JAL-2629 fix for hmmbuild failing due to whitespace in the name

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index faba183..dc24d9e 100644 (file)
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -296,6 +296,7 @@ public class HMMBuildThread implements Runnable
         {
         case "HMM Name":
           name = arg.getValue();
+          name = name.trim();
           break;
         case "Use Reference Annotation":
           command += "--hand ";
@@ -306,7 +307,7 @@ public class HMMBuildThread implements Runnable
       }
     }
 
-    name = name.trim();
+
 
     if (name == null || "".equals(name))
     {
@@ -327,7 +328,7 @@ 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