--- /dev/null
+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
+{
+ SequenceI refSeq = null;
+
+ MapList toSeq = null;
+
+ /**
+ * the length that refSeq is expected to be (excluding gaps, of course)
+ */
+ int length;
+
+ @Override
+ public boolean hasReferenceSeq()
+ {
+ return (refSeq != null);
+ }
+
+ @Override
+ public SequenceI getReferenceSeq()
+ {
+ 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)
+ {
+ while (mapSeq != refSeq && mapSeq.getDatasetSequence() != null)
+ {
+ mapSeq = mapSeq.getDatasetSequence();
+ }
+ if (mapSeq != refSeq)
+ {
+ return 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
+ *
+ * @param _refSeq
+ */
+ public void setRefSeq(SequenceI _refSeq)
+ {
+ refSeq = _refSeq;
+ while (refSeq.getDatasetSequence() != null)
+ {
+ refSeq = refSeq.getDatasetSequence();
+ }
+ length = _refSeq.getEnd() - _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);
+ }
+ }
+
+ public T liftOver(SequenceI newRefSeq, Mapping sp2sq)
+ {
+ if (sp2sq.getMappedWidth() != sp2sq.getWidth())
+ {
+ // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
+ // Protein reference frames
+ throw new Error(
+ "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
+ }
+ boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == refSeq) : false;
+
+ /**
+ * map from matrix to toSeq's coordinate frame
+ */
+ int[] refMap = toSeq.locateInFrom(0, length - 1);
+ ArrayList<Integer> newFromMap = new ArrayList<Integer>();
+ int last = -1;
+ for (int i = 0; i < refMap.length; i += 2)
+ {
+ /*
+ * for each contiguous range in toSeq, locate corresponding range in sequence mapped to toSeq by sp2sq
+ */
+ int[] sp2map = mapIsTo
+ ? sp2sq.getMap().locateInFrom(refMap[i], refMap[i + 1])
+ : sp2sq.getMap().locateInTo(refMap[i], refMap[i + 1]);
+ if (sp2map == null)
+ {
+ continue;
+ }
+
+ for (int spm = 0; spm < sp2map.length; spm += 2)
+ {
+
+ if (last > -1)
+ {
+ if (sp2map[spm] != last + 1)
+ {
+ newFromMap.add(sp2map[spm]);
+ }
+ else
+ {
+ newFromMap.remove(newFromMap.size() - 1);
+ }
+ }
+ else
+ {
+ newFromMap.add(sp2map[spm]);
+ }
+ last = sp2map[spm + 1];
+ newFromMap.add(last);
+ }
+ }
+ if ((newFromMap.size() % 2) != 0)
+ {
+ // should have had an even number of int ranges!
+ throw new Error("PAEMatrix liftover failed.");
+ }
+ int fromIntMap[] = new int[newFromMap.size()];
+ int ipos = 0;
+ for (Integer i : newFromMap)
+ {
+ fromIntMap[ipos++] = i;
+ }
+ MapList newFromMapList = new MapList(fromIntMap,
+ new int[]
+ { 0, length - 1 }, 1, 1);
+
+ T newCM = newMappableContactMatrix(newRefSeq, newFromMapList);
+ return newCM;
+ }
+
+ 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)
+ {
+ 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);
+
+ if (toSeq != null)
+ {
+ SequenceI lf = localFrame, uf = 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() + ")");
+ }
+ // check the mapping to see if localFrame _lcolumn exists
+ int[] word = toSeq.locateInTo(_lcolumn, _lcolumn);
+ if (word == null)
+ {
+ return null;
+ }
+ _column = word[0];
+ }
+ else
+ {
+ // no mapping
+ _column = _lcolumn;
+ }
+
+ // TODO - remove ? this may be a redundant check
+ if (_column < 0 || ((toSeq != null && _column > toSeq.getToHighest())
+ || (toSeq == null && getHeight() <= _column)))
+ {
+ return null;
+ }
+
+ // 2. resolve ranges in matrix corresponding to range in localFrame
+ final int[] matrixRange = toSeq == null
+ ? new int[]
+ { localFrame.getStart(), localFrame.getEnd() }
+ : toSeq.locateInTo(localFrame.getStart(), localFrame.getEnd());
+
+ int h = 0;
+ for (int p = 0; p < matrixRange.length; p += 2)
+ {
+ 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)
+ {
+ 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]);
+ }
+
+ @Override
+ public int[] getMappedPositionsFor(int cStart, int cEnd)
+ {
+ if (!hasReferenceSeq())
+ {
+ 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++)
+ {
+ 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]);
+ }
+ }
+ }
+ 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
+ *
+ * @param _column
+ * @param i
+ * @return
+ */
+ protected abstract double getElementAt(int _column, int i);
+
+}
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