Merge branch 'alpha/JAL-3066_Jalview_212_slivka-integration' into alpha/JAL-3362_Jalv...

[jalview.git] / src / jalview / datamodel / SequenceFeature.java

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 8a6cb61..c8a7def 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -27,9 +27,11 @@ import jalview.datamodel.features.FeatureSourceI;
 import jalview.datamodel.features.FeatureSources;
 import jalview.util.StringUtils;
 
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
@@ -343,6 +345,11 @@ public class SequenceFeature implements FeatureLocationI
     return featureGroup;
   }
 
+  /**
+   * Adds a hyperlink for the feature. This should have the format label|url.
+   * 
+   * @param labelLink
+   */
   public void addLink(String labelLink)
   {
     if (links == null)
@@ -600,9 +607,11 @@ public class SequenceFeature implements FeatureLocationI
   /**
    * Answers an html-formatted report of feature details
    * 
+   * @param seqName
+   * 
    * @return
    */
-  public String getDetailsReport()
+  public String getDetailsReport(String seqName)
   {
     FeatureSourceI metadata = FeatureSources.getInstance()
             .getSource(source);
@@ -610,9 +619,10 @@ public class SequenceFeature implements FeatureLocationI
     StringBuilder sb = new StringBuilder(128);
     sb.append("<br>");
     sb.append("<table>");
+    sb.append(String.format(ROW_DATA, "Location", seqName,
+            begin == end ? begin
+                    : begin + (isContactFeature() ? ":" : "-") + end));
     sb.append(String.format(ROW_DATA, "Type", type, ""));
-    sb.append(String.format(ROW_DATA, "Start/end", begin == end ? begin
-            : begin + (isContactFeature() ? ":" : "-") + end, ""));
     String desc = StringUtils.stripHtmlTags(description);
     sb.append(String.format(ROW_DATA, "Description", desc, ""));
     if (!Float.isNaN(score) && score != 0f)
@@ -643,9 +653,13 @@ public class SequenceFeature implements FeatureLocationI
         {
           /*
            * expand values in a Map attribute across separate lines
+           * copy to a TreeMap for alphabetical ordering
            */
-          Map<?, ?> values = (Map<?, ?>) value;
-          for (Entry<?, ?> e : values.entrySet())
+          Map<String, Object> values = (Map<String, Object>) value;
+          SortedMap<String, Object> sm = new TreeMap<>(
+                  String.CASE_INSENSITIVE_ORDER);
+          sm.putAll(values);
+          for (Entry<?, ?> e : sm.entrySet())
           {
             sb.append(String.format(ROW_DATA, key, e.getKey().toString(), e
                     .getValue().toString()));
@@ -731,3 +745,21 @@ public class SequenceFeature implements FeatureLocationI
     source = theSource;
   }
 }
+
+class SFSortByEnd implements Comparator<SequenceFeature>
+{
+  @Override
+  public int compare(SequenceFeature a, SequenceFeature b)
+  {
+    return a.getEnd() - b.getEnd();
+  }
+}
+
+class SFSortByBegin implements Comparator<SequenceFeature>
+{
+  @Override
+  public int compare(SequenceFeature a, SequenceFeature b)
+  {
+    return a.getBegin() - b.getBegin();
+  }
+}