import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactRange;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.gui.JalviewColourChooser.ColourChooserListener;
{
enum DragMode
{
- Select, Resize, Undefined
+ Select, Resize, Undefined, MatrixSelect
};
String HELIX = MessageManager.getString("label.helix");
int mouseDragLastY = -1;
+ int firstDragX = -1;
+
+ int firstDragY = -1;
+
DragMode dragMode = DragMode.Undefined;
boolean mouseDragging = false;
*/
int height = 0;
activeRow = -1;
-
+ int yOffset = 0;
+ // todo could reuse getRowIndexAndOffset ?
final int y = evt.getY();
+
for (int i = 0; i < aa.length; i++)
{
if (aa[i].visible)
* we have clicked on a resizable graph annotation
*/
graphStretch = i;
+ yOffset = height - y;
}
break;
}
return;
}
- ap.getScalePanel().mousePressed(evt);
+ if (graphStretch != -1)
+ {
+
+ if (aa[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER)
+ {
+ if (evt.isAltDown() || evt.isAltGraphDown())
+ {
+ dragMode = DragMode.MatrixSelect;
+ firstDragX = mouseDragLastX;
+ firstDragY = mouseDragLastY;
+ }
+ else
+ {
+ int currentX = getColumnForXPos(evt.getX());
+ ContactListI forCurrentX = av.getContactList(aa[graphStretch],
+ currentX);
+ if (forCurrentX != null)
+ {
+ 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);
+ for (int c = fr; c <= to; c++)
+ {
+ av.getColumnSelection().addElement(c);
+ }
+ av.getColumnSelection().addElement(currentX);
+ }
+ }
+ }
+ }
+ else
+ {
+ ap.getScalePanel().mousePressed(evt);
+ }
}
/**
@Override
public void mouseReleased(MouseEvent evt)
{
+ if (dragMode == DragMode.MatrixSelect)
+ {
+ matrixSelectRange(evt);
+ }
graphStretch = -1;
mouseDragLastX = -1;
mouseDragLastY = -1;
+ firstDragX = -1;
+ firstDragY = -1;
mouseDragging = false;
if (dragMode == DragMode.Resize)
{
* mostly vertical drag
*/
dragMode = DragMode.Resize;
+
+ /*
+ * but could also be a matrix drag
+ */
+ if ((evt.isAltDown() || evt.isAltGraphDown()) && (av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER))
+ {
+ /*
+ * dragging in a matrix
+ */
+ dragMode = DragMode.MatrixSelect;
+ firstDragX = mouseDragLastX;
+ firstDragY = mouseDragLastY;
+ }
}
}
if (dragMode == DragMode.Undefined)
+
{
/*
* drag is diagonal - defer deciding whether to
ap.paintAlignment(false, false);
}
}
+ else if (dragMode == DragMode.MatrixSelect)
+ {
+ /*
+ * TODO draw a rubber band for range
+ */
+ mouseDragLastX = x;
+ mouseDragLastY = y;
+ ap.paintAlignment(false, false);
+ }
else
{
/*
}
}
+ public void matrixSelectRange(MouseEvent evt)
+ {
+ /*
+ * get geometry of drag
+ */
+ int fromY = Math.min(firstDragY, evt.getY());
+ int toY = Math.max(firstDragY, evt.getY());
+ int fromX = Math.min(firstDragX, evt.getX());
+ int toX = Math.max(firstDragX, evt.getX());
+
+ int deltaY = toY - fromY;
+ int deltaX = toX - fromX;
+
+ int[] rowIndex = getRowIndexAndOffset(fromY,
+ av.getAlignment().getAlignmentAnnotation());
+ int[] toRowIndex = getRowIndexAndOffset(toY,
+ av.getAlignment().getAlignmentAnnotation());
+
+ if (rowIndex == null || toRowIndex == null)
+ {
+ System.out.println("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");
+ }
+
+ // rectangular selection on matrix style annotation
+ AlignmentAnnotation cma = av.getAlignment()
+ .getAlignmentAnnotation()[rowIndex[0]];
+
+ int lastX = getColumnForXPos(fromX);
+ int currentX = getColumnForXPos(toX);
+ int fromXc = Math.min(lastX, currentX);
+ int toXc = Math.max(lastX, currentX);
+ ContactListI forFromX = av.getContactList(cma, fromXc);
+ ContactListI forToX = av.getContactList(cma, toXc);
+
+ if (forFromX != null && forToX != null)
+ {
+ ContactGeometry lastXcgeom = new ContactGeometry(forFromX,
+ cma.graphHeight);
+ ContactGeometry.contactInterval lastXci = lastXcgeom
+ .mapFor(rowIndex[1], rowIndex[1] - deltaY);
+
+ ContactGeometry cXcgeom = new ContactGeometry(forToX,
+ cma.graphHeight);
+ ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1],
+ 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 + "])");
+ 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++)
+ {
+ if (cma.sequenceRef != null)
+ {
+ int col = cma.sequenceRef.findIndex(c);
+ av.getColumnSelection().addElement(col);
+ }
+ else
+ {
+ av.getColumnSelection().addElement(c);
+ }
+ }
+ 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++)
+ {
+ if (cma.sequenceRef != null)
+ {
+ int col = cma.sequenceRef.findIndex(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);
+ for (int c = fr; c <= to; c++)
+ {
+ av.getColumnSelection().addElement(c);
+ }
+ }
+
+ }
+
/**
* Constructs the tooltip, and constructs and displays a status message, for
* the current mouse position
return;
}
- int column = (evt.getX() / av.getCharWidth())
- + av.getRanges().getStartRes();
- column = Math.min(column, av.getRanges().getEndRes());
-
- if (av.hasHiddenColumns())
- {
- column = av.getAlignment().getHiddenColumns()
- .visibleToAbsoluteColumn(column);
- }
+ int column = getColumnForXPos(evt.getX());
AlignmentAnnotation ann = aa[row];
if (row > -1 && ann.annotations != null
&& column < ann.annotations.length)
{
- String toolTip = buildToolTip(ann, column, aa, rowAndOffset[1], av);
+ String toolTip = buildToolTip(ann, column, aa, rowAndOffset[1], av,
+ ap);
setToolTipText(toolTip == null ? null
: JvSwingUtils.wrapTooltip(true, toolTip));
String msg = getStatusMessage(av.getAlignment(), column, ann,
}
}
+ private int getColumnForXPos(int x)
+ {
+ int column = (x / av.getCharWidth()) + av.getRanges().getStartRes();
+ column = Math.min(column, av.getRanges().getEndRes());
+
+ if (av.hasHiddenColumns())
+ {
+ column = av.getAlignment().getHiddenColumns()
+ .visibleToAbsoluteColumn(column);
+ }
+ return column;
+ }
+
/**
* Answers the index in the annotations array of the visible annotation at the
* given y position. This is done by adding the heights of visible annotations
static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)
{
int[] res = new int[2];
+ res[0] = -1;
+ res[1] = 0;
if (aa == null)
{
- res[0] = -1;
- res[1] = 0;
return res;
}
int row = -1;
int height = 0, lheight = 0;
-
for (int i = 0; i < aa.length; i++)
{
if (aa[i].visible)
{
row = i;
res[0] = row;
- res[1] = yPos - lheight;
+ res[1] = height - yPos;
break;
}
}
* @param rowAndOffset
*/
static String buildToolTip(AlignmentAnnotation ann, int column,
- AlignmentAnnotation[] anns, int rowAndOffset, AlignViewportI av)
+ AlignmentAnnotation[] anns, int rowAndOffset, AlignViewportI av,
+ AlignmentPanel ap)
{
String tooltip = null;
if (ann.graphGroup > -1)
if (clist != null)
{
ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight);
- ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset,
- rowAndOffset);
- tooltip += "Contact from " + ci.cStart + " to " + ci.cEnd;
+ ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset);
+ 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);
+ ap.getStructureSelectionManager()
+ .highlightPositionsOn(ann.sequenceRef, new int[][]
+ { new int[] { col, col },
+ new int[]
+ { ci.cStart, ci.cEnd } }, null);
}
}
return tooltip;
{
fadedImage = oldFaded;
}
+ if (dragMode == DragMode.MatrixSelect)
+ {
+ g.setColor(Color.yellow);
+ g.drawRect(Math.min(firstDragX, mouseDragLastX),
+ Math.min(firstDragY, mouseDragLastY),
+ Math.max(firstDragX, mouseDragLastX)
+ - Math.min(firstDragX, mouseDragLastX),
+ Math.max(firstDragY, mouseDragLastY)
+ - Math.min(firstDragY, mouseDragLastY));
+
+ }
}
@Override
git://source.jalview.org / jalview.git / blobdiff