package jalview.ws.datamodel.alphafold;
+import java.awt.Color;
import java.util.ArrayList;
+import java.util.BitSet;
import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactListImpl;
import jalview.datamodel.ContactListProviderI;
+import jalview.datamodel.GroupSet;
+import jalview.datamodel.GroupSetI;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceI;
import jalview.util.MapList;
import jalview.ws.datamodel.MappableContactMatrixI;
-public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>> implements MappableContactMatrixI
+public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>>
+ implements MappableContactMatrixI
{
SequenceI refSeq = null;
+
MapList toSeq = null;
/**
*/
int length;
-
@Override
public boolean hasReferenceSeq()
{
{
return refSeq;
}
+
+ /**
+ * container for groups - defined on matrix columns
+ */
+ GroupSet grps = new GroupSet();
+
+ @Override
+ public GroupSetI getGroupSet()
+ {
+ return grps;
+ };
+
+ @Override
+ public void setGroupSet(GroupSet makeGroups)
+ {
+ grps = makeGroups;
+ }
+
@Override
public MapList getMapFor(SequenceI mapSeq)
{
- if (refSeq!=null)
+ if (refSeq != null)
{
- while (mapSeq!=refSeq && mapSeq.getDatasetSequence()!=null)
+ while (mapSeq != refSeq && mapSeq.getDatasetSequence() != null)
{
mapSeq = mapSeq.getDatasetSequence();
}
- if (mapSeq!=refSeq)
+ if (mapSeq != refSeq)
{
return null;
}
- } else {
- if (mapSeq!=null) {
+ }
+ else
+ {
+ if (mapSeq != null)
+ {
// our MapList does not concern this seq
return null;
}
}
-
+
return toSeq;
}
/**
- * set the reference sequence and construct the mapping between the start-end positions of given sequence and row/columns of contact matrix
+ * set the reference sequence and construct the mapping between the start-end
+ * positions of given sequence and row/columns of contact matrix
+ *
* @param _refSeq
*/
public void setRefSeq(SequenceI _refSeq)
refSeq = refSeq.getDatasetSequence();
}
length = _refSeq.getEnd() - _refSeq.getStart() + 1;
-// if (length!=refSeq.getLength() || _refSeq.getStart()!=1)
+ // if (length!=refSeq.getLength() || _refSeq.getStart()!=1)
{
- toSeq = new MapList(new int[] { _refSeq.getStart(), _refSeq.getEnd()}, new int[] { 0,length-1}, 1,1);
+ toSeq = new MapList(
+ new int[]
+ { _refSeq.getStart(), _refSeq.getEnd() },
+ new int[]
+ { 0, length - 1 }, 1, 1);
}
}
return newCM;
}
- protected abstract T newMappableContactMatrix(SequenceI newRefSeq,
+ protected abstract T newMappableContactMatrix(SequenceI newRefSeq,
MapList newFromMapList);
+
+ @Override
+ public int[] getMappedPositionsFor(final SequenceI localFrame,
+ final int column)
+ {
+ return getMappedPositionsFor(localFrame, column, column);
+ }
+
+ @Override
+ public int[] getMappedPositionsFor(final SequenceI localFrame, int from,
+ int to)
+ {
+ if (localFrame == null)
+ {
+ throw new Error("Unimplemented when no local sequence given.");
+ }
+ 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
+ || uf.getDatasetSequence() != null)
+ {
+ if (lf.getDatasetSequence() != null)
+ {
+ lf = lf.getDatasetSequence();
+ }
+ if (uf.getDatasetSequence() != null)
+ {
+ uf = uf.getDatasetSequence();
+ }
+ }
+ if (lf != uf)
+ {
+ // could try harder to find a mapping
+ throw new Error("This Matrix associated with '" + refSeq.getName()
+ + "' 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(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;
+ }
+
@Override
public ContactListI getMappableContactList(final SequenceI localFrame,
final int column)
{
final int _column;
final int _lcolumn;
- if (localFrame==null)
+ if (localFrame == null)
{
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 MappableContactMatrix us = this;
+ _lcolumn = localFrame.findPosition(column);
- _lcolumn=localFrame.findPosition(column);
-
if (toSeq != null)
{
SequenceI lf = localFrame, uf = refSeq;
}
else
{
- // no mapping
+ // no mapping
_column = _lcolumn;
}
- // TODO - remove ? this may be a redundant check
+ // TODO - remove ? this may be a redundant check
if (_column < 0 || ((toSeq != null && _column > toSeq.getToHighest())
|| (toSeq == null && getHeight() <= _column)))
{
int h = 0;
for (int p = 0; p < matrixRange.length; p += 2)
{
- h += 1+Math.abs(matrixRange[p + 1] - matrixRange[p]);
+ h += 1 + Math.abs(matrixRange[p + 1] - matrixRange[p]);
}
final int rangeHeight = h;
// 3. Construct ContactListImpl instance for just those segments.
-
+
return new ContactListImpl(new ContactListProviderI()
{
-
+
public int getColumn()
{
return column;
}
+
@Override
public int getPosition()
{
return _column;
}
-
+
@Override
public int getContactHeight()
{
return rangeHeight;
}
-
+
@Override
public double getContactAt(int mcolumn)
{
- if (mcolumn<0 || mcolumn>=rangeHeight)
+ if (mcolumn < 0 || mcolumn >= rangeHeight)
{
return -1;
}
return getElementAt(_column, locateInRange(mcolumn));
-
- // this code maps from mcolumn to localFrame - but that isn't what's needed
-// int loccolumn = localFrame.findPosition(mcolumn);
-// int[] lcolumn=(toSeq==null) ? new int[] {mcolumn} : toSeq.locateInTo(loccolumn,loccolumn);
-// if (lcolumn==null || lcolumn[0] < 0 || lcolumn[0] >= rangeHeight)
-// {
-// return -1;
-// }
-// return getElementAt(_column,lcolumn[0]);
- }
- /**
- * @return the mcolumn'th position in the matrixRange window on the matrix
- */
- private int locateInRange(int mcolumn)
- {
- int h=0,p=0;
- while (h < mcolumn && p+2 < matrixRange.length)
- {
- h += 1+Math.abs(matrixRange[p + 1] - matrixRange[p]);
- p+=2;
- }
- return matrixRange[p]+mcolumn-h;
+ // this code maps from mcolumn to localFrame - but that isn't what's
+ // needed
+ // int loccolumn = localFrame.findPosition(mcolumn);
+ // int[] lcolumn=(toSeq==null) ? new int[] {mcolumn} :
+ // toSeq.locateInTo(loccolumn,loccolumn);
+ // if (lcolumn==null || lcolumn[0] < 0 || lcolumn[0] >= rangeHeight)
+ // {
+ // return -1;
+ // }
+ // return getElementAt(_column,lcolumn[0]);
}
-
+
@Override
public int[] getMappedPositionsFor(int cStart, int cEnd)
{
if (!hasReferenceSeq())
{
- return ContactListProviderI.super.getMappedPositionsFor(cStart, cEnd);
+ return ContactListProviderI.super.getMappedPositionsFor(cStart,
+ cEnd);
}
// map into segment of matrix being shown
int realCstart = locateInRange(cStart);
int realCend = locateInRange(cEnd);
-
+
// TODO account for discontinuities in the mapping
- int[] mappedPositions = toSeq.locateInFrom(realCstart,realCend);
- if (mappedPositions!=null) {
- int s=-1,e=-1;
- for (int p=0;p<mappedPositions.length;p++)
+ int[] mappedPositions = toSeq.locateInFrom(realCstart, realCend);
+ if (mappedPositions != null)
+ {
+ int s = -1, e = -1;
+ for (int p = 0; p < mappedPositions.length; p++)
{
- if (s==-1 && mappedPositions[p]>=localFrame.getStart())
+ if (s == -1 && mappedPositions[p] >= localFrame.getStart())
{
- s=p; // remember first position within local frame
+ s = p; // remember first position within local frame
}
- if (e==-1 || mappedPositions[p]<=localFrame.getEnd())
+ if (e == -1 || mappedPositions[p] <= localFrame.getEnd())
{
// update end pointer
- e=p;
+ e = p;
// compute local map
mappedPositions[p] = localFrame.findIndex(mappedPositions[p]);
}
}
return mappedPositions;
}
+
+ /**
+ * @return the mcolumn'th position in the matrixRange window on the matrix
+ */
+ private int locateInRange(int mcolumn)
+ {
+
+ int h = 0, p = 0;
+ while (h < mcolumn && p + 2 < matrixRange.length)
+ {
+ h += 1 + Math.abs(matrixRange[p + 1] - matrixRange[p]);
+ p += 2;
+ }
+ return matrixRange[p] + mcolumn - h;
+ }
+
+ @Override
+ public Color getColourForGroup()
+ {
+ BitSet gp = us.getGroupsFor(_column);
+ Color col = us.getColourForGroup(gp);
+ return col;
+ }
});
}
/**
* get a specific element of the 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
+ * rather than the mapped frame. Implementations are allowed to throw
+ * RunTimeExceptions if _column/i are out of bounds
*
* @param _column
* @param i
* @return
*/
protected abstract double getElementAt(int _column, int i);
+
}
git://source.jalview.org / jalview.git / blobdiff