Merge branch 'develop' into features/JAL-250_hideredundantseqs

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

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 64fe053..4498f88 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -20,10 +20,12 @@
  */
 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 jalview.util.Comparison;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
@@ -33,7 +35,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
   final static int CHAR_TO_UPPER = 'A' - 'a';
 
-  AlignViewport av;
+  AlignViewportI av;
 
   FontMetrics fm;
 
@@ -52,14 +54,13 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   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;
   }
 
   /**
@@ -76,14 +77,13 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     // If EPS graphics, stringWidth will be a double, not an int
     double dwidth = fm.getStringBounds("M", g).getWidth();
 
-    monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av
-            .getCharWidth() == dwidth);
+    monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth()
+            && av.getCharWidth() == dwidth);
 
     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);
@@ -92,12 +92,12 @@ 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;
@@ -110,20 +110,18 @@ 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;
   }
@@ -131,21 +129,20 @@ 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);
+      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;
     }
@@ -184,7 +181,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
     drawBoxes(seq, start, end, y1);
 
-    if (av.validCharWidth)
+    if (av.isValidCharWidth())
     {
       drawText(seq, start, end, y1);
     }
@@ -219,8 +216,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     int length = seq.getLength();
 
     int curStart = -1;
-    int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(), avHeight = av
-            .getCharHeight();
+    int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(),
+            avHeight = av.getCharHeight();
 
     Color tempColour = null;
 
@@ -234,14 +231,14 @@ 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.getResidueShading(), seq, i);
         }
-
       }
 
       if (resBoxColour != tempColour)
@@ -310,8 +307,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       else
       {
         char gap = av.getGapCharacter();
-        graphics.drawString(seq.getSequenceAsString(start, end + 1)
-                .replace(gap, ' '), 0, y1);
+        graphics.drawString(
+                seq.getSequenceAsString(start, end + 1).replace(gap, ' '),
+                0, y1);
       }
     }
     else
@@ -319,8 +317,9 @@ 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;
+      boolean isgrep = currentSequenceGroup != null
+              ? currentSequenceGroup.getSeqrep() == seq
+              : false;
       char sr_c;
       for (int i = start; i <= end; i++)
       {
@@ -345,7 +344,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
                   || currentSequenceGroup.getColourText())
           {
             getboxColour = true;
-            getBoxColour(currentSequenceGroup.cs, seq, i);
+            getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+                    i);
 
             if (currentSequenceGroup.getColourText())
             {
@@ -355,7 +355,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
             if (currentSequenceGroup.thresholdTextColour > 0)
             {
               if (resBoxColour.getRed() + resBoxColour.getBlue()
-                      + resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
+                      + resBoxColour
+                              .getGreen() < currentSequenceGroup.thresholdTextColour)
               {
                 graphics.setColor(currentSequenceGroup.textColour2);
               }
@@ -385,7 +386,7 @@ 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())
             {
@@ -401,7 +402,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           {
             if (!getboxColour)
             {
-              getBoxColour(av.getGlobalColourScheme(), seq, i);
+              getBoxColour(av.getResidueShading(), seq, i);
             }
 
             if (resBoxColour.getRed() + resBoxColour.getBlue()
@@ -444,21 +445,25 @@ 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;
     }
@@ -512,8 +517,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    * @param height
    *          DOCUMENT ME!
    */
-  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 pady = av.getCharHeight() / 5;
     int charOffset = 0;