import jalview.util.Platform;
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
+import jalview.ws.datamodel.MappableContactMatrixI;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
/**
}
else
{
- // no row (or row that can be adjusted) was pressed. Simulate a ruler click
+ // no row (or row that can be adjusted) was pressed. Simulate a ruler
+ // click
ap.getScalePanel().mousePressed(evt);
}
}
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);
+ }
}
}
}
if (evt.isControlDown()
&& PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
{
- int c = fr - 1;
+ int c = fr;
ContactRange cr = forCurrentX.getRangeFor(fr, to);
double cval;
// TODO: could use GraphLine instead of arbitrary picking
// controls feathering - what other elements in row/column
// should we select
double thresh = cr.getMean() + (cr.getMax() - cr.getMean()) * .15;
- while (c > 0)
+ while (c >= 0)
{
cval = forCurrentX.getContactAt(c);
if (// cr.getMin() <= cval &&
}
c--;
}
- c = to;
- while (c < forCurrentX.getContactHeight())
+ c = to;
+ while (c < forCurrentX.getContactHeight())
+ {
+ cval = forCurrentX.getContactAt(c);
+ if (// cr.getMin() <= cval &&
+ cval <= thresh)
{
- 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
+ int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+ if (cols != null)
{
- break;
+ av.getColumnSelection().addRangeOfElements(cols, true);
}
- c++;
-
}
+ else
+ {
+ break;
+ }
+ c++;
+
}
+ }
}
}
ap.paintAlignment(false, false);
av.sendSelection();
return true;
}
+
/**
* Construct and display a context menu at the right-click position
*
}
if (rowIndex[0] != toRowIndex[0])
{
- jalview.bin.Console.trace("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
ContactGeometry lastXcgeom = new ContactGeometry(forFromX,
cma.graphHeight);
ContactGeometry.contactInterval lastXci = lastXcgeom
- .mapFor(rowIndex[1], rowIndex[1] - deltaY);
+ .mapFor(rowIndex[1], rowIndex[1] + deltaY);
ContactGeometry cXcgeom = new ContactGeometry(forToX,
cma.graphHeight);
ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1],
- rowIndex[1] - deltaY);
+ rowIndex[1] + deltaY);
// mark rectangular region formed by drag
jalview.bin.Console.trace("Matrix Selection from last(" + fromXc
for (int pair = 0; pair < mappedPos.length; pair += 2)
{
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);
- }
+ // {
+ // 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
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]);
+ + " 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
+ // if (cma.sequenceRef != null)
+ // {
+ // int col =
+ // cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
+ // av.getColumnSelection().addElement(col);
+ // }
+ // else
{
av.getColumnSelection().addElement(c);
}
{
row = i;
res[0] = row;
- res[1] = height - yPos;
+ res[1] = yPos-lheight;
break;
}
}
// TODO abstract tooltip generator so different implementations can be built
if (ann.graph == AlignmentAnnotation.CONTACT_MAP)
{
+ if (rowAndOffset>=ann.graphHeight)
+ {
+ return null;
+ }
ContactListI clist = av.getContactList(ann, column);
if (clist != null)
{
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);
return;
}
}
- imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
- + 1) * av.getCharWidth();
+ updateFadedImageWidth();
if (imgWidth < 1)
{
return;
tried = true;
} catch (IllegalArgumentException exc)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Serious issue with viewport geometry imgWidth requested was "
+ imgWidth);
return;
g.drawImage(image, 0, 0, this);
}
+ public void updateFadedImageWidth()
+ {
+ imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
+ + 1) * av.getCharWidth();
+
+ }
+
/**
* set true to enable redraw timing debug output on stderr
*/
&& (fadedImage == null || fadedImage.getWidth() != imgWidth
|| fadedImage.getHeight() != image.getHeight()))
{
- // System.err.println("redraw faded image ("+(fadedImage==null ?
+ // jalview.bin.Console.errPrintln("redraw faded image ("+(fadedImage==null ?
// "null image" : "") + " lastGood="+lastImageGood+")");
fadedImage = new BufferedImage(imgWidth, image.getHeight(),
BufferedImage.TYPE_INT_RGB);
@Override
public int getFadedImageWidth()
{
+ updateFadedImageWidth();
return imgWidth;
}
git://source.jalview.org / jalview.git / blobdiff