JAL-2629 add basic parameter adjustment to hmmsearch/align

[jalview.git] / src / jalview / hmmer / HMMBuildThread.java

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index 8bdb008..eb9fc2a 100644 (file)
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -16,6 +16,7 @@ import jalview.io.FileLoader;
 import jalview.io.FileParse;
 import jalview.io.HMMFile;
 import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -33,6 +34,8 @@ public class HMMBuildThread implements Runnable
   AlignmentI alignment;
   SequenceGroup group;
 
+  List<ArgumentI> params;
+
 
   boolean forGroup = false;
 
@@ -53,7 +56,7 @@ public class HMMBuildThread implements Runnable
     forGroup = false;
   }
 
-  public HMMBuildThread(AlignFrame af)
+  public HMMBuildThread(AlignFrame af, List<ArgumentI> args)
   {
     this.af = af;
     if (af.getViewport().getSelectionGroup() != null)
@@ -63,6 +66,7 @@ public class HMMBuildThread implements Runnable
     }
     viewport = af.getViewport();
     alignment = viewport.getAlignment();
+    params = args;
 
   }
 
@@ -215,7 +219,8 @@ public class HMMBuildThread implements Runnable
       String name = null;
       if (af != null)
       {
-        name = af.getTitle();
+        // name = af.getTitle();
+        name = "replace";
       }
       if (name == null || name == "" || name == " " || name == "  ")
       {