From cafaf4610c39cac8347bde424e6d9984c3959a51 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 23 Jun 2013 19:02:20 +0100
Subject: [PATCH] JAL-1230 simplify initialisation of consensus, conservation
 and structure consensus rows

---
 src/jalview/viewmodel/AlignmentViewport.java |  111 +++++++++++++++-----------
 1 file changed, 65 insertions(+), 46 deletions(-)

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 029280b..d65486d 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -402,7 +402,8 @@ public abstract class AlignmentViewport implements AlignViewportI
     if (autoCalculateStrucConsensus && strucConsensus == null
             && alignment.isNucleotide() && alignment.hasRNAStructure())
     {
-
+      // secondary structure has been added - so init the consensus line
+      initRNAStructure();
     }
 
     // see note in mantis : issue number 8585
@@ -1318,62 +1319,80 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       if (!alignment.isNucleotide())
       {
-        if (showConservation)
-        {
-          if (conservation == null)
-          {
-            conservation = new AlignmentAnnotation("Conservation",
-                    "Conservation of total alignment less than "
-                            + getConsPercGaps() + "% gaps",
-                    new Annotation[1], 0f, 11f,
-                    AlignmentAnnotation.BAR_GRAPH);
-            conservation.hasText = true;
-            conservation.autoCalculated = true;
-            alignment.addAnnotation(conservation);
-          }
-        }
-        if (showQuality)
-        {
-          if (quality == null)
-          {
-            quality = new AlignmentAnnotation("Quality",
-                    "Alignment Quality based on Blosum62 scores",
-                    new Annotation[1], 0f, 11f,
-                    AlignmentAnnotation.BAR_GRAPH);
-            quality.hasText = true;
-            quality.autoCalculated = true;
-            alignment.addAnnotation(quality);
-          }
-        }
+        initConservation();
+        initQuality();
       }
       else
       {
-        if (alignment.hasRNAStructure())
-        {
-          strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
-                  new Annotation[1], 0f, 100f,
-                  AlignmentAnnotation.BAR_GRAPH);
-          strucConsensus.hasText = true;
-          strucConsensus.autoCalculated = true;
-        }
+        initRNAStructure();
       }
+      initConsensus();
+    }
+  }
 
-      consensus = new AlignmentAnnotation("Consensus", "PID",
-              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      consensus.hasText = true;
-      consensus.autoCalculated = true;
+  private void initConsensus()
+  {
 
-      if (showConsensus)
+    consensus = new AlignmentAnnotation("Consensus", "PID",
+            new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+    consensus.hasText = true;
+    consensus.autoCalculated = true;
+
+    if (showConsensus)
+    {
+      alignment.addAnnotation(consensus);
+    }
+  }
+
+  private void initConservation()
+  {
+    if (showConservation)
+    {
+      if (conservation == null)
       {
-        alignment.addAnnotation(consensus);
-        if (strucConsensus != null)
-        {
-          alignment.addAnnotation(strucConsensus);
-        }
+        conservation = new AlignmentAnnotation("Conservation",
+                "Conservation of total alignment less than "
+                        + getConsPercGaps() + "% gaps",
+                new Annotation[1], 0f, 11f,
+                AlignmentAnnotation.BAR_GRAPH);
+        conservation.hasText = true;
+        conservation.autoCalculated = true;
+        alignment.addAnnotation(conservation);
+      }
+    }
+  }
+  private void initQuality()
+  {
+    if (showQuality)
+    {
+      if (quality == null)
+      {
+        quality = new AlignmentAnnotation("Quality",
+                "Alignment Quality based on Blosum62 scores",
+                new Annotation[1], 0f, 11f,
+                AlignmentAnnotation.BAR_GRAPH);
+        quality.hasText = true;
+        quality.autoCalculated = true;
+        alignment.addAnnotation(quality);
       }
     }
   }
+  private void initRNAStructure()
+  {
+    if (alignment.hasRNAStructure() && strucConsensus==null)
+    {
+      strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+              new Annotation[1], 0f, 100f,
+              AlignmentAnnotation.BAR_GRAPH);
+      strucConsensus.hasText = true;
+      strucConsensus.autoCalculated = true;
 
+      if (showConsensus)
+      {
+        alignment.addAnnotation(strucConsensus);
+      }
+    }
+  }
   /*
    * (non-Javadoc)
    * 
-- 
1.7.10.2