*/
package jalview.datamodel;
-import jalview.util.Comparison;
-import jalview.util.MapList;
-
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.Vector;
+import jalview.util.Comparison;
+import jalview.util.MapList;
+
public class Mapping
{
/**
}
if (!toRanges.hasNext())
{
- throw new NoSuchElementException("Ran out of peptide at position "
- + toPosition);
+ throw new NoSuchElementException(
+ "Ran out of peptide at position " + toPosition);
}
currentToRange = toRanges.next();
toPosition = currentToRange[0];
}
/**
- * gets boundary in direction of mapping
- *
- * @param position
- * in mapped reference frame
- * @return int{start, end} positions in associated sequence (in direction of
- * mapped word)
- */
- public int[] getWord(int mpos)
- {
- if (map != null)
- {
- return map.getToWord(mpos);
- }
- return null;
- }
-
- /**
* width of mapped unit in associated sequence
*
*/
to[f * 2] = r[0];
to[f * 2 + 1] = r[1];
}
- copy.setMap(new MapList(from, to, map.getFromRatio(), map
- .getToRatio()));
+ copy.setMap(
+ new MapList(from, to, map.getFromRatio(), map.getToRatio()));
}
return copy;
}
to = tto;
}
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#finalize()
- */
- @Override
- protected void finalize() throws Throwable
- {
- map = null;
- to = null;
- super.finalize();
- }
-
/**
* Returns an iterator which can serve up the aligned codon column positions
* and their corresponding peptide products
* @param gapChar
* @return
*/
- public Iterator<AlignedCodon> getCodonIterator(SequenceI seq, char gapChar)
+ public Iterator<AlignedCodon> getCodonIterator(SequenceI seq,
+ char gapChar)
{
return new AlignedCodonIterator(seq, gapChar);
}
@Override
public String toString()
{
- return String.format("%s %s", this.map.toString(), this.to == null ? ""
- : this.to.getName());
+ return String.format("%s %s", this.map.toString(),
+ this.to == null ? "" : this.to.getName());
}
/**