Merge branch 'develop' into features/JAL-250_hideredundantseqs

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

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 1bf5475..cde50e5 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -34,7 +34,7 @@ import java.util.List;
 public class SearchResults implements SearchResultsI
 {
 
-  private List<SearchResultMatchI> matches = new ArrayList<SearchResultMatchI>();
+  private List<SearchResultMatchI> matches = new ArrayList<>();
 
   /**
    * One match consists of a sequence reference, start and end positions.
@@ -42,17 +42,17 @@ public class SearchResults implements SearchResultsI
    */
   public class Match implements SearchResultMatchI
   {
-    SequenceI sequence;
+    final SequenceI sequence;
 
     /**
      * Start position of match in sequence (base 1)
      */
-    int start;
+    final int start;
 
     /**
      * End position (inclusive) (base 1)
      */
-    int end;
+    final int end;
 
     /**
      * create a Match on a range of sequence. Match always holds region in
@@ -133,11 +133,6 @@ public class SearchResults implements SearchResultsI
       return sb.toString();
     }
 
-    public void setSequence(SequenceI seq)
-    {
-      this.sequence = seq;
-    }
-
     /**
      * Hashcode is the hashcode of the matched sequence plus a hash of start and
      * end positions. Match objects that pass the test for equals are guaranteed
@@ -164,8 +159,8 @@ public class SearchResults implements SearchResultsI
         return false;
       }
       SearchResultMatchI m = (SearchResultMatchI) obj;
-      return (sequence == m.getSequence() && start == m.getStart() && end == m
-              .getEnd());
+      return (sequence == m.getSequence() && start == m.getStart()
+              && end == m.getEnd());
     }
   }
 
@@ -219,20 +214,15 @@ public class SearchResults implements SearchResultsI
       m = (Match) _m;
 
       mfound = false;
-      if (m.sequence == sequence)
-      {
-        mfound = true;
-        // locate aligned position
-        matchStart = sequence.findIndex(m.start) - 1;
-        matchEnd = sequence.findIndex(m.end) - 1;
-      }
-      else if (m.sequence == sequence.getDatasetSequence())
+      if (m.sequence == sequence
+              || m.sequence == sequence.getDatasetSequence())
       {
         mfound = true;
-        // locate region in local context
         matchStart = sequence.findIndex(m.start) - 1;
-        matchEnd = sequence.findIndex(m.end) - 1;
+        matchEnd = m.start == m.end ? matchStart : sequence
+                .findIndex(m.end) - 1;
       }
+
       if (mfound)
       {
         if (matchStart <= end && matchEnd >= start)
@@ -264,7 +254,7 @@ public class SearchResults implements SearchResultsI
         else
         {
           // debug
-          // System.err.println("Outwith bounds!" + matchStart+">"+end +"  or "
+          // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
           // + matchEnd+"<"+start);
         }
       }
@@ -363,4 +353,10 @@ public class SearchResults implements SearchResultsI
     SearchResultsI sr = (SearchResultsI) obj;
     return matches.equals(sr.getResults());
   }
+
+  @Override
+  public void addSearchResults(SearchResultsI toAdd)
+  {
+    matches.addAll(toAdd.getResults());
+  }
 }