JAL-2446 merged to spike branch

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

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 8cdf446..8d98fc4 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;
 
@@ -56,7 +55,10 @@ public class SearchResults implements SearchResultsI
     int end;
 
     /**
-     * Constructor
+     * create a Match on a range of sequence. Match always holds region in
+     * forwards order, even if given in reverse order (such as from a mapping to
+     * a reverse strand); this avoids trouble for routines that highlight search
+     * results etc
      * 
      * @param seq
      *          a sequence
@@ -81,6 +83,9 @@ public class SearchResults implements SearchResultsI
       }
       else
       {
+        // TODO: JBP could mark match as being specified in reverse direction
+        // for use
+        // by caller ? e.g. visualizing reverse strand highlight
         this.start = end;
         this.end = start;
       }
@@ -114,28 +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)
@@ -192,12 +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;
       }
@@ -226,20 +219,15 @@ public class SearchResults implements SearchResultsI
       m = (Match) _m;
 
       mfound = false;
-      if (m.sequence == sequence)
+      if (m.sequence == sequence
+              || m.sequence == sequence.getDatasetSequence())
       {
         mfound = true;
-        // locate aligned position
         matchStart = sequence.findIndex(m.start) - 1;
-        matchEnd = sequence.findIndex(m.end) - 1;
-      }
-      else if (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)
@@ -314,33 +302,6 @@ 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
@@ -359,44 +320,23 @@ 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()