Merge develop to Release_2_8_3_Branch

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

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index c6a3df2..70acb7b 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -21,7 +21,6 @@
 package jalview.gui;
 
 import jalview.api.FeatureRenderer;
-import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
@@ -38,6 +37,8 @@ import java.awt.Graphics;
  */
 public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
+  final static int CHAR_TO_UPPER = 'A' - 'a';
+
   AlignViewport av;
 
   FontMetrics fm;
@@ -81,7 +82,8 @@ 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.charWidth == dwidth);
+    monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av
+            .getCharWidth() == dwidth);
 
     this.renderGaps = renderGaps;
   }
@@ -222,7 +224,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     int length = seq.getLength();
 
     int curStart = -1;
-    int curWidth = av.charWidth;
+    int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(), avHeight = av
+            .getCharHeight();
 
     Color tempColour = null;
 
@@ -250,26 +253,25 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       {
         if (tempColour != null)
         {
-          graphics.fillRect(av.charWidth * (curStart - start), y1,
-                  curWidth, av.charHeight);
+          graphics.fillRect(avWidth * (curStart - start), y1, curWidth,
+                  avHeight);
         }
 
         graphics.setColor(resBoxColour);
 
         curStart = i;
-        curWidth = av.charWidth;
+        curWidth = avWidth;
         tempColour = resBoxColour;
       }
       else
       {
-        curWidth += av.charWidth;
+        curWidth += avWidth;
       }
 
       i++;
     }
 
-    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
-            av.charHeight);
+    graphics.fillRect(avWidth * (curStart - start), y1, curWidth, avHeight);
 
   }
 
@@ -293,7 +295,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    */
   public void drawText(SequenceI seq, int start, int end, int y1)
   {
-    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+    y1 += av.getCharHeight() - av.getCharHeight() / 5; // height/5 replaces pady
     int charOffset = 0;
     char s;
 
@@ -301,12 +303,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     {
       end = seq.getLength() - 1;
     }
-    graphics.setColor(av.textColour);
+    graphics.setColor(av.getTextColour());
 
-    if (monospacedFont && av.showText && allGroups.length == 0
-            && !av.getColourText() && av.thresholdTextColour == 0)
+    if (monospacedFont && av.getShowText() && allGroups.length == 0
+            && !av.getColourText() && av.getThresholdTextColour() == 0)
     {
-      if (av.renderGaps)
+      if (av.isRenderGaps())
       {
         graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
       }
@@ -323,7 +325,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       boolean getboxColour = false;
       for (int i = start; i <= end; i++)
       {
-        graphics.setColor(av.textColour);
+        graphics.setColor(av.getTextColour());
         getboxColour = false;
         s = seq.getCharAt(i);
         if (!renderGaps && jalview.util.Comparison.isGap(s))
@@ -393,7 +395,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
             }
           }
 
-          if (av.thresholdTextColour > 0)
+          if (av.getThresholdTextColour() > 0)
           {
             if (!getboxColour)
             {
@@ -401,9 +403,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
             }
 
             if (resBoxColour.getRed() + resBoxColour.getBlue()
-                    + resBoxColour.getGreen() < av.thresholdTextColour)
+                    + resBoxColour.getGreen() < av.getThresholdTextColour())
             {
-              graphics.setColor(av.textColour2);
+              graphics.setColor(av.getTextColour2());
             }
           }
           if (av.getShowUnconserved())
@@ -415,26 +417,39 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
         }
 
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s), charOffset + av.charWidth
+        charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                charOffset + av.getCharWidth()
                 * (i - start), y1);
 
       }
     }
   }
 
+  /**
+   * 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 s, char c)
+          char sequenceChar, char conservedChar)
   {
-    // TODO - use currentSequenceGroup rather than alignemnt 
+    // 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 != '-' && s == conschar)
+    if (conschar != '-'
+            && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
     {
-      s = c;
+      sequenceChar = conservedChar;
     }
-    return s;
+    return sequenceChar;
   }
 
   /**
@@ -487,17 +502,17 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   public void drawHighlightedText(SequenceI seq, int start, int end,
           int x1, int y1)
   {
-    int pady = av.charHeight / 5;
+    int pady = av.getCharHeight() / 5;
     int charOffset = 0;
     graphics.setColor(Color.BLACK);
-    graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
-            av.charHeight);
+    graphics.fillRect(x1, y1, av.getCharWidth() * (end - start + 1),
+            av.getCharHeight());
     graphics.setColor(Color.white);
 
     char s = '~';
 
     // Need to find the sequence position here.
-    if (av.validCharWidth)
+    if (av.isValidCharWidth())
     {
       for (int i = start; i <= end; i++)
       {
@@ -506,29 +521,30 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           s = seq.getCharAt(i);
         }
 
-        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-        graphics.drawString(String.valueOf(s), charOffset + x1
-                + (av.charWidth * (i - start)), (y1 + av.charHeight) - pady);
+        charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+        graphics.drawString(String.valueOf(s),
+                charOffset + x1 + (av.getCharWidth() * (i - start)),
+                (y1 + av.getCharHeight()) - pady);
       }
     }
   }
 
   public void drawCursor(SequenceI seq, int res, int x1, int y1)
   {
-    int pady = av.charHeight / 5;
+    int pady = av.getCharHeight() / 5;
     int charOffset = 0;
     graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+    graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
 
-    if (av.validCharWidth)
+    if (av.isValidCharWidth())
     {
       graphics.setColor(Color.white);
 
       char s = seq.getCharAt(res);
 
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s), charOffset + x1,
-              (y1 + av.charHeight) - pady);
+              (y1 + av.getCharHeight()) - pady);
     }
 
   }