X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FSequenceAnnotationReport.java;h=6d8ce5f9daeca0021b745e8fec3696c0b2ae15bd;hb=d131f05c68757d57e5e4a1f440196ae1b70f3b8a;hp=6fba9c62ef64e28b902b8954f25b7d65d4d509c4;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 6fba9c6..6d8ce5f 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,15 +20,17 @@
  */
 package jalview.io;
 
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Vector;
 
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.UrlLink;
 
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
+
 /**
  * generate HTML reports for a sequence
  * 
@@ -54,30 +56,30 @@ public class SequenceAnnotationReport
    *          TODO refactor to Jalview 'utilities' somehow.
    */
   public void appendFeatures(final StringBuffer tooltipText2, int rpos,
-          SequenceFeature[] features)
+          List<SequenceFeature> features)
   {
     appendFeatures(tooltipText2, rpos, features, null);
   }
 
   public void appendFeatures(final StringBuffer tooltipText2, int rpos,
-          SequenceFeature[] features, Hashtable minmax)
+          List<SequenceFeature> features, Hashtable minmax)
   {
     String tmpString;
     if (features != null)
     {
-      for (int i = 0; i < features.length; i++)
+      for (SequenceFeature feature:features)
       {
-        if (features[i].getType().equals("disulfide bond"))
+        if (feature.getType().equals("disulfide bond"))
         {
-          if (features[i].getBegin() == rpos
-                  || features[i].getEnd() == rpos)
+          if (feature.getBegin() == rpos
+                  || feature.getEnd() == rpos)
           {
             if (tooltipText2.length() > 6)
             {
               tooltipText2.append("<br>");
             }
-            tooltipText2.append("disulfide bond " + features[i].getBegin()
-                    + ":" + features[i].getEnd());
+            tooltipText2.append("disulfide bond " + feature.getBegin()
+                    + ":" + feature.getEnd());
           }
         }
         else
@@ -87,25 +89,25 @@ public class SequenceAnnotationReport
             tooltipText2.append("<br>");
           }
           // TODO: remove this hack to display link only features
-          boolean linkOnly = features[i].getValue("linkonly") != null;
+          boolean linkOnly = feature.getValue("linkonly") != null;
           if (!linkOnly)
           {
-            tooltipText2.append(features[i].getType() + " ");
+            tooltipText2.append(feature.getType() + " ");
             if (rpos != 0)
             {
               // we are marking a positional feature
-              tooltipText2.append(features[i].begin);
+              tooltipText2.append(feature.begin);
             }
-            if (features[i].begin != features[i].end)
+            if (feature.begin != feature.end)
             {
-              tooltipText2.append(" " + features[i].end);
+              tooltipText2.append(" " + feature.end);
             }
 
-            if (features[i].getDescription() != null
-                    && !features[i].description.equals(features[i]
+            if (feature.getDescription() != null
+                    && !feature.description.equals(feature
                             .getType()))
             {
-              tmpString = features[i].getDescription();
+              tmpString = feature.getDescription();
               String tmp2up = tmpString.toUpperCase();
               int startTag = tmp2up.indexOf("<HTML>");
               if (startTag > -1)
@@ -150,27 +152,27 @@ public class SequenceAnnotationReport
               }
             }
             // check score should be shown
-            if (features[i].getScore() != Float.NaN)
+            if (!Float.isNaN(feature.getScore()))
             {
               float[][] rng = (minmax == null) ? null : ((float[][]) minmax
-                      .get(features[i].getType()));
+                      .get(feature.getType()));
               if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
               {
-                tooltipText2.append(" Score=" + features[i].getScore());
+                tooltipText2.append(" Score=" + feature.getScore());
               }
             }
-            if (features[i].getValue("status") != null)
+            if (feature.getValue("status") != null)
             {
-              String status = features[i].getValue("status").toString();
+              String status = feature.getValue("status").toString();
               if (status.length() > 0)
               {
-                tooltipText2.append("; (" + features[i].getValue("status")
+                tooltipText2.append("; (" + feature.getValue("status")
                         + ")");
               }
             }
           }
         }
-        if (features[i].links != null)
+        if (feature.links != null)
         {
           if (linkImageURL != null)
           {
@@ -178,7 +180,7 @@ public class SequenceAnnotationReport
           }
           else
           {
-            for (String urlstring : (Vector<String>) features[i].links)
+            for (String urlstring : feature.links)
             {
               try
               {
@@ -363,8 +365,7 @@ public class SequenceAnnotationReport
     }
 
     // ADD NON POSITIONAL SEQUENCE INFO
-    SequenceFeature[] features = ds.getSequenceFeatures();
-    SequenceFeature[] tfeat = new SequenceFeature[1];
+    SequenceFeature[] features = sequence.getSequenceFeatures();
     if (showNpFeats && features != null)
     {
       for (int i = 0; i < features.length; i++)
@@ -372,7 +373,8 @@ public class SequenceAnnotationReport
         if (features[i].begin == 0 && features[i].end == 0)
         {
           int sz = -tip.length();
-          tfeat[0] = features[i];
+          List<SequenceFeature> tfeat = new ArrayList<SequenceFeature>();
+          tfeat.add(features[i]);
           appendFeatures(tip, 0, tfeat, minmax);
           sz += tip.length();
           maxWidth = Math.max(maxWidth, sz);