Sequence seq,\r
SeqCanvas seqcanvas)\r
{\r
+\r
pdb = entry;\r
sequence = seq;\r
\r
+ Thread worker = new Thread(this);\r
+ worker.start();\r
+\r
try\r
{\r
jbInit();\r
title.append( " Chain:" );\r
title.append( pdb.getProperty().get("chains"));\r
}\r
- Desktop.addInternalFrame(this,title.toString(),400, 400);\r
\r
- Thread worker = new Thread(this);\r
- worker.start();\r
+ Desktop.addInternalFrame(this,title.toString(),400, 400);\r
}\r
\r
public void run()\r
try\r
{\r
EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData("pdb:" + pdb.getId(), null,\r
- null);\r
+ String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");\r
\r
PDBfile pdbfile = new PDBfile(result);\r
\r
molecule_actionPerformed(e);\r
}\r
});\r
+ allchains.setSelected(true);\r
+ allchains.setText("Show All Chains");\r
+ allchains.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ allchains_itemStateChanged(e);\r
+ }\r
+ });\r
jMenuBar1.add(fileMenu);\r
jMenuBar1.add(coloursMenu);\r
fileMenu.add(saveMenu);\r
coloursMenu.add(depth);\r
coloursMenu.add(zbuffer);\r
coloursMenu.add(molecule);\r
+ coloursMenu.add(allchains);\r
ButtonGroup bg = new ButtonGroup();\r
bg.add(seqButton);\r
bg.add(chain);\r
JRadioButtonMenuItem chain = new JRadioButtonMenuItem();\r
JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();\r
JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();\r
+ JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();\r
\r
/**\r
* DOCUMENT ME!\r
public void mapping_actionPerformed(ActionEvent e)\r
{\r
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
- Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 500, 600);\r
+ Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);\r
cap.setText(pdbcanvas.mappingDetails.toString());\r
}\r
+\r
+ public void allchains_itemStateChanged(ItemEvent e)\r
+ {\r
+ pdbcanvas.setAllchainsVisible(allchains.getState());\r
+ }\r
}\r