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.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());
+ int yOffset = rowIndex[1];
+
+ if (rowIndex == null)
+ {
+ System.err.println("IMPLEMENTATION ERROR: matrix click out of range.");
+ }
+ 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);
+
+ if (evt.isControlDown())
+ {
+ 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 = matrix.getGroupsFor(currentX);
for (int c = fr; c <= to; c++)
{
- av.getColumnSelection().addElement(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))
+ {
+ int offp = (rseq != null)
+ ? rseq.findIndex(rseq.getStart() - 1 + p)
+ : p;
+
+ if (!av.hasHiddenColumns() || hc.isVisible(offp))
+ {
+ av.getColumnSelection().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
+
+ }
+ }
+ else
+ {
+ // select corresponding range in segment under mouse
+ {
+ for (int c = fr; c <= to; c++)
+ {
+ av.getColumnSelection().addElement(c);
+ }
+ 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()))
+ {
+ 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;
}
- av.getColumnSelection().addElement(currentX);
}
}
}
}
- else
- {
- ap.getScalePanel().mousePressed(evt);
- }
- }
+ ap.paintAlignment(false, false);
+ 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
* 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
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)
{
ContactListI clist = av.getContactList(ann, column);
if (clist != null)
git://source.jalview.org / jalview.git / blobdiff