/*\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.appletgui;\r
\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.Vector;\r
\r
import jalview.analysis.*;\r
+import jalview.commands.*;\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
-import jalview.commands.ChangeCaseCommand;\r
\r
public class APopupMenu\r
extends java.awt.PopupMenu implements ActionListener, ItemListener\r
{\r
Menu groupMenu = new Menu();\r
+ MenuItem editGroupName = new MenuItem();\r
protected MenuItem clustalColour = new MenuItem();\r
protected MenuItem zappoColour = new MenuItem();\r
protected MenuItem taylorColour = new MenuItem();\r
MenuItem revealAll = new MenuItem();\r
Menu menu1 = new Menu();\r
\r
- Dialog editNameDialog;\r
- Button okDialog = new Button("Accept");\r
- Button cancelDialog = new Button("Cancel");;\r
-\r
public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\r
{\r
///////////////////////////////////////////////////////////\r
e.printStackTrace();\r
}\r
\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;\r
+ i++)\r
{\r
- MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );\r
+ MenuItem item = new MenuItem(jalview.io.AppletFormatAdapter.\r
+ WRITEABLE_FORMATS[i]);\r
\r
item.addActionListener(this);\r
outputmenu.add(item);\r
\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
- if (sg != null && sg.getSize()>0)\r
+ if (sg != null && sg.getSize() > 0)\r
{\r
+ editGroupName.setLabel(sg.getName());\r
showText.setState(sg.getDisplayText());\r
showColourText.setState(sg.getColourText());\r
showBoxes.setState(sg.getDisplayBoxes());\r
remove(groupMenu);\r
}\r
\r
- if (links!=null)\r
+ if (links != null)\r
{\r
Menu linkMenu = new Menu("Link");\r
MenuItem item;\r
String link;\r
- for(int i=0; i<links.size(); i++)\r
+ for (int i = 0; i < links.size(); i++)\r
{\r
link = links.elementAt(i).toString();\r
final String target = link.substring(0, link.indexOf("|"));\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
link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
}\r
else\r
- url = link.substring(link.lastIndexOf("|")+1);\r
-\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ap.alignFrame.showURL(url, target);\r
- }\r
- });\r
- linkMenu.add(item);\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
+ ap.alignFrame.showURL(url, target);\r
+ }\r
+ });\r
+ linkMenu.add(item);\r
}\r
- if(seq!=null)\r
+ if (seq != null)\r
+ {\r
seqMenu.add(linkMenu);\r
+ }\r
else\r
+ {\r
add(linkMenu);\r
+ }\r
}\r
- if(seq!=null)\r
+ if (seq != null)\r
{\r
seqMenu.setLabel(seq.getName());\r
repGroup.setLabel("Represent Group with " + seq.getName());\r
}\r
else\r
+ {\r
remove(seqMenu);\r
+ }\r
\r
- if(!ap.av.hasHiddenRows)\r
+ if (!ap.av.hasHiddenRows)\r
+ {\r
remove(revealAll);\r
+ }\r
}\r
\r
public void itemStateChanged(ItemEvent evt)\r
{\r
- if(evt.getSource()==abovePIDColour)\r
+ if (evt.getSource() == abovePIDColour)\r
+ {\r
abovePIDColour_itemStateChanged();\r
- else if(evt.getSource()==showColourText)\r
+ }\r
+ else if (evt.getSource() == showColourText)\r
+ {\r
showColourText_itemStateChanged();\r
- else if(evt.getSource()==showText)\r
+ }\r
+ else if (evt.getSource() == showText)\r
+ {\r
showText_itemStateChanged();\r
- else if(evt.getSource()==showBoxes)\r
- showBoxes_itemStateChanged() ;\r
+ }\r
+ else if (evt.getSource() == showBoxes)\r
+ {\r
+ showBoxes_itemStateChanged();\r
+ }\r
}\r
\r
public void actionPerformed(ActionEvent evt)\r
{\r
Object source = evt.getSource();\r
- if(source==clustalColour)\r
+ if (source == clustalColour)\r
+ {\r
clustalColour_actionPerformed();\r
- else if(source==zappoColour)\r
+ }\r
+ else if (source == zappoColour)\r
+ {\r
zappoColour_actionPerformed();\r
- else if(source==taylorColour)\r
+ }\r
+ else if (source == taylorColour)\r
+ {\r
taylorColour_actionPerformed();\r
- else if(source==hydrophobicityColour)\r
+ }\r
+ else if (source == hydrophobicityColour)\r
+ {\r
hydrophobicityColour_actionPerformed();\r
- else if(source==helixColour)\r
+ }\r
+ else if (source == helixColour)\r
+ {\r
helixColour_actionPerformed();\r
- else if(source==strandColour)\r
+ }\r
+ else if (source == strandColour)\r
+ {\r
strandColour_actionPerformed();\r
- else if(source==turnColour)\r
+ }\r
+ else if (source == turnColour)\r
+ {\r
turnColour_actionPerformed();\r
- else if(source==buriedColour)\r
+ }\r
+ else if (source == buriedColour)\r
+ {\r
buriedColour_actionPerformed();\r
- else if(source==nucleotideMenuItem)\r
+ }\r
+ else if (source == nucleotideMenuItem)\r
+ {\r
nucleotideMenuItem_actionPerformed();\r
+ }\r
\r
else if (source == userDefinedColour)\r
+ {\r
userDefinedColour_actionPerformed();\r
+ }\r
else if (source == PIDColour)\r
+ {\r
PIDColour_actionPerformed();\r
+ }\r
else if (source == BLOSUM62Colour)\r
+ {\r
BLOSUM62Colour_actionPerformed();\r
+ }\r
else if (source == noColourmenuItem)\r
+ {\r
noColourmenuItem_actionPerformed();\r
+ }\r
else if (source == conservationMenuItem)\r
+ {\r
conservationMenuItem_itemStateChanged();\r
+ }\r
else if (source == unGroupMenuItem)\r
+ {\r
unGroupMenuItem_actionPerformed();\r
+ }\r
\r
- else if(source == sequenceName)\r
- editName();\r
- else if (source==okDialog || source==cancelDialog)\r
+ else if (source == sequenceName)\r
{\r
- editNameDialog.setVisible(false);\r
- if(source==cancelDialog)\r
- editNameDialog = null;\r
+ editName();\r
}\r
- else if(source == pdb)\r
+ else if (source == pdb)\r
+ {\r
addPDB();\r
- else if(source == hideSeqs)\r
+ }\r
+ else if (source == hideSeqs)\r
+ {\r
hideSequences(false);\r
- else if(source == repGroup)\r
+ }\r
+ else if (source == repGroup)\r
+ {\r
hideSequences(true);\r
- else if(source == revealAll)\r
+ }\r
+ else if (source == revealAll)\r
{\r
- ap.av.showAllHiddenSeqs();\r
+ ap.av.showAllHiddenSeqs();\r
}\r
\r
- else if(source==copy)\r
+ else if (source == editGroupName)\r
+ {\r
+ EditNameDialog dialog = new EditNameDialog(\r
+ getGroup().getName(),\r
+ getGroup().getDescription(),\r
+ " Group Name",\r
+ "Group Description",\r
+ ap,\r
+ "Edit Group Name / Description");\r
+\r
+ if (dialog.accept)\r
+ {\r
+\r
+ getGroup().setName(dialog.getName().replace(' ', '_'));\r
+ getGroup().setDescription(dialog.getDescription());\r
+ }\r
+\r
+ }\r
+ else if (source == copy)\r
+ {\r
ap.alignFrame.copy_actionPerformed();\r
- else if(source==cut)\r
- ap.alignFrame.cut_actionPerformed();\r
- else if(source==toUpper || source==toLower || source==toggleCase)\r
+ }\r
+ else if (source == cut)\r
{\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- Vector regions = new Vector();\r
- if (sg != null)\r
+ ap.alignFrame.cut_actionPerformed();\r
+ }\r
+ else if (source == toUpper || source == toLower || source == toggleCase)\r
{\r
- int start = sg.getStartRes();\r
- int end = sg.getEndRes() + 1;\r
-\r
- do\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ Vector regions = new Vector();\r
+ if (sg != null)\r
{\r
- if (ap.av.hasHiddenColumns)\r
+ int start = sg.getStartRes();\r
+ int end = sg.getEndRes() + 1;\r
+\r
+ do\r
{\r
- if(start==0)\r
- start = ap.av.colSel.adjustForHiddenColumns(start);\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
+ 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
- regions.addElement(new int[]\r
- {start, end});\r
-\r
- if (ap.av.hasHiddenColumns)\r
+ int[][] startEnd = new int[regions.size()][2];\r
+ for (int i = 0; i < regions.size(); i++)\r
{\r
- start = ap.av.colSel.adjustForHiddenColumns(end);\r
- start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
+ startEnd[i] = (int[]) regions.elementAt(i);\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
- String description;\r
- int caseChange;\r
-\r
- if(source==toggleCase)\r
- {\r
- description = "Toggle Case";\r
- caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
- }\r
- else if(source==toUpper)\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), startEnd, caseChange\r
- );\r
+ if (source == toggleCase)\r
+ {\r
+ description = "Toggle Case";\r
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
+ }\r
+ else if (source == toUpper)\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
- ap.alignFrame.addHistoryItem(caseCommand);\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
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
\r
- }\r
+ }\r
}\r
else\r
+ {\r
outputText(evt);\r
+ }\r
\r
}\r
\r
\r
cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(\r
e.getActionCommand(),\r
- new Alignment( ap.av.getSelectionAsNewSequence() ),\r
+ new Alignment(ap.av.getSelectionAsNewSequence()),\r
ap.av.showJVSuffix));\r
\r
}\r
\r
void editName()\r
{\r
- TextField id = new TextField(seq.getName(), 40);\r
- TextField description = new TextField(seq.getDescription(), 40);\r
- Panel panel = new Panel(new BorderLayout());\r
- Panel panel2 = new Panel(new BorderLayout());\r
- panel2.add(new Label(" Sequence Name "), BorderLayout.WEST);\r
- panel2.add(id, BorderLayout.CENTER);\r
- panel.add(panel2, BorderLayout.NORTH);\r
- panel2 = new Panel(new BorderLayout());\r
- panel2.add(new Label("Sequence Description "), BorderLayout.WEST);\r
- panel2.add(description, BorderLayout.CENTER);\r
- panel.add(panel2, BorderLayout.CENTER);\r
-\r
- panel2 = new Panel(new FlowLayout());\r
-\r
- panel2.add(okDialog);\r
- panel2.add(cancelDialog);\r
-\r
- panel.add(panel2, BorderLayout.SOUTH);\r
-\r
- editNameDialog = new Dialog(ap.alignFrame,\r
- "Edit Sequence Name / Description",\r
- true);\r
-\r
- editNameDialog.add(panel, BorderLayout.NORTH);\r
-\r
- editNameDialog.setBounds(ap.alignFrame.getBounds().x\r
- +(ap.alignFrame.getSize().width-500)/2 ,\r
- ap.alignFrame.getBounds().y\r
- +(ap.alignFrame.getSize().height-120)/2,\r
- 500, 120);\r
-\r
- editNameDialog.show();\r
-\r
- if (editNameDialog != null)\r
+ EditNameDialog dialog = new EditNameDialog(\r
+ seq.getName(),\r
+ seq.getDescription(),\r
+ " Sequence Name",\r
+ "Sequence Description",\r
+ ap,\r
+ "Edit Sequence Name / Description");\r
+\r
+ if (dialog.accept)\r
{\r
- seq.setName(id.getText());\r
- seq.setDescription(description.getText());\r
- ap.repaint();\r
+ seq.setName(dialog.getName());\r
+ seq.setDescription(dialog.getDescription());\r
+ ap.paintAlignment(false);\r
}\r
}\r
\r
groupMenu.setLabel("Group");\r
groupMenu.setLabel("Selection");\r
\r
+ editGroupName.addActionListener(this);\r
unGroupMenuItem.setLabel("Remove Group");\r
unGroupMenuItem.addActionListener(this);\r
\r
this.add(seqMenu);\r
this.add(hideSeqs);\r
this.add(revealAll);\r
+ groupMenu.add(editGroupName);\r
groupMenu.add(editMenu);\r
groupMenu.add(outputmenu);\r
groupMenu.add(menu1);\r
hideSeqs.addActionListener(this);\r
repGroup.addActionListener(this);\r
revealAll.addActionListener(this);\r
- okDialog.addActionListener(this);\r
- cancelDialog.addActionListener(this);\r
-\r
}\r
\r
void refresh()\r
{\r
- ap.seqPanel.seqCanvas.repaint();\r
- if(ap.overviewPanel!=null)\r
- ap.overviewPanel.updateOverviewImage();\r
+ ap.paintAlignment(true);\r
}\r
\r
protected void clustalColour_actionPerformed()\r
protected void abovePIDColour_itemStateChanged()\r
{\r
SequenceGroup sg = getGroup();\r
- if(sg.cs==null)\r
- return;\r
+ if (sg.cs == null)\r
+ {\r
+ return;\r
+ }\r
\r
if (abovePIDColour.getState())\r
{\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
+ hiddenRepSequences), 0,\r
ap.av.alignment.getWidth()));\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
getGroup().getName());\r
{\r
SequenceGroup sg = getGroup();\r
sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
+ hiddenRepSequences), 0,\r
ap.av.alignment.getWidth()));\r
refresh();\r
}\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
+ hiddenRepSequences), 0,\r
ap.av.alignment.getWidth()));\r
\r
refresh();\r
protected void conservationMenuItem_itemStateChanged()\r
{\r
SequenceGroup sg = getGroup();\r
- if(sg.cs==null)\r
- return;\r
+ if (sg.cs == null)\r
+ {\r
+ return;\r
+ }\r
\r
if (conservationMenuItem.getState())\r
{\r
\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.getSequences(ap.av.hiddenRepSequences), 0,\r
+ sg.getSequences(ap.av.\r
+ hiddenRepSequences), 0,\r
ap.av.alignment.getWidth());\r
\r
c.calculate();\r
refresh();\r
}\r
\r
-\r
SequenceGroup getGroup()\r
{\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
// this method won't add a new group if it already exists\r
- if(sg!=null)\r
+ if (sg != null)\r
+ {\r
ap.av.alignment.addGroup(sg);\r
+ }\r
\r
return sg;\r
}\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
ap.av.alignment.deleteGroup(sg);\r
ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
+ ap.paintAlignment(true);\r
}\r
\r
public void showColourText_itemStateChanged()\r
void hideSequences(boolean representGroup)\r
{\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg==null || sg.getSize()<1)\r
+ if (sg == null || sg.getSize() < 1)\r
{\r
- ap.av.hideSequence(new SequenceI[]{seq});\r
+ ap.av.hideSequence(new SequenceI[]\r
+ {seq});\r
return;\r
}\r
\r
}\r
\r
ap.av.hideSequence(hseqs);\r
- }\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff