\r
import javax.swing.*;\r
\r
+import java.util.Vector;\r
+\r
\r
/**\r
* DOCUMENT ME!\r
JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
-\r
- /**\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
+\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)\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
}\r
\r
\r
- if ((seq != null)\r
- && seq.getDatasetSequence().getPDBId() != null)\r
+ if (seq != null)\r
{\r
- java.util.Enumeration e = seq.getDatasetSequence().getPDBId().elements();\r
- while(e.hasMoreElements())\r
+ JMenuItem menuItem;\r
+ if( seq.getDatasetSequence().getPDBId() != null)\r
{\r
- final PDBEntry pdb = (PDBEntry)e.nextElement();\r
-\r
- JMenuItem pdbMenuItem = new JMenuItem();\r
- pdbMenuItem.setText("View PDB entry: "+pdb.getId());\r
- pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
+ elements();\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(pdbMenuItem);\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
+ sequenceMenu.add(menuItem);\r
+\r
+ if(ap.av.getSelectionGroup() !=null && 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
+\r
}\r
\r
+\r
+\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
if (sg != null)\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
{\r
sequenceMenu.setVisible(false);\r
}\r
- else\r
- {\r
- java.util.Vector links = Preferences.sequenceURLLinks;\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
- item = new JMenuItem(link.substring(0, link.indexOf("|")));\r
- String id = sequence.getName();\r
- if(id.indexOf("|")>-1)\r
- id = id.substring(id.lastIndexOf("|")+1);\r
-\r
- final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
- + id +\r
- link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\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
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
private void jbInit() throws Exception\r
{\r
groupMenu.setText("Group");\r
- groupMenu.setText("Define");\r
+ groupMenu.setText("Group");\r
groupName.setText("Name");\r
groupName.addActionListener(new java.awt.event.ActionListener()\r
{\r
}\r
});\r
sequenceMenu.setText("Sequence");\r
- sequenceName.setText("Edit Name/Desciption");\r
+ sequenceName.setText("Edit Name/Description");\r
sequenceName.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
showColourText_actionPerformed(e);\r
}\r
});\r
- add(groupMenu);\r
+ editMenu.setText("Edit");\r
+ cut.setText("Cut");\r
+ cut.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ upperCase.setText("To Upper Case");\r
+ upperCase.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ upperCase_actionPerformed(e);\r
+ }\r
+ });\r
+ copy.setText("Copy");\r
+ copy.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(e);\r
+ }\r
+ });\r
+ lowerCase.setText("To Lower Case");\r
+ lowerCase.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ lowerCase_actionPerformed(e);\r
+ }\r
+ });\r
+ toggle.setText("Toggle Case");\r
+ toggle.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ toggle_actionPerformed(e);\r
+ }\r
+ });\r
+ add(groupMenu);\r
add(sequenceMenu);\r
- groupMenu.add(groupName);\r
+ this.add(editMenu);\r
+ groupMenu.add(groupName);\r
groupMenu.addSeparator();\r
groupMenu.add(unGroupMenuItem);\r
groupMenu.add(colourMenu);\r
colourMenu.addSeparator();\r
colourMenu.add(abovePIDColour);\r
colourMenu.add(conservationMenuItem);\r
- noColourmenuItem.setText("None");\r
+ editMenu.add(copy);\r
+ editMenu.add(cut);\r
+ editMenu.add(upperCase);\r
+ editMenu.add(lowerCase);\r
+ editMenu.add(toggle);\r
+ noColourmenuItem.setText("None");\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
ex.printStackTrace();\r
}\r
}\r
+\r
+ void hideSequences(boolean representGroup)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if(sg==null || sg.getSize()<1)\r
+ {\r
+ ap.av.hideSequence(sequence);\r
+ return;\r
+ }\r
+\r
+ int index = 0;\r
+ while(index < sg.sequences.size())\r
+ {\r
+ if(representGroup && sg.getSequenceAt(index)!=sequence)\r
+ {\r
+ sequence.addHiddenSequence(sg.getSequenceAt(index));\r
+ ap.av.hideSequence(sg.getSequenceAt(index));\r
+ }\r
+ else if(!representGroup)\r
+ {\r
+ ap.av.hideSequence(sg.getSequenceAt(index));\r
+ }\r
+ index ++;\r
+ }\r
+\r
+ ap.av.setSelectionGroup(null);\r
+ refresh();\r
+ }\r
+\r
+ public void copy_actionPerformed(ActionEvent e)\r
+ {\r
+ ap.alignFrame.copy_actionPerformed(null);\r
+ }\r
+\r
+ public void cut_actionPerformed(ActionEvent e)\r
+ {\r
+ ap.alignFrame.cut_actionPerformed(null);\r
+ }\r
+\r
+ public void upperCase_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if(sg==null)\r
+ return;\r
+\r
+ for(int g=0; g<sg.getSize(); g++)\r
+ {\r
+ sg.getSequenceAt(g).changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
+ }\r
+ ap.repaint();\r
+ }\r
+\r
+ public void lowerCase_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if(sg==null)\r
+ return;\r
+\r
+ for(int g=0; g<sg.getSize(); g++)\r
+ {\r
+ sg.getSequenceAt(g).changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
+ }\r
+ ap.repaint();\r
+ }\r
+\r
+ public void toggle_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg == null)\r
+ return;\r
+\r
+ for (int g = 0; g < sg.getSize(); g++)\r
+ {\r
+ sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
+ }\r
+\r
+ ap.repaint();\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff