Merge branch 'feature/JAL-2664' into feature/JAL-2527

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

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 2ba1612..a270e37 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -21,7 +21,6 @@
 package jalview.datamodel;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.BitSet;
 import java.util.List;
 
@@ -120,28 +119,18 @@ public class SearchResults implements SearchResultsI
     }
 
     /**
-     * Returns the string of characters in the matched region, prefixed by the
-     * start position, e.g. "12CGT" or "208K"
+     * Returns a representation as "seqid/start-end"
      */
     @Override
     public String toString()
     {
-      final int from = Math.max(start - 1, 0);
-      String startPosition = String.valueOf(from);
-      return startPosition + getCharacters();
-    }
-
-    /* (non-Javadoc)
-     * @see jalview.datamodel.SearchResultMatchI#getCharacters()
-     */
-    @Override
-    public String getCharacters()
-    {
-      char[] chars = sequence.getSequence();
-      // convert start/end to base 0 (with bounds check)
-      final int from = Math.max(start - 1, 0);
-      final int to = Math.min(end, chars.length + 1);
-      return String.valueOf(Arrays.copyOfRange(chars, from, to));
+      StringBuilder sb = new StringBuilder();
+      if (sequence != null)
+      {
+        sb.append(sequence.getName()).append("/");
+      }
+      sb.append(start).append("-").append(end);
+      return sb.toString();
     }
 
     public void setSequence(SequenceI seq)
@@ -175,8 +164,8 @@ 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());
     }
   }
 
@@ -198,12 +187,10 @@ public class SearchResults implements SearchResultsI
   public boolean involvesSequence(SequenceI sequence)
   {
     SequenceI ds = sequence.getDatasetSequence();
-    Match m;
     for (SearchResultMatchI _m : matches)
     {
-      m = (Match) _m;
-      if (m.sequence != null
-              && (m.sequence == sequence || m.sequence == ds))
+      SequenceI matched = _m.getSequence();
+      if (matched != null && (matched == sequence || matched == ds))
       {
         return true;
       }
@@ -277,7 +264,7 @@ 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);
         }
       }
@@ -320,33 +307,6 @@ public class SearchResults implements SearchResultsI
   }
 
   /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#getResultSequence(int)
-   */
-  @Override
-  public SequenceI getResultSequence(int index)
-  {
-    return matches.get(index).getSequence();
-  }
-
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#getResultStart(int)
-   */
-  @Override
-  public int getResultStart(int i)
-  {
-    return matches.get(i).getStart();
-  }
-
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SearchResultsI#getResultEnd(int)
-   */
-  @Override
-  public int getResultEnd(int i)
-  {
-    return matches.get(i).getEnd();
-  }
-
-  /* (non-Javadoc)
    * @see jalview.datamodel.SearchResultsI#isEmpty()
    */
   @Override
@@ -365,44 +325,23 @@ public class SearchResults implements SearchResultsI
   }
 
   /**
-   * Return the results as a string of characters (bases) prefixed by start
-   * position(s). Meant for use when the context ensures that all matches are to
-   * regions of the same sequence (otherwise the result is meaningless).
+   * Return the results as a list of matches [seq1/from-to, seq2/from-to, ...]
    * 
    * @return
    */
   @Override
   public String toString()
   {
-    StringBuilder result = new StringBuilder(256);
-    for (SearchResultMatchI m : matches)
-    {
-      result.append(m.toString());
-    }
-    return result.toString();
-  }
-
-  /**
-   * Return the results as a string of characters (bases). Meant for use when
-   * the context ensures that all matches are to regions of the same sequence
-   * (otherwise the result is meaningless).
-   * 
-   * @return
-   */
-  public String getCharacters()
-  {
-    StringBuilder result = new StringBuilder(256);
-    for (SearchResultMatchI m : matches)
-    {
-      result.append(m.getCharacters());
-    }
-    return result.toString();
+    return matches == null ? "" : matches.toString();
   }
 
   /**
-   * Hashcode is has derived from the list of matches. This ensures that when
-   * two SearchResults objects satisfy the test for equals(), then they have the
+   * Hashcode is derived from the list of matches. This ensures that when two
+   * SearchResults objects satisfy the test for equals(), then they have the
    * same hashcode.
+   * 
+   * @see Match#hashCode()
+   * @see java.util.AbstractList#hashCode()
    */
   @Override
   public int hashCode()