package jalview.datamodel;
import java.util.ArrayList;
-import java.util.Arrays;
+import java.util.BitSet;
import java.util.List;
/**
*/
public class SearchResults implements SearchResultsI
{
+ private int count;
- private List<Match> matches = new ArrayList<Match>();
+ private List<SearchResultMatchI> matches = new ArrayList<>();
/**
* One match consists of a sequence reference, start and end positions.
*/
public class Match implements SearchResultMatchI
{
- SequenceI sequence;
+ final SequenceI sequence;
/**
* Start position of match in sequence (base 1)
*/
- int start;
+ final int start;
/**
* End position (inclusive) (base 1)
*/
- int end;
+ final 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;
}
}
- /* (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()
{
}
/**
- * 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));
- }
-
- public void setSequence(SequenceI seq)
- {
- this.sequence = seq;
+ StringBuilder sb = new StringBuilder();
+ if (sequence != null)
+ {
+ sb.append(sequence.getName()).append("/");
+ }
+ sb.append(start).append("-").append(end);
+ return sb.toString();
}
/**
@Override
public boolean equals(Object obj)
{
- if (obj == null || !(obj instanceof Match))
+ if (obj == null || !(obj instanceof SearchResultMatchI))
{
return false;
}
- Match m = (Match) obj;
- return (this.sequence == m.sequence && this.start == m.start && this.end == m.end);
+ SearchResultMatchI m = (SearchResultMatchI) obj;
+ return (sequence == m.getSequence() && start == m.getStart()
+ && end == m.getEnd());
+ }
+
+ @Override
+ public boolean contains(SequenceI seq, int from, int to)
+ {
+ return (sequence == seq && start <= from && end >= to);
}
}
- /* (non-Javadoc)
- * @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)
+ {
+ Match m = new Match(seq, start, end);
+ if (!matches.contains(m))
+ {
+ matches.add(m);
+ count++;
+ }
+ return m;
+ }
+
+ @Override
+ public void addResult(SequenceI seq, int[] positions)
{
- matches.add(new Match(seq, start, end));
+ /*
+ * 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;
+ }
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#involvesSequence(jalview.datamodel.SequenceI)
- */
@Override
public boolean involvesSequence(SequenceI sequence)
{
+ final int start = sequence.getStart();
+ final int end = sequence.getEnd();
+
SequenceI ds = sequence.getDatasetSequence();
- for (Match m : matches)
+ for (SearchResultMatchI m : matches)
{
- if (m.sequence != null
- && (m.sequence == sequence || m.sequence == ds))
+ SequenceI matched = m.getSequence();
+ if (matched != null && (matched == sequence || matched == ds)
+ && (m.getEnd() >= start) && (m.getStart() <= end))
{
return true;
}
return false;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResults(jalview.datamodel.SequenceI, int, int)
- */
@Override
public int[] getResults(SequenceI sequence, int start, int end)
{
int[] tmp = null;
int resultLength, matchStart = 0, matchEnd = 0;
boolean mfound;
- for (Match m : matches)
+ Match m;
+ for (SearchResultMatchI _m : matches)
{
+ m = (Match) _m;
+
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())
+ if (m.sequence == sequence
+ || 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)
else
{
// debug
- // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
+ // System.err.println("Outwith bounds!" + matchStart+">"+end +" or "
// + matchEnd+"<"+start);
}
}
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)
+ public int markColumns(SequenceCollectionI sqcol, BitSet bs)
{
- return matches.get(index).sequence;
- }
+ int count = 0;
+ BitSet mask = new BitSet();
+ int startRes = sqcol.getStartRes();
+ int endRes = sqcol.getEndRes();
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResultStart(int)
- */
- @Override
- public int getResultStart(int i)
- {
- return matches.get(i).start;
+ 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;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResultEnd(int)
- */
@Override
- public int getResultEnd(int i)
+ public int getCount()
{
- return matches.get(i).end;
+ return count;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#isEmpty()
- */
@Override
public boolean isEmpty()
{
return matches.isEmpty();
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResults()
- */
@Override
- public List<Match> getResults()
+ public List<SearchResultMatchI> 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 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 matches == null ? "" : matches.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
+ * 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()
@Override
public boolean equals(Object obj)
{
- if (obj == null || !(obj instanceof SearchResults))
+ if (obj == null || !(obj instanceof SearchResultsI))
{
return false;
}
- SearchResults sr = (SearchResults) obj;
- return ((ArrayList<Match>) this.matches).equals(sr.matches);
+ 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