{
ContactGeometry cXcgeom = new ContactGeometry(forCurrentX,
clicked.graphHeight);
- ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset,
- yOffset);
- /**
- * start and end range corresponding to the row range under the mouse at
- * column currentX
- */
- int fr, to;
- fr = Math.min(cXci.cStart, cXci.cEnd);
- to = Math.max(cXci.cStart, cXci.cEnd);
-
- // double click selects the whole group
- if (evt.getClickCount() == 2)
+ ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset);
+ if (cXci != null)
{
- ContactMatrixI matrix = av.getContactMatrix(clicked);
+ /**
+ * start and end range corresponding to the row range under the mouse at
+ * column currentX
+ */
+ int fr, to;
+ fr = Math.min(cXci.cStart, cXci.cEnd);
+ to = Math.max(cXci.cStart, cXci.cEnd);
- if (matrix != null)
+ // double click selects the whole group
+ if (evt.getClickCount() == 2)
{
- // simplest approach is to select all group containing column
- if (matrix.hasGroups())
+ ContactMatrixI matrix = av.getContactMatrix(clicked);
+
+ if (matrix != null)
{
- SequenceI rseq = clicked.sequenceRef;
- BitSet grp = new BitSet();
- grp.or(matrix.getGroupsFor(currentX));
- // TODO: cXci needs to be mapped to real groups
- for (int c = fr; c <= to; c++)
+ // simplest approach is to select all group containing column
+ if (matrix.hasGroups())
{
- BitSet additionalGrp = matrix.getGroupsFor(c);
- grp.or(additionalGrp);
- }
+ SequenceI rseq = clicked.sequenceRef;
+ BitSet grp = new BitSet();
+ grp.or(matrix.getGroupsFor(currentX));
+ // TODO: cXci needs to be mapped to real groups
+ for (int c = fr; c <= to; c++)
+ {
+ BitSet additionalGrp = matrix.getGroupsFor(c);
+ grp.or(additionalGrp);
+ }
- HiddenColumns hc = av.getAlignment().getHiddenColumns();
- ColumnSelection cs = av.getColumnSelection();
-
- for (int p=grp.nextSetBit(0); p >= 0; p = grp
- .nextSetBit(p + 1))
- {
- if (matrix instanceof MappableContactMatrixI)
+ HiddenColumns hc = av.getAlignment().getHiddenColumns();
+ ColumnSelection cs = av.getColumnSelection();
+
+ for (int p = grp.nextSetBit(0); p >= 0; p = grp
+ .nextSetBit(p + 1))
{
- // find the end of this run of set bits
- int nextp = grp.nextClearBit(p)-1;
- int[] pos = ((MappableContactMatrixI)matrix).getMappedPositionsFor(rseq, p,nextp);
- p=nextp;
-
- if (pos!=null)
+ if (matrix instanceof MappableContactMatrixI)
{
- for (int pos_p = pos[0];pos_p<=pos[1];pos_p++)
+ // find the end of this run of set bits
+ int nextp = grp.nextClearBit(p) - 1;
+ int[] pos = ((MappableContactMatrixI) matrix)
+ .getMappedPositionsFor(rseq, p, nextp);
+ p = nextp;
+
+ if (pos != null)
{
- int col = rseq.findIndex(pos_p)-1;
- if (col>=0 && (!av.hasHiddenColumns() || hc.isVisible(col)))
+ for (int pos_p = pos[0]; pos_p <= pos[1]; pos_p++)
{
- cs.addElement(col);
+ int col = rseq.findIndex(pos_p) - 1;
+ if (col >= 0 && (!av.hasHiddenColumns()
+ || hc.isVisible(col)))
+ {
+ cs.addElement(col);
+ }
}
}
}
- } else {
- int offp = (rseq != null)
- ? rseq.findIndex(rseq.getStart() - 1 + p)
- : p;
-
- if (!av.hasHiddenColumns() || hc.isVisible(offp))
+ else
{
- cs.addElement(offp);
+ int offp = (rseq != null)
+ ? rseq.findIndex(rseq.getStart() - 1 + p)
+ : p;
+
+ if (!av.hasHiddenColumns() || hc.isVisible(offp))
+ {
+ cs.addElement(offp);
+ }
}
}
}
- }
- // possible alternative for interactive selection - threshold
- // gives 'ceiling' for forming a cluster
- // when a row+column is selected, farthest common ancestor less
- // than thr is used to compute cluster
+ // possible alternative for interactive selection - threshold
+ // gives 'ceiling' for forming a cluster
+ // when a row+column is selected, farthest common ancestor less
+ // than thr is used to compute cluster
- }
- }
- else
- {
- // select corresponding range in segment under mouse
- {
- int[] rng = forCurrentX.getMappedPositionsFor(fr, to);
- if (rng != null)
- {
- av.getColumnSelection().addRangeOfElements(rng, true);
}
- av.getColumnSelection().addElement(currentX);
}
- // PAE SPECIFIC
- // and also select everything lower than the max range adjacent
- // (kind of works)
- if (evt.isControlDown()
- && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
+ else
{
- int c = fr;
- ContactRange cr = forCurrentX.getRangeFor(fr, to);
- double cval;
- // TODO: could use GraphLine instead of arbitrary picking
- // TODO: could report mean/median/variance for partitions
- // (contiguous selected vs unselected regions and inter-contig
- // regions)
- // controls feathering - what other elements in row/column
- // should we select
- double thresh = cr.getMean() + (cr.getMax() - cr.getMean()) * .15;
- while (c >= 0)
+ // select corresponding range in segment under mouse
{
- cval = forCurrentX.getContactAt(c);
- if (// cr.getMin() <= cval &&
- cval <= thresh)
+ int[] rng = forCurrentX.getMappedPositionsFor(fr, to);
+ if (rng != null)
{
- int[] cols = forCurrentX.getMappedPositionsFor(c, c);
- if (cols != null)
- {
- av.getColumnSelection().addRangeOfElements(cols, true);
- }
- else
- {
- break;
- }
+ av.getColumnSelection().addRangeOfElements(rng, true);
}
- c--;
+ av.getColumnSelection().addElement(currentX);
}
- c = to;
- while (c < forCurrentX.getContactHeight())
+ // PAE SPECIFIC
+ // and also select everything lower than the max range adjacent
+ // (kind of works)
+ if (evt.isControlDown()
+ && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
{
- cval = forCurrentX.getContactAt(c);
- if (// cr.getMin() <= cval &&
- cval <= thresh)
+ int c = fr;
+ ContactRange cr = forCurrentX.getRangeFor(fr, to);
+ double cval;
+ // TODO: could use GraphLine instead of arbitrary picking
+ // TODO: could report mean/median/variance for partitions
+ // (contiguous selected vs unselected regions and inter-contig
+ // regions)
+ // controls feathering - what other elements in row/column
+ // should we select
+ double thresh = cr.getMean()
+ + (cr.getMax() - cr.getMean()) * .15;
+ while (c >= 0)
{
- int[] cols = forCurrentX.getMappedPositionsFor(c, c);
- if (cols != null)
+ cval = forCurrentX.getContactAt(c);
+ if (// cr.getMin() <= cval &&
+ cval <= thresh)
{
- av.getColumnSelection().addRangeOfElements(cols, true);
+ int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+ if (cols != null)
+ {
+ av.getColumnSelection().addRangeOfElements(cols, true);
+ }
+ else
+ {
+ break;
+ }
}
+ c--;
}
- else
+ c = to;
+ while (c < forCurrentX.getContactHeight())
{
- break;
- }
- c++;
+ cval = forCurrentX.getContactAt(c);
+ if (// cr.getMin() <= cval &&
+ cval <= thresh)
+ {
+ int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+ if (cols != null)
+ {
+ av.getColumnSelection().addRangeOfElements(cols, true);
+ }
+ }
+ else
+ {
+ break;
+ }
+ c++;
+ }
}
+
}
}
}
if (forFromX != null && forToX != null)
{
- ContactGeometry lastXcgeom = new ContactGeometry(forFromX,
- cma.graphHeight);
- ContactGeometry.contactInterval lastXci = lastXcgeom
- .mapFor(rowIndex[1], rowIndex[1] + deltaY);
-
- ContactGeometry cXcgeom = new ContactGeometry(forToX,
+ // FIXME will need two ContactGeometry objects when handling contact matrices with differing numbers of rows at each
+ // column
+ ContactGeometry xcgeom = new ContactGeometry(forFromX,
cma.graphHeight);
- ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1],
- rowIndex[1] + deltaY);
+ ContactGeometry.contactInterval lastXci = xcgeom
+ .mapFor(rowIndex[1]);
+ ContactGeometry.contactInterval cXci = xcgeom.mapFor(rowIndex[1] + deltaY);
// mark rectangular region formed by drag
jalview.bin.Console.trace("Matrix Selection from last(" + fromXc
+ ",[" + lastXci.cStart + "," + lastXci.cEnd + "]) to cur("
+ toXc + ",[" + cXci.cStart + "," + cXci.cEnd + "])");
int fr, to;
- fr = Math.min(lastXci.cStart, lastXci.cEnd);
- to = Math.max(lastXci.cStart, lastXci.cEnd);
+ fr = Math.min(lastXci.cStart, cXci.cStart);
+ to = Math.max(lastXci.cEnd, cXci.cEnd);
int[] mappedPos = forFromX.getMappedPositionsFor(fr, to);
if (mappedPos != null)
{
// }
// else
{
- av.getColumnSelection().addElement(c);
- }
- }
- }
- // and again for most recent corner of drag
- fr = Math.min(cXci.cStart, cXci.cEnd);
- to = Math.max(cXci.cStart, cXci.cEnd);
- mappedPos = forFromX.getMappedPositionsFor(fr, to);
- if (mappedPos != null)
- {
- for (int pair = 0; pair < mappedPos.length; pair += 2)
- {
- jalview.bin.Console.trace("Marking " + fr + " to " + to
- + " mapping to sequence positions " + mappedPos[pair]
- + " to " + mappedPos[pair + 1]);
- for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++)
- {
- // if (cma.sequenceRef != null)
- // {
- // int col =
- // cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
- // av.getColumnSelection().addElement(col);
- // }
- // else
- {
- av.getColumnSelection().addElement(c);
- }
+ av.getColumnSelection().addElement(c-1);
}
}
}
git://source.jalview.org / jalview.git / blobdiff