Merge branch 'documentation/JAL-2675_release2102b1' into feature/JAL-2611

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

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 09b50c4..a382c60 100755 (executable)
--- 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.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 
 import java.awt.Color;
 import java.awt.Font;
@@ -32,6 +32,8 @@ import java.awt.Graphics;
 
 public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
+  final static int CHAR_TO_UPPER = 'A' - 'a';
+
   AlignViewport av;
 
   FontMetrics fm;
@@ -67,7 +69,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     this.renderGaps = renderGaps;
   }
 
-  public Color getResidueBoxColour(SequenceI seq, int i)
+  protected Color getResidueBoxColour(SequenceI seq, int i)
   {
     allGroups = av.getAlignment().findAllGroups(seq);
 
@@ -75,12 +77,12 @@ 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.getResidueShading(), seq, i);
     }
 
     return resBoxColour;
@@ -93,29 +95,29 @@ 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(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);
+      resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
     }
     else if (forOverview
             && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
@@ -160,8 +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)
@@ -173,12 +175,13 @@ 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.getResidueShading(), seq, i);
         }
       }
 
@@ -251,12 +254,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
         if (currentSequenceGroup.getColourText())
         {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
+          getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
           graphics.setColor(resBoxColour.darker());
         }
         if (currentSequenceGroup.getShowNonconserved())
         {
-          s = getDisplayChar(srep, i, s, '.');
+          s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
         }
       }
       else
@@ -268,7 +271,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
         if (av.getColourText())
         {
-          getBoxColour(av.getGlobalColourScheme(), seq, i);
+          getBoxColour(av.getResidueShading(), seq, i);
           if (av.getShowBoxes())
           {
             graphics.setColor(resBoxColour.darker());
@@ -280,7 +283,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (av.getShowUnconserved())
         {
-          s = getDisplayChar(srep, i, s, '.');
+          s = getDisplayChar(srep, i, s, '.', null);
 
         }
       }
@@ -306,26 +309,53 @@ 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);
     }
 
   }
 
-  private char getDisplayChar(final boolean usesrep, int position, char s,
-          char c)
+  /**
+   * Returns 'conservedChar' to represent the given position if the sequence
+   * character at that position is equal to the consensus (ignoring case), else
+   * returns the sequence character
+   * 
+   * @param usesrep
+   * @param position
+   * @param sequenceChar
+   * @param conservedChar
+   * @return
+   */
+  private char getDisplayChar(final boolean usesrep, int position,
+          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 (!jalview.util.Comparison.isGap(conschar) && s == 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))
     {
-      s = c;
+      sequenceChar = conservedChar;
     }
-    return s;
+    return sequenceChar;
   }
 
   boolean inCurrentSequenceGroup(int res)
@@ -348,14 +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 = '~';
@@ -370,8 +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);
       }
     }
   }