git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-3285 fix incorrect file paths on HMMAlign/Search results
[jalview.git]
/
src
/
jalview
/
hmmer
/
HMMAlign.java
diff --git
a/src/jalview/hmmer/HMMAlign.java
b/src/jalview/hmmer/HMMAlign.java
index
b5f047e
..
57e35e7
100644
(file)
--- a/
src/jalview/hmmer/HMMAlign.java
+++ b/
src/jalview/hmmer/HMMAlign.java
@@
-152,9
+152,9
@@
public class HMMAlign extends HmmerCommand
}
}
args.add("-o");
}
}
args.add("-o");
- args.add(getFilePath(resultFile));
- args.add(getFilePath(modelFile));
- args.add(getFilePath(alignmentFile));
+ args.add(getFilePath(resultFile, true));
+ args.add(getFilePath(modelFile, true));
+ args.add(getFilePath(alignmentFile, true));
return runCommand(args);
}
return runCommand(args);
}
@@
-172,7
+172,7
@@
public class HMMAlign extends HmmerCommand
private SequenceI[] importData(File resultFile,
List<AlignmentOrder> allOrders) throws IOException
{
private SequenceI[] importData(File resultFile,
List<AlignmentOrder> allOrders) throws IOException
{
- StockholmFile file = new StockholmFile(getFilePath(resultFile),
+ StockholmFile file = new StockholmFile(getFilePath(resultFile, false),
DataSourceType.FILE);
SequenceI[] result = file.getSeqsAsArray();
AlignmentOrder msaorder = new AlignmentOrder(result);
DataSourceType.FILE);
SequenceI[] result = file.getSeqsAsArray();
AlignmentOrder msaorder = new AlignmentOrder(result);