import jalview.structure.SelectionSource;
import jalview.util.Format;
import jalview.util.MessageManager;
+import jalview.ws.datamodel.MappableContactMatrixI;
/**
* DOCUMENT ME!
// stash colors in linked annotation row.
// doesn't work yet. TESTS!
int sstart=aa.sequenceRef!=null ? aa.sequenceRef.getStart()-1 : 0;
+ Annotation ae;
+ Color gpcol = null;
+ int[] seqpos=null;
for (BitSet gp : colors.keySet())
{
- Color gpcol = colors.get(gp);
- for (int p = gp.nextSetBit(0); p >= 0; p = gp.nextSetBit(p + 1))
+ gpcol = colors.get(gp);
+ for (int p = gp.nextSetBit(0); p >= 0 && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
{
- Annotation ae = aa.getAnnotationForPosition(p+sstart);
+ if (cm instanceof MappableContactMatrixI)
+ {
+ MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
+ seqpos = mcm.getMappedPositionsFor(aa.sequenceRef,p);
+ if (seqpos==null)
+ {
+ // no mapping for this column.
+ continue;
+ }
+ // TODO: handle ranges...
+ ae = aa.getAnnotationForPosition(seqpos[0]);
+ } else {
+ ae = aa.getAnnotationForPosition(p+sstart);
+ }
if (ae != null)
{
ae.colour = gpcol.brighter().darker();
Color col)
{
SequenceI rseq = tp.assocAnnotation.sequenceRef;
- if (av==null||av.getAlignment()==null)
+
+ if (av == null || av.getAlignment() == null)
{
// alignment is closed
return;
}
- for (BinaryNode bn:l)
+ for (BinaryNode bn : l)
{
- int colm=-1;
- try {
- colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1));
+ int colm = -1;
+ try
+ {
+ colm = Integer.parseInt(
+ bn.getName().substring(bn.getName().indexOf("c") + 1));
} catch (Exception e)
{
continue;
}
+ // TODO - sort indices for faster lookup
+
ColumnSelection cs = av.getColumnSelection();
HiddenColumns hc = av.getAlignment().getHiddenColumns();
+ ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation);
+ MappableContactMatrixI mcm = null;
+ int offp;
+ if (cm instanceof MappableContactMatrixI)
{
- int offp = (rseq!=null) ? rseq.findIndex(rseq.getStart()+colm) : colm;
-
- if (!av.hasHiddenColumns() || hc.isVisible(offp-1))
- {
- if (cs.contains(offp-1))
- {
- cs.removeElement(offp-1);
- } else {
- cs.addElement(offp-1);
- }
+ mcm = (MappableContactMatrixI) cm;
+ int[] seqpos = mcm.getMappedPositionsFor(tp.assocAnnotation.sequenceRef,colm);
+ if (seqpos==null)
+ {
+ // no mapping for this column.
+ continue;
+ }
+ // TODO: handle ranges...
+ offp=seqpos[0];
+ }
+ else
+ {
+ offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
+ : colm;
+ }
+ if (!av.hasHiddenColumns() || hc.isVisible(offp - 1))
+ {
+ if (cs.contains(offp - 1))
+ {
+ cs.removeElement(offp - 1);
+ }
+ else
+ {
+ cs.addElement(offp - 1);
}
}
- }
+ }
}
public void createSeqGroupFor(AlignmentPanel[] aps, Vector<BinaryNode> l,
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;
protected abstract T newMappableContactMatrix(SequenceI newRefSeq,
MapList newFromMapList);
@Override
+ public int[] getMappedPositionsFor(final SequenceI localFrame,
+ final int column)
+ {
+ return getMappedPositionsFor(localFrame,column,column);
+ }
+ public int[] getMappedPositionsFor(final SequenceI localFrame,
+ int from,int to)
+ {
+ 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 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;
+
+ // 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() + ")");
+ }
+
+ 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]);
+// }
+// }
+// }
+ return mappedPositions;
+ }
+
+ @Override
public ContactListI getMappableContactList(final SequenceI localFrame,
final int column)
{
// 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)
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;
+ }
});
}
git://source.jalview.org / jalview.git / commitdiff