From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 18 Oct 2017 13:22:57 +0000 (+0100)
Subject: Merge branch 'bugs/JAL-2777_whitespaceChain' into develop
X-Git-Tag: Release_2_10_3b1~107
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3f8731339024094fe6d68e8b96d2646805a19d34;hp=c4a72d18f6a7b2cf3de4a46b7a35cbfd0d76438f;p=jalview.git

Merge branch 'bugs/JAL-2777_whitespaceChain' into develop
---

diff --git a/src/jalview/ext/rbvi/chimera/AtomSpecModel.java b/src/jalview/ext/rbvi/chimera/AtomSpecModel.java
index f923f7f..39d6704 100644
--- a/src/jalview/ext/rbvi/chimera/AtomSpecModel.java
+++ b/src/jalview/ext/rbvi/chimera/AtomSpecModel.java
@@ -120,7 +120,7 @@ public class AtomSpecModel
 
       for (String chain : modelData.keySet())
       {
-        chain = chain.trim();
+        chain = " ".equals(chain) ? chain : chain.trim();
 
         List<int[]> rangeList = modelData.get(chain);
 
@@ -192,9 +192,10 @@ public class AtomSpecModel
     {
       sb.append(start).append("-").append(end);
     }
-    if (chain.length() > 0)
-    {
-      sb.append(".").append(chain);
+
+    sb.append(".");
+    if (!" ".equals(chain)) {
+      sb.append(chain);
     }
   }
 }
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index c5454ab..b768339 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -131,6 +131,11 @@ public class FeatureSettings extends JPanel
   private static final int MIN_WIDTH = 400;
 
   private static final int MIN_HEIGHT = 400;
+  
+  /**
+   * when true, constructor is still executing - so ignore UI events
+   */
+  protected volatile boolean inConstruction = true;
 
   /**
    * Constructor
@@ -303,6 +308,7 @@ public class FeatureSettings extends JPanel
               };
             });
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    inConstruction = false;
   }
 
   protected void popupSort(final int selectedRow, final String type,
@@ -1237,8 +1243,11 @@ public class FeatureSettings extends JPanel
       @Override
       public void stateChanged(ChangeEvent evt)
       {
-        fr.setTransparency((100 - transparency.getValue()) / 100f);
-        af.alignPanel.paintAlignment(true, true);
+        if (!inConstruction)
+        {
+          fr.setTransparency((100 - transparency.getValue()) / 100f);
+          af.alignPanel.paintAlignment(true,true);
+        }
       }
     });
 
diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index f16522f..1f47da3 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -216,7 +216,8 @@ public class FeatureRenderer extends FeatureRendererModel
       return null;
     }
 
-    if (Comparison.isGap(seq.getCharAt(column)))
+    // column is 'base 1' but getCharAt is an array index (ie from 0)
+    if (Comparison.isGap(seq.getCharAt(column - 1)))
     {
       /*
        * returning null allows the colour scheme to provide gap colour
diff --git a/test/jalview/ext/rbvi/chimera/AtomSpecModelTest.java b/test/jalview/ext/rbvi/chimera/AtomSpecModelTest.java
index c9e1cad..63d5e4e 100644
--- a/test/jalview/ext/rbvi/chimera/AtomSpecModelTest.java
+++ b/test/jalview/ext/rbvi/chimera/AtomSpecModelTest.java
@@ -29,6 +29,11 @@ public class AtomSpecModelTest
     assertEquals(model.getAtomSpec(), "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
     model.addRange(0, 3, 10, "C"); // subsumes 5-9
     assertEquals(model.getAtomSpec(), "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
+    model.addRange(5, 25, 35, " "); // empty chain code - e.g. from homology
+                                    // modelling
+    assertEquals(model.getAtomSpec(),
+            "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
+
   }
 
 }
diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index 7fd7abc..f6dfed6 100644
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -2,6 +2,7 @@ package jalview.renderer.seqfeatures;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotEquals;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
@@ -285,6 +286,28 @@ public class FeatureColourFinderTest
   }
 
   @Test(groups = "Functional")
+  public void testFindFeatureAtEnd()
+  {
+    /*
+     * terminal residue feature
+     */
+    seq.addSequenceFeature(new SequenceFeature("PDBRESNUM", "pdb res 1",
+            seq.getEnd(), seq.getEnd(), Float.NaN, "1seq.pdb"));
+    fr.setColour("PDBRESNUM", new FeatureColour(Color.red));
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+
+    /*
+     * final column should have PDBRESNUM feature, the others not
+     */
+    Color c = finder.findFeatureColour(Color.blue, seq,
+            seq.getLength() - 2);
+    assertNotEquals(c, Color.red);
+    c = finder.findFeatureColour(Color.blue, seq, seq.getLength() - 1);
+    assertEquals(c, Color.red);
+  }
+
+  @Test(groups = "Functional")
   public void testFindFeatureColour_graduatedFeatureColour()
   {
     seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2,