JAL-2015 JAL-1956 rollout of FeatureColourI in place of

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

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index d3a1d09..6573a7f 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -26,8 +26,8 @@ import jalview.datamodel.SequenceI;
 import jalview.util.UrlLink;
 
 import java.util.ArrayList;
-import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 
 /**
  * generate HTML reports for a sequence
@@ -60,7 +60,7 @@ public class SequenceAnnotationReport
   }
 
   public void appendFeatures(final StringBuffer tooltipText2, int rpos,
-          List<SequenceFeature> features, Hashtable minmax)
+          List<SequenceFeature> features, Map<String, float[][]> map)
   {
     String tmpString;
     if (features != null)
@@ -150,8 +150,8 @@ public class SequenceAnnotationReport
             // check score should be shown
             if (!Float.isNaN(feature.getScore()))
             {
-              float[][] rng = (minmax == null) ? null : ((float[][]) minmax
-                      .get(feature.getType()));
+              float[][] rng = (map == null) ? null : (map.get(feature
+                      .getType()));
               if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
               {
                 tooltipText2.append(" Score=" + feature.getScore());
@@ -321,7 +321,7 @@ public class SequenceAnnotationReport
 
   public void createSequenceAnnotationReport(final StringBuffer tip,
           SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
-          Hashtable minmax)
+          Map<String, float[][]> minmax)
   {
     createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats,
             true, minmax);
@@ -329,7 +329,7 @@ public class SequenceAnnotationReport
 
   public void createSequenceAnnotationReport(final StringBuffer tip,
           SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
-          boolean tableWrap, Hashtable minmax)
+          boolean tableWrap, Map<String, float[][]> map)
   {
     String tmp;
     tip.append("<i>");
@@ -369,7 +369,7 @@ public class SequenceAnnotationReport
           int sz = -tip.length();
           List<SequenceFeature> tfeat = new ArrayList<SequenceFeature>();
           tfeat.add(features[i]);
-          appendFeatures(tip, 0, tfeat, minmax);
+          appendFeatures(tip, 0, tfeat, map);
           sz += tip.length();
           maxWidth = Math.max(maxWidth, sz);
         }