JAL-2360 getColour() renamed to getColourScheme(), handling of "None"

corrected, tests added

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 4bd77b6..b025f64 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -208,8 +208,8 @@ public class AlignViewport extends AlignmentViewport implements
 
       if (colour != null)
       {
-        globalColourScheme = ColourSchemeProperty.getColour(alignment,
-                colour);
+        globalColourScheme = ColourSchemeProperty.getColourScheme(
+                alignment, colour);
         if (globalColourScheme != null)
         {
           globalColourScheme.setConsensus(hconsensus);

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 69e76f1..ca9f2d8 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -656,7 +656,7 @@ public class TreeCanvas extends Panel implements MouseListener,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sg,
+          cs = ColourSchemeProperty.getColourScheme(sg,
                   ColourSchemeProperty.getColourName(av
                           .getGlobalColourScheme()));
         }

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 39c0a5b..c52b562 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -511,7 +511,7 @@ public class Jalview
         {
           data.replaceAll("%20", " ");
 
-          ColourSchemeI cs = ColourSchemeProperty.getColour(af
+          ColourSchemeI cs = ColourSchemeProperty.getColourScheme(af
                   .getViewport().getAlignment(), data);
 
           if (cs == null)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 53d118b..2115617 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -292,7 +292,7 @@ public class AlignViewport extends AlignmentViewport implements
     }
     if (propertyValue != null)
     {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
+      globalColourScheme = ColourSchemeProperty.getColourScheme(alignment,
               propertyValue);
 
       if (globalColourScheme instanceof UserColourScheme)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 2629f0a..12e6d42 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -3344,7 +3344,7 @@ public class Jalview2XML
           }
           else
           {
-            cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
+            cs = ColourSchemeProperty.getColourScheme(al, jGroup.getColour());
           }
 
           if (cs != null)
@@ -4468,7 +4468,7 @@ public class Jalview2XML
       }
       else
       {
-        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
       }
 
       if (cs != null)
@@ -4749,7 +4749,7 @@ public class Jalview2XML
           {
             cs = new AnnotationColourGradient(
                     annAlignment.getAlignmentAnnotation()[i],
-                    ColourSchemeProperty.getColour(al,
+                    ColourSchemeProperty.getColourScheme(al,
                             viewAnnColour.getColourScheme()),
                     viewAnnColour.getAboveThreshold());
           }

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 52f61b1..aefc233 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -333,7 +333,7 @@ public class Jalview2XML_V1
           }
           else
           {
-            cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
+            cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour());
           }
 
           if (cs != null)
@@ -401,7 +401,7 @@ public class Jalview2XML_V1
       }
       else
       {
-        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
       }
 
       if (cs != null)

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 7acae98..8ad5699 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -997,7 +997,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sg,
+          cs = ColourSchemeProperty.getColourScheme(sg,
                   ColourSchemeProperty.getColourName(av
                           .getGlobalColourScheme()));
         }

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 1097617..f80adef 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1624,7 +1624,7 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("colour"))
         {
-          sg.cs = ColourSchemeProperty.getColour(al, value);
+          sg.cs = ColourSchemeProperty.getColourScheme(al, value);
         }
         else if (key.equalsIgnoreCase("pidThreshold"))
         {

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 9b91066..425b3a1 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -42,7 +42,7 @@ public class ColourSchemeProperty
 
   /**
    * Returns a colour scheme for the given name, with which the given data may
-   * be coloured. The name may be one of
+   * be coloured. The name is not case-sensitive, and may be one of
    * <ul>
    * <li>Clustal</li>
    * <li>Blosum62</li>
@@ -59,24 +59,27 @@ public class ColourSchemeProperty
    * <li>T-Coffee Scores</li>
    * <li>RNA Helices</li>
    * <li>User Defined</li>
-   * <li>None</li>
    * <li>an AWT colour name e.g. red</li>
    * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
    * </ul>
    * If none of these formats is matched, the string is converted to a colour
-   * using a hashing algorithm.
+   * using a hashing algorithm. For name "None", returns null.
    * 
    * @param forData
    * @param name
    * @return
    */
-  public static ColourSchemeI getColour(AnnotatedCollectionI forData,
+  public static ColourSchemeI getColourScheme(AnnotatedCollectionI forData,
           String name)
   {
+    if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
+    {
+      return null;
+
+    }
     JalviewColourScheme scheme = JalviewColourScheme.forName(name);
     if (scheme != null)
     {
-      // note JalviewColourScheme.None returns null here
       return scheme.getColourScheme(forData);
     }
 

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 434619e..af477f7 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -119,7 +119,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertSame("Didn't set T-coffee colourscheme", af.getViewport()
             .getGlobalColourScheme().getClass(), TCoffeeColourScheme.class);
     assertNotNull("Recognise T-Coffee score from string",
-            ColourSchemeProperty.getColour(af.getViewport()
+            ColourSchemeProperty.getColourScheme(af.getViewport()
                     .getAlignment(), af.getViewport()
                     .getGlobalColourScheme().getSchemeName()));
 

diff --git a/test/jalview/schemes/ColourSchemePropertyTest.java b/test/jalview/schemes/ColourSchemePropertyTest.java
index efea164..6fd830a 100644 (file)
--- a/test/jalview/schemes/ColourSchemePropertyTest.java
+++ b/test/jalview/schemes/ColourSchemePropertyTest.java
@@ -1,6 +1,8 @@
 package jalview.schemes;
 
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
 
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -65,4 +67,37 @@ public class ColourSchemePropertyTest
 
     assertEquals(ColourSchemeProperty.getColourName(null), "None");
   }
+
+  @Test
+  public void testGetColourScheme()
+  {
+    SequenceI seq = new Sequence("Seq1", "abcd");
+    AlignmentI al = new Alignment(new SequenceI[] { seq });
+    // the strings here correspond to JalviewColourScheme.toString() values
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "Clustal") instanceof ClustalxColourScheme);
+    // not case-sensitive
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "CLUSTAL") instanceof ClustalxColourScheme);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "clustal") instanceof ClustalxColourScheme);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "Blosum62") instanceof Blosum62ColourScheme);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "% Identity") instanceof PIDColourScheme);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "Zappo") instanceof ZappoColourScheme);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "Taylor") instanceof TaylorColourScheme);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "Hydrophobic") instanceof HydrophobicColourScheme);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "Helix Propensity") instanceof HelixColourScheme);
+    assertTrue(ColourSchemeProperty
+            .getColourScheme(al, "Strand Propensity") instanceof StrandColourScheme);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "Turn Propensity") instanceof TurnColourScheme);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "Buried Index") instanceof BuriedColourScheme);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "Nucleotide") instanceof NucleotideColourScheme);
+    assertTrue(ColourSchemeProperty
+            .getColourScheme(al, "Purine/Pyrimidine") instanceof PurinePyrimidineColourScheme);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "T-Coffee Scores") instanceof TCoffeeColourScheme);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "RNA Helices") instanceof RNAHelicesColour);
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "User Defined") instanceof UserColourScheme);
+    // 'None' is a special value
+    assertNull(ColourSchemeProperty.getColourScheme(al, "None"));
+    assertNull(ColourSchemeProperty.getColourScheme(al, "none"));
+    // default is to convert the name into a fixed coloour
+    assertTrue(ColourSchemeProperty.getColourScheme(al, "elephants") instanceof UserColourScheme);
+  }
 }