JAL-2588 (and JAL-2610, JAL-2603) mid refactor

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

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 764ef3f..9874fd2 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -20,11 +20,11 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShaderI;
 import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
@@ -34,14 +34,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
   final static int CHAR_TO_UPPER = 'A' - 'a';
 
-  AlignViewport av;
+  AlignViewportI av;
 
   FontMetrics fm;
 
   boolean renderGaps = true;
 
-  SequenceGroup currentSequenceGroup = null;
-
   SequenceGroup[] allGroups = null;
 
   Color resBoxColour;
@@ -50,17 +48,14 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
   boolean monospacedFont;
 
-  boolean forOverview = false;
-
   /**
-   * Creates a new SequenceRenderer object.
+   * Creates a new SequenceRenderer object
    * 
-   * @param av
-   *          DOCUMENT ME!
+   * @param viewport
    */
-  public SequenceRenderer(AlignViewport av)
+  public SequenceRenderer(AlignViewportI viewport)
   {
-    this.av = av;
+    this.av = viewport;
   }
 
   /**
@@ -83,13 +78,13 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     this.renderGaps = renderGaps;
   }
 
-  @Override
-  public Color getResidueBoxColour(SequenceI seq, int i)
+  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))
+    SequenceGroup currentSequenceGroup = inCurrentSequenceGroup(i);
+    if (currentSequenceGroup != null)
     {
       if (currentSequenceGroup.getDisplayBoxes())
       {
@@ -118,8 +113,6 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   public Color getResidueColour(final SequenceI seq, int position,
           FeatureColourFinder finder)
   {
-    // TODO replace 8 or so code duplications with calls to this method
-    // (refactored as needed)
     Color col = getResidueBoxColour(seq, position);
 
     if (finder != null)
@@ -141,14 +134,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    */
   void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {
-    if (shader != null)
+    if (shader.getColourScheme() != null)
     {
-      resBoxColour = shader.findColour(seq.getCharAt(i),
-              i, seq);
-    }
-    else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
-    {
-      resBoxColour = Color.lightGray;
+      resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
     }
     else
     {
@@ -185,7 +173,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
     drawBoxes(seq, start, end, y1);
 
-    if (av.validCharWidth)
+    if (av.isValidCharWidth())
     {
       drawText(seq, start, end, y1);
     }
@@ -231,7 +219,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
       if (i < length)
       {
-        if (inCurrentSequenceGroup(i))
+        SequenceGroup currentSequenceGroup = inCurrentSequenceGroup(i);
+        if (currentSequenceGroup != null)
         {
           if (currentSequenceGroup.getDisplayBoxes())
           {
@@ -320,9 +309,7 @@ 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;
+
       for (int i = start; i <= end; i++)
       {
 
@@ -335,7 +322,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           continue;
         }
 
-        if (inCurrentSequenceGroup(i))
+        SequenceGroup currentSequenceGroup = inCurrentSequenceGroup(i);
+        if (currentSequenceGroup != null)
         {
           if (!currentSequenceGroup.getDisplayText())
           {
@@ -367,6 +355,8 @@ 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
@@ -475,11 +465,11 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    * 
    * @return DOCUMENT ME!
    */
-  boolean inCurrentSequenceGroup(int res)
+  SequenceGroup inCurrentSequenceGroup(int res)
   {
     if (allGroups == null)
     {
-      return false;
+      return null;
     }
 
     for (int i = 0; i < allGroups.length; i++)
@@ -487,13 +477,11 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       if ((allGroups[i].getStartRes() <= res)
               && (allGroups[i].getEndRes() >= res))
       {
-        currentSequenceGroup = allGroups[i];
-
-        return true;
+        return (allGroups[i]);
       }
     }
 
-    return false;
+    return null;
   }
 
   /**