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
+ 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
- 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
+ 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