/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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 java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
import javax.swing.*;\r
\r
import MCview.*;\r
import jalview.analysis.*;\r
+import jalview.commands.*;\r
import jalview.datamodel.*;\r
import jalview.io.*;\r
import jalview.schemes.*;\r
\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class PopupMenu\r
extends JPopupMenu\r
{\r
JMenuItem sequenceName = new JMenuItem();\r
Sequence sequence;\r
JMenuItem unGroupMenuItem = new JMenuItem();\r
- JMenuItem pdbMenuItem = 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
-\r
- public PopupMenu(AlignmentPanel ap, Sequence seq)\r
+ JMenu editMenu = new JMenu();\r
+ JMenuItem cut = new JMenuItem();\r
+ JMenuItem copy = new JMenuItem();\r
+ JMenuItem upperCase = new JMenuItem();\r
+ JMenuItem lowerCase = new JMenuItem();\r
+ JMenuItem toggle = new JMenuItem();\r
+ JMenu pdbMenu = new JMenu();\r
+ JMenuItem pdbFromFile = new JMenuItem();\r
+ JMenuItem enterPDB = new JMenuItem();\r
+ JMenuItem discoverPDB = new JMenuItem();\r
+ JMenu outputMenu = new JMenu();\r
+ JMenuItem sequenceFeature = new JMenuItem();\r
+ JMenuItem textColour = new JMenuItem();\r
+ JMenu jMenu1 = new JMenu();\r
+\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
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
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
+ 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() > 1)\r
+ {\r
+ menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hideSequences(true);\r
+ }\r
+ });\r
+ sequenceMenu.add(menuItem);\r
+ }\r
+\r
+ if (ap.av.hasHiddenRows)\r
+ {\r
+ final int index = ap.av.alignment.findIndex(seq);\r
+\r
+ if (ap.av.adjustForHiddenSeqs(index) -\r
+ ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
+ {\r
+ menuItem = new JMenuItem("Reveal Sequences");\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ap.av.showSequence(index);\r
+ if (ap.overviewPanel != null)\r
+ {\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ }\r
+ });\r
+ add(menuItem);\r
+ }\r
+\r
+ menuItem = new JMenuItem("Reveal All");\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ap.av.showAllHiddenSeqs();\r
+ if (ap.overviewPanel != null)\r
+ {\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ }\r
+ });\r
+\r
+ add(menuItem);\r
+ }\r
+\r
+ }\r
+\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
if (sg != null)\r
noColourmenuItem.setSelected(true);\r
}\r
\r
- if (sg.cs instanceof ConservationColourScheme)\r
+ if (sg.cs != null && sg.cs.conservationApplied())\r
{\r
conservationMenuItem.setSelected(true);\r
}\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
- else\r
- {\r
- groupMenu.insertSeparator(3);\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
+ {\r
+ id = id.substring(id.lastIndexOf("|") + 1);\r
+ }\r
+\r
+ url = link.substring(link.indexOf("|") + 1,\r
+ link.indexOf("$SEQUENCE_ID$"))\r
+ + id +\r
+ link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+ }\r
+ else\r
+ {\r
+ url = link.substring(link.lastIndexOf("|") + 1);\r
+ }\r
+\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showLink(url);\r
+ }\r
+ });\r
+\r
+ linkMenu.add(item);\r
+ }\r
+ if (sequence != null)\r
+ {\r
+ sequenceMenu.add(linkMenu);\r
+ }\r
+ else\r
+ {\r
+ add(linkMenu);\r
+ }\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @throws Exception DOCUMENT ME!\r
+ */\r
private void jbInit()\r
throws Exception\r
{\r
groupMenu.setText("Group");\r
- groupMenu.setText("Define");\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
+ groupName_actionPerformed();\r
}\r
});\r
sequenceMenu.setText("Sequence");\r
- sequenceName.setText("Edit name");\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
+ sequenceName_actionPerformed();\r
}\r
});\r
PIDColour.setFocusPainted(false);\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- unGroupMenuItem_actionPerformed(e);\r
- }\r
- });\r
- pdbMenuItem.setText("View PDB structure");\r
- pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pdbMenuItem_actionPerformed(e);\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(e);\r
+ outline_actionPerformed();\r
}\r
});\r
nucleotideMenuItem.setText("Nucleotide");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- nucleotideMenuItem_actionPerformed(e);\r
+ nucleotideMenuItem_actionPerformed();\r
}\r
});\r
colourMenu.setText("Group Colour");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- showBoxes_actionPerformed(e);\r
+ showBoxes_actionPerformed();\r
}\r
});\r
showText.setText("Text");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- showText_actionPerformed(e);\r
+ showText_actionPerformed();\r
}\r
});\r
showColourText.setText("Colour Text");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- showColourText_actionPerformed(e);\r
+ showColourText_actionPerformed();\r
}\r
});\r
+ editMenu.setText("Edit");\r
+ cut.setText("Cut");\r
+ cut.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ });\r
+ upperCase.setText("To Upper Case");\r
+ upperCase.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e);\r
+ }\r
+ });\r
+ copy.setText("Copy");\r
+ copy.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ });\r
+ lowerCase.setText("To Lower Case");\r
+ lowerCase.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e);\r
+ }\r
+ });\r
+ toggle.setText("Toggle Case");\r
+ toggle.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e);\r
+ }\r
+ });\r
+ pdbMenu.setText("Associate Structure with Sequence");\r
+ pdbFromFile.setText("From File");\r
+ pdbFromFile.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pdbFromFile_actionPerformed();\r
+ }\r
+ });\r
+ enterPDB.setText("Enter PDB Id");\r
+ enterPDB.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ enterPDB_actionPerformed();\r
+ }\r
+ });\r
+ discoverPDB.setText("Discover PDB ids");\r
+ discoverPDB.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ discoverPDB_actionPerformed();\r
+ }\r
+ });\r
+ outputMenu.setText("Output to Textbox...");\r
+ sequenceFeature.setText("Create Sequence Feature");\r
+ sequenceFeature.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sequenceFeature_actionPerformed();\r
+ }\r
+ });\r
+ textColour.setText("Text Colour");\r
+ textColour.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ textColour_actionPerformed();\r
+ }\r
+ });\r
+ jMenu1.setText("Group");\r
add(groupMenu);\r
+\r
add(sequenceMenu);\r
- groupMenu.add(groupName);\r
- groupMenu.addSeparator();\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(colourMenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(showBoxes);\r
- groupMenu.add(showText);\r
- groupMenu.add(showColourText);\r
- groupMenu.addSeparator();\r
- groupMenu.add(outline);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputMenu);\r
+ groupMenu.add(sequenceFeature);\r
+ groupMenu.add(jMenu1);\r
sequenceMenu.add(sequenceName);\r
- sequenceMenu.add(pdbMenuItem);\r
+ sequenceMenu.add(pdbMenu);\r
+ colourMenu.add(textColour);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\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(e);\r
+ noColourmenuItem_actionPerformed();\r
}\r
});\r
\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- clustalColour_actionPerformed(e);\r
+ clustalColour_actionPerformed();\r
}\r
});\r
zappoColour.setText("Zappo");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- zappoColour_actionPerformed(e);\r
+ zappoColour_actionPerformed();\r
}\r
});\r
taylorColour.setText("Taylor");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- taylorColour_actionPerformed(e);\r
+ taylorColour_actionPerformed();\r
}\r
});\r
hydrophobicityColour.setText("Hydrophobicity");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- hydrophobicityColour_actionPerformed(e);\r
+ hydrophobicityColour_actionPerformed();\r
}\r
});\r
helixColour.setText("Helix propensity");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- helixColour_actionPerformed(e);\r
+ helixColour_actionPerformed();\r
}\r
});\r
strandColour.setText("Strand propensity");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- strandColour_actionPerformed(e);\r
+ strandColour_actionPerformed();\r
}\r
});\r
turnColour.setText("Turn propensity");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- turnColour_actionPerformed(e);\r
+ turnColour_actionPerformed();\r
}\r
});\r
buriedColour.setText("Buried Index");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- buriedColour_actionPerformed(e);\r
+ buriedColour_actionPerformed();\r
}\r
});\r
abovePIDColour.setText("Above % Identity");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- abovePIDColour_actionPerformed(e);\r
+ abovePIDColour_actionPerformed();\r
}\r
});\r
- userDefinedColour.setText("User Defined");\r
+ userDefinedColour.setText("User Defined...");\r
userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- PIDColour_actionPerformed(e);\r
+ PIDColour_actionPerformed();\r
}\r
});\r
BLOSUM62Colour.setText("BLOSUM62");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- BLOSUM62Colour_actionPerformed(e);\r
+ BLOSUM62Colour_actionPerformed();\r
}\r
});\r
conservationMenuItem.setText("Conservation");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- conservationMenuItem_actionPerformed(e);\r
+ conservationMenuItem_actionPerformed();\r
}\r
});\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
void refresh()\r
{\r
- SequenceGroup sg = getGroup();\r
- SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
-\r
- if (superG != null)\r
+ if (ap.overviewPanel != null)\r
{\r
- superG.setSuperGroupProperties(sg);\r
+ ap.overviewPanel.updateOverviewImage();\r
}\r
\r
- ap.seqPanel.repaint();\r
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
}\r
\r
- protected void clustalColour_actionPerformed(ActionEvent e)\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.sequences,\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
ap.av.alignment.getWidth());\r
refresh();\r
}\r
\r
- protected void zappoColour_actionPerformed(ActionEvent e)\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
- protected void taylorColour_actionPerformed(ActionEvent e)\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
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\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
- protected void helixColour_actionPerformed(ActionEvent e)\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
- protected void strandColour_actionPerformed(ActionEvent e)\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
- protected void turnColour_actionPerformed(ActionEvent e)\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
- protected void buriedColour_actionPerformed(ActionEvent e)\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
- public void nucleotideMenuItem_actionPerformed(ActionEvent e)\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
- protected void abovePIDColour_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void abovePIDColour_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
+ if (sg.cs == null)\r
+ {\r
+ return;\r
+ }\r
\r
if (abovePIDColour.isSelected())\r
{\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
getGroup().getName());\r
\r
- if (sg.cs instanceof ResidueColourScheme)\r
- {\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
- }\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- {\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
- }\r
+ sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
\r
SliderPanel.showPIDSlider();\r
}\r
else // remove PIDColouring\r
{\r
- ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
- rcs.setThreshold(0);\r
- sg.cs = rcs;\r
+ sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
}\r
\r
refresh();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- new UserDefinedColours(ap, getGroup());\r
+ SequenceGroup sg = getGroup();\r
+\r
+ if (e.getActionCommand().equals("User Defined..."))\r
+ {\r
+ new UserDefinedColours(ap, sg);\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
+ getUserColourSchemes().get(e.getActionCommand());\r
+\r
+ sg.cs = udc;\r
+ }\r
+ refresh();\r
}\r
\r
- protected void PIDColour_actionPerformed(ActionEvent e)\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.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
+ hiddenRepSequences),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
refresh();\r
}\r
\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void BLOSUM62Colour_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
+ hiddenRepSequences),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
\r
refresh();\r
}\r
\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\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
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void conservationMenuItem_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
+ if (sg.cs == null)\r
+ {\r
+ return;\r
+ }\r
\r
if (conservationMenuItem.isSelected())\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
- ap.av.alignment.getWidth());\r
+ sg.getSequences(ap.av.\r
+ hiddenRepSequences),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
\r
c.calculate();\r
c.verdict(false, ap.av.ConsPercGaps);\r
\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+ sg.cs.setConservation(c);\r
\r
- sg.cs = ccs;\r
-\r
- SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
SliderPanel.showConservationSlider();\r
}\r
else // remove ConservationColouring\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
- sg.cs = ccs.cs;\r
+ sg.cs.setConservation(null);\r
}\r
\r
refresh();\r
}\r
\r
- protected void groupName_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void groupName_actionPerformed()\r
{\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
+ EditNameDialog dialog = new EditNameDialog(sg.getName(),\r
+ sg.getDescription(),\r
+ " Group Name ",\r
+ "Group Description ",\r
+ "Edit Group Name/Description");\r
\r
- if (reply == null)\r
+ if (!dialog.accept)\r
{\r
return;\r
}\r
\r
- sg.setName(reply);\r
- groupName.setText(reply);\r
+ sg.setName(dialog.getName());\r
+ sg.setDescription(dialog.getDescription());\r
}\r
\r
- protected void analyze_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ SequenceGroup getGroup()\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(cap);\r
- Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\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
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\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
- for (int i = 0; i < sg.sequences.size(); i++)\r
+ if (!dialog.accept)\r
{\r
- Sequence tmp = (Sequence) sg.sequences.get(i);\r
- sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
- sb.append("\n");\r
+ return;\r
}\r
\r
- sb.append("Something amazing will happen soon");\r
- cap.setText(sb.toString());\r
+ if (dialog.getName() != null)\r
+ {\r
+ if (dialog.getName().indexOf(" ") > -1)\r
+ {\r
+ JOptionPane.showMessageDialog(ap,\r
+ "Spaces have been converted to \"_\"",\r
+ "No spaces allowed in Sequence Name",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+\r
+ sequence.setName(dialog.getName().replace(' ', '_'));\r
+ ap.repaint();\r
+ }\r
+\r
+ sequence.setDescription(dialog.getDescription());\r
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+\r
}\r
\r
- SequenceGroup getGroup()\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
- // this method won't add a new group if it already exists\r
- ap.av.alignment.addGroup(sg);\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
- return sg;\r
+ if (col != null)\r
+ {\r
+ sg.setOutlineColour(col);\r
+ }\r
+\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void showBoxes_actionPerformed()\r
+ {\r
+ getGroup().setDisplayBoxes(showBoxes.isSelected());\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void showText_actionPerformed()\r
+ {\r
+ getGroup().setDisplayText(showText.isSelected());\r
+ refresh();\r
}\r
\r
- void sequenceName_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void showColourText_actionPerformed()\r
{\r
- String id = sequence.getName();\r
- String s = (String) JOptionPane.showInternalInputDialog(ap,\r
- "Edit sequence name",\r
- "Edit sequence name (" + sequence.getName() + ")",\r
- JOptionPane.PLAIN_MESSAGE, null, null, id);\r
+ getGroup().setColourText(showColourText.isSelected());\r
+ refresh();\r
+ }\r
\r
- if (s != null)\r
+ public void showLink(String url)\r
+ {\r
+ try\r
{\r
- sequence.setName(s);\r
- ap.repaint();\r
+ jalview.util.BrowserLauncher.openURL(url);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Unixers: Couldn't find default web browser."\r
+ +\r
+ "\nAdd the full path to your browser in Preferences.",\r
+ "Web browser not found",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ ex.printStackTrace();\r
}\r
}\r
\r
- void unGroupMenuItem_actionPerformed(ActionEvent e)\r
+ void hideSequences(boolean representGroup)\r
{\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
+ if (sg == null || sg.getSize() < 1)\r
+ {\r
+ ap.av.hideSequence(new SequenceI[]\r
+ {sequence});\r
+ return;\r
+ }\r
+\r
ap.av.setSelectionGroup(null);\r
- refresh();\r
- }\r
\r
- void pdbMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (sequence.getPDBId() == null)\r
+ if (representGroup)\r
{\r
+ ap.av.hideRepSequences(sequence, sg);\r
+\r
return;\r
}\r
\r
- try\r
+ int gsize = sg.getSize();\r
+ SequenceI[] hseqs;\r
+\r
+ hseqs = new SequenceI[gsize];\r
+\r
+ int index = 0;\r
+ for (int i = 0; i < gsize; i++)\r
{\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,\r
- null);\r
+ hseqs[index++] = sg.getSequenceAt(i);\r
+ }\r
\r
- PDBfile pdb = new PDBfile(result);\r
+ ap.av.hideSequence(hseqs);\r
+ }\r
+\r
+ public void copy_actionPerformed()\r
+ {\r
+ ap.alignFrame.copy_actionPerformed(null);\r
+ }\r
+\r
+ public void cut_actionPerformed()\r
+ {\r
+ ap.alignFrame.cut_actionPerformed(null);\r
+ }\r
+\r
+ void changeCase(ActionEvent e)\r
+ {\r
+ Object source = e.getSource();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ Vector regions = new Vector();\r
+ if (sg != null)\r
+ {\r
+ int start = sg.getStartRes();\r
+ int end = sg.getEndRes() + 1;\r
+\r
+ do\r
+ {\r
+ if (ap.av.hasHiddenColumns)\r
+ {\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
+ {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
+ while (end < sg.getEndRes());\r
+\r
+ int[][] startEnd = new int[regions.size()][2];\r
+ for (int i = 0; i < regions.size(); i++)\r
+ {\r
+ startEnd[i] = (int[]) regions.elementAt(i);\r
+ }\r
+\r
+ String description;\r
+ int caseChange;\r
+\r
+ if (source == toggle)\r
+ {\r
+ description = "Toggle Case";\r
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
+ }\r
+ else if (source == upperCase)\r
+ {\r
+ description = "To Upper Case";\r
+ caseChange = ChangeCaseCommand.TO_UPPER;\r
+ }\r
+ else\r
+ {\r
+ description = "To Lower Case";\r
+ caseChange = ChangeCaseCommand.TO_LOWER;\r
+ }\r
+\r
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
+ description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
+ startEnd, caseChange\r
+ );\r
+\r
+ ap.alignFrame.addHistoryItem(caseCommand);\r
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
\r
- rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(rc);\r
- Desktop.addInternalFrame(frame,\r
- sequence.getName() + " " + sequence.getPDBId(),\r
- 400, 400);\r
}\r
- catch (Exception ex)\r
+ }\r
+\r
+ public void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput(null);\r
+ Desktop.addInternalFrame(cap,\r
+ "Alignment output - " + e.getActionCommand(), 600,\r
+ 500);\r
+\r
+ String[] omitHidden = null;\r
+\r
+ if (ap.av.hasHiddenColumns)\r
{\r
- ex.printStackTrace();\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 outline_actionPerformed(ActionEvent e)\r
+ public void pdbFromFile_actionPerformed()\r
{\r
- SequenceGroup sg = getGroup();\r
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
- Color.BLUE);\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
- if (col != null)\r
+ int value = chooser.showOpenDialog(null);\r
+\r
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
{\r
- sg.setOutlineColour(col);\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
- refresh();\r
}\r
\r
- public void showBoxes_actionPerformed(ActionEvent e)\r
+ public void enterPDB_actionPerformed()\r
{\r
- getGroup().setDisplayBoxes(showBoxes.isSelected());\r
- refresh();\r
+ String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (id != null && id.length() > 0)\r
+ {\r
+ PDBEntry entry = new PDBEntry();\r
+ entry.setId(id);\r
+ sequence.getDatasetSequence()\r
+ .addPDBId(entry);\r
+ }\r
}\r
\r
- public void showText_actionPerformed(ActionEvent e)\r
+ public void discoverPDB_actionPerformed()\r
{\r
- getGroup().setDisplayText(showText.isSelected());\r
- refresh();\r
+ new jalview.io.DBRefFetcher(\r
+ ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
}\r
\r
- public void showColourText_actionPerformed(ActionEvent e)\r
+ public void sequenceFeature_actionPerformed()\r
{\r
- getGroup().setColourText(showColourText.isSelected());\r
- refresh();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ int gSize = sg.getSize();\r
+ SequenceI[] seqs = new SequenceI[gSize];\r
+ SequenceFeature[] features = new SequenceFeature[gSize];\r
+\r
+ for (int i = 0; i < gSize; i++)\r
+ {\r
+ seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
+ int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
+ int end = sg.findEndRes(sg.getSequenceAt(i));\r
+ features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");\r
+ }\r
+\r
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
+ .createNewFeatures(seqs, features))\r
+ {\r
+ ap.alignFrame.showSeqFeatures.setSelected(true);\r
+ ap.av.setShowSequenceFeatures(true);\r
+ ap.highlightSearchResults(null);\r
+ }\r
+ }\r
+\r
+ public void textColour_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ if (sg != null)\r
+ {\r
+ new TextColourChooser().chooseColour(ap, sg);\r
+ }\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff