import jalview.util.Platform;
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
+import jalview.ws.datamodel.MappableContactMatrixI;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
/**
fr = Math.min(cXci.cStart, cXci.cEnd);
to = Math.max(cXci.cStart, cXci.cEnd);
- if (evt.isControlDown())
+ // double click selects the whole group
+ if (evt.getClickCount() == 2)
{
ContactMatrixI matrix = av.getContactMatrix(clicked);
if (matrix.hasGroups())
{
SequenceI rseq = clicked.sequenceRef;
- BitSet grp = matrix.getGroupsFor(currentX);
+ 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();
- for (int p = grp.nextSetBit(0); p >= 0; p = grp
+ ColumnSelection cs = av.getColumnSelection();
+
+ for (int p=grp.nextSetBit(0); p >= 0; p = grp
.nextSetBit(p + 1))
{
- int offp = (rseq != null)
- ? rseq.findIndex(rseq.getStart() - 1 + p)
- : p;
-
- if (!av.hasHiddenColumns() || hc.isVisible(offp))
+ if (matrix instanceof MappableContactMatrixI)
{
- av.getColumnSelection().addElement(offp);
+ // 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)
+ {
+ for (int pos_p = pos[0];pos_p<=pos[1];pos_p++)
+ {
+ 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))
+ {
+ cs.addElement(offp);
+ }
}
}
}
{
// select corresponding range in segment under mouse
{
- for (int c = fr; c <= to; c++)
+ int[] rng = forCurrentX.getMappedPositionsFor(fr, to);
+ if (rng != null)
{
- av.getColumnSelection().addElement(c);
+ 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 (PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
+ if (evt.isControlDown()
+ && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
{
int c = fr - 1;
ContactRange cr = forCurrentX.getRangeFor(fr, to);
if (// cr.getMin() <= cval &&
cval <= thresh)
{
- av.getColumnSelection().addElement(c--);
- }
- else
- {
- break;
+ int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+ if (cols != null)
+ {
+ av.getColumnSelection().addRangeOfElements(cols, true);
+ }
+ else
+ {
+ break;
+ }
}
+ c--;
}
c = to;
while (c < forCurrentX.getContactHeight())
if (// cr.getMin() <= cval &&
cval <= thresh)
{
- av.getColumnSelection().addElement(c++);
+ int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+ if (cols != null)
+ {
+ av.getColumnSelection().addRangeOfElements(cols, true);
+ }
}
else
{
break;
}
+ c++;
+
}
}
}
int fr, to;
fr = Math.min(lastXci.cStart, lastXci.cEnd);
to = Math.max(lastXci.cStart, lastXci.cEnd);
- jalview.bin.Console.trace("Marking " + fr + " to " + to);
- for (int c = fr; c <= to; c++)
+ int[] mappedPos = forFromX.getMappedPositionsFor(fr, to);
+ if (mappedPos != null)
{
- if (cma.sequenceRef != null)
+ jalview.bin.Console.trace("Marking " + fr + " to " + to
+ + " mapping to sequence positions " + mappedPos[0] + " to "
+ + mappedPos[1]);
+ for (int pair = 0; pair < mappedPos.length; pair += 2)
{
- int col = cma.sequenceRef.findIndex(c);
- av.getColumnSelection().addElement(col);
- }
- else
- {
- av.getColumnSelection().addElement(c);
+ 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);
+ }
}
}
+ // and again for most recent corner of drag
fr = Math.min(cXci.cStart, cXci.cEnd);
to = Math.max(cXci.cStart, cXci.cEnd);
- jalview.bin.Console.trace("Marking " + fr + " to " + to);
- for (int c = fr; c <= to; c++)
+ mappedPos = forFromX.getMappedPositionsFor(fr, to);
+ if (mappedPos != null)
{
- if (cma.sequenceRef != null)
- {
- int col = cma.sequenceRef.findIndex(c);
- av.getColumnSelection().addElement(col);
- }
- else
+ for (int pair = 0; pair < mappedPos.length; pair += 2)
{
- av.getColumnSelection().addElement(c);
+ 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);
+ }
+ }
}
}
fr = Math.min(lastX, currentX);
ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
+ " - " + ci.cEnd + "]" + "<br/>Mean:" + cr.getMean();
+
int col = ann.sequenceRef.findPosition(column);
+ int[][] highlightPos;
+ int[] mappedPos = clist.getMappedPositionsFor(ci.cStart, ci.cEnd);
+ if (mappedPos != null)
+ {
+ highlightPos = new int[1 + mappedPos.length][2];
+ highlightPos[0] = new int[] { col, col };
+ for (int p = 0, h = 0; p < mappedPos.length; h++, p += 2)
+ {
+ highlightPos[h][0] = ann.sequenceRef
+ .findPosition(mappedPos[p] - 1);
+ highlightPos[h][1] = ann.sequenceRef
+ .findPosition(mappedPos[p + 1] - 1);
+ }
+ }
+ else
+ {
+ highlightPos = new int[][] { new int[] { col, col } };
+ }
ap.getStructureSelectionManager()
- .highlightPositionsOn(ann.sequenceRef, new int[][]
- { new int[] { col, col },
- new int[]
- { ci.cStart, ci.cEnd } }, null);
+ .highlightPositionsOn(ann.sequenceRef, highlightPos, null);
}
}
return tooltip;
git://source.jalview.org / jalview.git / blobdiff