/*\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) 2006 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
import jalview.io.EBIFetchClient;\r
import java.awt.event.ActionListener;\r
import java.awt.event.ActionEvent;\r
+import java.io.*;\r
+import jalview.io.JalviewFileChooser;\r
+import jalview.io.JalviewFileView;\r
\r
public class PDBViewer extends JInternalFrame implements Runnable\r
{\r
PDBEntry pdb;\r
Sequence sequence;\r
PDBCanvas pdbcanvas;\r
+ String tmpPDBFile;\r
\r
\r
public PDBViewer(PDBEntry entry,\r
Sequence seq,\r
SeqCanvas seqcanvas)\r
{\r
- /*Uncomment this to modify in Jbuilder\r
try\r
{\r
jbInit();\r
catch (Exception ex)\r
{\r
ex.printStackTrace();\r
- }*/\r
+ }\r
+\r
\r
if (entry==null)\r
return;\r
pdb = entry;\r
sequence = seq;\r
+ pdbcanvas = new PDBCanvas(seqcanvas, sequence);\r
+\r
+ if(pdb.getFile()!=null)\r
+ {\r
+ try{\r
+ tmpPDBFile = pdb.getFile();\r
+ PDBfile pdbfile = new PDBfile(tmpPDBFile,\r
+ jalview.io.AppletFormatAdapter.FILE);\r
+ pdbcanvas.setPDBFile(pdbfile);\r
+\r
+ }catch(java.io.IOException ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Thread worker = new Thread(this);\r
+ worker.start();\r
+ }\r
\r
- Thread worker = new Thread(this);\r
- worker.start();\r
\r
- pdbcanvas = new PDBCanvas(seqcanvas, seq);\r
\r
setContentPane(pdbcanvas);\r
StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());\r
{\r
try\r
{\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String query = "pdb:" + pdb.getId();\r
- String[] result = ebi.fetchData(query, "default","raw");\r
- if (result!=null) {\r
- PDBfile pdbfile = new PDBfile(result);\r
- pdbcanvas.setPDBFile(pdbfile);\r
- } else {\r
- throw new Exception("Empty result for WSDbFetch Query: "+query);\r
- }\r
-\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ String query = "pdb:" + pdb.getId();\r
+ tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();\r
+ if (tmpPDBFile != null)\r
+ {\r
+ PDBfile pdbfile = new PDBfile(tmpPDBFile, jalview.io.AppletFormatAdapter.FILE);\r
+ pdbcanvas.setPDBFile(pdbfile);\r
+ }\r
+ else\r
+ {\r
+ throw new Exception("Empty result for WSDbFetch Query: " + query);\r
+ }\r
}\r
catch (Exception ex)\r
{\r
background_actionPerformed(e);\r
}\r
});\r
+ savePDB.setText("PDB File");\r
+ savePDB.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ savePDB_actionPerformed(e);\r
+ }\r
+ });\r
jMenuBar1.add(fileMenu);\r
jMenuBar1.add(coloursMenu);\r
jMenuBar1.add(viewMenu);\r
fileMenu.add(saveMenu);\r
fileMenu.add(mapping);\r
+ saveMenu.add(savePDB);\r
saveMenu.add(png);\r
saveMenu.add(eps);\r
coloursMenu.add(seqButton);\r
JRadioButtonMenuItem helix = new JRadioButtonMenuItem();\r
JMenu viewMenu = new JMenu();\r
JMenuItem background = new JMenuItem();\r
+ JMenuItem savePDB = new JMenuItem();\r
\r
/**\r
* DOCUMENT ME!\r
pdbcanvas.repaint();\r
}\r
}\r
+\r
+ public void savePDB_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save PDB File");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ try\r
+ {\r
+ BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));\r
+ File outFile = chooser.getSelectedFile();\r
+\r
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
+ String data;\r
+ while ( (data = in.readLine()) != null)\r
+ {\r
+ if (\r
+ !( data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1)\r
+ )\r
+ out.println(data);\r
+ }\r
+ out.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
}\r