Merge branch 'features/sequenceFeatureRefactor' into develop

[jalview.git] / src / jalview / renderer / seqfeatures / FeatureRenderer.java

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 362ef5e..648f776 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -77,7 +77,6 @@ public class FeatureRenderer extends
         charOffset = (av_charWidth - fm.charWidth(s)) / 2;
         g.drawString(String.valueOf(s), charOffset
                 + (av_charWidth * (i - start)), pady);
-
       }
     }
   }
@@ -142,7 +141,6 @@ public class FeatureRenderer extends
         charOffset = (av_charWidth - fm.charWidth(s)) / 2;
         g.drawString(String.valueOf(s), charOffset
                 + (av_charWidth * (i - start)), pady);
-
       }
     }
   }
@@ -293,26 +291,24 @@ public class FeatureRenderer extends
       // current feature to render
       for (sfindex = 0; sfindex < sfSize; sfindex++)
       {
-        if (!lastSequenceFeatures[sfindex].type.equals(type))
+        final SequenceFeature sequenceFeature = lastSequenceFeatures[sfindex];
+        if (!sequenceFeature.type.equals(type))
         {
           continue;
         }
 
         if (featureGroups != null
-                && lastSequenceFeatures[sfindex].featureGroup != null
-                && lastSequenceFeatures[sfindex].featureGroup.length() != 0
-                && featureGroups
-                        .containsKey(lastSequenceFeatures[sfindex].featureGroup)
-                && !featureGroups
-.get(
-                        lastSequenceFeatures[sfindex].featureGroup)
+                && sequenceFeature.featureGroup != null
+                && sequenceFeature.featureGroup.length() != 0
+                && featureGroups.containsKey(sequenceFeature.featureGroup)
+                && !featureGroups.get(sequenceFeature.featureGroup)
                         .booleanValue())
         {
           continue;
         }
 
         if (!offscreenRender
-                && (lastSequenceFeatures[sfindex].getBegin() > epos || lastSequenceFeatures[sfindex]
+                && (sequenceFeature.getBegin() > epos || sequenceFeature
                         .getEnd() < spos))
         {
           continue;
@@ -320,59 +316,51 @@ public class FeatureRenderer extends
 
         if (offscreenRender && offscreenImage == null)
         {
-          if (lastSequenceFeatures[sfindex].begin <= start
-                  && lastSequenceFeatures[sfindex].end >= start)
+          if (sequenceFeature.begin <= start
+                  && sequenceFeature.end >= start)
           {
             // this is passed out to the overview and other sequence renderers
             // (e.g. molecule viewer) to get displayed colour for rendered
             // sequence
-            currentColour = new Integer(
-getColour(
-                    lastSequenceFeatures[sfindex]).getRGB());
+            currentColour = new Integer(getColour(sequenceFeature).getRGB());
             // used to be retreived from av.featuresDisplayed
             // currentColour = av.featuresDisplayed
             // .get(sequenceFeatures[sfindex].type);
 
           }
         }
-        else if (lastSequenceFeatures[sfindex].type
-                .equals("disulfide bond"))
+        else if (sequenceFeature.type.equals("disulfide bond"))
         {
-
-          renderFeature(g, seq,
-                  seq.findIndex(lastSequenceFeatures[sfindex].begin) - 1,
-                  seq.findIndex(lastSequenceFeatures[sfindex].begin) - 1,
-                  getColour(lastSequenceFeatures[sfindex])
+          renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
+                  seq.findIndex(sequenceFeature.begin) - 1,
+                  getColour(sequenceFeature)
                   // new Color(((Integer) av.featuresDisplayed
                   // .get(sequenceFeatures[sfindex].type)).intValue())
                   , start, end, y1);
-          renderFeature(g, seq,
-                  seq.findIndex(lastSequenceFeatures[sfindex].end) - 1,
-                  seq.findIndex(lastSequenceFeatures[sfindex].end) - 1,
-                  getColour(lastSequenceFeatures[sfindex])
+          renderFeature(g, seq, seq.findIndex(sequenceFeature.end) - 1,
+                  seq.findIndex(sequenceFeature.end) - 1,
+                  getColour(sequenceFeature)
                   // new Color(((Integer) av.featuresDisplayed
                   // .get(sequenceFeatures[sfindex].type)).intValue())
                   , start, end, y1);
 
         }
-        else if (showFeature(lastSequenceFeatures[sfindex]))
+        else if (showFeature(sequenceFeature))
         {
           if (av_isShowSeqFeatureHeight
-                  && lastSequenceFeatures[sfindex].score != Float.NaN)
+                  && sequenceFeature.score != Float.NaN)
           {
             renderScoreFeature(g, seq,
-                    seq.findIndex(lastSequenceFeatures[sfindex].begin) - 1,
-                    seq.findIndex(lastSequenceFeatures[sfindex].end) - 1,
-                    getColour(lastSequenceFeatures[sfindex]), start, end,
-                    y1, normaliseScore(lastSequenceFeatures[sfindex]));
+                    seq.findIndex(sequenceFeature.begin) - 1,
+                    seq.findIndex(sequenceFeature.end) - 1,
+                    getColour(sequenceFeature), start, end, y1,
+                    normaliseScore(sequenceFeature));
           }
           else
           {
-            renderFeature(g, seq,
-                    seq.findIndex(lastSequenceFeatures[sfindex].begin) - 1,
-                    seq.findIndex(lastSequenceFeatures[sfindex].end) - 1,
-                    getColour(lastSequenceFeatures[sfindex]), start, end,
-                    y1);
+            renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
+                    seq.findIndex(sequenceFeature.end) - 1,
+                    getColour(sequenceFeature), start, end, y1);
           }
         }