+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 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 jalview.datamodel.*;\r
+import MCview.*;\r
+\r
import jalview.analysis.*;\r
+\r
+import jalview.datamodel.*;\r
+\r
+\r
import jalview.schemes.*;\r
-import javax.swing.*;\r
+\r
+import java.awt.*;\r
import java.awt.event.*;\r
\r
+import javax.swing.*;\r
+\r
+import java.util.Vector;\r
+import jalview.io.FormatAdapter;\r
+\r
\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class PopupMenu extends JPopupMenu\r
{\r
- JMenu groupMenu = new JMenu();\r
- JMenuItem copyGroup = new JMenuItem();\r
- JMenuItem moveGroup = new JMenuItem();\r
- JMenuItem deleteSequences = new JMenuItem();\r
- JMenuItem analyze = new JMenuItem();\r
- JMenu defineMenu = new JMenu();\r
- JMenuItem groupName = new JMenuItem();\r
- JMenuItem groupAnnotation = 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 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 JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();\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
-\r
-\r
- AlignmentPanel ap;\r
- JMenu sequenceMenu = new JMenu();\r
- JMenuItem sequenceName = new JMenuItem();\r
- JMenu residueMenu = new JMenu();\r
- JMenuItem annotateResidue = new JMenuItem();\r
-\r
- SequenceI sequence;\r
-\r
- public PopupMenu(AlignmentPanel ap, SequenceI seq)\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
-\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
- try\r
- { jbInit(); }\r
- catch(Exception e)\r
- { e.printStackTrace(); }\r
-\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
- if(sg!=null)\r
- groupName.setText( sg.getName() );\r
-\r
- if(seq!=null)\r
- {\r
- residueMenu.setVisible(false);\r
- sequenceName.setText( sequence.getName() );\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 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
+\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[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
+\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
+\r
+ if (seq != null)\r
+ {\r
+ int start = Math.max(sequence.getName().length()-15, 0);\r
+ sequenceMenu.setText(sequence.getName().substring(start));\r
+\r
+ JMenuItem menuItem;\r
+ if( seq.getDatasetSequence().getPDBId() != null)\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("View PDB entry: " + pdb.getId());\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
+ }\r
+ });\r
+ sequenceMenu.add(menuItem);\r
+ }\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(false)>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
+ ap.overviewPanel.updateOverviewImage();\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
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ });\r
+\r
+ add(menuItem);\r
+ }\r
+\r
+\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
+\r
+ if (seq == null)\r
+ {\r
+ sequenceMenu.setVisible(false);\r
+ pdbMenu.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
+ id = id.substring(id.lastIndexOf("|") + 1);\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
+ 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
+ sequenceMenu.add(linkMenu);\r
+ else\r
+ add(linkMenu);\r
+ }\r
}\r
- else\r
- sequenceMenu.setVisible(false);\r
\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- groupMenu.setText("Group");\r
- copyGroup.setText("Copy region to new Alignment");\r
- copyGroup.addActionListener(new java.awt.event.ActionListener()\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @throws Exception DOCUMENT ME!\r
+ */\r
+ private void jbInit() throws Exception\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copyGroup_actionPerformed(e);\r
- }\r
- });\r
- moveGroup.setText("Move sequences to new Alignment");\r
- moveGroup.addActionListener(new java.awt.event.ActionListener()\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(e);\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(e);\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(e);\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(e);\r
+ }\r
+ });\r
+ nucleotideMenuItem.setText("Nucleotide");\r
+ nucleotideMenuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ nucleotideMenuItem_actionPerformed(e);\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(e);\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(e);\r
+ }\r
+ });\r
+ showColourText.setText("Colour Text");\r
+ showColourText.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showColourText_actionPerformed(e);\r
+ }\r
+ });\r
+ editMenu.setText("Edit");\r
+ cut.setText("Cut");\r
+ cut.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- moveGroup_actionPerformed(e);\r
+ cut_actionPerformed(e);\r
}\r
});\r
- deleteSequences.setText("Delete sequences");\r
- deleteSequences.addActionListener(new java.awt.event.ActionListener()\r
+ upperCase.setText("To Upper Case");\r
+ upperCase.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- deleteSequences_actionPerformed(e);\r
+ upperCase_actionPerformed(e);\r
}\r
});\r
- analyze.setText("Analyze");\r
- analyze.addActionListener(new java.awt.event.ActionListener()\r
+ copy.setText("Copy");\r
+ copy.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- analyze_actionPerformed(e);\r
+ copy_actionPerformed(e);\r
}\r
});\r
- defineMenu.setText("Define");\r
- groupName.setText("Name");\r
- groupName.addActionListener(new java.awt.event.ActionListener()\r
+ lowerCase.setText("To Lower Case");\r
+ lowerCase.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- groupName_actionPerformed(e);\r
+ lowerCase_actionPerformed(e);\r
}\r
});\r
- groupAnnotation.setText("Annotation");\r
- groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
+ toggle.setText("Toggle Case");\r
+ toggle.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- groupAnnotation_actionPerformed(e);\r
+ toggle_actionPerformed(e);\r
}\r
});\r
- sequenceMenu.setText("Sequence");\r
- sequenceName.setText("sequenceName");\r
- sequenceName.addActionListener(new java.awt.event.ActionListener()\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
- sequenceName_actionPerformed(e);\r
+ pdbFromFile_actionPerformed(e);\r
}\r
});\r
- residueMenu.setText("Residue");\r
- annotateResidue.setText("annotate residue???");\r
- PIDColour.setFocusPainted(false);\r
- add(groupMenu);\r
- this.add(sequenceMenu);\r
- this.add(residueMenu);\r
- groupMenu.add(defineMenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(copyGroup);\r
- groupMenu.add(moveGroup);\r
- groupMenu.add(deleteSequences);\r
- groupMenu.addSeparator();\r
- groupMenu.add(analyze);\r
- defineMenu.add(groupName);\r
- defineMenu.add(groupAnnotation);\r
- defineMenu.addSeparator();\r
- defineMenu.add(noColourmenuItem);\r
- defineMenu.add(clustalColour);\r
- defineMenu.add(zappoColour);\r
- defineMenu.add(taylorColour);\r
- defineMenu.add(hydrophobicityColour);\r
- defineMenu.add(helixColour);\r
- defineMenu.add(strandColour);\r
- defineMenu.add(turnColour);\r
- defineMenu.add(buriedColour);\r
- defineMenu.add(userDefinedColour);\r
- defineMenu.add(PIDColour);\r
- defineMenu.add(BLOSUM62Colour);\r
- defineMenu.addSeparator();\r
- defineMenu.add(abovePIDColour);\r
- defineMenu.add(conservationMenuItem);\r
-\r
- sequenceMenu.add(sequenceName);\r
- residueMenu.add(annotateResidue);\r
-\r
- noColourmenuItem.setText("None");\r
- noColourmenuItem.setSelected(true);\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ enterPDB.setText("Enter PDB Id");\r
+ enterPDB.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- noColourmenuItem_actionPerformed(e);\r
+ enterPDB_actionPerformed(e);\r
}\r
});\r
-\r
- clustalColour.setSelected(false);\r
- clustalColour.setText("Clustalx colours");\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
+ discoverPDB.setText("Discover PDB ids");\r
+ discoverPDB.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- clustalColour_actionPerformed(e);\r
+ discoverPDB_actionPerformed(e);\r
}\r
});\r
- zappoColour.setText("Zappo colour scheme");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
+ outputMenu.setText("Output to Textbox...");\r
+ add(groupMenu);\r
+\r
+ add(sequenceMenu);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputMenu);\r
+ groupMenu.addSeparator();\r
+ groupMenu.add(groupName);\r
+ groupMenu.add(unGroupMenuItem);\r
+ groupMenu.add(colourMenu);\r
+ groupMenu.add(showBoxes);\r
+ groupMenu.add(showText);\r
+ groupMenu.add(showColourText);\r
+ groupMenu.add(outline);\r
+ sequenceMenu.add(sequenceName);\r
+ sequenceMenu.add(pdbMenu);\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
+\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(abovePIDColour);\r
+ colourMenu.add(conservationMenuItem);\r
+ editMenu.add(copy);\r
+ editMenu.add(cut);\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
+ noColourmenuItem.setText("None");\r
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ noColourmenuItem_actionPerformed(e);\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(e);\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(e);\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(e);\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(e);\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(e);\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(e);\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(e);\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(e);\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(e);\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(e);\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(e);\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(e);\r
+ }\r
+ });\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ void refresh()\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
- taylorColour.setText("Taylor colour scheme");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
+ if (ap.overviewPanel != null)\r
+ ap.overviewPanel.updateOverviewImage();\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(ActionEvent e)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
- hydrophobicityColour.setText("By hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
+ SequenceGroup sg = getGroup();\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(true),\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(ActionEvent e)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
- helixColour.setText("Helix propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\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(ActionEvent e)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
- strandColour.setText("Strand propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\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(ActionEvent e)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
- turnColour.setText("Turn propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\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(ActionEvent e)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
- buriedColour.setText("Buried index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\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(ActionEvent e)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\r
- abovePIDColour.setText("Above PID threshold only");\r
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()\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(ActionEvent e)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- abovePIDColour_actionPerformed(e);\r
- }\r
- });\r
- userDefinedColour.setText("User defined colours");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()\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(ActionEvent e)\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
+ getGroup().cs = new BuriedColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
- BLOSUM62Colour.setText("BLOSUM62 score");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\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(ActionEvent e)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.setText("By conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ SequenceGroup sg = getGroup();\r
+ if(sg.cs==null)\r
+ return;\r
\r
+ if (abovePIDColour.isSelected())\r
+ {\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(true), 0,\r
+ ap.av.alignment.getWidth()));\r
\r
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
+ getGroup().getName());\r
\r
- }\r
+ sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
\r
- void refresh()\r
- {\r
- ap.seqPanel.seqCanvas.paintFlag=true;\r
- ap.seqPanel.repaint();\r
- }\r
+ SliderPanel.showPIDSlider();\r
+ }\r
+ else // remove PIDColouring\r
+ {\r
+ sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
+ }\r
\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new ClustalxColourScheme();\r
- refresh();\r
- }\r
+ refresh();\r
+ }\r
\r
- protected void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new ZappoColourScheme();\r
- refresh();\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
- protected void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new TaylorColourScheme();\r
- refresh();\r
- }\r
+ if (e.getActionCommand().equals("User Defined..."))\r
+ new UserDefinedColours(ap, sg);\r
+ else\r
+ {\r
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
+ getUserColourSchemes().get(e.getActionCommand());\r
\r
+ sg.cs = udc;\r
+ }\r
+ }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void PIDColour_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ sg.cs = new PIDColourScheme();\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
+ ap.av.alignment.getWidth()));\r
+ refresh();\r
+ }\r
\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new HydrophobicColourScheme();\r
- refresh();\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = getGroup();\r
\r
- protected void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new HelixColourScheme();\r
- refresh();\r
- }\r
+ sg.cs = new Blosum62ColourScheme();\r
\r
- protected void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new StrandColourScheme();\r
- refresh();\r
- }\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
+ ap.av.alignment.getWidth()));\r
\r
- protected void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new TurnColourScheme();\r
- refresh();\r
- }\r
+ refresh();\r
+ }\r
\r
- protected void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new BuriedColourScheme();\r
- refresh();\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)\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(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ if(sg.cs==null)\r
+ return;\r
+\r
+ if (conservationMenuItem.isSelected())\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.getSequences(true), 0,\r
+ ap.av.alignment.getWidth());\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
-/*\r
-public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
-{\r
-ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);\r
-JInternalFrame frame = new JInternalFrame();\r
-frame.setContentPane(cip);\r
-Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);\r
-frame.setMaximizable(false);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void groupName_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Enter new group name", "Edit group name",\r
+ JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (reply == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ sg.setName(reply);\r
+ groupName.setText(reply);\r
+ }\r
\r
- }*/\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void analyze_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(cap);\r
+ Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
+\r
+ SequenceGroup sg = getGroup();\r
+ StringBuffer sb = new StringBuffer();\r
+\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
+ {\r
+ Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
+ sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
+ sb.append("\n");\r
+ }\r
+\r
+ sb.append("Something amazing will happen soon");\r
+ cap.setText(sb.toString());\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
+ ap.av.alignment.addGroup(sg);\r
\r
- protected void abovePIDColour_actionPerformed(ActionEvent e)\r
- {\r
- SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs );\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(sp);\r
- Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400,90);\r
- frame.setMaximizable(false);\r
+ return sg;\r
+ }\r
\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ void sequenceName_actionPerformed(ActionEvent e)\r
+ {\r
+ JLabel idlabel = new JLabel( " Sequence Name ");\r
+ JLabel desclabel = new JLabel("Sequence Description ");\r
+ idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
+ desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
+ JTextField id = new JTextField(sequence.getName(), 40);\r
+ JTextField description = new JTextField(sequence.getDescription(), 40);\r
+ JPanel panel = new JPanel(new BorderLayout());\r
+ JPanel panel2 = new JPanel(new BorderLayout());\r
+ panel2.add(idlabel, BorderLayout.WEST);\r
+ panel2.add(id, BorderLayout.CENTER);\r
+ panel.add(panel2, BorderLayout.NORTH);\r
+ panel2 = new JPanel(new BorderLayout());\r
+ panel2.add(desclabel, BorderLayout.WEST);\r
+ panel2.add(description, BorderLayout.CENTER);\r
+ panel.add(panel2, BorderLayout.SOUTH);\r
+\r
+\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ panel, "Edit Sequence Name/Description",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
+\r
+\r
+ if (reply != JOptionPane.OK_OPTION )\r
+ {\r
+ return;\r
+ }\r
+\r
+ String s = id.getText();\r
+\r
+ if (s != null)\r
+ {\r
+ if (s.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
+ s = s.replace(' ', '_');\r
+ sequence.getDatasetSequence().setName(s);\r
+ sequence.setName(s);\r
+ ap.repaint();\r
+ }\r
+\r
+ sequence.getDatasetSequence().setDescription(description.getText());\r
+ sequence.setDescription(description.getText());\r
+ }\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ void unGroupMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ ap.av.alignment.deleteGroup(sg);\r
+ ap.av.setSelectionGroup(null);\r
+ refresh();\r
+ }\r
\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());\r
- frame.setContentPane(chooser);\r
- Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
- frame.setResizable(false);\r
- frame.setIconifiable(false);\r
- frame.setMaximizable(false);\r
\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void outline_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
+ Color.BLUE);\r
\r
- protected void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
+ if (col != null)\r
+ {\r
+ sg.setOutlineColour(col);\r
+ }\r
\r
- }\r
+ refresh();\r
+ }\r
\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new Blosum62ColourScheme(ap.av);\r
- refresh();\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void showBoxes_actionPerformed(ActionEvent e)\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(ActionEvent e)\r
+ {\r
+ getGroup().setDisplayText(showText.isSelected());\r
+ refresh();\r
+ }\r
\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = null;\r
- refresh();\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void showColourText_actionPerformed(ActionEvent e)\r
+ {\r
+ getGroup().setColourText(showColourText.isSelected());\r
+ refresh();\r
+ }\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\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
+ +"\nAdd the full path to your browser in Preferences.",\r
+ "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),\r
- sg.getEndRes() );\r
\r
- c.calculate();\r
- c.verdict(false, 100);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
\r
- sg.cs = ccs;\r
+ void hideSequences(boolean representGroup)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if(sg==null || sg.getSize(false)<1)\r
+ {\r
+ ap.av.hideSequence(new SequenceI[]{sequence});\r
+ return;\r
+ }\r
\r
- refresh();\r
- }\r
+ int gsize = sg.getSize(false);\r
+ SequenceI [] hseqs;\r
+\r
+ hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
+\r
+ int index = 0;\r
+ while(index < gsize)\r
+ {\r
+ if(representGroup && sg.getSequenceAt(index)!=sequence)\r
+ {\r
+ sequence.addHiddenSequence(sg.getSequenceAt(index));\r
+ hseqs[index] = sg.getSequenceAt(index);\r
+ }\r
+ else if(!representGroup)\r
+ {\r
+ hseqs[index] = sg.getSequenceAt(index);\r
+ }\r
+ index ++;\r
+ }\r
+\r
+ ap.av.hideSequence(hseqs);\r
+\r
+ ap.av.setSelectionGroup(null);\r
+ }\r
\r
- protected void groupAnnotation_actionPerformed(ActionEvent e)\r
+ public void copy_actionPerformed(ActionEvent e)\r
{\r
-\r
+ ap.alignFrame.copy_actionPerformed(null);\r
}\r
\r
- protected void groupName_actionPerformed(ActionEvent e)\r
+ public void cut_actionPerformed(ActionEvent e)\r
{\r
- SequenceGroup sg = getGroup();\r
- String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
- if(reply==null)\r
- return;\r
-\r
- sg.setName(reply);\r
- groupName.setText(reply);\r
+ ap.alignFrame.cut_actionPerformed(null);\r
}\r
\r
- protected void copyGroup_actionPerformed(ActionEvent e)\r
+ public void upperCase_actionPerformed(ActionEvent e)\r
{\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
+ changeCase(e.getSource());\r
+ }\r
\r
- SequenceI[] s = new Sequence[sg.sequences.size()];\r
- for (int i=0; i < sg.sequences.size(); i++)\r
- {\r
- s[i] = new Sequence( sg.getSequenceAt(i));\r
- s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );\r
- }\r
- AlignFrame af = new AlignFrame(new Alignment(s));\r
- int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
- if (newHeight > 500)\r
- newHeight = 500;\r
- Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
- }\r
-\r
- protected void moveGroup_actionPerformed(ActionEvent e)\r
+ public void lowerCase_actionPerformed(ActionEvent e)\r
{\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
-\r
- SequenceI[] s = new Sequence[sg.sequences.size()];\r
-\r
- for (int i=0; i < sg.sequences.size(); i++)\r
- s[i] = new Sequence( sg.getSequenceAt(i));\r
-\r
- AlignFrame af = new AlignFrame(new Alignment(s));\r
- int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
- if(newHeight>500)\r
- newHeight=500;\r
- Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
+ changeCase(e.getSource());\r
+ }\r
\r
+ public void toggle_actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e.getSource());\r
+ }\r
\r
- for (int i=0; i < sg.sequences.size(); i++)\r
- ap.av.alignment.deleteSequence(sg.getSequenceAt(i));\r
+ void changeCase(Object source)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg != null)\r
+ {\r
+ for (int g = 0; g < sg.getSize(true); g++)\r
+ {\r
+ int start = sg.getStartRes();\r
+ int end = sg.getEndRes() + 1;\r
+\r
+ do\r
+ {\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ end = ap.av.colSel.getHiddenBoundaryRight(start);\r
+ if (start == end)\r
+ end = sg.getEndRes() + 1;\r
+ if (end > sg.getEndRes())\r
+ end = sg.getEndRes() + 1;\r
+ }\r
+\r
+ if (source == toggle)\r
+ ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+ .toggleCase(start, end);\r
+ else\r
+ ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+ .changeCase(source == upperCase, start, end);\r
+\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ start = ap.av.colSel.adjustForHiddenColumns(end);\r
+ start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
+ }\r
+\r
+ }\r
+ while (end < sg.getEndRes());\r
+ }\r
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
+ }\r
+ }\r
\r
+ public void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ Desktop.addInternalFrame(cap,\r
+ "Alignment output - " + e.getActionCommand(), 600,\r
+ 500);\r
\r
- ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
- ap.RefreshPanels();\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
- protected void deleteSequences_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
- for (int i=0;i < sg.sequences.size(); i++)\r
- ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
- ap.seqPanel.parent.RefreshPanels();\r
+ public void pdbFromFile_actionPerformed(ActionEvent e)\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
- }\r
+ int value = chooser.showOpenDialog(null);\r
\r
- protected void analyze_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- JInternalFrame frame = new JInternalFrame();\r
- cap.formatForOutput();\r
- frame.setContentPane(cap);\r
- Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\r
-\r
- for(int i=0; i<sg.sequences.size(); i++)\r
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
{\r
- Sequence tmp = (Sequence)sg.sequences.get(i);\r
- sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
- sb.append("\n");\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
+ return;\r
+\r
+ entry.setId(reply);\r
+ }\r
+ else\r
+ entry.setId(pdbfile.id);\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
- sb.append("Something amazing will happen soon");\r
- cap.setText( sb.toString() );\r
-\r
}\r
\r
- SequenceGroup getGroup()\r
+ public void enterPDB_actionPerformed(ActionEvent e)\r
{\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
+ String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
\r
- // this method won't add a new group if it already exists\r
- ap.av.alignment.addGroup(sg);\r
- return sg;\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
- void sequenceName_actionPerformed(ActionEvent e)\r
+ public void discoverPDB_actionPerformed(ActionEvent e)\r
{\r
- String id = sequence.getName();\r
- String s = (String)JOptionPane.showInternalInputDialog(\r
- ap,\r
- "Edit sequence name",\r
- "Edit sequence name",\r
- JOptionPane.PLAIN_MESSAGE,\r
- null,\r
- null,\r
- id);\r
-\r
- if(s!=null)\r
- {\r
- sequence.setName(s);\r
- ap.RefreshPanels();\r
- }\r
-\r
+ new jalview.io.DBRefFetcher(\r
+ ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff