*/
package jalview.datamodel;
-public class SearchResults
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.List;
+
+/**
+ * Holds a list of search result matches, where each match is a contiguous
+ * stretch of a single sequence.
+ *
+ * @author gmcarstairs amwaterhouse
+ *
+ */
+public class SearchResults implements SearchResultsI
{
+ private int count;
- Match[] matches;
+ private List<SearchResultMatchI> 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 implements SearchResultMatchI
{
- if (matches == null)
+ final SequenceI sequence;
+
+ /**
+ * Start position of match in sequence (base 1)
+ */
+ final int start;
+
+ /**
+ * End position (inclusive) (base 1)
+ */
+ final int end;
+
+ /**
+ * 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
+ * @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
+ {
+ // 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;
+ }
+ }
+
+ @Override
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
+
+ @Override
+ public int getStart()
+ {
+ return start;
+ }
+
+ @Override
+ public int getEnd()
{
- matches = new Match[]
- { new Match(seq, start, end) };
- return;
+ return end;
}
- int mSize = matches.length;
+ /**
+ * Returns a representation as "seqid/start-end"
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder sb = new StringBuilder();
+ if (sequence != null)
+ {
+ sb.append(sequence.getName()).append("/");
+ }
+ sb.append(start).append("-").append(end);
+ return sb.toString();
+ }
- Match[] tmp = new Match[mSize + 1];
- int m;
- for (m = 0; m < mSize; m++)
+ /**
+ * 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()
{
- tmp[m] = matches[m];
+ int hash = sequence == null ? 0 : sequence.hashCode();
+ hash += 31 * start;
+ hash += 67 * end;
+ return hash;
}
- tmp[m] = new Match(seq, start, end);
+ /**
+ * 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 SearchResultMatchI))
+ {
+ return false;
+ }
+ SearchResultMatchI m = (SearchResultMatchI) obj;
+ return (sequence == m.getSequence() && start == m.getStart()
+ && end == m.getEnd());
+ }
- matches = tmp;
+ @Override
+ public boolean contains(SequenceI seq, int from, int to)
+ {
+ return (sequence == seq && start <= from && end >= to);
+ }
}
- /**
- * 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)
+ @Override
+ public SearchResultMatchI addResult(SequenceI seq, int start, int end)
{
- if (matches == null || matches.length == 0)
+ Match m = new Match(seq, start, end);
+ if (!matches.contains(m))
{
- return false;
+ matches.add(m);
+ count++;
}
+ return m;
+ }
+
+ @Override
+ public void addResult(SequenceI seq, int[] positions)
+ {
+ /*
+ * we only increment the match count by 1 - or not at all,
+ * if the matches are all duplicates of existing
+ */
+ int beforeCount = count;
+ for (int i = 0; i < positions.length - 1; i += 2)
+ {
+ addResult(seq, positions[i], positions[i + 1]);
+ }
+ if (count > beforeCount)
+ {
+ count = beforeCount + 1;
+ }
+ }
+
+ @Override
+ public boolean involvesSequence(SequenceI sequence)
+ {
+ final int start = sequence.getStart();
+ final int end = sequence.getEnd();
+
SequenceI ds = sequence.getDatasetSequence();
- for (int m = 0; m < matches.length; m++)
+ for (SearchResultMatchI m : matches)
{
- if (matches[m].sequence != null
- && (matches[m].sequence == sequence || matches[m].sequence == ds))
+ SequenceI matched = m.getSequence();
+ if (matched != null && (matched == sequence || matched == ds)
+ && (m.getEnd() >= start) && (m.getStart() <= end))
{
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
- */
+ @Override
public int[] getResults(SequenceI sequence, int start, int end)
{
- if (matches == null)
+ if (matches.isEmpty())
{
return null;
}
int[] tmp = null;
int resultLength, matchStart = 0, matchEnd = 0;
boolean mfound;
- for (int m = 0; m < matches.length; m++)
+ Match m;
+ for (SearchResultMatchI _m : matches)
{
+ m = (Match) _m;
+
mfound = false;
- if (matches[m].sequence == sequence)
+ if (m.sequence == sequence
+ || m.sequence == sequence.getDatasetSequence())
{
mfound = true;
- // locate aligned position
- matchStart = sequence.findIndex(matches[m].start) - 1;
- matchEnd = sequence.findIndex(matches[m].end) - 1;
- }
- else if (matches[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 = m.start == m.end ? matchStart : sequence
+ .findIndex(m.end) - 1;
}
+
if (mfound)
{
if (matchStart <= end && matchEnd >= start)
if (result == null)
{
- result = new int[]
- { matchStart, matchEnd };
+ result = new int[] { matchStart, matchEnd };
}
else
{
else
{
// debug
- // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
+ // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
// + matchEnd+"<"+start);
}
}
return result;
}
- public int getSize()
+ @Override
+ public int markColumns(SequenceCollectionI sqcol, BitSet bs)
{
- return matches == null ? 0 : matches.length;
+ int count = 0;
+ BitSet mask = new BitSet();
+ int startRes = sqcol.getStartRes();
+ int endRes = sqcol.getEndRes();
+
+ for (SequenceI s : sqcol.getSequences())
+ {
+ int[] cols = getResults(s, startRes, endRes);
+ if (cols != null)
+ {
+ for (int pair = 0; pair < cols.length; pair += 2)
+ {
+ mask.set(cols[pair], cols[pair + 1] + 1);
+ }
+ }
+ }
+ // compute columns that were newly selected
+ BitSet original = (BitSet) bs.clone();
+ original.and(mask);
+ count = mask.cardinality() - original.cardinality();
+ // and mark ranges not already marked
+ bs.or(mask);
+ return count;
}
- public SequenceI getResultSequence(int index)
+ @Override
+ public int getCount()
{
- return matches[index].sequence;
+ return count;
}
- public int getResultStart(int index)
+ @Override
+ public boolean isEmpty()
{
- return matches[index].start;
+ return matches.isEmpty();
}
- public int getResultEnd(int index)
+ @Override
+ public List<SearchResultMatchI> getResults()
{
- return matches[index].end;
+ return matches;
}
- class Match
+ /**
+ * Return the results as a list of matches [seq1/from-to, seq2/from-to, ...]
+ *
+ * @return
+ */
+ @Override
+ public String toString()
{
- SequenceI sequence;
-
- int start;
+ return matches == null ? "" : matches.toString();
+ }
- int end;
+ /**
+ * 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()
+ {
+ return matches.hashCode();
+ }
- public Match(SequenceI seq, int start, int end)
+ /**
+ * 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 SearchResultsI))
{
- sequence = seq;
- this.start = start;
- this.end = end;
+ return false;
}
+ SearchResultsI sr = (SearchResultsI) obj;
+ return matches.equals(sr.getResults());
+ }
+
+ @Override
+ public void addSearchResults(SearchResultsI toAdd)
+ {
+ matches.addAll(toAdd.getResults());
}
}
git://source.jalview.org / jalview.git / blobdiff