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Can load PDB file from disk
author
amwaterhouse
<Andrew Waterhouse>
Tue, 25 Jul 2006 09:32:17 +0000
(09:32 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 25 Jul 2006 09:32:17 +0000
(09:32 +0000)
src/MCview/PDBViewer.java
patch
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diff --git
a/src/MCview/PDBViewer.java
b/src/MCview/PDBViewer.java
index
87c2739
..
69a131c
100755
(executable)
--- a/
src/MCview/PDBViewer.java
+++ b/
src/MCview/PDBViewer.java
@@
-38,7
+38,6
@@
public class PDBViewer extends JInternalFrame implements Runnable
Sequence seq,
\r
SeqCanvas seqcanvas)
\r
{
\r
Sequence seq,
\r
SeqCanvas seqcanvas)
\r
{
\r
- /*Uncomment this to modify in Jbuilder
\r
try
\r
{
\r
jbInit();
\r
try
\r
{
\r
jbInit();
\r
@@
-46,17
+45,34
@@
public class PDBViewer extends JInternalFrame implements Runnable
catch (Exception ex)
\r
{
\r
ex.printStackTrace();
\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
\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
+ PDBfile pdbfile = new PDBfile(pdb.getFile(),
\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
\r
- Thread worker = new Thread(this);
\r
- worker.start();
\r
\r
\r
- pdbcanvas = new PDBCanvas(seqcanvas, seq);
\r
\r
setContentPane(pdbcanvas);
\r
StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
\r
\r
setContentPane(pdbcanvas);
\r
StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
\r
@@
-80,24
+96,18
@@
public class PDBViewer extends JInternalFrame implements Runnable
{
\r
try
\r
{
\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
+ String file = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
\r
+ if (file != null)
\r
+ {
\r
+ PDBfile pdbfile = new PDBfile(file, 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
}
\r
catch (Exception ex)
\r
{
\r