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
if(pdb.getProperty()!=null)\r
{\r
- title.append( " Method: " );\r
- title.append(pdb.getProperty().get("method"));\r
- title.append( " Chain:" );\r
- title.append( pdb.getProperty().get("chains"));\r
+ if (pdb.getProperty().get("method")!=null)\r
+ {\r
+ title.append(" Method: ");\r
+ title.append(pdb.getProperty().get("method"));\r
+ }\r
+ if (pdb.getProperty().get("chains") != null)\r
+ {\r
+ title.append(" Chain:");\r
+ title.append(pdb.getProperty().get("chains"));\r
+ }\r
}\r
-\r
Desktop.addInternalFrame(this,title.toString(),400, 400);\r
}\r
\r
{\r
try\r
{\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");\r
-\r
- PDBfile pdbfile = new PDBfile(result);\r
-\r
- pdbcanvas.setPDBFile(pdbfile);\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
ex.printStackTrace();\r
+ showErrorMessage("Failed to retrieve PDB structure.");\r
+// this.dispose();\r
}\r
}\r
\r
}\r
});\r
viewMenu.setText("View");\r
+ background.setText("Background Colour...");\r
+ background.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\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
coloursMenu.add(turn);\r
coloursMenu.add(buried);\r
coloursMenu.add(user);\r
+ coloursMenu.add(background);\r
ButtonGroup bg = new ButtonGroup();\r
bg.add(seqButton);\r
bg.add(chain);\r
JRadioButtonMenuItem strand = new JRadioButtonMenuItem();\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
{\r
pdbcanvas.setAllchainsVisible(allchains.getState());\r
}\r
+ void showErrorMessage(String error)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);\r
+ }\r
+\r
\r
public void zappo_actionPerformed(ActionEvent e)\r
{\r
pdbcanvas.repaint();\r
}\r
}\r
+\r
+ public void background_actionPerformed(ActionEvent e)\r
+ {\r
+ java.awt.Color col = JColorChooser.showDialog(this, "Select Background Colour",\r
+ pdbcanvas.backgroundColour);\r
+\r
+ if(col!=null)\r
+ {\r
+ pdbcanvas.backgroundColour = col;\r
+ pdbcanvas.redrawneeded = true;\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 (data.indexOf("<PRE>") == -1 && data.indexOf("</PRE>") == -1)\r
+ out.println(data);\r
+ }\r
+ out.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff