* Holds a list of search result matches, where each match is a contiguous
* stretch of a single sequence.
*
- * @author gmcarstairs
+ * @author gmcarstairs amwaterhouse
*
*/
-public class SearchResults
+public class SearchResults implements SearchResultsI
{
private List<Match> matches = new ArrayList<Match>();
- public class 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 implements SearchResultMatchI
{
SequenceI sequence;
public Match(SequenceI seq, int start, int end)
{
sequence = seq;
- this.start = start;
- this.end = end;
+
+ /*
+ * 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;
+ }
}
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultMatchI#getSequence()
+ */
+ @Override
public SequenceI getSequence()
{
return sequence;
}
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultMatchI#getStart()
+ */
+ @Override
public int getStart()
{
return start;
}
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultMatchI#getEnd()
+ */
+ @Override
public int getEnd()
{
return end;
}
/**
- * Returns the string of characters in the matched region.
+ * 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();
+ }
+
+ /* (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));
}
+
+ 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
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultsI#addResult(jalview.datamodel.SequenceI, int, int)
*/
+ @Override
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
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultsI#involvesSequence(jalview.datamodel.SequenceI)
*/
+ @Override
public boolean involvesSequence(SequenceI sequence)
{
SequenceI ds = sequence.getDatasetSequence();
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
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultsI#getResults(jalview.datamodel.SequenceI, int, int)
*/
+ @Override
public int[] getResults(SequenceI sequence, int start, int end)
{
if (matches.isEmpty())
if (result == null)
{
- result = new int[]
- { matchStart, matchEnd };
+ result = new int[] { matchStart, matchEnd };
}
else
{
return result;
}
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultsI#getSize()
+ */
+ @Override
public int getSize()
{
return matches.size();
}
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultsI#getResultSequence(int)
+ */
+ @Override
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
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultsI#getResultStart(int)
*/
+ @Override
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
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultsI#getResultEnd(int)
*/
+ @Override
public int getResultEnd(int i)
{
return matches.get(i).end;
}
- /**
- * Returns true if no search result matches are held.
- *
- * @return
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultsI#isEmpty()
*/
+ @Override
public boolean isEmpty()
{
return matches.isEmpty();
}
- /**
- * Returns the list of matches.
- *
- * @return
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultsI#getResults()
*/
+ @Override
public List<Match> getResults()
{
return matches;
}
/**
- * 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 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
*/
public String toString()
{
StringBuilder result = new StringBuilder(256);
- for (Match m : matches)
+ 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();
+ }
+
+ /**
+ * 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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff