/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
*/\r
package jalview.gui;\r
\r
-import MCview.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.commands.ChangeCaseCommand;\r
+import java.util.*;\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
+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
* @author $author$\r
* @version $Revision$\r
*/\r
-public class PopupMenu extends JPopupMenu\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 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 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
JMenu jMenu1 = 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
+ * 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
+ {\r
+ java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
+ elements();\r
+\r
+ while (e.hasMoreElements())\r
{\r
- JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );\r
+ final PDBEntry pdb = (PDBEntry) e.nextElement();\r
\r
- item.addActionListener(new java.awt.event.ActionListener()\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
- outputText_actionPerformed(e);\r
+ new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
}\r
});\r
-\r
- outputMenu.add(item);\r
+ sequenceMenu.add(menuItem);\r
}\r
+ }\r
\r
-\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception e)\r
+ menuItem = new JMenuItem("Hide Sequences");\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
{\r
- e.printStackTrace();\r
+ hideSequences(false);\r
}\r
+ });\r
+ add(menuItem);\r
\r
-\r
- if (seq != null)\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
- sequenceMenu.setText(sequence.getName());\r
-\r
- JMenuItem menuItem;\r
- if( seq.getDatasetSequence().getPDBId() != null)\r
+ public void actionPerformed(ActionEvent e)\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
+ hideSequences(true);\r
}\r
+ });\r
+ sequenceMenu.add(menuItem);\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
+ if (ap.av.hasHiddenRows)\r
+ {\r
+ final int index = ap.av.alignment.findIndex(seq);\r
\r
- if(ap.av.getSelectionGroup() !=null\r
- && ap.av.getSelectionGroup().getSize()>1)\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
- menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
+ public void actionPerformed(ActionEvent e)\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ ap.av.showSequence(index);\r
+ if (ap.overviewPanel != null)\r
{\r
- hideSequences(true);\r
+ ap.overviewPanel.updateOverviewImage();\r
}\r
- });\r
- sequenceMenu.add(menuItem);\r
- }\r
+ }\r
+ });\r
+ add(menuItem);\r
+ }\r
\r
- if (ap.av.hasHiddenRows)\r
+ menuItem = new JMenuItem("Reveal All");\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\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
+ ap.av.showAllHiddenSeqs();\r
+ if (ap.overviewPanel != null)\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
+ ap.overviewPanel.updateOverviewImage();\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
+ add(menuItem);\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
- SequenceGroup sg = ap.av.getSelectionGroup();\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 (sg != null)\r
- {\r
- groupName.setText(sg.getName());\r
+ if (!ap.av.alignment.getGroups().contains(sg))\r
+ {\r
+ unGroupMenuItem.setVisible(false);\r
+ }\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
+ if (seq == null)\r
+ {\r
+ sequenceMenu.setVisible(false);\r
+ pdbMenu.setVisible(false);\r
+ }\r
\r
- if (sg.cs!=null && sg.cs.conservationApplied())\r
- {\r
- conservationMenuItem.setSelected(true);\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
- showText.setSelected(sg.getDisplayText());\r
- showColourText.setSelected(sg.getColourText());\r
- showBoxes.setSelected(sg.getDisplayBoxes());\r
- }\r
- else\r
+ if (link.indexOf("$SEQUENCE_ID$") > -1)\r
{\r
- groupMenu.setVisible(false);\r
- editMenu.setVisible(false);\r
- }\r
+ String id = seq.getName();\r
+ if (id.indexOf("|") > -1)\r
+ {\r
+ id = id.substring(id.lastIndexOf("|") + 1);\r
+ }\r
\r
- if (!ap.av.alignment.getGroups().contains(sg))\r
- {\r
- unGroupMenuItem.setVisible(false);\r
+ url = link.substring(link.indexOf("|") + 1,\r
+ link.indexOf("$SEQUENCE_ID$"))\r
+ + id +\r
+ link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
}\r
-\r
-\r
- if (seq == null)\r
+ else\r
{\r
- sequenceMenu.setVisible(false);\r
- pdbMenu.setVisible(false);\r
+ url = link.substring(link.lastIndexOf("|") + 1);\r
}\r
\r
- if(links != null && links.size()>0)\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
{\r
- JMenu linkMenu = new JMenu("Link");\r
- JMenuItem item;\r
- for(int i=0; i<links.size(); i++)\r
+ public void actionPerformed(ActionEvent e)\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
+ showLink(url);\r
}\r
- if(sequence!=null)\r
- sequenceMenu.add(linkMenu);\r
- else\r
- add(linkMenu);\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @throws Exception DOCUMENT ME!\r
- */\r
- private void jbInit() throws Exception\r
+ outline.setText("Border colour");\r
+ outline.addActionListener(new java.awt.event.ActionListener()\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
+ 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
jMenu1.setText("Group");\r
add(groupMenu);\r
\r
- add(sequenceMenu);\r
- groupMenu.add(editMenu);\r
- groupMenu.add(outputMenu);\r
- groupMenu.add(sequenceFeature);\r
- groupMenu.add(jMenu1);\r
- sequenceMenu.add(sequenceName);\r
- sequenceMenu.add(pdbMenu);\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
+ add(sequenceMenu);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputMenu);\r
+ groupMenu.add(sequenceFeature);\r
+ groupMenu.add(jMenu1);\r
+ sequenceMenu.add(sequenceName);\r
+ sequenceMenu.add(pdbMenu);\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
+ 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
+ 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
+ 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
+ if (ap.overviewPanel != null)\r
+ {\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+\r
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
+ }\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
+ * 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
- 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
- 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
- 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
+ * 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
- void refresh()\r
- {\r
- if (ap.overviewPanel != null)\r
- ap.overviewPanel.updateOverviewImage();\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
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\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 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
+ * 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 zappoColour_actionPerformed()\r
- {\r
- getGroup().cs = new ZappoColourScheme();\r
- refresh();\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 taylorColour_actionPerformed()\r
- {\r
- getGroup().cs = new TaylorColourScheme();\r
- refresh();\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
- protected void hydrophobicityColour_actionPerformed()\r
- {\r
- getGroup().cs = new HydrophobicColourScheme();\r
- refresh();\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 helixColour_actionPerformed()\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
- getGroup().cs = new HelixColourScheme();\r
- refresh();\r
+ return;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void strandColour_actionPerformed()\r
+ if (abovePIDColour.isSelected())\r
{\r
- getGroup().cs = new StrandColourScheme();\r
- refresh();\r
- }\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void turnColour_actionPerformed()\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
- getGroup().cs = new TurnColourScheme();\r
- refresh();\r
+ sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void buriedColour_actionPerformed()\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
- getGroup().cs = new BuriedColourScheme();\r
- refresh();\r
+ new UserDefinedColours(ap, sg);\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void nucleotideMenuItem_actionPerformed()\r
+ else\r
{\r
- getGroup().cs = new NucleotideColourScheme();\r
- refresh();\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 abovePIDColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if(sg.cs==null)\r
- return;\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
- if (abovePIDColour.isSelected())\r
- {\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void BLOSUM62Colour_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
- getGroup().getName());\r
+ sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
+ hiddenRepSequences),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
\r
- SliderPanel.showPIDSlider();\r
- }\r
- else // remove PIDColouring\r
- {\r
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
- }\r
+ refresh();\r
+ }\r
\r
- refresh();\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 userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\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
- refresh();\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.hiddenRepSequences),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
- refresh();\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void BLOSUM62Colour_actionPerformed()\r
+ if (conservationMenuItem.isSelected())\r
{\r
- SequenceGroup sg = getGroup();\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
- sg.cs = new Blosum62ColourScheme();\r
+ c.calculate();\r
+ c.verdict(false, ap.av.ConsPercGaps);\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
+ sg.cs.setConservation(c);\r
\r
- refresh();\r
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
+ SliderPanel.showConservationSlider();\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void noColourmenuItem_actionPerformed()\r
+ else // remove ConservationColouring\r
{\r
- getGroup().cs = null;\r
- refresh();\r
+ sg.cs.setConservation(null);\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
- return;\r
-\r
- if (conservationMenuItem.isSelected())\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(ap.av.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
+ refresh();\r
+ }\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
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void groupName_actionPerformed()\r
+ {\r
\r
- refresh();\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void groupName_actionPerformed()\r
+ if (!dialog.accept)\r
{\r
+ return;\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
+ sg.setName(dialog.getName());\r
+ sg.setDescription(dialog.getDescription());\r
+ }\r
\r
- sg.setName(dialog.getName());\r
- sg.setDescription(dialog.getDescription());\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- SequenceGroup getGroup()\r
+ if (!dialog.accept)\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
- return sg;\r
+ return;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- void sequenceName_actionPerformed()\r
+ if (dialog.getName() != null)\r
{\r
- EditNameDialog dialog = new EditNameDialog(sequence.getName(),\r
- sequence.getDescription(),\r
- " Sequence Name ",\r
- "Sequence Description ",\r
- "Edit Sequence Name/Description");\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
- if (!dialog.accept)\r
- {\r
- return;\r
- }\r
+ sequence.setName(dialog.getName().replace(' ', '_'));\r
+ ap.repaint();\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
+ sequence.setDescription(dialog.getDescription());\r
\r
- sequence.setName(dialog.getName().replace(' ', '_'));\r
- ap.repaint();\r
- }\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
\r
- sequence.setDescription(dialog.getDescription());\r
+ }\r
\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\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
+ /**\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
- /**\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
+ 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
- protected void outline_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
- Color.BLUE);\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
- if (col != null)\r
- {\r
- sg.setOutlineColour(col);\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
- refresh();\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void showBoxes_actionPerformed()\r
+ public void showLink(String url)\r
+ {\r
+ try\r
{\r
- getGroup().setDisplayBoxes(showBoxes.isSelected());\r
- refresh();\r
+ jalview.util.BrowserLauncher.openURL(url);\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void showText_actionPerformed()\r
+ catch (Exception ex)\r
{\r
- getGroup().setDisplayText(showText.isSelected());\r
- refresh();\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void showColourText_actionPerformed()\r
+ void hideSequences(boolean representGroup)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg == null || sg.getSize() < 1)\r
{\r
- getGroup().setColourText(showColourText.isSelected());\r
- refresh();\r
+ ap.av.hideSequence(new SequenceI[]\r
+ {sequence});\r
+ return;\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
- +"\nAdd the full path to your browser in Preferences.",\r
- "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
-\r
-\r
- ex.printStackTrace();\r
- }\r
- }\r
+ ap.av.setSelectionGroup(null);\r
\r
- void hideSequences(boolean representGroup)\r
+ if (representGroup)\r
{\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg==null || sg.getSize()<1)\r
- {\r
- ap.av.hideSequence(new SequenceI[]{sequence});\r
- return;\r
- }\r
-\r
- ap.av.setSelectionGroup(null);\r
-\r
- if (representGroup)\r
- {\r
- ap.av.hideRepSequences(sequence, sg);\r
+ ap.av.hideRepSequences(sequence, sg);\r
\r
- return;\r
- }\r
-\r
- int gsize = sg.getSize();\r
- SequenceI[] hseqs;\r
+ return;\r
+ }\r
\r
- hseqs = new SequenceI[gsize];\r
+ int gsize = sg.getSize();\r
+ SequenceI[] hseqs;\r
\r
- int index = 0;\r
- for (int i = 0; i < gsize; i++)\r
- {\r
- hseqs[index++] = sg.getSequenceAt(i);\r
- }\r
+ hseqs = new SequenceI[gsize];\r
\r
- ap.av.hideSequence(hseqs);\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
if (ap.av.hasHiddenColumns)\r
{\r
- if(start==0)\r
+ if (start == 0)\r
+ {\r
start = ap.av.colSel.adjustForHiddenColumns(start);\r
+ }\r
\r
end = ap.av.colSel.getHiddenBoundaryRight(start);\r
if (start == end)\r
+ {\r
end = sg.getEndRes() + 1;\r
+ }\r
if (end > sg.getEndRes())\r
+ {\r
end = sg.getEndRes() + 1;\r
+ }\r
}\r
\r
regions.addElement(new int[]\r
startEnd[i] = (int[]) regions.elementAt(i);\r
}\r
\r
-\r
String description;\r
int caseChange;\r
\r
- if(source==toggle)\r
+ if (source == toggle)\r
{\r
description = "Toggle Case";\r
caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
}\r
- else if(source==upperCase)\r
+ else if (source == upperCase)\r
{\r
description = "To Upper Case";\r
caseChange = ChangeCaseCommand.TO_UPPER;\r
\r
ap.alignFrame.addHistoryItem(caseCommand);\r
\r
-\r
ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
+ ap.av.getAlignment().getSequences());\r
\r
}\r
}\r
"Alignment output - " + e.getActionCommand(), 600,\r
500);\r
\r
- String [] omitHidden = null;\r
+ String[] omitHidden = null;\r
\r
- if(ap.av.hasHiddenColumns)\r
+ if (ap.av.hasHiddenColumns)\r
{\r
System.out.println("PROMPT USER HERE");\r
omitHidden = ap.av.getViewAsString(true);\r
omitHidden));\r
}\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
- 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
+ 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 discoverPDB_actionPerformed()\r
{\r
new jalview.io.DBRefFetcher(\r
- ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
+ ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
}\r
\r
public void sequenceFeature_actionPerformed()\r
{\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg==null)\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
+ 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
+ features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");\r
}\r
\r
if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
{\r
SequenceGroup sg = getGroup();\r
if (sg != null)\r
+ {\r
new TextColourChooser().chooseColour(ap, sg);\r
+ }\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff