JAL-969 - refactor colourscheme machinery from GUI code to core alignment view model

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6ce68c3..fce736f 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -2346,68 +2346,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
     }             \r
     viewport.setGlobalColourScheme(cs);\r
 \r
-    if (viewport.getColourAppliesToAllGroups())\r
-    {\r
-      Vector groups = viewport.getAlignment().getGroups();\r
-      for (int i = 0; i < groups.size(); i++)\r
-      {\r
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
-        if (cs == null)\r
-        {\r
-          sg.cs = null;\r
-          continue;\r
-        }\r
-        if (cs instanceof ClustalxColourScheme)\r
-        {\r
-          sg.cs = new ClustalxColourScheme(\r
-                  sg.getSequences(viewport.getHiddenRepSequences()),\r
-                  sg.getWidth());\r
-        }\r
-        else\r
-        {\r
-          try\r
-          {\r
-            sg.cs = cs.getClass().newInstance();\r
-          } catch (Exception ex)\r
-          {\r
-            ex.printStackTrace();\r
-            sg.cs = cs;\r
-          }\r
-        }\r
-\r
-        if (viewport.getAbovePIDThreshold()\r
-                || cs instanceof PIDColourScheme\r
-                || cs instanceof Blosum62ColourScheme)\r
-        {\r
-          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-          sg.cs.setConsensus(AAFrequency.calculate(\r
-                  sg.getSequences(viewport.getHiddenRepSequences()), 0,\r
-                  sg.getWidth()));\r
-        }\r
-        else\r
-        {\r
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
-        }\r
-\r
-        if (viewport.getConservationSelected())\r
-        {\r
-          Conservation c = new Conservation("Group",\r
-                  ResidueProperties.propHash, 3,\r
-                  sg.getSequences(viewport.getHiddenRepSequences()), 0,\r
-                  viewport.getAlignment().getWidth() - 1);\r
-          c.calculate();\r
-          c.verdict(false, viewport.getConsPercGaps());\r
-          sg.cs.setConservation(c);\r
-        }\r
-        else\r
-        {\r
-          sg.cs.setConservation(null);\r
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
-        }\r
-\r
-      }\r
-    }\r
 \r
     if (alignPanel.getOverviewPanel() != null)\r
     {\r

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 9258e3a..e0a6a71 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -63,11 +63,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
 
   boolean upperCasebold = false;
 
-  boolean colourAppliesToAllGroups = true;
-
-  boolean conservationColourSelected = false;
-
-  boolean abovePIDThreshold = false;
 
   int charHeight;
 
@@ -300,26 +295,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     return sq;
   }
 
-  public boolean getConservationSelected()
-  {
-    return conservationColourSelected;
-  }
-
-  public void setConservationSelected(boolean b)
-  {
-    conservationColourSelected = b;
-  }
-
-  public boolean getAbovePIDThreshold()
-  {
-    return abovePIDThreshold;
-  }
-
-  public void setAbovePIDThreshold(boolean b)
-  {
-    abovePIDThreshold = b;
-  }
-
   public int getStartRes()
   {
     return startRes;
@@ -538,16 +513,6 @@ public class AlignViewport extends AlignmentViewport implements AlignViewportI,
     return currentTree;
   }
 
-  public void setColourAppliesToAllGroups(boolean b)
-  {
-    colourAppliesToAllGroups = b;
-  }
-
-  public boolean getColourAppliesToAllGroups()
-  {
-    return colourAppliesToAllGroups;
-  }
-
   public boolean getShowJVSuffix()
   {
     return showJVSuffix;

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 76001a5..3a0e3f5 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -718,7 +718,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     showSeqFeatures.setSelected(av.showSequenceFeatures);
     hiddenMarkers.setState(av.showHiddenMarkers);
-    applyToAllGroups.setState(av.colourAppliesToAllGroups);
+    applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
     autoCalculate.setSelected(av.autoCalculateConsensus);

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 8bb40a1..7294bae 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -93,12 +93,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   boolean showAnnotation = true;
 
-  boolean colourAppliesToAllGroups = true;
-
-  boolean conservationColourSelected = false;
-
-  boolean abovePIDThreshold = false;
-
   int charHeight;
 
   int charWidth;
@@ -111,9 +105,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
 
   boolean seqNameItalics;
 
-  int threshold;
-
-  int increment;
 
   NJTree currentTree = null;
 
@@ -437,50 +428,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
     return sq;
   }
 
-
-  /**
-   * GUI state
-   * 
-   * @return true if conservation based shading is enabled
-   */
-  public boolean getConservationSelected()
-  {
-    return conservationColourSelected;
-  }
-
-  /**
-   * GUI state
-   * 
-   * @param b
-   *          enable conservation based shading
-   */
-  public void setConservationSelected(boolean b)
-  {
-    conservationColourSelected = b;
-  }
-
-  /**
-   * GUI state
-   * 
-   * @return true if percent identity threshold is applied to shading
-   */
-  public boolean getAbovePIDThreshold()
-  {
-    return abovePIDThreshold;
-  }
-
-  /**
-   * GUI state
-   * 
-   * 
-   * @param b
-   *          indicate if percent identity threshold is applied to shading
-   */
-  public void setAbovePIDThreshold(boolean b)
-  {
-    abovePIDThreshold = b;
-  }
-
   /**
    * DOCUMENT ME!
    * 
@@ -831,48 +778,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
   /**
    * DOCUMENT ME!
    * 
-   * @param thresh
-   *          DOCUMENT ME!
-   */
-  public void setThreshold(int thresh)
-  {
-    threshold = thresh;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public int getThreshold()
-  {
-    return threshold;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param inc
-   *          DOCUMENT ME!
-   */
-  public void setIncrement(int inc)
-  {
-    increment = inc;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public int getIncrement()
-  {
-    return increment;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @return DOCUMENT ME!
    */
   public ColumnSelection getColumnSelection()
@@ -904,27 +809,6 @@ public class AlignViewport extends AlignmentViewport implements SelectionSource,
   /**
    * DOCUMENT ME!
    * 
-   * @param b
-   *          DOCUMENT ME!
-   */
-  public void setColourAppliesToAllGroups(boolean b)
-  {
-    colourAppliesToAllGroups = b;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public boolean getColourAppliesToAllGroups()
-  {
-    return colourAppliesToAllGroups;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @return DOCUMENT ME!
    */
   public boolean getShowJVSuffix()

diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java
index 1627ab7..614bfee 100644 (file)
--- a/src/jalview/gui/TextColourChooser.java
+++ b/src/jalview/gui/TextColourChooser.java
@@ -137,7 +137,7 @@ public class TextColourChooser
     if (sg == null)
     {
       ap.av.textColour = col;
-      if (ap.av.colourAppliesToAllGroups)
+      if (ap.av.getColourAppliesToAllGroups())
       {
         setGroupTextColour();
       }
@@ -155,7 +155,7 @@ public class TextColourChooser
     if (sg == null)
     {
       ap.av.textColour2 = col;
-      if (ap.av.colourAppliesToAllGroups)
+      if (ap.av.getColourAppliesToAllGroups())
       {
         setGroupTextColour();
       }
@@ -173,7 +173,7 @@ public class TextColourChooser
     if (sg == null)
     {
       ap.av.thresholdTextColour = value;
-      if (ap.av.colourAppliesToAllGroups)
+      if (ap.av.getColourAppliesToAllGroups())
       {
         setGroupTextColour();
       }