JAL-2089 Merge branch releases/Release_2_10_Branch to master

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

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 8469355..dd0664b 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,6 +23,7 @@ package jalview.io;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.io.gff.GffConstants;
 import jalview.util.DBRefUtils;
 import jalview.util.UrlLink;
 
@@ -140,8 +141,7 @@ public class SequenceAnnotationReport
           }
           else
           {
-            if (tmpString.indexOf("<") > -1
-                    || tmpString.indexOf(">") > -1)
+            if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
             {
               // The description does not specify html is to
               // be used, so we must remove < > symbols
@@ -166,8 +166,7 @@ public class SequenceAnnotationReport
                   .getType());
           if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
           {
-            sb.append(" Score=").append(
-                    String.valueOf(feature.getScore()));
+            sb.append(" Score=").append(String.valueOf(feature.getScore()));
           }
         }
         String status = (String) feature.getValue("status");
@@ -175,7 +174,8 @@ public class SequenceAnnotationReport
         {
           sb.append("; (").append(status).append(")");
         }
-        String clinSig = (String) feature.getValue("clinical_significance");
+        String clinSig = (String) feature
+                .getValue(GffConstants.CLINICAL_SIGNIFICANCE);
         if (clinSig != null)
         {
           sb.append("; ").append(clinSig);
@@ -310,8 +310,7 @@ public class SequenceAnnotationReport
             String unq = urls[u] + "|" + urls[u + 1];
             if (!uniques.contains(unq))
             {
-              result.add(new String[] { target, label, urls[u],
-                  urls[u + 1] });
+              result.add(new String[] { target, label, urls[u], urls[u + 1] });
               uniques.add(unq);
             }
           }
@@ -329,8 +328,7 @@ public class SequenceAnnotationReport
           String unq = urls[u] + "|" + urls[u + 1];
           if (!uniques.contains(unq))
           {
-            result.add(new String[] { target, label, urls[u],
-                urls[u + 1] });
+            result.add(new String[] { target, label, urls[u], urls[u + 1] });
             uniques.add(unq);
           }
         }
@@ -347,8 +345,7 @@ public class SequenceAnnotationReport
           String unq = urls[u] + "|" + urls[u + 1];
           if (!uniques.contains(unq))
           {
-            result.add(new String[] { target, label, urls[u],
-                urls[u + 1] });
+            result.add(new String[] { target, label, urls[u], urls[u + 1] });
             uniques.add(unq);
           }
         }