X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=d9d12db3e166a381810fafce0c885585c191337e;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=b0535b6bab324a3773effe38bb37367fff67c3aa;hpb=df1c58f9669c477db082016aa919d6c6cc9da071;p=jalview.git

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index b0535b6..d9d12db 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -1,130 +1,370 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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 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.
- *
- * 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
- */
-package jalview.datamodel;
-
-public class SearchResults
-{
-
-  Match [] matches;
-
-    /**
-     * This method replaces the old search results which merely
-     * held an alignment index of search matches. This broke
-     * when sequences were moved around the alignment
-     * @param seq Sequence
-     * @param start int
-     * @param end 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;
-  }
-
-  /**
-  * 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 for drawing on SequenceCanvas
-  */
-  public int [] getResults(SequenceI sequence, int start, int end)
-  {
-    if(matches==null)
-      return null;
-
-    int [] result = null;
-    int [] tmp = null;
-    int resultLength;
-
-    for(int m=0; m<matches.length; m++)
-    {
-      if( matches[m].sequence == sequence )
-      {
-        int matchStart = matches[m].sequence.findIndex( matches[m].start ) - 1;
-        int matchEnd = matches[m].sequence.findIndex( matches[m].end ) - 1;
-
-        if(matchStart<=end && matchEnd>=start)
-        {
-          if(matchStart<start)
-            matchStart = start;
-
-          if(matchEnd>end)
-            matchEnd = end;
-
-
-          if(result==null)
-            result = new int[]{matchStart, matchEnd};
-          else
-          {
-            resultLength = result.length;
-            tmp = new int[resultLength+2];
-            System.arraycopy(result,0,tmp,0,resultLength);
-            result = tmp;
-            result[resultLength] = matchStart;
-            result[resultLength+1] = matchEnd;
-          }
-        }
-      }
-    }
-    return result;
-  }
-
-  public int getSize()
-  {
-    return matches==null ? 0 : matches.length;
-  }
-
-  public SequenceI getResultSequence(int index)
-  {    return matches[index].sequence;  }
-
-  public int getResultStart(int index)
-  {    return matches[index].start;  }
-
-  public int getResultEnd(int index)
-  {    return matches[index].end;  }
-
-  class Match
-  {
-    SequenceI sequence;
-    int start;
-    int end;
-
-    public Match(SequenceI seq, int start, int end)
-    {
-     sequence = seq;
-     this.start = start;
-     this.end = end;
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ *  
+ * 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/>.
+ * 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
+{
+
+  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;
+      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, 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
+   * index of search matches. This broke when sequences were moved around the
+   * alignment
+   * 
+   * @param seq
+   *          Sequence
+   * @param start
+   *          int
+   * @param end
+   *          int
+   */
+  public void addResult(SequenceI seq, int start, int end)
+  {
+    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)
+   * @return true if the results involve sequence
+   */
+  public boolean involvesSequence(SequenceI sequence)
+  {
+    SequenceI ds = sequence.getDatasetSequence();
+    for (Match m : matches)
+    {
+      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
+   * for drawing on SequenceCanvas
+   */
+  public int[] getResults(SequenceI sequence, int start, int end)
+  {
+    if (matches.isEmpty())
+    {
+      return null;
+    }
+
+    int[] result = null;
+    int[] tmp = null;
+    int resultLength, matchStart = 0, matchEnd = 0;
+    boolean mfound;
+    for (Match m : matches)
+    {
+      mfound = false;
+      if (m.sequence == sequence)
+      {
+        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;
+      }
+      if (mfound)
+      {
+        if (matchStart <= end && matchEnd >= start)
+        {
+          if (matchStart < start)
+          {
+            matchStart = start;
+          }
+
+          if (matchEnd > end)
+          {
+            matchEnd = end;
+          }
+
+          if (result == null)
+          {
+            result = new int[] { matchStart, matchEnd };
+          }
+          else
+          {
+            resultLength = result.length;
+            tmp = new int[resultLength + 2];
+            System.arraycopy(result, 0, tmp, 0, resultLength);
+            result = tmp;
+            result[resultLength] = matchStart;
+            result[resultLength + 1] = matchEnd;
+          }
+        }
+        else
+        {
+          // debug
+          // System.err.println("Outwith bounds!" + matchStart+">"+end +"  or "
+          // + matchEnd+"<"+start);
+        }
+      }
+    }
+    return result;
+  }
+
+  public int getSize()
+  {
+    return matches.size();
+  }
+
+  public SequenceI getResultSequence(int index)
+  {
+    return matches.get(index).sequence;
+  }
+
+  /**
+   * Returns the start position of the i'th match in the search results.
+   * 
+   * @param i
+   * @return
+   */
+  public int getResultStart(int i)
+  {
+    return matches.get(i).start;
+  }
+
+  /**
+   * Returns the end position of the i'th match in the search results.
+   * 
+   * @param i
+   * @return
+   */
+  public int getResultEnd(int i)
+  {
+    return matches.get(i).end;
+  }
+
+  /**
+   * Returns true if no search result matches are held.
+   * 
+   * @return
+   */
+  public boolean isEmpty()
+  {
+    return matches.isEmpty();
+  }
+
+  /**
+   * Returns the list of matches.
+   * 
+   * @return
+   */
+  public List<Match> getResults()
+  {
+    return matches;
+  }
+
+  /**
+   * 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();
+  }
+
+  /**
+   * 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)
+    {
+      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);
+  }
+}