X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=e62e58a8192f0ab64f351a8ab005568ca53ca6ec;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=329f447fcc6eb6de89434be8bfdb6776ce6eefd9;hpb=5c212e384ee48b37d899cc88fc3d12c5028cc3b4;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 329f447..e62e58a 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -1,27 +1,100 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * Holds a list of search result matches, where each match is a contiguous
+ * stretch of a single sequence.
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class SearchResults
 {
 
-  Match[] matches;
+  private List<Match> matches = new ArrayList<Match>();
+
+  public class Match
+  {
+    SequenceI sequence;
+
+    /**
+     * Start position of match in sequence (base 1)
+     */
+    int start;
+
+    /**
+     * End position (inclusive) (base 1)
+     */
+    int end;
+
+    /**
+     * Constructor
+     * 
+     * @param seq
+     *          a sequence
+     * @param start
+     *          start position of matched range (base 1)
+     * @param end
+     *          end of matched range (inclusive, base 1)
+     */
+    public Match(SequenceI seq, int start, int end)
+    {
+      sequence = seq;
+      this.start = start;
+      this.end = end;
+    }
+
+    public SequenceI getSequence()
+    {
+      return sequence;
+    }
+
+    public int getStart()
+    {
+      return start;
+    }
+
+    public int getEnd()
+    {
+      return end;
+    }
+
+    /**
+     * Returns the string of characters in the matched region.
+     */
+    @Override
+    public String toString()
+    {
+      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));
+    }
+  }
 
   /**
    * This method replaces the old search results which merely held an alignment
@@ -29,57 +102,38 @@ public class SearchResults
    * alignment
    * 
    * @param seq
-   *                Sequence
+   *          Sequence
    * @param start
-   *                int
+   *          int
    * @param end
-   *                int
+   *          int
    */
   public void addResult(SequenceI seq, int start, int end)
   {
-    if (matches == null)
-    {
-      matches = new Match[]
-      { new Match(seq, start, end) };
-      return;
-    }
-
-    int mSize = matches.length;
-
-    Match[] tmp = new Match[mSize + 1];
-    int m;
-    for (m = 0; m < mSize; m++)
-    {
-      tmp[m] = matches[m];
-    }
-
-    tmp[m] = new Match(seq, start, end);
-
-    matches = tmp;
+    matches.add(new Match(seq, start, end));
   }
+
   /**
    * Quickly check if the given sequence is referred to in the search results
-   * @param sequence (specific alignment sequence or a dataset sequence)
+   * 
+   * @param sequence
+   *          (specific alignment sequence or a dataset sequence)
    * @return true if the results involve sequence
    */
   public boolean involvesSequence(SequenceI sequence)
   {
-    if (matches==null || matches.length==0)
-    {
-      return false;
-    }
     SequenceI ds = sequence.getDatasetSequence();
-    for (int m=0; m<matches.length; m++)
+    for (Match m : matches)
     {
-      if (matches[m].sequence!=null &&
-              (matches[m].sequence==sequence 
-              || matches[m].sequence==ds))
+      if (m.sequence != null
+              && (m.sequence == sequence || m.sequence == ds))
       {
         return true;
       }
     }
     return false;
   }
+
   /**
    * This Method returns the search matches which lie between the start and end
    * points of the sequence in question. It is optimised for returning objects
@@ -87,7 +141,7 @@ public class SearchResults
    */
   public int[] getResults(SequenceI sequence, int start, int end)
   {
-    if (matches == null)
+    if (matches.isEmpty())
     {
       return null;
     }
@@ -96,22 +150,22 @@ public class SearchResults
     int[] tmp = null;
     int resultLength, matchStart = 0, matchEnd = 0;
     boolean mfound;
-    for (int m = 0; m < matches.length; m++)
+    for (Match m : matches)
     {
       mfound = false;
-      if (matches[m].sequence == sequence)
+      if (m.sequence == sequence)
       {
         mfound = true;
         // locate aligned position
-        matchStart = sequence.findIndex(matches[m].start) - 1;
-        matchEnd = sequence.findIndex(matches[m].end) - 1;
+        matchStart = sequence.findIndex(m.start) - 1;
+        matchEnd = sequence.findIndex(m.end) - 1;
       }
-      else if (matches[m].sequence == sequence.getDatasetSequence())
+      else if (m.sequence == sequence.getDatasetSequence())
       {
         mfound = true;
         // locate region in local context
-        matchStart = sequence.findIndex(matches[m].start) - 1;
-        matchEnd = sequence.findIndex(matches[m].end) - 1;
+        matchStart = sequence.findIndex(m.start) - 1;
+        matchEnd = sequence.findIndex(m.end) - 1;
       }
       if (mfound)
       {
@@ -142,6 +196,12 @@ public class SearchResults
             result[resultLength + 1] = matchEnd;
           }
         }
+        else
+        {
+          // debug
+          // System.err.println("Outwith bounds!" + matchStart+">"+end +"  or "
+          // + matchEnd+"<"+start);
+        }
       }
     }
     return result;
@@ -149,37 +209,71 @@ public class SearchResults
 
   public int getSize()
   {
-    return matches == null ? 0 : matches.length;
+    return matches.size();
   }
 
   public SequenceI getResultSequence(int index)
   {
-    return matches[index].sequence;
+    return matches.get(index).sequence;
   }
 
-  public int getResultStart(int index)
+  /**
+   * Returns the start position of the i'th match in the search results.
+   * 
+   * @param i
+   * @return
+   */
+  public int getResultStart(int i)
   {
-    return matches[index].start;
+    return matches.get(i).start;
   }
 
-  public int getResultEnd(int index)
+  /**
+   * Returns the end position of the i'th match in the search results.
+   * 
+   * @param i
+   * @return
+   */
+  public int getResultEnd(int i)
   {
-    return matches[index].end;
+    return matches.get(i).end;
   }
 
-  class Match
+  /**
+   * Returns true if no search result matches are held.
+   * 
+   * @return
+   */
+  public boolean isEmpty()
   {
-    SequenceI sequence;
-
-    int start;
+    return matches.isEmpty();
+  }
 
-    int end;
+  /**
+   * Returns the list of matches.
+   * 
+   * @return
+   */
+  public List<Match> getResults()
+  {
+    return matches;
+  }
 
-    public Match(SequenceI seq, int start, int end)
+  /**
+   * Return the results as a string of characters. Meant for use when the
+   * context ensures that all matches are to regions of the same sequence
+   * (otherwise the result is meaningless).
+   * 
+   * @return
+   */
+  @Override
+  public String toString()
+  {
+    StringBuilder result = new StringBuilder(256);
+    for (Match m : matches)
     {
-      sequence = seq;
-      this.start = start;
-      this.end = end;
+      result.append(m.toString());
     }
+    return result.toString();
   }
 }