import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactListImpl;
import jalview.datamodel.ContactListProviderI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.GroupSet;
import jalview.datamodel.GroupSetI;
import jalview.datamodel.Mapping;
public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>>
implements MappableContactMatrixI
{
- SequenceI refSeq = null;
-
- MapList toSeq = null;
-
/**
- * the length that refSeq is expected to be (excluding gaps, of course)
+ * the matrix that is being mapped to
*/
- int length;
+ protected ContactMatrixI mappedMatrix=null;
+
+ public ContactListI getContactList(int column)
+ {
+ return mappedMatrix.getContactList(column);
+ }
+
+ public float getMin()
+ {
+ return mappedMatrix.getMin();
+ }
+
+ public float getMax()
+ {
+ return mappedMatrix.getMax();
+ }
+
+ public int getWidth()
+ {
+ return mappedMatrix.getWidth();
+ }
+
+ public int getHeight()
+ {
+ return mappedMatrix.getHeight();
+ }
@Override
- public boolean hasReferenceSeq()
+ public ContactMatrixI getMappedMatrix()
{
- return (refSeq != null);
+ return mappedMatrix;
}
+
+ @Override
+ public GroupSetI getGroupSet()
+ {
+ return mappedMatrix.getGroupSet();
+ };
@Override
- public SequenceI getReferenceSeq()
+ public void setGroupSet(GroupSet makeGroups)
{
- return refSeq;
+ mappedMatrix.setGroupSet(makeGroups);
}
+
+ /**
+ * the sequence and how it is mapped to the matrix
+ */
+
+ SequenceI refSeq = null;
+
+ MapList toSeq = null;
/**
- * container for groups - defined on matrix columns
+ * the length that refSeq is expected to be (excluding gaps, of course)
*/
- GroupSet grps = new GroupSet();
+ int length;
@Override
- public GroupSetI getGroupSet()
+ public boolean hasReferenceSeq()
{
- return grps;
- };
+ return (refSeq != null);
+ }
@Override
- public void setGroupSet(GroupSet makeGroups)
+ public SequenceI getReferenceSeq()
{
- grps = makeGroups;
+ return refSeq;
}
@Override
return getMappedPositionsFor(localFrame, column, column);
}
+ @Override
public int[] getMappedPositionsFor(final SequenceI localFrame, int from,
int to)
{
{
throw new Error("Unimplemented when no local sequence given.");
}
- // return a ContactListI for column
- // column is index into localFrame
- // 1. map column to corresponding column in matrix
-
- final int _lcolumn = localFrame.findPosition(from);
- final int _rcolumn = (from == to) ? _lcolumn
- : localFrame.findPosition(to);
- if (toSeq == null)
- {
- // no mapping
- return new int[] { _lcolumn, _rcolumn };
- }
-
SequenceI lf = localFrame, uf = refSeq;
+ // check that localFrame is derived from refSeq
// just look for dataset sequences and check they are the same.
// in future we could use DBRefMappings/whatever.
while (lf.getDatasetSequence() != null
+ "' is not mappable for the given localFrame sequence. ("
+ localFrame.getName() + ")");
}
+
+ // now look up from-to matrix columns in toSeq frame
+
+ if (toSeq == null)
+ {
+ // no mapping - so we assume 1:1
+ return new int[] { from, to };
+ }
+ // from-to are matrix columns
+ // first locate on reference sequence
- int[] mappedPositions = toSeq.locateInFrom(_lcolumn, _rcolumn);
- // TODO - trim to localFrame ?
- // if (mappedPositions!=null) {
- // int s=-1,e=-1;
- // for (int p=0;p<mappedPositions.length;p++)
- // {
- // if (s==-1 && mappedPositions[p]>=localFrame.getStart())
- // {
- // s=p; // remember first position within local frame
- // }
- // if (e==-1 || mappedPositions[p]<=localFrame.getEnd())
- // {
- // // update end pointer
- // e=p;
- // // compute local map
- // mappedPositions[p] = localFrame.findIndex(mappedPositions[p]);
- // }
- // }
- // }
+ int[] mappedPositions = toSeq.locateInFrom(from, to);
+ if (mappedPositions==null)
+ {
+ return null;
+ }
+
+ // and now map to localFrame
+ // from-to columns on the associated sequence should be
+ // i. restricted to positions in localFrame
+ // ii.
+
+// int s = -1, e = -1;
+// for (int p = 0; p < mappedPositions.length; p++)
+// {
+// if (s == -1 && mappedPositions[p] >= localFrame.getStart())
+// {
+// s = p; // remember first position within local frame
+// }
+// if (e == -1 || mappedPositions[p] <= localFrame.getEnd())
+// {
+// // update end pointer
+// e = p;
+// // compute local map
+// mappedPositions[p] = localFrame.findIndex(mappedPositions[p]);
+// }
+// }
+// int[] _trimmed = new int[e - s + 1];
+// return _trimmed;
return mappedPositions;
}
}
/**
- * get a specific element of the contact matrix in its data-local coordinates
+ * get a specific element of the underlying contact matrix in its data-local coordinates
* rather than the mapped frame. Implementations are allowed to throw
* RunTimeExceptions if _column/i are out of bounds
*
* @param i
* @return
*/
- protected abstract double getElementAt(int _column, int i);
+ public double getElementAt(int _column, int i) {
+ return mappedMatrix.getElementAt(_column, i);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return 7 * (refSeq != null ? refSeq.hashCode() : 0)
+ + 11 * (toSeq != null ? toSeq.hashCode() : 0)
+ + 13 * (mappedMatrix != null ? mappedMatrix.hashCode() : 0)
+ + length * 3;
+ }
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == null || !(obj.getClass().equals(getClass())))
+ {
+ return false;
+ }
+ T them = (T) obj;
+ return mappedMatrix == them.mappedMatrix && length == them.length
+ && refSeq == them.refSeq && toSeq.equals(them.toSeq);
+
+ }
}
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