X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMBuildThread.java;fp=src%2Fjalview%2Fhmmer%2FHMMBuildThread.java;h=d5e938a6fd5694fc61f1ef6c72960d48fd672c8c;hb=5602a9c0504dd5849e3ce69814907f6b1a77f660;hp=faba1839c9c7dc451413b6c27c414b4c32832244;hpb=6076783c7a50cc6d318b2478b10800aedb9288c4;p=jalview.git

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index faba183..d5e938a 100644
--- 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;
 
+  boolean multiJob;
 
   boolean forGroup = false;
 
@@ -95,12 +96,14 @@ public class HMMBuildThread implements Runnable
           {
             alignment = viewport.getAlignment();
             groups.addAll(viewport.getAlignment().getGroups());
+            multiJob = true;
             break;
           }
           else if ("All groups".equals(value))
           {
             alignment = null;
             groups = viewport.getAlignment().getGroups();
+            multiJob = true;
             break;
           }
           else if ("Selected group".equals(value))
@@ -295,7 +298,11 @@ public class HMMBuildThread implements Runnable
         switch (argName)
         {
         case "HMM Name":
-          name = arg.getValue();
+          if (!multiJob)
+          {
+            name = arg.getValue();
+            name = name.trim();
+          }
           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)
@@ -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