Merge branch 'develop' into features/JAL-1705_ensembl

[jalview.git] / src / jalview / io / SequenceAnnotationReport.java

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 7c96d45..72f8044 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -20,7 +20,6 @@
  */
 package jalview.io;
 
-
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -30,7 +29,6 @@ import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
 
-
 /**
  * generate HTML reports for a sequence
  * 
@@ -67,12 +65,11 @@ public class SequenceAnnotationReport
     String tmpString;
     if (features != null)
     {
-      for (SequenceFeature feature:features)
+      for (SequenceFeature feature : features)
       {
         if (feature.getType().equals("disulfide bond"))
         {
-          if (feature.getBegin() == rpos
-                  || feature.getEnd() == rpos)
+          if (feature.getBegin() == rpos || feature.getEnd() == rpos)
           {
             if (tooltipText2.length() > 6)
             {
@@ -104,8 +101,7 @@ public class SequenceAnnotationReport
             }
 
             if (feature.getDescription() != null
-                    && !feature.description.equals(feature
-                            .getType()))
+                    && !feature.description.equals(feature.getType()))
             {
               tmpString = feature.getDescription();
               String tmp2up = tmpString.toUpperCase();
@@ -152,7 +148,7 @@ public class SequenceAnnotationReport
               }
             }
             // check score should be shown
-            if (feature.getScore() != Float.NaN)
+            if (!Float.isNaN(feature.getScore()))
             {
               float[][] rng = (minmax == null) ? null : ((float[][]) minmax
                       .get(feature.getType()));
@@ -235,8 +231,7 @@ public class SequenceAnnotationReport
 
       // collect matching db-refs
       DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
-              new String[]
-              { target });
+              new String[] { target });
       // collect id string too
       String id = seq.getName();
       String descr = seq.getDescription();
@@ -263,8 +258,8 @@ public class SequenceAnnotationReport
               String unq = urls[u] + "|" + urls[u + 1];
               if (!uniques.contains(unq))
               {
-                urlSets.add(new String[]
-                { target, label, urls[u], urls[u + 1] });
+                urlSets.add(new String[] { target, label, urls[u],
+                    urls[u + 1] });
                 uniques.add(unq);
               }
             }
@@ -282,8 +277,8 @@ public class SequenceAnnotationReport
             String unq = urls[u] + "|" + urls[u + 1];
             if (!uniques.contains(unq))
             {
-              urlSets.add(new String[]
-              { target, label, urls[u], urls[u + 1] });
+              urlSets.add(new String[] { target, label, urls[u],
+                  urls[u + 1] });
               uniques.add(unq);
             }
           }
@@ -300,8 +295,8 @@ public class SequenceAnnotationReport
             String unq = urls[u] + "|" + urls[u + 1];
             if (!uniques.contains(unq))
             {
-              urlSets.add(new String[]
-              { target, label, urls[u], urls[u + 1] });
+              urlSets.add(new String[] { target, label, urls[u],
+                  urls[u + 1] });
               uniques.add(unq);
             }
           }
@@ -316,13 +311,12 @@ public class SequenceAnnotationReport
       {
         uniques.add(unq);
         // Add a non-dynamic link
-        urlSets.add(new String[]
-        { target, label, null, urlLink.getUrl_prefix() });
+        urlSets.add(new String[] { target, label, null,
+            urlLink.getUrl_prefix() });
       }
     }
 
-    return urlSets.toArray(new String[][]
-    {});
+    return urlSets.toArray(new String[][] {});
   }
 
   public void createSequenceAnnotationReport(final StringBuffer tip,