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JAL-4187 JAL-629 JAL-3830 adjustments to Cygwin and WSL parts of bash launcher script...
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
Pdb.java
diff --git
a/src/jalview/ws/dbsources/Pdb.java
b/src/jalview/ws/dbsources/Pdb.java
index
e4326d1
..
bb5c165
100644
(file)
--- a/
src/jalview/ws/dbsources/Pdb.java
+++ b/
src/jalview/ws/dbsources/Pdb.java
@@
-165,8
+165,8
@@
public class Pdb extends EbiFileRetrievedProxy
// todo get rid of Type and use FileFormatI instead?
FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
: FileFormat.MMCif;
// todo get rid of Type and use FileFormatI instead?
FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
: FileFormat.MMCif;
- pdbAlignment = new FormatAdapter().readFile(file, DataSourceType.FILE,
- fileFormat);
+ pdbAlignment = new FormatAdapter().readFile(tmpFile,
+ DataSourceType.FILE, fileFormat);
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();