X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=b9db46123c335bd5f703045adbecd9f6e0107c84;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=dd021cfeaf0235fe546e792094fbc8e7b67810f9;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index dd021cf..b9db461 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -1,27 +1,163 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * 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>();
+
+  /**
+   * One match consists of a sequence reference, start and end positions.
+   * Discontiguous ranges in a sequence require two or more Match objects.
+   */
+  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;
+
+      /*
+       * always hold 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
+       */
+      if (start <= end)
+      {
+        this.start = start;
+        this.end = end;
+      }
+      else
+      {
+        this.start = end;
+        this.end = start;
+      }
+    }
+
+    public SequenceI getSequence()
+    {
+      return sequence;
+    }
+
+    public int getStart()
+    {
+      return start;
+    }
+
+    public int getEnd()
+    {
+      return end;
+    }
+
+    /**
+     * Returns the string of characters in the matched region, prefixed by the
+     * start position, e.g. "12CGT" or "208K"
+     */
+    @Override
+    public String toString()
+    {
+      final int from = Math.max(start - 1, 0);
+      String startPosition = String.valueOf(from);
+      return startPosition + getCharacters();
+    }
+
+    /**
+     * Returns the string of characters in the matched region.
+     */
+    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));
+    }
+
+    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
+     * to have the same hashcode.
+     */
+    @Override
+    public int hashCode()
+    {
+      int hash = sequence == null ? 0 : sequence.hashCode();
+      hash += 31 * start;
+      hash += 67 * end;
+      return hash;
+    }
+
+    /**
+     * Two Match objects are equal if they are for the same sequence, start and
+     * end positions
+     */
+    @Override
+    public boolean equals(Object obj)
+    {
+      if (obj == null || !(obj instanceof Match))
+      {
+        return false;
+      }
+      Match m = (Match) obj;
+      return (this.sequence == m.sequence && this.start == m.start && this.end == m.end);
+    }
+  }
 
   /**
    * This method replaces the old search results which merely held an alignment
@@ -37,25 +173,7 @@ public class SearchResults
    */
   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));
   }
 
   /**
@@ -67,15 +185,11 @@ public class SearchResults
    */
   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;
       }
@@ -90,7 +204,7 @@ public class SearchResults
    */
   public int[] getResults(SequenceI sequence, int start, int end)
   {
-    if (matches == null)
+    if (matches.isEmpty())
     {
       return null;
     }
@@ -99,22 +213,22 @@ 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)
       {
@@ -132,8 +246,7 @@ public class SearchResults
 
           if (result == null)
           {
-            result = new int[]
-            { matchStart, matchEnd };
+            result = new int[] { matchStart, matchEnd };
           }
           else
           {
@@ -158,37 +271,114 @@ 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;
+    return matches.isEmpty();
+  }
 
-    int start;
+  /**
+   * Returns the list of matches.
+   * 
+   * @return
+   */
+  public List<Match> getResults()
+  {
+    return matches;
+  }
 
-    int end;
+  /**
+   * 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
+   */
+  @Override
+  public String toString()
+  {
+    StringBuilder result = new StringBuilder(256);
+    for (Match m : matches)
+    {
+      result.append(m.toString());
+    }
+    return result.toString();
+  }
 
-    public Match(SequenceI seq, int start, int end)
+  /**
+   * 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 (Match m : matches)
     {
-      sequence = seq;
-      this.start = start;
-      this.end = end;
+      result.append(m.getCharacters());
+    }
+    return result.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
+   * same hashcode.
+   */
+  @Override
+  public int hashCode()
+  {
+    return matches.hashCode();
+  }
+
+  /**
+   * Two SearchResults are considered equal if they contain the same matches in
+   * the same order.
+   */
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (obj == null || !(obj instanceof SearchResults))
+    {
+      return false;
     }
+    SearchResults sr = (SearchResults) obj;
+    return ((ArrayList<Match>) this.matches).equals(sr.matches);
   }
 }