\r
- }\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+import MCview.*;
+import jalview.analysis.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
+import jalview.util.GroupUrlLink;
+import jalview.util.GroupUrlLink.UrlStringTooLongException;
+import jalview.util.UrlLink;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision: 1.118 $
+ */
+public class PopupMenu extends JPopupMenu
+{
+ JMenu groupMenu = new JMenu();
+
+ JMenuItem groupName = new JMenuItem();
+
+ protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
+ protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+
+ protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+
+ protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
+ AlignmentPanel ap;
+
+ JMenu sequenceMenu = new JMenu();
+
+ JMenuItem sequenceName = new JMenuItem();
+
+ SequenceI sequence;
+
+ JMenuItem unGroupMenuItem = new JMenuItem();
+
+ JMenuItem outline = new JMenuItem();
+
+ JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
+
+ JMenu colourMenu = new JMenu();
+
+ JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
+
+ JMenu editMenu = new JMenu();
+
+ JMenuItem cut = new JMenuItem();
+
+ JMenuItem copy = new JMenuItem();
+
+ JMenuItem upperCase = new JMenuItem();
+
+ JMenuItem lowerCase = new JMenuItem();
+
+ JMenuItem toggle = new JMenuItem();
+
+ JMenu pdbMenu = new JMenu();
+
+ JMenuItem pdbFromFile = new JMenuItem();
+
+ JMenuItem enterPDB = new JMenuItem();
+
+ JMenuItem discoverPDB = new JMenuItem();
+
+ JMenu outputMenu = new JMenu();
+
+ JMenuItem sequenceFeature = new JMenuItem();
+
+ JMenuItem textColour = new JMenuItem();
+
+ JMenu jMenu1 = new JMenu();
+
+ JMenu structureMenu = new JMenu();
+
+ JMenu viewStructureMenu = new JMenu();
+
+ // JMenu colStructureMenu = new JMenu();
+ JMenuItem editSequence = new JMenuItem();
+
+ // JMenuItem annotationMenuItem = new JMenuItem();
+
+ JMenu groupLinksMenu;
+
+ /**
+ * Creates a new PopupMenu object.
+ *
+ * @param ap
+ * DOCUMENT ME!
+ * @param seq
+ * DOCUMENT ME!
+ */
+ public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
+ {
+ this(ap, seq, links, null);
+ }
+
+ /**
+ *
+ * @param ap
+ * @param seq
+ * @param links
+ * @param groupLinks
+ */
+ public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links,
+ Vector groupLinks)
+ {
+ // /////////////////////////////////////////////////////////
+ // If this is activated from the sequence panel, the user may want to
+ // edit or annotate a particular residue. Therefore display the residue menu
+ //
+ // If from the IDPanel, we must display the sequence menu
+ // ////////////////////////////////////////////////////////
+ this.ap = ap;
+ sequence = seq;
+
+ ButtonGroup colours = new ButtonGroup();
+ colours.add(noColourmenuItem);
+ colours.add(clustalColour);
+ colours.add(zappoColour);
+ colours.add(taylorColour);
+ colours.add(hydrophobicityColour);
+ colours.add(helixColour);
+ colours.add(strandColour);
+ colours.add(turnColour);
+ colours.add(buriedColour);
+ colours.add(abovePIDColour);
+ colours.add(userDefinedColour);
+ colours.add(PIDColour);
+ colours.add(BLOSUM62Colour);
+ colours.add(purinePyrimidineColour);
+ // colours.add(covariationColour);
+
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+ {
+ JMenuItem item = new JMenuItem(
+ jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ outputText_actionPerformed(e);
+ }
+ });
+
+ outputMenu.add(item);
+ }
+
+ try
+ {
+ jbInit();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ JMenuItem menuItem;
+ if (seq != null)
+ {
+ sequenceMenu.setText(sequence.getName());
+
+ if (seq.getDatasetSequence().getPDBId() != null
+ && seq.getDatasetSequence().getPDBId().size() > 0)
+ {
+ java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
+ .elements();
+
+ while (e.hasMoreElements())
+ {
+ final PDBEntry pdb = (PDBEntry) e.nextElement();
+
+ menuItem = new JMenuItem();
+ menuItem.setText(pdb.getId());
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence
+ new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap);
+ // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
+ }
+
+ });
+ viewStructureMenu.add(menuItem);
+
+ /*
+ * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
+ * menuItem.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * colourByStructure(pdb.getId()); } });
+ * colStructureMenu.add(menuItem);
+ */
+ }
+ }
+ else
+ {
+ if (ap.av.alignment.isNucleotide() == false)
+ {
+ structureMenu.remove(viewStructureMenu);
+ }
+ // structureMenu.remove(colStructureMenu);
+ }
+
+ if (ap.av.alignment.isNucleotide() == true)
+ {
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].getRNAStruc() != null)
+ {
+ final String rnastruc = aa[i].getRNAStruc();
+
+ menuItem = new JMenuItem();
+ menuItem.setText("RNA structure - consensus");
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+ .getName(), ap);
+ }
+ });
+ viewStructureMenu.add(menuItem);
+ }
+ }
+
+ // SequenceFeatures[] test = seq.getSequenceFeatures();
+
+ if (seq.getAnnotation() != null)
+ {
+ AlignmentAnnotation seqAnno[] = seq.getAnnotation();
+ for (int i = 0; i < seqAnno.length; i++)
+ {
+ if (seqAnno[i].getRNAStruc() != null)
+ {
+ final String rnastruc = seqAnno[i].getRNAStruc();
+
+ // TODO: make rnastrucF a bit more nice
+ menuItem = new JMenuItem();
+ menuItem.setText("RNA structure - "+seq.getName());
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: VARNA does'nt print gaps in the sequence
+ new AppVarna(seq.getSequenceAsString(), rnastruc, seq
+ .getName(), ap);
+ }
+ });
+ viewStructureMenu.add(menuItem);
+ }
+ }
+ }
+
+
+ }
+
+ menuItem = new JMenuItem("Hide Sequences");
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSequences(false);
+ }
+ });
+ add(menuItem);
+
+ if (ap.av.getSelectionGroup() != null
+ && ap.av.getSelectionGroup().getSize() > 1)
+ {
+ menuItem = new JMenuItem("Represent Group with " + seq.getName());
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSequences(true);
+ }
+ });
+ sequenceMenu.add(menuItem);
+ }
+
+ if (ap.av.hasHiddenRows)
+ {
+ final int index = ap.av.alignment.findIndex(seq);
+
+ if (ap.av.adjustForHiddenSeqs(index)
+ - ap.av.adjustForHiddenSeqs(index - 1) > 1)
+ {
+ menuItem = new JMenuItem("Reveal Sequences");
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.showSequence(index);
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ }
+ });
+ add(menuItem);
+ }
+ }
+ }
+ // for the case when no sequences are even visible
+ if (ap.av.hasHiddenRows) {
+ {
+ menuItem = new JMenuItem("Reveal All");
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.showAllHiddenSeqs();
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ }
+ });
+
+ add(menuItem);
+ }
+
+ }
+
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ if (sg != null&& sg.getSize()>0)
+ {
+ groupName.setText("Name: "+sg.getName());
+ groupName.setText("Edit name and description of 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>();
+ SequenceI sqass=null;
+ for (SequenceI sq: ap.av.getSequenceSelection())
+ {
+ Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence().getPDBId();
+ if (pes!=null) {
+ for (PDBEntry pe: pes)
+ {
+ pdbe.put(pe.getId(), pe);
+ if (sqass==null)
+ {
+ sqass = sq;
+ }
+ }
+ }
+ }
+ if (pdbe.size()>0)
+ {
+ final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
+ final JMenuItem gpdbview;
+ if (pdbe.size()==1)
+ {
+ structureMenu.add(gpdbview=new JMenuItem("View structure for "+sqass.getDisplayId(false)));
+ } else {
+ structureMenu.add(gpdbview=new JMenuItem("View all "+pdbe.size()+" structures."));
+ }
+ gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
+ gpdbview.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new AppJmol(ap, pe, ap.av.collateForPDB(pe));
+ }
+ });
+ }
+ }
+ else
+ {
+ groupMenu.setVisible(false);
+ editMenu.setVisible(false);
+ }
+
+ if (!ap.av.alignment.getGroups().contains(sg))
+ {
+ unGroupMenuItem.setVisible(false);
+ }
+
+ if (seq == null)
+ {
+ sequenceMenu.setVisible(false);
+ structureMenu.setVisible(false);
+ }
+
+ if (links != null && links.size() > 0)
+ {
+
+ JMenu linkMenu = new JMenu("Link");
+ Vector linkset = new Vector();
+ for (int i = 0; i < links.size(); i++)
+ {
+ String link = links.elementAt(i).toString();
+ UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(link);
+ } catch (Exception foo)
+ {
+ jalview.bin.Cache.log.error("Exception for URLLink '" + link
+ + "'", foo);
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
+ {
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ if (seq!=null && urlLink.isDynamic())
+ {
+
+ // collect matching db-refs
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+ seq.getDBRef(), new String[]
+ { urlLink.getTarget() });
+ // collect id string too
+ String id = seq.getName();
+ String descr = seq.getDescription();
+ if (descr != null && descr.length() < 1)
+ {
+ descr = null;
+ }
+
+ if (dbr != null)
+ {
+ for (int r = 0; r < dbr.length; r++)
+ {
+ if (id != null && dbr[r].getAccessionId().equals(id))
+ {
+ // suppress duplicate link creation for the bare sequence ID
+ // string with this link
+ id = null;
+ }
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
+ true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+ {
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ addshowLink(linkMenu, label + "|" + urls[u],
+ urls[u + 1]);
+ }
+ }
+ }
+ }
+ }
+ if (id != null)
+ {
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(id, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+ {
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
+ }
+ }
+ }
+ // Create urls from description but only for URL links which are regex
+ // links
+ if (descr != null && urlLink.getRegexReplace() != null)
+ {
+ // create link for this URL from description where regex matches
+ String[] urls = urlLink.makeUrls(descr, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+ {
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
+ {
+ linkset.addElement(label + "|" + urlLink.getUrl_prefix());
+ // Add a non-dynamic link
+ addshowLink(linkMenu, label, urlLink.getUrl_prefix());
+ }
+ }
+ }
+ if (sequence != null)
+ {
+ sequenceMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+ }
+ }
+
+ private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
+ {
+
+ // TODO: usability: thread off the generation of group url content so root
+ // menu appears asap
+ // sequence only URLs
+ // ID/regex match URLs
+ groupLinksMenu = new JMenu("Group Link");
+ JMenu[] linkMenus = new JMenu[]
+ { null, new JMenu("IDS"), new JMenu("Sequences"),
+ new JMenu("IDS and 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("Group Links");
+ 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("open URL: " + url);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ showLink(url);
+ }
+
+ }).start();
+ }
+ });
+
+ linkMenu.add(item);
+ }
+
+ /**
+ * add a late bound groupURL item to the given linkMenu
+ *
+ * @param linkMenu
+ * @param label
+ * - menu label string
+ * @param urlgenerator
+ * GroupURLLink used to generate URL
+ * @param urlstub
+ * Object array returned from the makeUrlStubs function.
+ */
+ private void addshowLink(JMenu linkMenu, String label,
+ final GroupUrlLink urlgenerator, final Object[] urlstub)
+ {
+ JMenuItem item = new JMenuItem(label);
+ item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
+ + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
+ // put
+ // in
+ // info
+ // about
+ // what
+ // is
+ // being
+ // sent.
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ try
+ {
+ showLink(urlgenerator.constructFrom(urlstub));
+ } catch (UrlStringTooLongException e)
+ {
+ }
+ }
+
+ }).start();
+ }
+ });
+
+ linkMenu.add(item);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception
+ * DOCUMENT ME!
+ */
+ private void jbInit() throws Exception
+ {
+ groupMenu.setText("Group");
+ groupMenu.setText("Selection");
+ groupName.setText("Name");
+ groupName.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ groupName_actionPerformed();
+ }
+ });
+ sequenceMenu.setText("Sequence");
+ sequenceName.setText("Edit Name/Description");
+ sequenceName.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceName_actionPerformed();
+ }
+ });
+ PIDColour.setFocusPainted(false);
+ unGroupMenuItem.setText("Remove Group");
+ unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ unGroupMenuItem_actionPerformed();
+ }
+ });
+
+ outline.setText("Border colour");
+ outline.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ outline_actionPerformed();
+ }
+ });
+ nucleotideMenuItem.setText("Nucleotide");
+ nucleotideMenuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideMenuItem_actionPerformed();
+ }
+ });
+ colourMenu.setText("Group Colour");
+ showBoxes.setText("Boxes");
+ showBoxes.setState(true);
+ showBoxes.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showBoxes_actionPerformed();
+ }
+ });
+ showText.setText("Text");
+ showText.setState(true);
+ showText.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showText_actionPerformed();
+ }
+ });
+ showColourText.setText("Colour Text");
+ showColourText.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showColourText_actionPerformed();
+ }
+ });
+ displayNonconserved.setText("Show Nonconserved");
+ displayNonconserved.setState(true);
+ displayNonconserved.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showNonconserved_actionPerformed();
+ }
+ });
+ editMenu.setText("Edit");
+ cut.setText("Cut");
+ cut.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ cut_actionPerformed();
+ }
+ });
+ upperCase.setText("To Upper Case");
+ upperCase.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
+ copy.setText("Copy");
+ copy.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed();
+ }
+ });
+ lowerCase.setText("To Lower Case");
+ lowerCase.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
+ toggle.setText("Toggle Case");
+ toggle.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
+ pdbMenu.setText("Associate Structure with Sequence");
+ pdbFromFile.setText("From File");
+ pdbFromFile.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pdbFromFile_actionPerformed();
+ }
+ });
+ enterPDB.setText("Enter PDB Id");
+ enterPDB.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ enterPDB_actionPerformed();
+ }
+ });
+ discoverPDB.setText("Discover PDB ids");
+ discoverPDB.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ discoverPDB_actionPerformed();
+ }
+ });
+ outputMenu.setText("Output to Textbox...");
+ sequenceFeature.setText("Create Sequence Feature");
+ sequenceFeature.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceFeature_actionPerformed();
+ }
+ });
+ textColour.setText("Text Colour");
+ textColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed();
+ }
+ });
+ jMenu1.setText("Group");
+ structureMenu.setText("Structure");
+ viewStructureMenu.setText("View Structure");
+ // colStructureMenu.setText("Colour By Structure");
+ editSequence.setText("Edit Sequence...");
+ editSequence.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ editSequence_actionPerformed(actionEvent);
+ }
+ });
+ /*
+ * annotationMenuItem.setText("By Annotation");
+ * annotationMenuItem.addActionListener(new ActionListener() { public void
+ * actionPerformed(ActionEvent actionEvent) {
+ * annotationMenuItem_actionPerformed(actionEvent); } });
+ */
+
+ add(groupMenu);
+
+ add(sequenceMenu);
+ this.add(structureMenu);
+ groupMenu.add(editMenu);
+ groupMenu.add(outputMenu);
+ groupMenu.add(sequenceFeature);
+ groupMenu.add(jMenu1);
+ sequenceMenu.add(sequenceName);
+ colourMenu.add(textColour);
+ colourMenu.add(noColourmenuItem);
+ colourMenu.add(clustalColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.add(PIDColour);
+ colourMenu.add(zappoColour);
+ colourMenu.add(taylorColour);
+ colourMenu.add(hydrophobicityColour);
+ colourMenu.add(helixColour);
+ colourMenu.add(strandColour);
+ colourMenu.add(turnColour);
+ colourMenu.add(buriedColour);
+ colourMenu.add(nucleotideMenuItem);
+ if (ap.getAlignment().isNucleotide()) {
+ colourMenu.add(purinePyrimidineColour);
+ }
+ // colourMenu.add(covariationColour);
+ colourMenu.add(userDefinedColour);
+
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ .getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ JMenuItem item = new JMenuItem(userColours.nextElement().toString());
+ item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ colourMenu.add(item);
+ }
+ }
+
+ colourMenu.addSeparator();
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(conservationMenuItem);
+ // colourMenu.add(annotationMenuItem);
+ editMenu.add(copy);
+ editMenu.add(cut);
+ editMenu.add(editSequence);
+ editMenu.add(upperCase);
+ editMenu.add(lowerCase);
+ editMenu.add(toggle);
+ pdbMenu.add(pdbFromFile);
+ pdbMenu.add(enterPDB);
+ pdbMenu.add(discoverPDB);
+ jMenu1.add(groupName);
+ jMenu1.add(unGroupMenuItem);
+ 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("None");
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ noColourmenuItem_actionPerformed();
+ }
+ });
+
+ clustalColour.setText("Clustalx colours");
+ clustalColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ clustalColour_actionPerformed();
+ }
+ });
+ zappoColour.setText("Zappo");
+ zappoColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zappoColour_actionPerformed();
+ }
+ });
+ taylorColour.setText("Taylor");
+ taylorColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ taylorColour_actionPerformed();
+ }
+ });
+ hydrophobicityColour.setText("Hydrophobicity");
+ hydrophobicityColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed();
+ }
+ });
+ helixColour.setText("Helix propensity");
+ helixColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ helixColour_actionPerformed();
+ }
+ });
+ strandColour.setText("Strand propensity");
+ strandColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ strandColour_actionPerformed();
+ }
+ });
+ turnColour.setText("Turn propensity");
+ turnColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ turnColour_actionPerformed();
+ }
+ });
+ buriedColour.setText("Buried Index");
+ buriedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ buriedColour_actionPerformed();
+ }
+ });
+ abovePIDColour.setText("Above % Identity");
+ abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDColour_actionPerformed();
+ }
+ });
+ userDefinedColour.setText("User Defined...");
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ userDefinedColour_actionPerformed(e);
+ }
+ });
+ PIDColour.setText("Percentage Identity");
+ PIDColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ PIDColour_actionPerformed();
+ }
+ });
+ BLOSUM62Colour.setText("BLOSUM62");
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ BLOSUM62Colour_actionPerformed();
+ }
+ });
+ purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed();
+ }
+ });
+ /*
+ * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * covariationColour_actionPerformed(); } });
+ */
+
+ conservationMenuItem.setText("Conservation");
+ conservationMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ });
+ }
+
+ 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.getSequences(ap.av.hiddenRepSequences),
+ ap.av.alignment.getWidth());
+ 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.hiddenRepSequences), 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.getActionCommand().equals("User Defined..."))
+ {
+ new UserDefinedColours(ap, sg);
+ }
+ else
+ {
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours
+ .getUserColourSchemes().get(e.getActionCommand());
+
+ sg.cs = udc;
+ }
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void PIDColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new PIDColourScheme();
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.hiddenRepSequences), 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.hiddenRepSequences), sg.getStartRes(),
+ sg.getEndRes() + 1));
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void noColourmenuItem_actionPerformed()
+ {
+ getGroup().cs = null;
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void conservationMenuItem_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (conservationMenuItem.isSelected())
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3,
+ sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+ sg.getEndRes() + 1);
+
+ c.calculate();
+ c.verdict(false, ap.av.ConsPercGaps);
+
+ sg.cs.setConservation(c);
+
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ else
+ // remove ConservationColouring
+ {
+ sg.cs.setConservation(null);
+ }
+
+ refresh();
+ }
+
+ 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.predefinedColours = 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(), " Group Name ",
+ "Group Description ", "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.alignment.addGroup(sg);
+ }
+
+ return sg;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ void sequenceName_actionPerformed()
+ {
+ EditNameDialog dialog = new EditNameDialog(sequence.getName(),
+ sequence.getDescription(), " Sequence Name ",
+ "Sequence Description ", "Edit Sequence Name/Description",
+ ap.alignFrame);
+
+ if (!dialog.accept)
+ {
+ return;
+ }
+
+ if (dialog.getName() != null)
+ {
+ if (dialog.getName().indexOf(" ") > -1)
+ {
+ JOptionPane.showMessageDialog(ap,
+ "Spaces have been converted to \"_\"",
+ "No spaces allowed in 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.alignment.deleteGroup(sg);
+ ap.av.setSelectionGroup(null);
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void outline_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ Color col = JColorChooser.showDialog(this, "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,
+ "Unixers: Couldn't find default web browser."
+ + "\nAdd the full path to your browser in Preferences.",
+ "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 = "Toggle Case";
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;
+ }
+ else if (source == upperCase)
+ {
+ description = "To Upper Case";
+ caseChange = ChangeCaseCommand.TO_UPPER;
+ }
+ else
+ {
+ description = "To Lower Case";
+ caseChange = ChangeCaseCommand.TO_LOWER;
+ }
+
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+ sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
+ caseChange);
+
+ ap.alignFrame.addHistoryItem(caseCommand);
+
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
+
+ }
+ }
+
+ public void outputText_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+ Desktop.addInternalFrame(cap,
+ "Alignment output - " + e.getActionCommand(), 600, 500);
+
+ String[] omitHidden = null;
+
+ System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+ // or we simply trust the user wants
+ // wysiwig behaviour
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
+ omitHidden = ap.av.getViewAsString(true);
+ Alignment oal = new Alignment(ap.av.getSequenceSelection());
+ AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
+ if (nala != null)
+ {
+ for (int i = 0; i < nala.length; i++)
+ {
+ AlignmentAnnotation na = nala[i];
+ oal.addAnnotation(na);
+ }
+ }
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+ oal, omitHidden, csel, sg));
+ oal = null;
+ }
+
+ public void pdbFromFile_actionPerformed()
+ {
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false));
+ chooser.setToolTipText("Load a PDB file and associate it with sequence '"+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);
+ }
+
+ }
+
+ public void enterPDB_actionPerformed()
+ {
+ String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ "Enter PDB Id", "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.selectionGroup == null) ? new SequenceI[]
+ { sequence }
+ : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
+ Thread discpdb = new Thread(new Runnable()
+ {
+ public void run()
+ {
+
+ new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
+ .fetchDBRefs(false);
+ }
+
+ });
+ discpdb.start();
+ }
+
+ public void sequenceFeature_actionPerformed()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ int rsize = 0, gSize = sg.getSize();
+ SequenceI[] rseqs, seqs = new SequenceI[gSize];
+ SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+
+ for (int i = 0; i < gSize; i++)
+ {
+ int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+ int end = sg.findEndRes(sg.getSequenceAt(i));
+ if (start <= end)
+ {
+ seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
+ features[rsize] = new SequenceFeature(null, null, null, start, end,
+ "Jalview");
+ rsize++;
+ }
+ }
+ rseqs = new SequenceI[rsize];
+ tfeatures = new SequenceFeature[rsize];
+ System.arraycopy(seqs, 0, rseqs, 0, rsize);
+ System.arraycopy(features, 0, tfeatures, 0, rsize);
+ features = tfeatures;
+ seqs = rseqs;
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
+ {
+ ap.alignFrame.setShowSeqFeatures(true);
+ ap.highlightSearchResults(null);
+ }
+ }
+
+ public void textColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg != null)
+ {
+ new TextColourChooser().chooseColour(ap, sg);
+ }
+ }
+
+ public void colourByStructure(String pdbid)
+ {
+ Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure(
+ sequence, pdbid);
+
+ AlignmentAnnotation an = new AlignmentAnnotation("Structure",
+ "Coloured by " + pdbid, anots);
+
+ ap.av.alignment.addAnnotation(an);
+ an.createSequenceMapping(sequence, 0, true);
+ // an.adjustForAlignment();
+ ap.av.alignment.setAnnotationIndex(an, 0);
+
+ ap.adjustAnnotationHeight();
+
+ sequence.addAlignmentAnnotation(an);
+
+ }
+
+ public void editSequence_actionPerformed(ActionEvent actionEvent)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ if (sg != null)
+ {
+ if (sequence == null)
+ sequence = (Sequence) sg.getSequenceAt(0);
+
+ EditNameDialog dialog = new EditNameDialog(
+ sequence.getSequenceAsString(sg.getStartRes(),
+ sg.getEndRes() + 1), null, "Edit Sequence ", null,
+ "Edit Sequence", ap.alignFrame);
+
+ if (dialog.accept)
+ {
+ EditCommand editCommand = new EditCommand("Edit Sequences",
+ EditCommand.REPLACE, dialog.getName().replace(' ',
+ ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+ sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
+
+ ap.alignFrame.addHistoryItem(editCommand);
+
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
+ }
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff