JAL-674 make temperature factor, local secondary structure and service based secondar...

[jalview.git] / src / MCview / PDBChain.java

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 2dd6d37..e8f1bc9 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -267,7 +267,7 @@ public class PDBChain
     bonds.addElement(new Bond(start, end, at1, at2));
   }
 
-  public void makeResidueList()
+  public void makeResidueList(boolean visibleChainAnnotation)
   {
     int count = 0;
     Object symbol;
@@ -377,23 +377,27 @@ public class PDBChain
               .elementAt(i));
       resFeatures.setElementAt(null, i);
     }
-    Annotation[] annots = new Annotation[resAnnotation.size()];
-    float max = 0;
-    for (i = 0, iSize = annots.length; i < iSize; i++)
+    if (visibleChainAnnotation)
     {
-      annots[i] = (Annotation) resAnnotation.elementAt(i);
-      if (annots[i].value > max)
+      Annotation[] annots = new Annotation[resAnnotation.size()];
+      float max = 0;
+      for (i = 0, iSize = annots.length; i < iSize; i++)
       {
-        max = annots[i].value;
+        annots[i] = (Annotation) resAnnotation.elementAt(i);
+        if (annots[i].value > max)
+        {
+          max = annots[i].value;
+        }
+        resAnnotation.setElementAt(null, i);
       }
-      resAnnotation.setElementAt(null, i);
+
+      AlignmentAnnotation tfactorann = new AlignmentAnnotation(
+              "PDB.TempFactor", "Temperature Factor for "
+                      + sequence.getName(), annots, 0, max,
+              AlignmentAnnotation.LINE_GRAPH);
+      tfactorann.setSequenceRef(sequence);
+      sequence.addAlignmentAnnotation(tfactorann);
     }
-    AlignmentAnnotation tfactorann = new AlignmentAnnotation(
-            "PDB.TempFactor", "Temperature Factor for "
-                    + sequence.getName(), annots, 0, max,
-            AlignmentAnnotation.LINE_GRAPH);
-    tfactorann.setSequenceRef(sequence);
-    sequence.addAlignmentAnnotation(tfactorann);
   }
 
   public void setChargeColours()