From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 15 Jun 2017 09:26:40 +0000 (+0100)
Subject: Merge branch 'bug/JAL-2589gapColour' into develop
X-Git-Tag: Release_2_10_3b1~183^2~4^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a07bb83b2db533506ec098ec05cd920d4109314c;hp=12d4dfa00a5e93ae1de1d8409c6d5ca2bc8af13f;p=jalview.git

Merge branch 'bug/JAL-2589gapColour' into develop
---

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 77ec373..86610a2 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -836,12 +836,15 @@ public class APopupMenu extends java.awt.PopupMenu implements
         }
       }
 
-      if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
-              features, true, ap))
+      if (!seqs.isEmpty())
       {
-        ap.alignFrame.sequenceFeatures.setState(true);
-        ap.av.setShowSequenceFeatures(true);
-        ap.highlightSearchResults(null);
+        if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+                features, true, ap))
+        {
+          ap.alignFrame.sequenceFeatures.setState(true);
+          ap.av.setShowSequenceFeatures(true);
+          ap.highlightSearchResults(null);
+        }
       }
     }
     else
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 9a6c760..756b77b 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1944,11 +1944,17 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       }
     }
 
-    if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
-            features, true, ap))
+    /*
+     * an entirely gapped region will generate empty lists of sequence / features
+     */
+    if (!seqs.isEmpty())
     {
-      ap.alignFrame.setShowSeqFeatures(true);
-      ap.highlightSearchResults(null);
+      if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(
+              seqs, features, true, ap))
+      {
+        ap.alignFrame.setShowSeqFeatures(true);
+        ap.highlightSearchResults(null);
+      }
     }
   }
 
diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 72ac2c8..98f5bff 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -223,7 +223,11 @@ public class FeatureRenderer extends FeatureRendererModel
 
     if (Comparison.isGap(seq.getCharAt(column)))
     {
-      return Color.white;
+      /*
+       * returning null allows the colour scheme to provide gap colour
+       * - normally white, but can be customised otherwise
+       */
+      return null;
     }
 
     Color renderedColour = null;
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 03fc129..b47b82e 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -24,7 +24,6 @@ import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.Map;
@@ -91,7 +90,7 @@ public abstract class ResidueColourScheme implements ColourSchemeI
   {
     Color colour = Color.white;
 
-    if (!Comparison.isGap(c) && colors != null && symbolIndex != null
+    if (colors != null && symbolIndex != null
             && c < symbolIndex.length
             && symbolIndex[c] < colors.length)
     {
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index aa20121..e1b60ca 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -23,6 +23,7 @@ package jalview.schemes;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.Map;
@@ -35,13 +36,10 @@ import java.util.Map;
  */
 public class ScoreColourScheme extends ResidueColourScheme
 {
-  /** DOCUMENT ME!! */
   public double min;
 
-  /** DOCUMENT ME!! */
   public double max;
 
-  /** DOCUMENT ME!! */
   public double[] scores;
 
   /**
@@ -65,25 +63,38 @@ public class ScoreColourScheme extends ResidueColourScheme
 
     // Make colours in constructor
     // Why wasn't this done earlier?
-    int i, iSize = scores.length;
+    int iSize = scores.length;
     colors = new Color[scores.length];
-    for (i = 0; i < iSize; i++)
+    for (int i = 0; i < iSize; i++)
     {
-      float red = (float) (scores[i] - (float) min) / (float) (max - min);
+      /*
+       * scale score between min and max to the range 0.0 - 1.0
+       */
+      float score = (float) (scores[i] - (float) min) / (float) (max - min);
 
-      if (red > 1.0f)
+      if (score > 1.0f)
       {
-        red = 1.0f;
+        score = 1.0f;
       }
 
-      if (red < 0.0f)
+      if (score < 0.0f)
       {
-        red = 0.0f;
+        score = 0.0f;
       }
-      colors[i] = makeColour(red);
+      colors[i] = makeColour(score);
     }
   }
 
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
+  {
+    if (Comparison.isGap(c))
+    {
+      return Color.white;
+    }
+    return super.findColour(c);
+  }
+
   /**
    * DOCUMENT ME!
    * 
diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index 59566ed..9b68b43 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.assertNull;
 import static org.testng.Assert.assertTrue;
 
 import jalview.api.FeatureColourI;
@@ -126,6 +127,10 @@ public class FeatureColourFinderTest
     assertEquals(c, Color.red);
   }
 
+  /**
+   * feature colour at a gap is null (not white) - a user defined colour scheme
+   * can then provide a bespoke gap colour if configured to do so
+   */
   @Test(groups = "Functional")
   public void testFindFeatureColour_gapPosition()
   {
@@ -135,7 +140,7 @@ public class FeatureColourFinderTest
     fr.featuresAdded();
     av.setShowSequenceFeatures(true);
     Color c = finder.findFeatureColour(null, seq, 6);
-    assertEquals(c, Color.white);
+    assertNull(c);
   }
 
   @Test(groups = "Functional")
diff --git a/test/jalview/schemes/BuriedColourSchemeTest.java b/test/jalview/schemes/BuriedColourSchemeTest.java
new file mode 100644
index 0000000..cdb0e80
--- /dev/null
+++ b/test/jalview/schemes/BuriedColourSchemeTest.java
@@ -0,0 +1,33 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class BuriedColourSchemeTest
+{
+  /**
+   * Turn colours are based on the scores in ResidueProperties.buried A = 1.7, R
+   * = 0.1, N = 0.4, D = 0.4... min = 0.05 max = 4.6
+   * <p>
+   * scores are scaled to c 0-1 between min and max and colour is (0, 1-c, c)
+   */
+  @Test(groups = "Functional")
+  public void testFindColour()
+  {
+    ScoreColourScheme scheme = new BuriedColourScheme();
+
+    float min = 0.05f;
+    float max = 4.6f;
+    float a = (1.7f - min) / (max - min);
+    assertEquals(scheme.findColour('A', 0, null), new Color(0, 1 - a, a));
+
+    float d = (0.4f - min) / (max - min);
+    assertEquals(scheme.findColour('D', 0, null), new Color(0, 1 - d, d));
+
+    assertEquals(scheme.findColour('-', 0, null), Color.WHITE);
+  }
+
+}
diff --git a/test/jalview/schemes/HelixColourSchemeTest.java b/test/jalview/schemes/HelixColourSchemeTest.java
new file mode 100644
index 0000000..ed46419
--- /dev/null
+++ b/test/jalview/schemes/HelixColourSchemeTest.java
@@ -0,0 +1,33 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class HelixColourSchemeTest
+{
+  /**
+   * Turn colours are based on the scores in ResidueProperties.helix A = 1.42, R
+   * = 0.98, N = 0.67, D = 1.01... min = 0.57 max = 1.51
+   * <p>
+   * scores are scaled to c 0-1 between min and max and colour is (c, 1-c, c)
+   */
+  @Test(groups = "Functional")
+  public void testFindColour()
+  {
+    ScoreColourScheme scheme = new HelixColourScheme();
+
+    float min = 0.57f;
+    float max = 1.51f;
+    float a = (1.42f - min) / (max - min);
+    assertEquals(scheme.findColour('A', 0, null), new Color(a, 1 - a, a));
+
+    float d = (1.01f - min) / (max - min);
+    assertEquals(scheme.findColour('D', 0, null), new Color(d, 1 - d, d));
+
+    assertEquals(scheme.findColour('-', 0, null), Color.WHITE);
+  }
+
+}
diff --git a/test/jalview/schemes/HydrophobicColourSchemeTest.java b/test/jalview/schemes/HydrophobicColourSchemeTest.java
new file mode 100644
index 0000000..f3b93a9
--- /dev/null
+++ b/test/jalview/schemes/HydrophobicColourSchemeTest.java
@@ -0,0 +1,35 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class HydrophobicColourSchemeTest
+{
+  /**
+   * Turn colours are based on the scores in ResidueProperties.hyd A = 1.8, R =
+   * -4.5, N = -3.5, D = -3.5... min = -3.9 max = 4.5
+   * <p>
+   * scores are scaled to c 0-1 between min and max and colour is (c, 0, 1-c)
+   */
+  @Test(groups = "Functional")
+  public void testFindColour()
+  {
+    ScoreColourScheme scheme = new HydrophobicColourScheme();
+
+    float min = -3.9f;
+    float max = 4.5f;
+    float a = (1.8f - min) / (max - min);
+    assertEquals(scheme.findColour('A', 0, null),
+ new Color(a, 0, 1 - a));
+
+    float d = (-3.5f - min) / (max - min);
+    assertEquals(scheme.findColour('D', 0, null),
+ new Color(d, 0, 1 - d));
+
+    assertEquals(scheme.findColour('-', 0, null), Color.WHITE);
+  }
+
+}
diff --git a/test/jalview/schemes/StrandColourSchemeTest.java b/test/jalview/schemes/StrandColourSchemeTest.java
new file mode 100644
index 0000000..4a8d0e9
--- /dev/null
+++ b/test/jalview/schemes/StrandColourSchemeTest.java
@@ -0,0 +1,35 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class StrandColourSchemeTest
+{
+  /**
+   * Turn colours are based on the scores in ResidueProperties.strand A = 0.83,
+   * R = 0.93, N = 0.89, D = 0.54... min = 0.37 max = 1.7
+   * <p>
+   * scores are scaled to c 0-1 between min and max and colour is (c, c, 1-c)
+   */
+  @Test(groups = "Functional")
+  public void testFindColour()
+  {
+    ScoreColourScheme scheme = new StrandColourScheme();
+
+    float min = 0.37f;
+    float max = 1.7f;
+    float a = (0.83f - min) / (max - min);
+    assertEquals(scheme.findColour('A', 0, null),
+ new Color(a, a, 1 - a));
+
+    float d = (0.54f - min) / (max - min);
+    assertEquals(scheme.findColour('D', 0, null),
+ new Color(d, d, 1 - d));
+
+    assertEquals(scheme.findColour('-', 0, null), Color.WHITE);
+  }
+
+}
diff --git a/test/jalview/schemes/TurnColourSchemeTest.java b/test/jalview/schemes/TurnColourSchemeTest.java
new file mode 100644
index 0000000..5e6baf0
--- /dev/null
+++ b/test/jalview/schemes/TurnColourSchemeTest.java
@@ -0,0 +1,35 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+
+public class TurnColourSchemeTest
+{
+  /**
+   * Turn colours are based on the scores in ResidueProperties.turn A = 0.66, R
+   * = 0.95, N = 1.56, D = 1.46... min = 0.47 max = 1.56
+   * <p>
+   * scores are scaled to c 0-1 between min and max and colour is (c, 1-c, 1-c)
+   */
+  @Test(groups = "Functional")
+  public void testFindColour()
+  {
+    ScoreColourScheme scheme = new TurnColourScheme();
+
+    float min = 0.47f;
+    float max = 1.56f;
+    float a = (0.66f - min) / (max - min);
+    assertEquals(scheme.findColour('A', 0, null),
+            new Color(a, 1 - a, 1 - a));
+
+    float d = (1.46f - min) / (max - min);
+    assertEquals(scheme.findColour('D', 0, null),
+            new Color(d, 1 - d, 1 - d));
+
+    assertEquals(scheme.findColour('-', 0, null), Color.WHITE);
+  }
+
+}
diff --git a/test/jalview/schemes/UserColourSchemeTest.java b/test/jalview/schemes/UserColourSchemeTest.java
index 497014e..2a482ee 100644
--- a/test/jalview/schemes/UserColourSchemeTest.java
+++ b/test/jalview/schemes/UserColourSchemeTest.java
@@ -54,6 +54,10 @@ public class UserColourSchemeTest
     assertEquals(c1, cs.findColour('h'));
     Color c2 = new Color(10, 20, 30);
     assertEquals(c2, cs.findColour('c'));
+    assertEquals(Color.WHITE, cs.findColour('G'));
+    assertEquals(Color.WHITE, cs.findColour('-'));
+    assertEquals(Color.WHITE, cs.findColour('.'));
+    assertEquals(Color.WHITE, cs.findColour(' '));
 
     cs = new UserColourScheme("white");
     cs.parseAppletParameter("D,E=red; K,R,H=0022FF; c=10 , 20,30;t=orange;lowercase=blue;s=pink");
@@ -80,4 +84,29 @@ public class UserColourSchemeTest
     String param = cs.toAppletParameter();
     assertEquals("D,E=ff0000;H,K,R=0022ff;c=0a141e", param);
   }
+
+  /**
+   * Test for user colour scheme constructed with a colour per residue,
+   * including gap. Note this can currently be done from the User Defined
+   * Colours dialog, but not by parsing a colours parameter, as
+   * parseAppletParameter only recognises amino acid codes.
+   */
+  @Test(groups = "Functional")
+  public void testConstructor_coloursArray()
+  {
+    Color g = Color.green;
+    Color y = Color.yellow;
+    Color b = Color.blue;
+    Color r = Color.red;
+    // colours for ARNDCQEGHILKMFPSTWYVBZ and gap
+    Color[] colours = new Color[] { g, y, b, r, g, y, r, b, g, y, r, b, g,
+        y, r, b, g, y, r, b, g, y, r, g };
+    UserColourScheme cs = new UserColourScheme(colours);
+
+    assertEquals(g, cs.findColour('A'));
+    assertEquals(b, cs.findColour('n'));
+    assertEquals(g, cs.findColour('-'));
+    assertEquals(g, cs.findColour('.'));
+    assertEquals(g, cs.findColour(' '));
+  }
 }