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JAL-2629 default HMMBuild to alignment if not specified by args
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 10 May 2018 14:17:53 +0000
(15:17 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 10 May 2018 14:17:53 +0000
(15:17 +0100)
src/jalview/hmmer/HMMBuild.java
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diff --git
a/src/jalview/hmmer/HMMBuild.java
b/src/jalview/hmmer/HMMBuild.java
index
3c3bd40
..
6de7029
100644
(file)
--- a/
src/jalview/hmmer/HMMBuild.java
+++ b/
src/jalview/hmmer/HMMBuild.java
@@
-96,11
+96,14
@@
public class HMMBuild extends HmmerCommand
AlignViewportI viewport)
{
List<AnnotatedCollectionI> runBuildFor = new ArrayList<>();
AlignViewportI viewport)
{
List<AnnotatedCollectionI> runBuildFor = new ArrayList<>();
+ boolean foundArg = false;
+
for (ArgumentI arg : params)
{
String name = arg.getName();
if (MessageManager.getString("label.hmmbuild_for").equals(name))
{
for (ArgumentI arg : params)
{
String name = arg.getName();
if (MessageManager.getString("label.hmmbuild_for").equals(name))
{
+ foundArg = true;
String value = arg.getValue();
if (MessageManager.getString("label.alignment").equals(value))
{
String value = arg.getValue();
if (MessageManager.getString("label.alignment").equals(value))
{
@@
-134,6
+137,15
@@
public class HMMBuild extends HmmerCommand
}
}
}
}
}
}
+
+ /*
+ * default is to build for the whole alignment
+ */
+ if (!foundArg)
+ {
+ runBuildFor.add(alignment);
+ }
+
return runBuildFor;
}
return runBuildFor;
}