replacing @j2sNative with @j2sIgnore where appropriate - requires NEW

[jalview.git] / src / jalview / renderer / AnnotationRenderer.java

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 17bc6df..548291c 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -416,8 +416,6 @@ public class AnnotationRenderer
     return null;
   }
 
-  boolean rna = false;
-
   /**
    * Render the annotation rows associated with an alignment.
    * 
@@ -470,10 +468,6 @@ public class AnnotationRenderer
             .getAlignmentStrucConsensusAnnotation();
     final AlignmentAnnotation complementConsensusAnnot = av
             .getComplementConsensusAnnotation();
-    boolean renderHistogram = true;
-    boolean renderProfile = false;
-    boolean normaliseProfile = false;
-    boolean isRNA = rna;
 
     BitSet graphGroupDrawn = new BitSet();
     int charOffset = 0; // offset for a label
@@ -484,32 +478,29 @@ public class AnnotationRenderer
     for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
-      isRNA = row.isRNA();
+      boolean renderHistogram = true;
+      boolean renderProfile = false;
+      boolean normaliseProfile = false;
+      boolean isRNA = row.isRNA();
+
+      // check if this is a consensus annotation row and set the display
+      // settings appropriately
+      // TODO: generalise this to have render styles for consensus/profile
+      // data
+      if (row.groupRef != null && row == row.groupRef.getConsensus())
       {
-        // check if this is a consensus annotation row and set the display
-        // settings appropriately
-        // TODO: generalise this to have render styles for consensus/profile
-        // data
-        if (row.groupRef != null && row == row.groupRef.getConsensus())
-        {
-          renderHistogram = row.groupRef.isShowConsensusHistogram();
-          renderProfile = row.groupRef.isShowSequenceLogo();
-          normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
-        }
-        else if (row == consensusAnnot || row == structConsensusAnnot
-                || row == complementConsensusAnnot)
-        {
-          renderHistogram = av_renderHistogram;
-          renderProfile = av_renderProfile;
-          normaliseProfile = av_normaliseProfile;
-        }
-        else
-        {
-          renderHistogram = true;
-          // don't need to set render/normaliseProfile since they are not
-          // currently used in any other annotation track renderer
-        }
+        renderHistogram = row.groupRef.isShowConsensusHistogram();
+        renderProfile = row.groupRef.isShowSequenceLogo();
+        normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
       }
+      else if (row == consensusAnnot || row == structConsensusAnnot
+              || row == complementConsensusAnnot)
+      {
+        renderHistogram = av_renderHistogram;
+        renderProfile = av_renderProfile;
+        normaliseProfile = av_normaliseProfile;
+      }
+
       Annotation[] row_annotations = row.annotations;
       if (!row.visible)
       {
@@ -1398,7 +1389,8 @@ public class AnnotationRenderer
           boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
           boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
           float ht = normaliseProfile ? y - _aa.graphHeight : y1;
-          final double normaliseFactor = normaliseProfile ? _aa.graphHeight : (y2 - y1);
+          final double normaliseFactor = normaliseProfile ? _aa.graphHeight
+                  : (y2 - y1);
 
           /**
            * Render a single base for a sequence profile, a base pair for
@@ -1449,7 +1441,7 @@ public class AnnotationRenderer
               s = new String(dc);
             }
             // next profl[] position is profile % for the character(s)
-            
+
             int percent = profl[c++];
             if (percent == 0)
             {
@@ -1482,9 +1474,9 @@ public class AnnotationRenderer
             // (int)(scl));
             // g.setColor(profcolour.findColour(dc[0]).darker());
 
-            double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);            
+            double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);
             double sy = newHeight / asc;
-            double newAsc = asc * sy; 
+            double newAsc = asc * sy;
             double newDec = dec * sy;
             // it is not necessary to recalculate lm for the new font.
             // note: lm.getBaselineOffsets()[lm.getBaselineIndex()]) must be 0
@@ -1510,10 +1502,14 @@ public class AnnotationRenderer
               ht2 += newHeight;
             }
             else
+            /**
+             * Java only
+             * 
+             * @j2sIgnore
+             */
             {
-              /*
-               * Java ('normal') method is to scale the font to fit
-               */
+              // Java ('normal') method is to scale the font to fit
+
               final int hght = (int) (ht + (newAsc - newDec));
               Font font = ofont
                       .deriveFont(AffineTransform.getScaleInstance(sx, sy));
@@ -1532,7 +1528,7 @@ public class AnnotationRenderer
       Graphics2D g2 = (Graphics2D) g;
       g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
               BasicStroke.JOIN_ROUND, 3f, new float[]
-      { 5f, 3f }, 0f));
+              { 5f, 3f }, 0f));
 
       y2 = (int) (y
               - ((_aa.threshold.value - min) / range) * _aa.graphHeight);