JAL-2371 CollectionColourScheme renamed ResidueShader and moved to

jalview.renderer

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index ee03852..9fcf89a 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -31,7 +31,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
 
 import java.awt.Color;
@@ -80,7 +80,7 @@ public interface AlignViewportI extends ViewStyleI
 
   ColourSchemeI getGlobalColourScheme();
 
-  CollectionColourSchemeI getViewportColourScheme();
+  ResidueShaderI getViewportColourScheme();
 
   AlignmentI getAlignment();
 

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 018b227..4ae0ed2 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -39,11 +39,11 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
 import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.CollectionColourScheme;
-import jalview.schemes.CollectionColourSchemeI;
 import jalview.schemes.HelixColourScheme;
 import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.JalviewColourScheme;
@@ -330,7 +330,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
    * 
    * @param cs
    */
-  protected void setSelectedColour(CollectionColourSchemeI cs)
+  protected void setSelectedColour(ResidueShaderI cs)
   {
     if (cs == null || cs.getColourScheme() == null)
     {
@@ -1147,62 +1147,62 @@ public class APopupMenu extends java.awt.PopupMenu implements
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new CollectionColourScheme(new ClustalxColourScheme(sg,
+    sg.cs = new ResidueShader(new ClustalxColourScheme(sg,
             ap.av.getHiddenRepSequences()));
     refresh();
   }
 
   protected void zappoColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new ZappoColourScheme());
+    getGroup().cs = new ResidueShader(new ZappoColourScheme());
     refresh();
   }
 
   protected void taylorColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new TaylorColourScheme());
+    getGroup().cs = new ResidueShader(new TaylorColourScheme());
     refresh();
   }
 
   protected void hydrophobicityColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new HydrophobicColourScheme());
+    getGroup().cs = new ResidueShader(new HydrophobicColourScheme());
     refresh();
   }
 
   protected void helixColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new HelixColourScheme());
+    getGroup().cs = new ResidueShader(new HelixColourScheme());
     refresh();
   }
 
   protected void strandColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new StrandColourScheme());
+    getGroup().cs = new ResidueShader(new StrandColourScheme());
     refresh();
   }
 
   protected void turnColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new TurnColourScheme());
+    getGroup().cs = new ResidueShader(new TurnColourScheme());
     refresh();
   }
 
   protected void buriedColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new BuriedColourScheme());
+    getGroup().cs = new ResidueShader(new BuriedColourScheme());
     refresh();
   }
 
   public void nucleotideMenuItem_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(new NucleotideColourScheme());
+    getGroup().cs = new ResidueShader(new NucleotideColourScheme());
     refresh();
   }
 
   public void purinePyrimidineColour_actionPerformed()
   {
-    getGroup().cs = new CollectionColourScheme(
+    getGroup().cs = new ResidueShader(
             new PurinePyrimidineColourScheme());
     refresh();
   }
@@ -1245,7 +1245,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
   protected void PIDColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new CollectionColourScheme(new PIDColourScheme());
+    sg.cs = new ResidueShader(new PIDColourScheme());
     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
             .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
     refresh();
@@ -1255,7 +1255,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
   {
     SequenceGroup sg = getGroup();
 
-    sg.cs = new CollectionColourScheme(new Blosum62ColourScheme());
+    sg.cs = new ResidueShader(new Blosum62ColourScheme());
 
     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
             .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 2e76e1a..29df968 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -32,7 +32,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.CollectionColourScheme;
+import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.CommandListener;
@@ -209,7 +209,7 @@ public class AlignViewport extends AlignmentViewport implements
 
       if (colour != null)
       {
-        globalColourScheme = new CollectionColourScheme(
+        globalColourScheme = new ResidueShader(
                 ColourSchemeProperty.getColourScheme(alignment, colour));
         if (globalColourScheme != null)
         {
@@ -219,7 +219,7 @@ public class AlignViewport extends AlignmentViewport implements
 
       if (applet.getParameter("userDefinedColour") != null)
       {
-        globalColourScheme = new CollectionColourScheme(
+        globalColourScheme = new ResidueShader(
                 new UserColourScheme(
                         applet.getParameter("userDefinedColour")));
       }

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 4d9d37c..1c7c4ce 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -23,7 +23,7 @@ package jalview.appletgui;
 import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShaderI;
 
 import java.awt.Color;
 import java.awt.Font;
@@ -114,13 +114,11 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     return col;
   }
 
-  void getBoxColour(CollectionColourSchemeI collectionColourSchemeI,
-          SequenceI seq, int i)
+  void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {
-    if (collectionColourSchemeI != null)
+    if (shader != null)
     {
-      resBoxColour = collectionColourSchemeI.findColour(seq.getCharAt(i),
-              i, seq);
+      resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
     }
     else if (forOverview
             && !jalview.util.Comparison.isGap(seq.getCharAt(i)))

diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index 1beb82b..2354ba1 100644 (file)
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -21,7 +21,7 @@
 package jalview.appletgui;
 
 import jalview.datamodel.SequenceGroup;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShaderI;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -53,14 +53,14 @@ public class SliderPanel extends Panel implements ActionListener,
 
   boolean forConservation = true;
 
-  CollectionColourSchemeI cs;
+  ResidueShaderI cs;
 
   static Frame conservationSlider;
 
   static Frame PIDSlider;
 
   public static int setConservationSlider(AlignmentPanel ap,
-          CollectionColourSchemeI ccs, String source)
+          ResidueShaderI ccs, String source)
   {
     SliderPanel sp = null;
 
@@ -121,7 +121,7 @@ public class SliderPanel extends Panel implements ActionListener,
   }
 
   public static int setPIDSliderSource(AlignmentPanel ap,
-          CollectionColourSchemeI ccs, String source)
+          ResidueShaderI ccs, String source)
   {
     SliderPanel pid = null;
     if (PIDSlider == null)
@@ -204,7 +204,7 @@ public class SliderPanel extends Panel implements ActionListener,
     }
   }
   public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
-          CollectionColourSchemeI collectionColourSchemeI)
+          ResidueShaderI shader)
   {
     try
     {
@@ -214,7 +214,7 @@ public class SliderPanel extends Panel implements ActionListener,
       e.printStackTrace();
     }
     this.ap = ap;
-    this.cs = collectionColourSchemeI;
+    this.cs = shader;
     forConservation = forConserve;
     undoButton.setVisible(false);
     applyButton.setVisible(false);
@@ -249,7 +249,7 @@ public class SliderPanel extends Panel implements ActionListener,
       return;
     }
 
-    CollectionColourSchemeI toChange = cs;
+    ResidueShaderI toChange = cs;
     Iterator<SequenceGroup> allGroups = null;
 
     if (allGroupsCheck.getState())

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index aecc0c9..b794724 100644 (file)
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -22,7 +22,7 @@ package jalview.appletgui;
 
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceGroup;
-import jalview.schemes.CollectionColourScheme;
+import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.FeatureColour;
 import jalview.schemes.ResidueProperties;
@@ -506,7 +506,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = new CollectionColourScheme(ucs);
+        seqGroup.cs = new ResidueShader(ucs);
         seqGroup.getGroupColourScheme().setThreshold(0,
                 ap.av.isIgnoreGapsConsensus());
       }
@@ -592,7 +592,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = new CollectionColourScheme(ucs);
+        seqGroup.cs = new ResidueShader(ucs);
       }
       else
       {

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index c77569e..a1579c5 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -22,8 +22,8 @@ package jalview.datamodel;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
-import jalview.schemes.CollectionColourScheme;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
 
 import java.awt.Color;
@@ -71,7 +71,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * Colourscheme applied to group if any
    */
-  public CollectionColourSchemeI cs;
+  public ResidueShaderI cs;
 
   // start column (base 0)
   int startRes = 0;
@@ -118,7 +118,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   public SequenceGroup()
   {
     groupName = "JGroup:" + this.hashCode();
-    cs = new CollectionColourScheme();
+    cs = new ResidueShader();
   }
 
   /**
@@ -145,7 +145,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     this.displayBoxes = displayBoxes;
     this.displayText = displayText;
     this.colourText = colourText;
-    this.cs = new CollectionColourScheme(scheme);
+    this.cs = new ResidueShader(scheme);
     startRes = start;
     endRes = end;
     recalcConservation();
@@ -1371,12 +1371,12 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     if (cs == null)
     {
-      cs = new CollectionColourScheme();
+      cs = new ResidueShader();
     }
     cs.setColourScheme(scheme);
   }
 
-  public void setGroupColourScheme(CollectionColourSchemeI scheme)
+  public void setGroupColourScheme(ResidueShaderI scheme)
   {
     cs = scheme;
   }
@@ -1386,7 +1386,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     return cs == null ? null : cs.getColourScheme();
   }
 
-  public CollectionColourSchemeI getGroupColourScheme()
+  public ResidueShaderI getGroupColourScheme()
   {
     return cs;
   }

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 35a87d4..a201757 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -41,7 +41,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.CollectionColourScheme;
+import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
@@ -295,11 +295,11 @@ public class AlignViewport extends AlignmentViewport implements
     {
       ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
               alignment, propertyValue);
-      globalColourScheme = new CollectionColourScheme(colourScheme);
+      globalColourScheme = new ResidueShader(colourScheme);
 
       if (colourScheme instanceof UserColourScheme)
       {
-        globalColourScheme = new CollectionColourScheme(
+        globalColourScheme = new ResidueShader(
                 UserDefinedColours.loadDefaultColours());
         globalColourScheme.setThreshold(0, isIgnoreGapsConsensus());
       }

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8393693..d5ec6ac 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -39,6 +39,7 @@ import jalview.ext.varna.RnaModel;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemabinding.version2.AlcodMap;
 import jalview.schemabinding.version2.AlcodonFrame;
 import jalview.schemabinding.version2.Annotation;
@@ -73,7 +74,6 @@ import jalview.schemabinding.version2.Tree;
 import jalview.schemabinding.version2.UserColours;
 import jalview.schemabinding.version2.Viewport;
 import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.CollectionColourSchemeI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.FeatureColour;
@@ -1178,7 +1178,7 @@ public class Jalview2XML
         ColourSchemeI colourScheme = sg.getColourScheme();
         if (colourScheme != null)
         {
-          CollectionColourSchemeI groupColourScheme = sg
+          ResidueShaderI groupColourScheme = sg
                   .getGroupColourScheme();
           if (groupColourScheme.conservationApplied())
           {
@@ -1294,7 +1294,7 @@ public class Jalview2XML
                 .getGlobalColourScheme()));
       }
 
-      CollectionColourSchemeI vcs = av.getViewportColourScheme();
+      ResidueShaderI vcs = av.getViewportColourScheme();
       ColourSchemeI cs = av.getGlobalColourScheme();
 
       if (cs != null)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 47b0694..07dad72 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -35,7 +35,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.SequenceAnnotationReport;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.SelectionListener;
 import jalview.structure.SelectionSource;
@@ -1733,7 +1733,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       stretchGroup.cs.alignmentChanged(stretchGroup,
               av.getHiddenRepSequences());
 
-      CollectionColourSchemeI groupColourScheme = stretchGroup.getGroupColourScheme();
+      ResidueShaderI groupColourScheme = stretchGroup.getGroupColourScheme();
       String name = stretchGroup.getName();
       if (stretchGroup.cs.conservationApplied())
       {

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 311439a..e77536d 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -23,7 +23,7 @@ package jalview.gui;
 import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShaderI;
 import jalview.util.Comparison;
 
 import java.awt.Color;
@@ -132,19 +132,18 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   /**
    * DOCUMENT ME!
    * 
-   * @param collectionColourSchemeI
+   * @param shader
    *          DOCUMENT ME!
    * @param seq
    *          DOCUMENT ME!
    * @param i
    *          DOCUMENT ME!
    */
-  void getBoxColour(CollectionColourSchemeI collectionColourSchemeI,
-          SequenceI seq, int i)
+  void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {
-    if (collectionColourSchemeI != null)
+    if (shader != null)
     {
-      resBoxColour = collectionColourSchemeI.findColour(seq.getCharAt(i),
+      resBoxColour = shader.findColour(seq.getCharAt(i),
               i, seq);
     }
     else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 40f86b8..1793a9b 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -22,7 +22,7 @@ package jalview.gui;
 
 import jalview.datamodel.SequenceGroup;
 import jalview.jbgui.GSliderPanel;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShaderI;
 import jalview.util.MessageManager;
 
 import java.awt.event.MouseAdapter;
@@ -52,7 +52,7 @@ public class SliderPanel extends GSliderPanel
 
   boolean forConservation = true;
 
-  CollectionColourSchemeI cs;
+  ResidueShaderI cs;
 
   private static SliderPanel sliderPanel;
 
@@ -79,7 +79,7 @@ public class SliderPanel extends GSliderPanel
    *          DOCUMENT ME!
    */
   public SliderPanel(final AlignmentPanel ap, int value,
-          boolean forConserve, CollectionColourSchemeI scheme)
+          boolean forConserve, ResidueShaderI scheme)
   {
     this.ap = ap;
     this.cs = scheme;
@@ -138,7 +138,7 @@ public class SliderPanel extends GSliderPanel
    * @return DOCUMENT ME!
    */
   public static int setConservationSlider(AlignmentPanel ap,
-          CollectionColourSchemeI ccs, String source)
+          ResidueShaderI ccs, String source)
   {
     sliderPanel = null;
 
@@ -244,7 +244,7 @@ public class SliderPanel extends GSliderPanel
    * @return DOCUMENT ME!
    */
   public static int setPIDSliderSource(AlignmentPanel ap,
-          CollectionColourSchemeI ccs, String source)
+          ResidueShaderI ccs, String source)
   {
     int threshold = ccs.getThreshold();
 
@@ -339,7 +339,7 @@ public class SliderPanel extends GSliderPanel
    * @param percent
    * @param scheme
    */
-  protected void updateColourScheme(int percent, CollectionColourSchemeI scheme)
+  protected void updateColourScheme(int percent, ResidueShaderI scheme)
   {
     if (scheme == null)
     {

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 5973710..9b0d938 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -29,8 +29,6 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ProfilesI;
-import jalview.schemes.CollectionColourScheme;
-import jalview.schemes.CollectionColourSchemeI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.ResidueProperties;
@@ -74,7 +72,7 @@ public class AnnotationRenderer
   boolean av_renderHistogram = true, av_renderProfile = true,
           av_normaliseProfile = false;
 
-  CollectionColourSchemeI profcolour = null;
+  ResidueShaderI profcolour = null;
 
   private ColumnSelection columnSelection;
 
@@ -326,7 +324,7 @@ public class AnnotationRenderer
        */
       ColourSchemeI col = av.getAlignment().isNucleotide() ? new NucleotideColourScheme()
               : new ZappoColourScheme();
-      profcolour = new CollectionColourScheme(col);
+      profcolour = new ResidueShader(col);
     }
     columnSelection = av.getColumnSelection();
     hconsensus = av.getSequenceConsensusHash();

diff --git a/src/jalview/schemes/CollectionColourScheme.java b/src/jalview/renderer/ResidueShader.java
similarity index 86%
rename from src/jalview/schemes/CollectionColourScheme.java
rename to src/jalview/renderer/ResidueShader.java
index ebff6e6..c591031 100644 (file)
--- a/src/jalview/schemes/CollectionColourScheme.java
+++ b/src/jalview/renderer/ResidueShader.java
@@ -1,4 +1,4 @@
-package jalview.schemes;
+package jalview.renderer;
 
 import jalview.analysis.Conservation;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -6,6 +6,7 @@ import jalview.datamodel.ProfileI;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
 import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 
@@ -24,7 +25,7 @@ import java.util.Map;
  * @author gmcarstairs
  *
  */
-public class CollectionColourScheme implements CollectionColourSchemeI
+public class ResidueShader implements ResidueShaderI
 {
   private ColourSchemeI colourScheme;
 
@@ -40,7 +41,7 @@ public class CollectionColourScheme implements CollectionColourSchemeI
 
   private int inc;
 
-  public CollectionColourScheme(ColourSchemeI cs)
+  public ResidueShader(ColourSchemeI cs)
   {
     colourScheme = cs;
   }
@@ -48,12 +49,12 @@ public class CollectionColourScheme implements CollectionColourSchemeI
   /**
    * Default constructor
    */
-  public CollectionColourScheme()
+  public ResidueShader()
   {
   }
 
   /**
-   * @see jalview.schemes.CollectionColourSchemeI#setConsensus(jalview.datamodel.ProfilesI)
+   * @see jalview.renderer.ResidueShaderI#setConsensus(jalview.datamodel.ProfilesI)
    */
   @Override
   public void setConsensus(ProfilesI cons)
@@ -62,7 +63,7 @@ public class CollectionColourScheme implements CollectionColourSchemeI
   }
 
   /**
-   * @see jalview.schemes.CollectionColourSchemeI#conservationApplied()
+   * @see jalview.renderer.ResidueShaderI#conservationApplied()
    */
   @Override
   public boolean conservationApplied()
@@ -71,7 +72,7 @@ public class CollectionColourScheme implements CollectionColourSchemeI
   }
 
   /**
-   * @see jalview.schemes.CollectionColourSchemeI#setConservationApplied(boolean)
+   * @see jalview.renderer.ResidueShaderI#setConservationApplied(boolean)
    */
   @Override
   public void setConservationApplied(boolean conservationApplied)
@@ -80,7 +81,7 @@ public class CollectionColourScheme implements CollectionColourSchemeI
   }
 
   /**
-   * @see jalview.schemes.CollectionColourSchemeI#setConservation(jalview.analysis.Conservation)
+   * @see jalview.renderer.ResidueShaderI#setConservation(jalview.analysis.Conservation)
    */
   @Override
   public void setConservation(Conservation cons)
@@ -100,7 +101,7 @@ public class CollectionColourScheme implements CollectionColourSchemeI
   }
 
   /**
-   * @see jalview.schemes.CollectionColourSchemeI#alignmentChanged(jalview.datamodel.AnnotatedCollectionI,
+   * @see jalview.renderer.ResidueShaderI#alignmentChanged(jalview.datamodel.AnnotatedCollectionI,
    *      java.util.Map)
    */
   @Override
@@ -114,7 +115,7 @@ public class CollectionColourScheme implements CollectionColourSchemeI
   }
 
   /**
-   * @see jalview.schemes.CollectionColourSchemeI#setThreshold(int, boolean)
+   * @see jalview.renderer.ResidueShaderI#setThreshold(int, boolean)
    */
   @Override
   public void setThreshold(int consensusThreshold, boolean ignoreGaps)
@@ -124,7 +125,7 @@ public class CollectionColourScheme implements CollectionColourSchemeI
   }
 
   /**
-   * @see jalview.schemes.CollectionColourSchemeI#setConservationInc(int)
+   * @see jalview.renderer.ResidueShaderI#setConservationInc(int)
    */
   @Override
   public void setConservationInc(int i)
@@ -133,7 +134,7 @@ public class CollectionColourScheme implements CollectionColourSchemeI
   }
 
   /**
-   * @see jalview.schemes.CollectionColourSchemeI#getConservationInc()
+   * @see jalview.renderer.ResidueShaderI#getConservationInc()
    */
   @Override
   public int getConservationInc()
@@ -142,7 +143,7 @@ public class CollectionColourScheme implements CollectionColourSchemeI
   }
 
   /**
-   * @see jalview.schemes.CollectionColourSchemeI#getThreshold()
+   * @see jalview.renderer.ResidueShaderI#getThreshold()
    */
   @Override
   public int getThreshold()
@@ -151,7 +152,7 @@ public class CollectionColourScheme implements CollectionColourSchemeI
   }
 
   /**
-   * @see jalview.schemes.CollectionColourSchemeI#findColour(char, int,
+   * @see jalview.renderer.ResidueShaderI#findColour(char, int,
    *      jalview.datamodel.SequenceI)
    */
   @Override
@@ -313,7 +314,7 @@ public class CollectionColourScheme implements CollectionColourSchemeI
   }
 
   /**
-   * @see jalview.schemes.CollectionColourSchemeI#getColourScheme()
+   * @see jalview.renderer.ResidueShaderI#getColourScheme()
    */
   @Override
   public ColourSchemeI getColourScheme()
@@ -322,7 +323,7 @@ public class CollectionColourScheme implements CollectionColourSchemeI
   }
 
   /**
-   * @see jalview.schemes.CollectionColourSchemeI#setColourScheme(jalview.schemes.ColourSchemeI)
+   * @see jalview.renderer.ResidueShaderI#setColourScheme(jalview.schemes.ColourSchemeI)
    */
   @Override
   public void setColourScheme(ColourSchemeI cs)

diff --git a/src/jalview/schemes/CollectionColourSchemeI.java b/src/jalview/renderer/ResidueShaderI.java
similarity index 94%
rename from src/jalview/schemes/CollectionColourSchemeI.java
rename to src/jalview/renderer/ResidueShaderI.java
index 152b02a..a914a1a 100644 (file)
--- a/src/jalview/schemes/CollectionColourSchemeI.java
+++ b/src/jalview/renderer/ResidueShaderI.java
@@ -1,15 +1,16 @@
-package jalview.schemes;
+package jalview.renderer;
 
 import jalview.analysis.Conservation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
 
 import java.awt.Color;
 import java.util.Map;
 
-public interface CollectionColourSchemeI
+public interface ResidueShaderI
 {
 
   public abstract void setConsensus(ProfilesI cons);

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 69879b7..1352cf2 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -42,9 +42,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.CollectionColourScheme;
-import jalview.schemes.CollectionColourSchemeI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.structure.CommandListener;
@@ -599,7 +599,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected boolean ignoreGapsInConsensusCalculation = false;
 
-  protected CollectionColourSchemeI globalColourScheme;
+  protected ResidueShaderI globalColourScheme;
 
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
@@ -619,7 +619,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
      */
     if (globalColourScheme == null)
     {
-      globalColourScheme = new CollectionColourScheme();
+      globalColourScheme = new ResidueShader();
     }
     globalColourScheme.setColourScheme(cs);
 
@@ -670,7 +670,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public CollectionColourSchemeI getViewportColourScheme()
+  public ResidueShaderI getViewportColourScheme()
   {
     return globalColourScheme;
   }
@@ -1850,7 +1850,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   void resetAllColourSchemes()
   {
-    CollectionColourSchemeI cs = globalColourScheme;
+    ResidueShaderI cs = globalColourScheme;
     if (cs != null)
     {
       cs.alignmentChanged(alignment, hiddenRepSequences);

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 0278a3b..fa3fe75 100644 (file)
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -28,7 +28,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.CollectionColourSchemeI;
+import jalview.renderer.ResidueShaderI;
 
 public class ConsensusThread extends AlignCalcWorker
 {
@@ -147,7 +147,7 @@ public class ConsensusThread extends AlignCalcWorker
    */
   protected void setColourSchemeConsensus(ProfilesI hconsensus)
   {
-    CollectionColourSchemeI cs = alignViewport.getViewportColourScheme();
+    ResidueShaderI cs = alignViewport.getViewportColourScheme();
     if (cs != null)
     {
       cs.setConsensus(hconsensus);

diff --git a/test/jalview/schemes/CollectionColourSchemeTest.java b/test/jalview/renderer/ResidueShaderTest.java
similarity index 94%
rename from test/jalview/schemes/CollectionColourSchemeTest.java
rename to test/jalview/renderer/ResidueShaderTest.java
index 9dffdb4..76fd9b4 100644 (file)
--- a/test/jalview/schemes/CollectionColourSchemeTest.java
+++ b/test/jalview/renderer/ResidueShaderTest.java
@@ -1,4 +1,4 @@
-package jalview.schemes;
+package jalview.renderer;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
@@ -10,13 +10,14 @@ import jalview.datamodel.ProfileI;
 import jalview.datamodel.Profiles;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.PIDColourScheme;
 
 import java.awt.Color;
 import java.util.Collections;
 
 import org.testng.annotations.Test;
 
-public class CollectionColourSchemeTest
+public class ResidueShaderTest
 {
 
   @Test(groups = "Functional")
@@ -34,10 +35,9 @@ public class CollectionColourSchemeTest
     profiles[1] = new Profile(4, 0, 4, "R");
     profiles[2] = new Profile(4, 4, 0, "");
     profiles[3] = new Profile(4, 1, 2, "T");
-    CollectionColourScheme ccs = new CollectionColourScheme(
-            new PIDColourScheme());
+    ResidueShader ccs = new ResidueShader(new PIDColourScheme());
     ccs.setConsensus(new Profiles(profiles));
-    
+
     /*
      * no threshold
      */
@@ -49,7 +49,7 @@ public class CollectionColourSchemeTest
     assertTrue(ccs.aboveThreshold('W', 2));
     assertTrue(ccs.aboveThreshold('t', 3));
     assertTrue(ccs.aboveThreshold('Q', 3));
-  
+
     /*
      * with threshold, include gaps
      */
@@ -59,7 +59,7 @@ public class CollectionColourSchemeTest
     assertTrue(ccs.aboveThreshold('R', 1));
     assertFalse(ccs.aboveThreshold('W', 2));
     assertFalse(ccs.aboveThreshold('t', 3)); // 50% < 60%
-  
+
     /*
      * with threshold, ignore gaps
      */
@@ -78,12 +78,11 @@ public class CollectionColourSchemeTest
   @Test(groups = "Functional")
   public void testApplyConservation()
   {
-    CollectionColourScheme ccs = new CollectionColourScheme(
-            new PIDColourScheme());
-  
+    ResidueShader ccs = new ResidueShader(new PIDColourScheme());
+
     // no conservation present - no fading
     assertEquals(Color.RED, ccs.applyConservation(Color.RED, 12));
-    
+
     /*
      * stub Conservation to return a given consensus string
      */
@@ -92,16 +91,17 @@ public class CollectionColourSchemeTest
             Collections.<SequenceI> emptyList(), 0, 0)
     {
       @Override
-      public SequenceI getConsSequence() {
+      public SequenceI getConsSequence()
+      {
         return new Sequence("seq", consSequence);
       }
     };
     ccs.setConservation(cons);
-  
+
     // column out of range:
     assertEquals(Color.RED,
             ccs.applyConservation(Color.RED, consSequence.length()));
-  
+
     /*
      * with 100% threshold, 'fade factor' is 
      * (11-score)/10 * 100/20 = (11-score)/2
@@ -121,7 +121,7 @@ public class CollectionColourSchemeTest
     assertEquals(Color.RED, ccs.applyConservation(Color.RED, 10));
     assertEquals(Color.RED, ccs.applyConservation(Color.RED, 11));
     assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 12));
-  
+
     /*
      * with 0% threshold, there should be no fading
      */
@@ -139,7 +139,7 @@ public class CollectionColourSchemeTest
     assertEquals(Color.RED, ccs.applyConservation(Color.RED, 10));
     assertEquals(Color.RED, ccs.applyConservation(Color.RED, 11));
     assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 12)); // gap
-  
+
     /*
      * with 40% threshold, 'fade factor' is 
      * (11-score)/10 * 40/20 = (11-score)/5