package jalview.datamodel;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.BitSet;
import java.util.List;
int end;
/**
- * Constructor
+ * create a Match on a range of sequence. Match always holds region 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
*
* @param seq
* a sequence
}
else
{
+ // TODO: JBP could mark match as being specified in reverse direction
+ // for use
+ // by caller ? e.g. visualizing reverse strand highlight
this.start = end;
this.end = start;
}
}
/**
- * Returns the string of characters in the matched region, prefixed by the
- * start position, e.g. "12CGT" or "208K"
+ * Returns a representation as "seqid/start-end"
*/
@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));
+ StringBuilder sb = new StringBuilder();
+ if (sequence != null)
+ {
+ sb.append(sequence.getName()).append("/");
+ }
+ sb.append(start).append("-").append(end);
+ return sb.toString();
}
public void setSequence(SequenceI seq)
* @see jalview.datamodel.SearchResultsI#addResult(jalview.datamodel.SequenceI, int, int)
*/
@Override
- public void addResult(SequenceI seq, int start, int end)
+ public SearchResultMatchI addResult(SequenceI seq, int start, int end)
{
- matches.add(new Match(seq, start, end));
+ Match m = new Match(seq, start, end);
+ matches.add(m);
+ return m;
}
/* (non-Javadoc)
public boolean involvesSequence(SequenceI sequence)
{
SequenceI ds = sequence.getDatasetSequence();
- Match m;
for (SearchResultMatchI _m : matches)
{
- m = (Match) _m;
- if (m.sequence != null
- && (m.sequence == sequence || m.sequence == ds))
+ SequenceI matched = _m.getSequence();
+ if (matched != null && (matched == sequence || matched == ds))
{
return true;
}
m = (Match) _m;
mfound = false;
- if (m.sequence == sequence)
+ if (m.sequence == sequence
+ || m.sequence == sequence.getDatasetSequence())
{
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;
+ matchEnd = m.start == m.end ? matchStart : sequence
+ .findIndex(m.end) - 1;
}
+
if (mfound)
{
if (matchStart <= end && matchEnd >= start)
}
/* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResultSequence(int)
- */
- @Override
- public SequenceI getResultSequence(int index)
- {
- return matches.get(index).getSequence();
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResultStart(int)
- */
- @Override
- public int getResultStart(int i)
- {
- return matches.get(i).getStart();
- }
-
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResultEnd(int)
- */
- @Override
- public int getResultEnd(int i)
- {
- return matches.get(i).getEnd();
- }
-
- /* (non-Javadoc)
* @see jalview.datamodel.SearchResultsI#isEmpty()
*/
@Override
}
/**
- * 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 the results as a list of matches [seq1/from-to, seq2/from-to, ...]
*
* @return
*/
@Override
public String toString()
{
- StringBuilder result = new StringBuilder(256);
- 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();
+ return matches == null ? "" : matches.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
+ * Hashcode is derived from the list of matches. This ensures that when two
+ * SearchResults objects satisfy the test for equals(), then they have the
* same hashcode.
+ *
+ * @see Match#hashCode()
+ * @see java.util.AbstractList#hashCode()
*/
@Override
public int hashCode()