From: Daniel Barton <daluke.barton@gmail.com>
Date: Tue, 27 Aug 2013 16:37:06 +0000 (+0100)
Subject: JAL-1358 jalview displays some RNA struture annotation but the format is very messed up
X-Git-Tag: Jalview_2_9~200^2~21^2~19
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=9daf267d40a67e589a92d3d8fe14f9e535d10ee2;p=jalview.git

JAL-1358 jalview displays some RNA struture annotation but the format is very messed up
---

diff --git a/lib/min-jabaws-client-3.0.0.jar b/lib/min-jabaws-client-3.0.0.jar
new file mode 100644
index 0000000..c70a615
Binary files /dev/null and b/lib/min-jabaws-client-3.0.0.jar differ
diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index 9592142..7d06701 100644
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -157,7 +157,11 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
 			
 			
 			if (ourAnnot.size() > 0) {
+				
+				// Modify the visible annotation on the alignment viewport with the
+        // new alignment annotation rows created.
 				updateOurAnnots(ourAnnot);
+				ap.adjustAnnotationHeight();
 			}
 			
 		}
diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index d57eae4..e985f41 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -61,17 +61,20 @@ public class SequenceAnnotationWSClient extends Jws2Client
     initSequenceAnnotationWSClient(sh, alignFrame, preset, editParams);
   }
 
+  // dan think. Do I need to change this method to run RNAalifold through the GUI
+  
   public void initSequenceAnnotationWSClient(final Jws2Instance sh,
           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
   {
-    if (alignFrame.getViewport().getAlignment().isNucleotide())
-    {
-      JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
-              + " can only be used\nfor amino acid alignments.",
-              "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
-      return;
-
-    }
+	// dan changed! dan test. comment out if conditional
+//    if (alignFrame.getViewport().getAlignment().isNucleotide())
+//    {
+//      JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
+//              + " can only be used\nfor amino acid alignments.",
+//              "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
+//      return;
+//
+//    }
     if (sh.action.toLowerCase().contains("conservation"))
     {
       // Build an AACon style client - take alignment, return annotation for
@@ -131,7 +134,65 @@ public class SequenceAnnotationWSClient extends Jws2Client
               .startWorker(
                       new AADisorderClient(sh, alignFrame, preset, paramset));
     }
+    
+    
+    // dan test dan changed!
+    if (sh.action.toLowerCase().contains("rna structure prediction"))
+    {
 
+    	List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
+    			.getCalcManager()
+    			.getRegisteredWorkersOfClass(RNAalifoldClient.class);
+    	if (clnts == null || clnts.size() == 0)
+    	{
+    		if (!processParams(sh, editParams))
+    		{
+    			return;
+    		}
+    		RNAalifoldClient worker;
+    		alignFrame
+    						.getViewport()
+    						.getCalcManager()
+    						.registerWorker(
+    									worker = new RNAalifoldClient(sh, alignFrame,
+    													this.preset, paramset));
+    		alignFrame.getViewport().getCalcManager().startWorker(worker);
+    	}
+    	else 
+    	{
+    		RNAalifoldClient worker = (RNAalifoldClient) clnts.get(0);
+    		if (editParams)
+    		{
+    			paramset = worker.getArguments();
+    			preset = worker.getPreset();
+    		}
+    		
+    		if (!processParams(sh, editParams, true))
+        {
+          return;
+        }
+    		
+    		// reinstate worker if it was blacklisted (might have happened due to
+        // invalid parameters)
+        alignFrame.getViewport().getCalcManager().workerMayRun(worker);
+        worker.updateParameters(this.preset, paramset);
+    	}
+    	
+    }
+    
+//	
+//	if (!processParams(sh, editParams, true))
+//	{
+//		return;
+//	}
+//
+//	alignFrame
+//			.getViewport()
+//			.getCalcManager()
+//			.startWorker(
+//					new RNAalifoldClient(sh, alignFrame, preset, paramset));
+//	
+    
   }
 
   public SequenceAnnotationWSClient(AAConSettings fave,