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JAL-2629 corrected cutoff parameter passing to hmmsearch
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 18 Apr 2018 11:13:23 +0000
(12:13 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 18 Apr 2018 11:13:23 +0000
(12:13 +0100)
src/jalview/hmmer/HMMSearch.java
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diff --git
a/src/jalview/hmmer/HMMSearch.java
b/src/jalview/hmmer/HMMSearch.java
index
7413d14
..
d4c9656
100644
(file)
--- a/
src/jalview/hmmer/HMMSearch.java
+++ b/
src/jalview/hmmer/HMMSearch.java
@@
-160,7
+160,7
@@
public class HMMSearch extends HmmerCommand
}
else if (MessageManager.getString("label.seq_e_value").equals(name))
{
}
else if (MessageManager.getString("label.seq_e_value").equals(name))
{
- args.add("--incE");
+ args.add("-E");
args.add(arg.getValue());
}
else if (MessageManager.getString("label.seq_score").equals(name))
args.add(arg.getValue());
}
else if (MessageManager.getString("label.seq_score").equals(name))
@@
-168,10
+168,10
@@
public class HMMSearch extends HmmerCommand
args.add("-incT");
args.add(arg.getValue());
}
args.add("-incT");
args.add(arg.getValue());
}
- else if (MessageManager.getString("label.dom_e_value_desc")
+ else if (MessageManager.getString("label.dom_e_value")
.equals(name))
{
.equals(name))
{
- args.add("--incdomE");
+ args.add("--domE");
args.add(arg.getValue());
}
else if (MessageManager.getString("label.dom_score").equals(name))
args.add(arg.getValue());
}
else if (MessageManager.getString("label.dom_score").equals(name))