From: Daniel Barton <daluke.barton@gmail.com>
Date: Fri, 30 Aug 2013 16:11:12 +0000 (+0100)
Subject: Colour be RNA helices bug fixed
X-Git-Tag: Jalview_2_9~200^2~21^2~16
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=2efd78f2ea2ca9cb61b259fbb22d6d125db7fd4c

Colour be RNA helices bug fixed
---

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 168aa31..a2ffff5 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -66,7 +66,8 @@ public class RNAHelicesColour extends ResidueColourScheme
 
   public void refresh()
   {
-    if (lastrefresh != annotation._rnasecstr.hashCode()
+    if ((annotation._rnasecstr == null
+    		|| lastrefresh != annotation._rnasecstr.hashCode())
             && annotation.isValidStruc())
     {
       annotation.getRNAStruc();
diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index 25b65b3..cef7eb6 100644
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -97,8 +97,24 @@ public class RNAHelicesColourChooser
       return;
     }
 
-    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
-
+    // This loop will find the first rna structure annotation by which to colour
+    //  the sequences.
+    AlignmentAnnotation[] annotations = av.getAlignment().getAlignmentAnnotation();
+    for (int i = 0; i < annotations.length; i++) {
+    	
+    	// is this a sensible way of determining type of annotation?
+    	if (annotations[i].getRNAStruc() != null) { 
+    		currentAnnotation = annotations[i];
+    		break;
+    	}
+    }
+    if (currentAnnotation == null)   
+    {
+    	System.err.println("Jalview is about to try and colour by RNAHelices even"
+    			+ " though there are no RNA secondary structure annotations present!");
+    	currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
+    }
+    
     RNAHelicesColour rhc = null;
 
     rhc = new RNAHelicesColour(currentAnnotation);
diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index 6f4dc48..7cd4230 100644
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -4,16 +4,14 @@ import jalview.api.AlignCalcWorkerI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.gui.AlignFrame;
+import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 
 import java.text.MessageFormat;
 import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
 import java.util.LinkedHashMap;
+import java.util.List;
 import java.util.TreeSet;
 import java.util.regex.Pattern;
 
@@ -47,8 +45,17 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
 		
 		nucleotidesAllowed = true;
 		proteinAllowed = false;
-		
-	}
+		initViewportParams();
+  }
+
+  protected void initViewportParams()
+  {
+    ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
+            getCalcId(),
+            new AAConSettings(true, service, this.preset,
+                    (arguments != null) ? JabaParamStore
+                            .getJwsArgsfromJaba(arguments) : null), true);
+  }
 	
 	@Override
 	public String getServiceActionText()
@@ -71,8 +78,6 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
 			List<String> structs = ((RNAStructScoreManager) scoremanager).getStructs();
 			List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager).getData();
 			
-			System.out.println("Length of RNAStructScoreManager is: " + structs.size());
-			
 			// test to see if this data object contains base pair contacts 
 			Score fscore = data.get(0).first();
 		  this.bpScores = (fscore.getMethod().equals(
@@ -153,7 +158,8 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
 		annotation.belowAlignment = false;
 //		annotation.showAllColLabels = true;
 		
-		annotation.validateRangeAndDisplay();
+		alignViewport.getAlignment().validateAnnotation(annotation);
+		af.setMenusForViewport();
 		
 		ourAnnot.add(annotation);
 	}
@@ -220,6 +226,8 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
 		String typename = "";
 		String datatype = score.getMethod();
 		
+		
+		// Look up java switch syntax and use one here
 		if (datatype.equals(AlifoldResult.mfeStructure.toString())) {
 			
 			description = MessageFormat.format("Minimum Free Energy Structure. Energy: {0} = {1} + {2}", 
@@ -279,7 +287,7 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
 	}
 	
 	private char isSS (char chr) {
-		String regex = "\\(|\\)|\\{|\\}|\\[|\\]";
+		String regex = "\\(|\\)|\\{|\\}|\\[|\\]"; 
 		char ss = (Pattern.matches(regex, Character.toString(chr))) ? 'S': ' ';
 		return ss;
 	}