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jal-2629 fix for hmmbuild failing due to whitespace in the name
[jalview.git]
/
src
/
jalview
/
hmmer
/
HMMBuildThread.java
diff --git
a/src/jalview/hmmer/HMMBuildThread.java
b/src/jalview/hmmer/HMMBuildThread.java
index
faba183
..
d5e938a
100644
(file)
--- a/
src/jalview/hmmer/HMMBuildThread.java
+++ b/
src/jalview/hmmer/HMMBuildThread.java
@@
-36,6
+36,7
@@
public class HMMBuildThread implements Runnable
SequenceGroup group;
List<ArgumentI> params;
SequenceGroup group;
List<ArgumentI> params;
+ boolean multiJob;
boolean forGroup = false;
boolean forGroup = false;
@@
-95,12
+96,14
@@
public class HMMBuildThread implements Runnable
{
alignment = viewport.getAlignment();
groups.addAll(viewport.getAlignment().getGroups());
{
alignment = viewport.getAlignment();
groups.addAll(viewport.getAlignment().getGroups());
+ multiJob = true;
break;
}
else if ("All groups".equals(value))
{
alignment = null;
groups = viewport.getAlignment().getGroups();
break;
}
else if ("All groups".equals(value))
{
alignment = null;
groups = viewport.getAlignment().getGroups();
+ multiJob = true;
break;
}
else if ("Selected group".equals(value))
break;
}
else if ("Selected group".equals(value))
@@
-295,7
+298,11
@@
public class HMMBuildThread implements Runnable
switch (argName)
{
case "HMM Name":
switch (argName)
{
case "HMM Name":
- name = arg.getValue();
+ if (!multiJob)
+ {
+ name = arg.getValue();
+ name = name.trim();
+ }
break;
case "Use Reference Annotation":
command += "--hand ";
break;
case "Use Reference Annotation":
command += "--hand ";
@@
-306,8
+313,6
@@
public class HMMBuildThread implements Runnable
}
}
}
}
- name = name.trim();
-
if (name == null || "".equals(name))
{
if (forGroup)
if (name == null || "".equals(name))
{
if (forGroup)
@@
-327,7
+332,8
@@
public class HMMBuildThread implements Runnable
}
}
}
}
- command += "-n " + name + cmds.SPACE;
+
+ command += "-n " + name.replace(' ', '_') + cmds.SPACE;
if (!alignment.isNucleotide())
{
command += cmds.FORCEAMINO; // TODO check for rna
if (!alignment.isNucleotide())
{
command += cmds.FORCEAMINO; // TODO check for rna