firstDragX = mouseDragLastX;
firstDragY = mouseDragLastY;
}
- else
+ }
+ }
+ else
+ {
+ // no row (or row that can be adjusted) was pressed. Simulate a ruler click
+ ap.getScalePanel().mousePressed(evt);
+ }
+ }
+
+ /**
+ * checks whether the annotation row under the mouse click evt's handles the
+ * event
+ *
+ * @param evt
+ * @return false if evt was not handled
+ */
+ boolean matrix_clicked(MouseEvent evt)
+ {
+ int[] rowIndex = getRowIndexAndOffset(evt.getY(),
+ av.getAlignment().getAlignmentAnnotation());
+ if (rowIndex == null)
+ {
+ jalview.bin.Console
+ .error("IMPLEMENTATION ERROR: matrix click out of range.");
+ return false;
+ }
+ int yOffset = rowIndex[1];
+
+ AlignmentAnnotation clicked = av.getAlignment()
+ .getAlignmentAnnotation()[rowIndex[0]];
+ if (clicked.graph != AlignmentAnnotation.CONTACT_MAP)
+ {
+ return false;
+ }
+
+ // TODO - use existing threshold to select related sections of matrix
+ GraphLine thr = clicked.getThreshold();
+
+ int currentX = getColumnForXPos(evt.getX());
+ ContactListI forCurrentX = av.getContactList(clicked, currentX);
+ if (forCurrentX != null)
+ {
+ 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)
+ {
+ ContactMatrixI matrix = av.getContactMatrix(clicked);
+
+ if (matrix != null)
{
- GraphLine thr = aa[graphStretch].getThreshold();
-
- // 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
- int currentX = getColumnForXPos(evt.getX());
- ContactMatrixI matrix = av.getContactMatrix(aa[graphStretch]);
- if (matrix!=null)
+ // simplest approach is to select all group containing column
+ if (matrix.hasGroups())
{
- if (matrix.hasGroups())
- {
- SequenceI rseq = aa[graphStretch].sequenceRef;
+ SequenceI rseq = clicked.sequenceRef;
BitSet grp = matrix.getGroupsFor(currentX);
- ColumnSelection cs = av.getColumnSelection();
+ for (int c = fr; c <= to; c++)
+ {
+ BitSet additionalGrp = matrix.getGroupsFor(c);
+ grp.or(additionalGrp);
+ }
HiddenColumns hc = av.getAlignment().getHiddenColumns();
- for (int p=grp.nextSetBit(0); p>=0; p = grp.nextSetBit(p+1))
+ for (int p = grp.nextSetBit(0); p >= 0; p = grp
+ .nextSetBit(p + 1))
{
- int offp = (rseq!=null) ? rseq.findIndex(rseq.getStart()-1+p) : p;
-
+ int offp = (rseq != null)
+ ? rseq.findIndex(rseq.getStart() - 1 + p)
+ : p;
+
if (!av.hasHiddenColumns() || hc.isVisible(offp))
- {
+ {
av.getColumnSelection().addElement(offp);
}
}
- } else
+ }
+ // 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
+ {
+ for (int c = fr; c <= to; c++)
{
- ContactListI forCurrentX = av.getContactList(aa[graphStretch],
- currentX);
- if (forCurrentX != null)
+ av.getColumnSelection().addElement(c);
+ }
+ 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()))
+ {
+ int c = fr - 1;
+ 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)
{
- ContactGeometry cXcgeom = new ContactGeometry(forCurrentX,
- aa[graphStretch].graphHeight);
- ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset,
- yOffset);
- int fr, to;
- fr = Math.min(cXci.cStart, cXci.cEnd);
- to = Math.max(cXci.cStart, cXci.cEnd);
- // select corresponding range in segment under mouse
+ cval = forCurrentX.getContactAt(c);
+ if (// cr.getMin() <= cval &&
+ cval <= thresh)
{
- for (int c = fr; c <= to; c++)
- {
- av.getColumnSelection().addElement(c);
- }
- av.getColumnSelection().addElement(currentX);
+ av.getColumnSelection().addElement(c--);
}
- // PAE SPECIFIC
- // and also select everything lower than the max range adjacent
- // (kind of works)
- if (PAEContactMatrix.PAEMATRIX.equals(aa[graphStretch].getCalcId()))
+ else
{
- int c = fr - 1;
- 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)
- {
- cval = forCurrentX.getContactAt(c);
- if (// cr.getMin() <= cval &&
- cval <= thresh)
- {
- av.getColumnSelection().addElement(c--);
- }
- else
- {
- break;
- }
- }
- c = to;
- while (c < forCurrentX.getContactHeight())
- {
- cval = forCurrentX.getContactAt(c);
- if (// cr.getMin() <= cval &&
- cval <= thresh)
- {
- av.getColumnSelection().addElement(c++);
- }
- else
- {
- break;
- }
- }
+ break;
}
+ }
+ c = to;
+ while (c < forCurrentX.getContactHeight())
+ {
+ cval = forCurrentX.getContactAt(c);
+ if (// cr.getMin() <= cval &&
+ cval <= thresh)
+ {
+ av.getColumnSelection().addElement(c++);
+ }
+ else
+ {
+ break;
}
}
}
- }}
- }
- else
- {
- ap.getScalePanel().mousePressed(evt);
+ }
}
+ ap.paintAlignment(false, false);
+ PaintRefresher.Refresh(ap, av.getSequenceSetId());
+ av.sendSelection();
+ return true;
}
-
/**
* Construct and display a context menu at the right-click position
*
ap.adjustAnnotationHeight();
}
dragMode = DragMode.Undefined;
- ap.getScalePanel().mouseReleased(evt);
+ if (!matrix_clicked(evt))
+ {
+ ap.getScalePanel().mouseReleased(evt);
+ }
/*
* isPopupTrigger is set in mouseReleased on Windows
if (rowIndex == null || toRowIndex == null)
{
- System.out.println("Drag out of range. needs to be clipped");
+ jalview.bin.Console.trace("Drag out of range. needs to be clipped");
}
if (rowIndex[0] != toRowIndex[0])
{
- System.out.println("Drag went to another row. needs to be clipped");
+ jalview.bin.Console.trace("Drag went to another row. needs to be clipped");
}
// rectangular selection on matrix style annotation
rowIndex[1] - deltaY);
// mark rectangular region formed by drag
- System.err.println("Matrix Selection from last(" + fromXc + ",["
+ 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);
- System.err.println("Marking " + fr + " to " + to);
+ jalview.bin.Console.trace("Marking " + fr + " to " + to);
for (int c = fr; c <= to; c++)
{
if (cma.sequenceRef != null)
}
fr = Math.min(cXci.cStart, cXci.cEnd);
to = Math.max(cXci.cStart, cXci.cEnd);
- System.err.println("Marking " + fr + " to " + to);
+ jalview.bin.Console.trace("Marking " + fr + " to " + to);
for (int c = fr; c <= to; c++)
{
if (cma.sequenceRef != null)
fr = Math.min(lastX, currentX);
to = Math.max(lastX, currentX);
- System.err.println("Marking " + fr + " to " + to);
+ jalview.bin.Console.trace("Marking " + fr + " to " + to);
for (int c = fr; c <= to; c++)
{
av.getColumnSelection().addElement(c);
git://source.jalview.org / jalview.git / blobdiff