}\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(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(pdbMenuItem);\r
+ sequenceMenu.add(menuItem);\r
}\r
\r
+\r
}\r
\r
+\r
+\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
if (sg != null)\r
}\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
}\r
});\r
sequenceMenu.setText("Sequence");\r
- sequenceName.setText("Edit name");\r
+ sequenceName.setText("Edit Name/Desciption");\r
sequenceName.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
*/\r
void refresh()\r
{\r
- SequenceGroup sg = getGroup();\r
- if(sg!=null)\r
- {\r
- SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
-\r
- if (superG != null)\r
- {\r
- superG.setSuperGroupProperties(sg);\r
- }\r
- }\r
if (ap.overviewPanel != null)\r
ap.overviewPanel.updateOverviewImage();\r
\r
*/\r
void sequenceName_actionPerformed(ActionEvent e)\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
+ JLabel idlabel = new JLabel( " Sequence Name ");\r
+ JLabel desclabel = new JLabel("Sequence Description ");\r
+ idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
+ desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
+ JTextField id = new JTextField(sequence.getName(), 40);\r
+ JTextField description = new JTextField(sequence.getDescription(), 40);\r
+ JPanel panel = new JPanel(new BorderLayout());\r
+ JPanel panel2 = new JPanel(new BorderLayout());\r
+ panel2.add(idlabel, BorderLayout.WEST);\r
+ panel2.add(id, BorderLayout.CENTER);\r
+ panel.add(panel2, BorderLayout.NORTH);\r
+ panel2 = new JPanel(new BorderLayout());\r
+ panel2.add(desclabel, BorderLayout.WEST);\r
+ panel2.add(description, BorderLayout.CENTER);\r
+ panel.add(panel2, BorderLayout.SOUTH);\r
+\r
+\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ panel, "Edit Sequence Name/Description",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
+\r
+\r
+ if (reply != JOptionPane.OK_OPTION )\r
+ {\r
+ return;\r
+ }\r
+\r
+ String s = id.getText();\r
\r
if (s != null)\r
{\r
}\r
\r
s = s.replace(' ', '_');\r
+ sequence.getDatasetSequence().setName(s);\r
sequence.setName(s);\r
ap.repaint();\r
}\r
+\r
+ sequence.getDatasetSequence().setDescription(description.getText());\r
+ sequence.setDescription(description.getText());\r
}\r
\r
/**\r
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
}\r