From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Fri, 25 Aug 2017 13:52:18 +0000 (+0100)
Subject: Revert "jal-2629 fix for hmmbuild failing due to whitespace in the name"
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=48d729681b0bf78441514aff3d084d16d86e876a;p=jalview.git

Revert "jal-2629 fix for hmmbuild failing due to whitespace in the name"

This reverts commit b0516b5aff64734bd343fe5b2178f64677c02863.
---

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index d5e938a..faba183 100644
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -36,7 +36,6 @@ public class HMMBuildThread implements Runnable
   SequenceGroup group;
   List<ArgumentI> params;
 
-  boolean multiJob;
 
   boolean forGroup = false;
 
@@ -96,14 +95,12 @@ 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))
@@ -298,11 +295,7 @@ public class HMMBuildThread implements Runnable
         switch (argName)
         {
         case "HMM Name":
-          if (!multiJob)
-          {
-            name = arg.getValue();
-            name = name.trim();
-          }
+          name = arg.getValue();
           break;
         case "Use Reference Annotation":
           command += "--hand ";
@@ -313,6 +306,8 @@ public class HMMBuildThread implements Runnable
       }
     }
 
+    name = name.trim();
+
     if (name == null || "".equals(name))
     {
       if (forGroup)
@@ -332,8 +327,7 @@ public class HMMBuildThread implements Runnable
       }
     }
 
-
-    command += "-n " + name.replace(' ', '_') + cmds.SPACE;
+    command += "-n " + name + cmds.SPACE;
     if (!alignment.isNucleotide())
     {
       command += cmds.FORCEAMINO; // TODO check for rna