JAL-2371 CollectionColourScheme renamed ResidueShader and moved to

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

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 70acb7b..e77536d 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -23,18 +23,13 @@ package jalview.gui;
 import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
+import jalview.util.Comparison;
 
 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';
@@ -91,18 +86,19 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   @Override
   public 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.cs, seq, i);
+        getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
       }
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.getGlobalColourScheme(), seq, i);
+      getBoxColour(av.getViewportColourScheme(), seq, i);
     }
 
     return resBoxColour;
@@ -136,21 +132,21 @@ 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 != null)
     {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
+      resBoxColour = shader.findColour(seq.getCharAt(i),
+              i, seq);
     }
-    else if (forOverview
-            && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
     {
       resBoxColour = Color.lightGray;
     }
@@ -217,7 +213,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           int y1)
   {
     if (seq == null)
-     {
+    {
       return; // fix for racecondition
     }
     int i = start;
@@ -239,14 +235,14 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         {
           if (currentSequenceGroup.getDisplayBoxes())
           {
-            getBoxColour(currentSequenceGroup.cs, seq, i);
+            getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+                    i);
           }
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
+          getBoxColour(av.getViewportColourScheme(), seq, i);
         }
-
       }
 
       if (resBoxColour != tempColour)
@@ -323,11 +319,17 @@ 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++)
       {
+
         graphics.setColor(av.getTextColour());
         getboxColour = false;
         s = seq.getCharAt(i);
+
         if (!renderGaps && jalview.util.Comparison.isGap(s))
         {
           continue;
@@ -344,7 +346,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
                   || currentSequenceGroup.getColourText())
           {
             getboxColour = true;
-            getBoxColour(currentSequenceGroup.cs, seq, i);
+            getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+                    i);
 
             if (currentSequenceGroup.getColourText())
             {
@@ -364,11 +367,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           {
             graphics.setColor(currentSequenceGroup.textColour);
           }
-          if (currentSequenceGroup.getShowNonconserved()) // todo optimize
+          if (!isarep && !isgrep
+                  && currentSequenceGroup.getShowNonconserved()) // todo
+                                                                 // optimize
           {
             // todo - use sequence group consensus
-            s = getDisplayChar(srep, i, s,
-                    '.');
+            s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
 
           }
 
@@ -383,7 +387,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (av.getColourText())
           {
             getboxColour = true;
-            getBoxColour(av.getGlobalColourScheme(), seq, i);
+            getBoxColour(av.getViewportColourScheme(), seq, i);
 
             if (av.getShowBoxes())
             {
@@ -399,7 +403,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           {
             if (!getboxColour)
             {
-              getBoxColour(av.getGlobalColourScheme(), seq, i);
+              getBoxColour(av.getViewportColourScheme(), seq, i);
             }
 
             if (resBoxColour.getRed() + resBoxColour.getBlue()
@@ -408,10 +412,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
               graphics.setColor(av.getTextColour2());
             }
           }
-          if (av.getShowUnconserved())
+          if (!isarep && av.getShowUnconserved())
           {
-            s = getDisplayChar(srep, i, s,
-                    '.');
+            s = getDisplayChar(srep, i, s, '.', null);
 
           }
 
@@ -419,8 +422,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
         charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
         graphics.drawString(String.valueOf(s),
-                charOffset + av.getCharWidth()
-                * (i - start), y1);
+                charOffset + av.getCharWidth() * (i - start), y1);
 
       }
     }
@@ -438,13 +440,26 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    * @return
    */
   private char getDisplayChar(final boolean usesrep, int position,
-          char sequenceChar, char conservedChar)
+          char sequenceChar, char conservedChar, SequenceGroup currentGroup)
   {
     // TODO - use currentSequenceGroup rather than alignment
     // currentSequenceGroup.getConsensus()
-    char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
-            .charAt(0);
-    if (conschar != '-'
+    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
+                    && position >= currentGroup.getStartRes()
+                    && position <= currentGroup.getEndRes() && currentGroup
+                    .getConsensus().annotations.length > position) ? currentGroup
+                    .getConsensus().annotations[position].displayCharacter
+                    .charAt(0)
+                    : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+                            .charAt(0);
+    if (!jalview.util.Comparison.isGap(conschar)
             && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
     {
       sequenceChar = conservedChar;