JAL-2629 add simple jackhmmer functionality

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4587368..d1ebdb7 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -69,6 +69,7 @@ import jalview.hmmer.HMMERParamStore;
 import jalview.hmmer.HMMERPreset;
 import jalview.hmmer.HMMSearch;
 import jalview.hmmer.HmmerCommand;
+import jalview.hmmer.JackHMMER;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BackupFiles;
@@ -1111,6 +1112,36 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     new Thread(new HMMSearch(this, args)).start();
     alignPanel.repaint();
   }
+  
+  @Override
+  public void jackhmmer_actionPerformed(boolean withDefaults)
+  {
+    
+    /*
+     * get default parameters, and (if requested) show 
+     * dialog to allow modification
+     */
+    
+    ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
+    List<ArgumentI> args = store.getServiceParameters();
+
+    if (!withDefaults)
+    {
+      WsParamSetI set = new HMMERPreset();
+      WsJobParameters params = new WsJobParameters(store, set, args);
+      if (params.showRunDialog())
+      {
+        args = params.getJobParams();
+      }
+      else
+      {
+        return; // user cancelled
+      }
+    }
+    new Thread(new JackHMMER(this, args)).start();
+    alignPanel.repaint();
+    
+  }
 
   /**
    * Checks if the alignment has at least one hidden Markov model, if not shows