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 8c4ead8..9874fd2 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,33 +20,26 @@
  */
 package jalview.gui;
 
-import jalview.api.FeatureRenderer;
+import jalview.api.AlignViewportI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
 
-/**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
- */
 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;
@@ -55,17 +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;
   }
 
   /**
@@ -88,21 +78,22 @@ 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())
       {
-        getBoxColour(currentSequenceGroup.cs, seq, i);
+        getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
       }
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.getGlobalColourScheme(), seq, i);
+      getBoxColour(av.getResidueShading(), seq, i);
     }
 
     return resBoxColour;
@@ -115,20 +106,18 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    * 
    * @param seq
    * @param position
-   * @param fr
+   * @param finder
    * @return
    */
   @Override
   public Color getResidueColour(final SequenceI seq, int position,
-          FeatureRenderer fr)
+          FeatureColourFinder finder)
   {
-    // TODO replace 8 or so code duplications with calls to this method
-    // (refactored as needed)
     Color col = getResidueBoxColour(seq, position);
 
-    if (fr != null)
+    if (finder != null)
     {
-      col = fr.findFeatureColour(col, seq, position);
+      col = finder.findFeatureColour(col, seq, position);
     }
     return col;
   }
@@ -136,23 +125,18 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   /**
    * DOCUMENT ME!
    * 
-   * @param cs
+   * @param shader
    *          DOCUMENT ME!
    * @param seq
    *          DOCUMENT ME!
    * @param i
    *          DOCUMENT ME!
    */
-  void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+  void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {
-    if (cs != null)
+    if (shader.getColourScheme() != null)
     {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
-    }
-    else if (forOverview
-            && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
-    {
-      resBoxColour = Color.lightGray;
+      resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
     }
     else
     {
@@ -189,7 +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);
     }
@@ -235,18 +219,19 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
       if (i < length)
       {
-        if (inCurrentSequenceGroup(i))
+        SequenceGroup currentSequenceGroup = inCurrentSequenceGroup(i);
+        if (currentSequenceGroup != null)
         {
           if (currentSequenceGroup.getDisplayBoxes())
           {
-            getBoxColour(currentSequenceGroup.cs, seq, i);
+            getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+                    i);
           }
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
+          getBoxColour(av.getResidueShading(), seq, i);
         }
-
       }
 
       if (resBoxColour != tempColour)
@@ -324,9 +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++)
       {
 
@@ -339,7 +322,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           continue;
         }
 
-        if (inCurrentSequenceGroup(i))
+        SequenceGroup currentSequenceGroup = inCurrentSequenceGroup(i);
+        if (currentSequenceGroup != null)
         {
           if (!currentSequenceGroup.getDisplayText())
           {
@@ -350,7 +334,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
                   || currentSequenceGroup.getColourText())
           {
             getboxColour = true;
-            getBoxColour(currentSequenceGroup.cs, seq, i);
+            getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+                    i);
 
             if (currentSequenceGroup.getColourText())
             {
@@ -370,6 +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
@@ -390,7 +377,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (av.getColourText())
           {
             getboxColour = true;
-            getBoxColour(av.getGlobalColourScheme(), seq, i);
+            getBoxColour(av.getResidueShading(), seq, i);
 
             if (av.getShowBoxes())
             {
@@ -406,7 +393,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           {
             if (!getboxColour)
             {
-              getBoxColour(av.getGlobalColourScheme(), seq, i);
+              getBoxColour(av.getResidueShading(), seq, i);
             }
 
             if (resBoxColour.getRed() + resBoxColour.getBlue()
@@ -417,7 +404,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           }
           if (!isarep && av.getShowUnconserved())
           {
-            s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
+            s = getDisplayChar(srep, i, s, '.', null);
 
           }
 
@@ -447,12 +434,17 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   {
     // TODO - use currentSequenceGroup rather than alignment
     // currentSequenceGroup.getConsensus()
-    char conschar = (usesrep) ? (currentGroup == null ? av.getAlignment()
+    char conschar = (usesrep) ? (currentGroup == null
+            || position < currentGroup.getStartRes()
+            || position > currentGroup.getEndRes() ? av.getAlignment()
             .getSeqrep().getCharAt(position)
             : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
                     .getCharAt(position) : av.getAlignment().getSeqrep()
                     .getCharAt(position)))
-            : (currentGroup != null && currentGroup.getConsensus() != null) ? currentGroup
+            : (currentGroup != null && currentGroup.getConsensus() != null
+                    && position >= currentGroup.getStartRes()
+                    && position <= currentGroup.getEndRes() && currentGroup
+                    .getConsensus().annotations.length > position) ? currentGroup
                     .getConsensus().annotations[position].displayCharacter
                     .charAt(0)
                     : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
@@ -473,11 +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++)
@@ -485,13 +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;
   }
 
   /**