Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'

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

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 36825ea..4498f88 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -77,8 +77,8 @@ 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
-            .getCharWidth() == dwidth);
+    monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth()
+            && av.getCharWidth() == dwidth);
 
     this.renderGaps = renderGaps;
   }
@@ -140,8 +140,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   {
     if (shader.getColourScheme() != null)
     {
-      resBoxColour = shader.findColour(seq.getCharAt(i),
-              i, seq);
+      resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
     }
     else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
     {
@@ -217,8 +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;
 
@@ -308,8 +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
@@ -317,8 +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++)
       {
@@ -354,7 +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);
               }
@@ -443,21 +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;
     }
@@ -511,8 +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;