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JAL-2344 corrected conversion of Type enum to FileFormat
features/JAL-2344FileFormatI
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 29 Nov 2016 10:57:10 +0000
(10:57 +0000)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 29 Nov 2016 10:57:10 +0000
(10:57 +0000)
src/jalview/ws/dbsources/Pdb.java
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diff --git
a/src/jalview/ws/dbsources/Pdb.java
b/src/jalview/ws/dbsources/Pdb.java
index
0aae38f
..
68dda88
100644
(file)
--- a/
src/jalview/ws/dbsources/Pdb.java
+++ b/
src/jalview/ws/dbsources/Pdb.java
@@
-40,7
+40,6
@@
import jalview.ws.ebi.EBIFetchClient;
import java.util.ArrayList;
import java.util.List;
import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
import com.stevesoft.pat.Regex;
import com.stevesoft.pat.Regex;
@@
-155,9
+154,10
@@
public class Pdb extends EbiFileRetrievedProxy
}
try
{
}
try
{
- // convert Type.PDB/MMCIF to FileFormat.PDB/MMCIF
- // todo get rid of Type?
- FileFormatI fileFormat = FileFormat.valueOf(pdbFileFormat.toString());
+ // todo get rid of Type and use FileFormatI instead?
+ // todo get rid of "ext" and just use "tmp"?
+ FileFormatI fileFormat = pdbFileFormat == Type.PDB ? FileFormat.PDB
+ : FileFormat.MMCif;
pdbAlignment = new FormatAdapter().readFile(file,
DataSourceType.FILE, fileFormat);
if (pdbAlignment != null)
pdbAlignment = new FormatAdapter().readFile(file,
DataSourceType.FILE, fileFormat);
if (pdbAlignment != null)