Merge branch 'feature/2588' into merge/develop_feature/2588_JAL-2588

[jalview.git] / src / jalview / gui / SequenceRenderer.java

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 4498f88..5be7f55 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -23,9 +23,8 @@ package jalview.gui;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.renderer.ResidueShaderI;
+import jalview.renderer.ResidueColourFinder;
 import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
@@ -41,17 +40,15 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
   boolean renderGaps = true;
 
-  SequenceGroup currentSequenceGroup = null;
-
   SequenceGroup[] allGroups = null;
 
-  Color resBoxColour;
+  // Color resBoxColour;
 
   Graphics graphics;
 
   boolean monospacedFont;
 
-  boolean forOverview = false;
+  ResidueColourFinder resColourFinder;
 
   /**
    * Creates a new SequenceRenderer object
@@ -61,6 +58,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   public SequenceRenderer(AlignViewportI viewport)
   {
     this.av = viewport;
+    resColourFinder = new ResidueColourFinder();
   }
 
   /**
@@ -83,26 +81,6 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     this.renderGaps = renderGaps;
   }
 
-  protected Color getResidueBoxColour(SequenceI seq, int i)
-  {
-    // rate limiting step when rendering overview for lots of groups
-    allGroups = av.getAlignment().findAllGroups(seq);
-
-    if (inCurrentSequenceGroup(i))
-    {
-      if (currentSequenceGroup.getDisplayBoxes())
-      {
-        getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
-      }
-    }
-    else if (av.getShowBoxes())
-    {
-      getBoxColour(av.getResidueShading(), seq, i);
-    }
-
-    return resBoxColour;
-  }
-
   /**
    * Get the residue colour at the given sequence position - as determined by
    * the sequence group colour (if any), else the colour scheme, possibly
@@ -117,39 +95,10 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   public Color getResidueColour(final SequenceI seq, int position,
           FeatureColourFinder finder)
   {
-    Color col = getResidueBoxColour(seq, position);
-
-    if (finder != null)
-    {
-      col = finder.findFeatureColour(col, seq, position);
-    }
-    return col;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param shader
-   *          DOCUMENT ME!
-   * @param seq
-   *          DOCUMENT ME!
-   * @param i
-   *          DOCUMENT ME!
-   */
-  void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
-  {
-    if (shader.getColourScheme() != null)
-    {
-      resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
-    }
-    else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
-    {
-      resBoxColour = Color.lightGray;
-    }
-    else
-    {
-      resBoxColour = Color.white;
-    }
+    return resColourFinder.getResidueColour(av.getShowBoxes(),
+            av.getResidueShading(),
+            allGroups, seq, position,
+            finder);
   }
 
   /**
@@ -208,6 +157,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   public synchronized void drawBoxes(SequenceI seq, int start, int end,
           int y1)
   {
+    Color resBoxColour = Color.white;
+
     if (seq == null)
     {
       return; // fix for racecondition
@@ -227,17 +178,22 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
       if (i < length)
       {
-        if (inCurrentSequenceGroup(i))
+        SequenceGroup currentSequenceGroup = resColourFinder
+                .getCurrentSequenceGroup(
+                allGroups, i);
+        if (currentSequenceGroup != null)
         {
           if (currentSequenceGroup.getDisplayBoxes())
           {
-            getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+            resBoxColour = resColourFinder.getBoxColour(
+                    currentSequenceGroup.getGroupColourScheme(), seq,
                     i);
           }
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.getResidueShading(), seq, i);
+          resBoxColour = resColourFinder
+                  .getBoxColour(av.getResidueShading(), seq, i);
         }
       }
 
@@ -317,10 +273,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       boolean srep = av.isDisplayReferenceSeq();
       boolean getboxColour = false;
       boolean isarep = av.getAlignment().getSeqrep() == seq;
-      boolean isgrep = currentSequenceGroup != null
-              ? currentSequenceGroup.getSeqrep() == seq
-              : false;
-      char sr_c;
+      Color resBoxColour = Color.white;
+
       for (int i = start; i <= end; i++)
       {
 
@@ -333,7 +287,10 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           continue;
         }
 
-        if (inCurrentSequenceGroup(i))
+        SequenceGroup currentSequenceGroup = resColourFinder
+                .getCurrentSequenceGroup(
+                allGroups, i);
+        if (currentSequenceGroup != null)
         {
           if (!currentSequenceGroup.getDisplayText())
           {
@@ -344,7 +301,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
                   || currentSequenceGroup.getColourText())
           {
             getboxColour = true;
-            getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+            resBoxColour = resColourFinder.getBoxColour(
+                    currentSequenceGroup.getGroupColourScheme(), seq,
                     i);
 
             if (currentSequenceGroup.getColourText())
@@ -366,6 +324,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           {
             graphics.setColor(currentSequenceGroup.textColour);
           }
+          boolean isgrep = currentSequenceGroup != null
+                  ? currentSequenceGroup.getSeqrep() == seq : false;
           if (!isarep && !isgrep
                   && currentSequenceGroup.getShowNonconserved()) // todo
                                                                  // optimize
@@ -386,7 +346,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (av.getColourText())
           {
             getboxColour = true;
-            getBoxColour(av.getResidueShading(), seq, i);
+            resBoxColour = resColourFinder
+                    .getBoxColour(av.getResidueShading(), seq, i);
 
             if (av.getShowBoxes())
             {
@@ -402,7 +363,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           {
             if (!getboxColour)
             {
-              getBoxColour(av.getResidueShading(), seq, i);
+              resBoxColour = resColourFinder
+                      .getBoxColour(av.getResidueShading(), seq, i);
             }
 
             if (resBoxColour.getRed() + resBoxColour.getBlue()
@@ -473,35 +435,6 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   /**
    * DOCUMENT ME!
    * 
-   * @param res
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  boolean inCurrentSequenceGroup(int res)
-  {
-    if (allGroups == null)
-    {
-      return false;
-    }
-
-    for (int i = 0; i < allGroups.length; i++)
-    {
-      if ((allGroups[i].getStartRes() <= res)
-              && (allGroups[i].getEndRes() >= res))
-      {
-        currentSequenceGroup = allGroups[i];
-
-        return true;
-      }
-    }
-
-    return false;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param seq
    *          DOCUMENT ME!
    * @param start