X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=a382c604a4937f0d54a03395780236d15c6cb6d0;hb=28d2a0b7dde7f6751d9e063fc2e11da065d284a4;hp=1c7c4ce85c32ad89ab7b32d6d2f562078a88a437;hpb=b2b7e99113e1f0962140fc72d989cc826799a2d4;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 1c7c4ce..a382c60 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -20,10 +20,10 @@
  */
 package jalview.appletgui;
 
-import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShaderI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 
 import java.awt.Color;
 import java.awt.Font;
@@ -69,8 +69,7 @@ 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)
   {
     allGroups = av.getAlignment().findAllGroups(seq);
 
@@ -83,7 +82,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.getViewportColourScheme(), seq, i);
+      getBoxColour(av.getResidueShading(), seq, i);
     }
 
     return resBoxColour;
@@ -96,27 +95,27 @@ 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;
   }
 
   void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {
-    if (shader != null)
+    if (shader.getColourScheme() != null)
     {
       resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
     }
@@ -163,8 +162,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     int length = seq.getLength();
 
     int curStart = -1;
-    int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(), avCharHeight = av
-            .getCharHeight();
+    int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(),
+            avCharHeight = av.getCharHeight();
 
     Color tempColour = null;
     while (i <= end)
@@ -182,7 +181,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.getViewportColourScheme(), seq, i);
+          getBoxColour(av.getResidueShading(), seq, i);
         }
       }
 
@@ -272,7 +271,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
         if (av.getColourText())
         {
-          getBoxColour(av.getViewportColourScheme(), seq, i);
+          getBoxColour(av.getResidueShading(), seq, i);
           if (av.getShowBoxes())
           {
             graphics.setColor(resBoxColour.darker());
@@ -310,8 +309,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       }
 
       charOffset = (avCharWidth - fm.charWidth(s)) / 2;
-      graphics.drawString(String.valueOf(s), charOffset + avCharWidth
-              * (i - start), y1);
+      graphics.drawString(String.valueOf(s),
+              charOffset + avCharWidth * (i - start), y1);
     }
 
   }
@@ -334,21 +333,25 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     // currentSequenceGroup.getConsensus()
     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)))
+            || 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);
+                    && 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 == conschar
+                    || sequenceChar + CHAR_TO_UPPER == conschar))
     {
       sequenceChar = conservedChar;
     }
@@ -375,14 +378,15 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     return false;
   }
 
-  public void drawHighlightedText(SequenceI seq, int start, int end,
-          int x1, int y1)
+  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+          int y1)
   {
     int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
     int pady = avCharHeight / 5;
     int charOffset = 0;
     graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, avCharWidth * (end - start + 1), avCharHeight);
+    graphics.fillRect(x1, y1, avCharWidth * (end - start + 1),
+            avCharHeight);
     graphics.setColor(Color.white);
 
     char s = '~';
@@ -397,8 +401,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
 
         charOffset = (avCharWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s), charOffset + x1
-                + avCharWidth * (i - start), y1 + avCharHeight - pady);
+        graphics.drawString(String.valueOf(s),
+                charOffset + x1 + avCharWidth * (i - start),
+                y1 + avCharHeight - pady);
       }
     }
   }