/**
*
- * Implements the SequenceI interface for a char[] based sequence object.
- *
- * @author $author$
- * @version $Revision$
+ * Implements the SequenceI interface for a char[] based sequence object
*/
public class Sequence extends ASequence implements SequenceI
{
*/
Vector<AlignmentAnnotation> annotation;
- /**
- * The index of the sequence in a MSA
- */
- int index = -1;
-
private SequenceFeaturesI sequenceFeatureStore;
/*
* preserve end residue column provided cursor was valid
*/
int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0;
+
if (residuePos == this.end)
{
endColumn = column;
/*
* move left or right to find pos from hint.position
*/
- int col = curs.columnPosition - 1; // convert from base 1 to 0-based array
- // index
+ int col = curs.columnPosition - 1; // convert from base 1 to base 0
int newPos = curs.residuePosition;
int delta = newPos > pos ? -1 : 1;
boolean createNewDs = false;
// TODO: take a (second look) at the dataset creation validation method for
// the very large sequence case
+
int startIndex = findIndex(start) - 1;
int endIndex = findIndex(end) - 1;
int startDeleteColumn = -1; // for dataset sequence deletions
int deleteCount = 0;
- for (int s = i; s < j; s++)
+ for (int s = i; s < j && s < sequence.length; s++)
{
if (Comparison.isGap(sequence[s]))
{
}
}
- /**
- * @return The index (zero-based) of this sequence in the MSA. It returns
- * {@code -1} if this information is not available.
- */
- @Override
- public int getIndex()
- {
- return index;
- }
-
- /**
- * Defines the (zero-based) position of this sequence in the MSA. Use the
- * value {@code -1} if this information is undefined.
- *
- * @param value
- */
- @Override
- public void setIndex(int value)
- {
- index = value;
- }
-
@Override
public void setRNA(RNA r)
{
List<SequenceFeature> result = getFeatures().findFeatures(startPos,
endPos, types);
+ if (datasetSequence != null)
+ {
+ result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
+ types);
+ }
+ else
+ {
+ result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
+ }
/*
* if end column is gapped, endPos may be to the right,
public int findPosition(int i);
/**
- * Returns the from-to sequence positions (start..) for the given column
- * positions (1..), or null if no residues are included in the range
+ * Returns the sequence positions for first and last residues lying within the
+ * given column positions [fromColum,toColumn] (where columns are numbered
+ * from 1), or null if no residues are included in the range
*
* @param fromColum
+ * - first column base 1
* @param toColumn
+ * - last column, base 1
* @return
*/
public Range findPositions(int fromColum, int toColumn);
public void transferAnnotation(SequenceI entry, Mapping mp);
/**
- * @param index
- * The sequence index in the MSA
- */
- public void setIndex(int index);
-
- /**
- * @return The index of the sequence in the alignment
- */
- public int getIndex();
-
- /**
* @return The RNA of the sequence in the alignment
*/
* @param c1
* @param c2
*/
- public int replace(char c1, char c2);
+ int replace(char c1, char c2);
}