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pdb fetchDataAsFile
author
amwaterhouse
<Andrew Waterhouse>
Tue, 25 Jul 2006 09:37:41 +0000
(09:37 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 25 Jul 2006 09:37:41 +0000
(09:37 +0000)
src/jalview/gui/SequenceFetcher.java
patch
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diff --git
a/src/jalview/gui/SequenceFetcher.java
b/src/jalview/gui/SequenceFetcher.java
index
795276b
..
99c1d5e
100755
(executable)
--- a/
src/jalview/gui/SequenceFetcher.java
+++ b/
src/jalview/gui/SequenceFetcher.java
@@
-327,17
+327,18
@@
public class SequenceFetcher
}
\r
\r
EBIFetchClient ebi = new EBIFetchClient();
\r
}
\r
\r
EBIFetchClient ebi = new EBIFetchClient();
\r
- String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");
\r
- if (reply == null)
\r
+ String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
\r
+ if (file == null)
\r
return null;
\r
try
\r
{
\r
return null;
\r
try
\r
{
\r
- PDBfile pdbfile = new PDBfile(reply);
\r
+ PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
\r
for (int i = 0; i < pdbfile.chains.size(); i++)
\r
{
\r
if (chain == null ||
\r
( (PDBChain) pdbfile.chains.elementAt(i)).id.
\r
toUpperCase().equals(chain))
\r
for (int i = 0; i < pdbfile.chains.size(); i++)
\r
{
\r
if (chain == null ||
\r
( (PDBChain) pdbfile.chains.elementAt(i)).id.
\r
toUpperCase().equals(chain))
\r
+
\r
result.append("\n>PDB|" + id + "|" +
\r
( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
\r
getName() +
\r
result.append("\n>PDB|" + id + "|" +
\r
( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
\r
getName() +
\r