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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
6300c4b
..
57e35e7
100644
(file)
--- a/
src/jalview/hmmer/HMMAlign.java
+++ b/
src/jalview/hmmer/HMMAlign.java
@@
-64,12
+64,7
@@
public class HMMAlign extends HmmerCommand
@Override
public void run()
{
@Override
public void run()
{
- HiddenMarkovModel hmm = af.getSelectedHMM();
- if (hmm == null)
- {
- System.err.println("Can't run hmmalign as no HMM profile selected");
- return;
- }
+ HiddenMarkovModel hmm = getHmmProfile();
long msgId = System.currentTimeMillis();
af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
long msgId = System.currentTimeMillis();
af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
@@
-97,8
+92,8
@@
public class HMMAlign extends HmmerCommand
boolean ran = runCommand(modelFile, alignmentFile, resultFile);
if (!ran)
{
boolean ran = runCommand(modelFile, alignmentFile, resultFile);
if (!ran)
{
- JvOptionPane.showInternalMessageDialog(af,
- MessageManager.getString("warn.hmmalign_failed"));
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .formatMessage("warn.command_failed", "hmmalign"));
return;
}
return;
}
@@
-157,9
+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);
}
@@
-177,7
+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);
@@
-212,14
+207,6
@@
public class HMMAlign extends HmmerCommand
al.setDataset(dataset);
}
al.setDataset(dataset);
}
- /*
- * hack to ensure hmm set on alignment
- */
- if (al.getSequenceAt(0).hasHMMProfile())
- {
- al.setHmmConsensus(al.getSequenceAt(0));
- }
-
displayInNewFrame(al, allOrders, hidden, title);
}
displayInNewFrame(al, allOrders, hidden, title);
}