import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Collections;
import java.util.List;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.ContactRange;
+import jalview.datamodel.GraphLine;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.util.Platform;
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
+import jalview.ws.datamodel.MappableContactMatrixI;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
/**
* AnnotationPanel displays visible portion of annotation rows below unwrapped
if (graphStretch != -1)
{
- if (aa[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER)
+ if (aa[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP)
{
+ // data in row has position on y as well as x axis
if (evt.isAltDown() || evt.isAltGraphDown())
{
dragMode = DragMode.MatrixSelect;
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)
{
- int currentX = getColumnForXPos(evt.getX());
- ContactListI forCurrentX = av.getContactList(aa[graphStretch],
- currentX);
- if (forCurrentX != null)
+ // simplest approach is to select all group containing column
+ if (matrix.hasGroups())
{
- 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);
+ 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++)
{
- av.getColumnSelection().addElement(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)
+ {
+ // 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);
+ }
+ }
}
- av.getColumnSelection().addElement(currentX);
+ }
+ // 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()))
+ {
+ 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)
+ {
+ 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--;
+ }
+ c = to;
+ while (c < forCurrentX.getContactHeight())
+ {
+ 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++;
+
}
}
}
}
- else
- {
- ap.getScalePanel().mousePressed(evt);
- }
+ ap.paintAlignment(false, false);
+ PaintRefresher.Refresh(ap, av.getSequenceSetId());
+ av.sendSelection();
+ return true;
}
/**
ap.adjustAnnotationHeight();
}
dragMode = DragMode.Undefined;
- ap.getScalePanel().mouseReleased(evt);
+ if (!matrix_clicked(evt))
+ {
+ ap.getScalePanel().mouseReleased(evt);
+ }
/*
* isPopupTrigger is set in mouseReleased on Windows
* but could also be a matrix drag
*/
if ((evt.isAltDown() || evt.isAltGraphDown()) && (av.getAlignment()
- .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER))
+ .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP))
{
/*
* dragging in a matrix
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
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
- System.err.println("Matrix Selection from last(" + fromXc + ",["
- + lastXci.cStart + "," + lastXci.cEnd + "]) to cur(" + toXc
- + ",[" + cXci.cStart + "," + cXci.cEnd + "])");
+ 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);
- 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);
- System.err.println("Marking " + fr + " to " + to);
- for (int c = fr; c <= to; c++)
+ mappedPos = forFromX.getMappedPositionsFor(fr, to);
+ if (mappedPos != null)
{
- if (cma.sequenceRef != null)
+ for (int pair = 0; pair < mappedPos.length; pair += 2)
{
- int col = cma.sequenceRef.findIndex(c);
- av.getColumnSelection().addElement(col);
- }
- else
- {
- 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);
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);
{
row = i;
res[0] = row;
- res[1] = height - yPos;
+ res[1] = yPos-lheight;
break;
}
}
tooltip = ann.annotations[column].description;
}
// TODO abstract tooltip generator so different implementations can be built
- if (ann.graph == AlignmentAnnotation.CUSTOMRENDERER)
+ 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);
+ 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;
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