JAL-2839 Finder refactoring prior to fixing the defect

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

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 8d98fc4..63a87a8 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
@@ -91,27 +91,18 @@ public class SearchResults implements SearchResultsI
       }
     }
 
-    /* (non-Javadoc)
-     * @see jalview.datamodel.SearchResultMatchI#getSequence()
-     */
     @Override
     public SequenceI getSequence()
     {
       return sequence;
     }
 
-    /* (non-Javadoc)
-     * @see jalview.datamodel.SearchResultMatchI#getStart()
-     */
     @Override
     public int getStart()
     {
       return start;
     }
 
-    /* (non-Javadoc)
-     * @see jalview.datamodel.SearchResultMatchI#getEnd()
-     */
     @Override
     public int getEnd()
     {
@@ -133,11 +124,6 @@ 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 +150,14 @@ 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());
+    }
+
+    @Override
+    public boolean contains(SequenceI seq, int from, int to)
+    {
+      return (sequence == seq && start <= from && end >= to);
     }
   }
 
@@ -259,7 +251,7 @@ 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);
         }
       }
@@ -358,4 +350,10 @@ public class SearchResults implements SearchResultsI
     SearchResultsI sr = (SearchResultsI) obj;
     return matches.equals(sr.getResults());
   }
+
+  @Override
+  public void addSearchResults(SearchResultsI toAdd)
+  {
+    matches.addAll(toAdd.getResults());
+  }
 }