import java.util.ArrayList;
import java.util.Arrays;
+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
+ * @author gmcarstairs amwaterhouse
*
*/
-public class SearchResults
+public class SearchResults implements SearchResultsI
{
- private List<Match> matches = new ArrayList<Match>();
+ private List<SearchResultMatchI> matches = new ArrayList<SearchResultMatchI>();
/**
* 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
+ public class Match implements SearchResultMatchI
{
SequenceI sequence;
}
}
+ /* (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;
return startPosition + getCharacters();
}
- /**
- * Returns the string of characters in the matched region.
+ /* (non-Javadoc)
+ * @see jalview.datamodel.SearchResultMatchI#getCharacters()
*/
+ @Override
public String getCharacters()
{
char[] chars = sequence.getSequence();
@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());
}
}
- /**
- * 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();
- for (Match m : matches)
+ Match m;
+ for (SearchResultMatchI _m : matches)
{
+ m = (Match) _m;
if (m.sequence != null
&& (m.sequence == sequence || m.sequence == ds))
{
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())
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)
{
return result;
}
+ @Override
+ public int markColumns(SequenceCollectionI sqcol, BitSet bs)
+ {
+ int count = 0;
+ BitSet mask = new BitSet();
+ for (SequenceI s : sqcol.getSequences())
+ {
+ int[] cols = getResults(s, sqcol.getStartRes(), sqcol.getEndRes());
+ 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#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;
+ return matches.get(index).getSequence();
}
- /**
- * 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;
+ return matches.get(i).getStart();
}
- /**
- * 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;
+ return matches.get(i).getEnd();
}
- /**
- * 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()
*/
- public List<Match> getResults()
+ @Override
+ public List<SearchResultMatchI> getResults()
{
return matches;
}
public String toString()
{
StringBuilder result = new StringBuilder(256);
- for (Match m : matches)
+ for (SearchResultMatchI m : matches)
{
result.append(m.toString());
}
public String getCharacters()
{
StringBuilder result = new StringBuilder(256);
- for (Match m : matches)
+ for (SearchResultMatchI m : matches)
{
result.append(m.getCharacters());
}
@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());
}
}
git://source.jalview.org / jalview.git / blobdiff