X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSearchResults.java;h=629edb74e4d084cd9f8cd2db0cbb6865b31c1daa;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=240052464ef1842fa1686be892d3af4cbe89f8b7;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 2400524..629edb7 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -1,85 +1,188 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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 .
+ * 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 matches = new ArrayList();
/**
- * 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
+ * One match consists of a sequence reference, start and end positions.
+ * Discontiguous ranges in a sequence require two or more Match objects.
*/
- public void addResult(SequenceI seq, int start, int end)
+ public class Match
{
- if (matches == null)
+ 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)
{
- matches = new Match[]
- { new Match(seq, start, end) };
- return;
+ sequence = seq;
+ this.start = start;
+ this.end = end;
}
- int mSize = matches.length;
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
- Match[] tmp = new Match[mSize + 1];
- int m;
- for (m = 0; m < mSize; m++)
+ public int getStart()
{
- tmp[m] = matches[m];
+ return start;
}
- tmp[m] = new Match(seq, start, end);
+ public int getEnd()
+ {
+ return end;
+ }
- matches = tmp;
+ /**
+ * 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)
+ *
+ * @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"+end +" or "
+ // + matchEnd+"<"+start);
+ }
}
}
return result;
@@ -149,37 +257,114 @@ 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 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) this.matches).equals(sr.matches);
}
}