import javax.swing.Scrollable;
import javax.swing.ToolTipManager;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
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;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+import jalview.renderer.ContactGeometry;
import jalview.schemes.ResidueProperties;
import jalview.util.Comparison;
import jalview.util.MessageManager;
{
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;
@Override
public void colourSelected(Color c)
{
- HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
+ HiddenColumns hiddenColumns = av.getAlignment()
+ .getHiddenColumns();
for (int index : av.getColumnSelection().getSelected())
{
if (hiddenColumns.isVisible(index))
}
fAnot[index].colour = c;
}
- }};
+ }
+ };
};
- JalviewColourChooser.showColourChooser(this,
- title, Color.black, listener);
+ JalviewColourChooser.showColourChooser(this, title, Color.black,
+ listener);
}
else
// HELIX, SHEET or STEM
*/
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)
{
activeRow = i;
}
- else if (aa[i].graph > 0)
+ else if (aa[i].graph != 0)
{
/*
* 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 deltaY = toY - fromY;
+
+ 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 fromXp = Math.min(firstDragX, evt.getX());
+ int toXp = Math.max(firstDragX, evt.getX());
+ int lastX = getColumnForXPos(fromXp);
+ int currentX = getColumnForXPos(toXp);
+ ContactListI forLastX = av.getContactList(cma, lastX);
+ ContactListI forCurrentX = av.getContactList(cma, currentX);
+ if (forLastX != null && forCurrentX != null)
+ {
+ ContactGeometry lastXcgeom = new ContactGeometry(forLastX,
+ cma.graphHeight);
+ ContactGeometry.contactInterval lastXci = lastXcgeom.mapFor(
+ rowIndex[1],
+ rowIndex[1] + ((fromY == firstDragY) ? -deltaY : deltaY));
+ ContactGeometry cXcgeom = new ContactGeometry(forCurrentX,
+ 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(" + lastXci.cStart
+ + "," + lastXci.cEnd + ") to cur(" + 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++)
+ {
+ 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++)
+ {
+ 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
{
int yPos = evt.getY();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-
- int row = getRowIndex(yPos, aa);
+ int rowAndOffset[] = getRowIndexAndOffset(yPos, aa);
+ int row = rowAndOffset[0];
if (row == -1)
{
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);
+ 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);
+ String msg = getStatusMessage(av.getAlignment(), column, ann,
+ rowAndOffset[1], av);
ap.alignFrame.setStatus(msg);
}
else
}
}
+ 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
{
return -1;
}
+ return getRowIndexAndOffset(yPos, aa)[0];
+ }
+
+ static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)
+ {
+ int[] res = new int[2];
+ if (aa == null)
+ {
+ res[0] = -1;
+ res[1] = 0;
+ return res;
+ }
int row = -1;
- int height = 0;
+ int height = 0, lheight = 0;
for (int i = 0; i < aa.length; i++)
{
if (aa[i].visible)
{
+ lheight = height;
height += aa[i].height;
}
if (height > yPos)
{
row = i;
+ res[0] = row;
+ res[1] = height - yPos;
break;
}
}
- return row;
+ return res;
}
/**
* @param ann
* @param column
* @param anns
+ * @param rowAndOffset
*/
static String buildToolTip(AlignmentAnnotation ann, int column,
- AlignmentAnnotation[] anns)
+ AlignmentAnnotation[] anns, int rowAndOffset, AlignViewportI av,
+ AlignmentPanel ap)
{
String tooltip = null;
if (ann.graphGroup > -1)
{
tooltip = ann.annotations[column].description;
}
+ // TODO abstract tooltip generator so different implementations can be built
+ if (ann.graph == AlignmentAnnotation.CUSTOMRENDERER)
+ {
+ ContactListI clist = av.getContactList(ann, column);
+ 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;
+ // ap.getStructureSelectionManager().mouseOverSequence(ann.sequenceRef,
+ // new int[] {column, ci.cStart,ci.cEnd}, -1, null)
+ }
+ }
return tooltip;
}
* @param al
* @param column
* @param ann
+ * @param rowAndOffset
*/
static String getStatusMessage(AlignmentI al, int column,
- AlignmentAnnotation ann)
+ AlignmentAnnotation ann, int rowAndOffset, AlignViewportI av)
{
/*
* show alignment column and annotation description if any
}
private volatile boolean imageFresh = false;
- private Rectangle visibleRect = new Rectangle(), clipBounds = new Rectangle();
+
+ private Rectangle visibleRect = new Rectangle(),
+ clipBounds = new Rectangle();
/**
* DOCUMENT ME!
@Override
public void paintComponent(Graphics g)
{
-
- // BH: note that this method is generally recommended to
- // call super.paintComponent(g). Otherwise, the children of this
- // component will not be rendered. That is not needed here
- // because AnnotationPanel does not have any children. It is
- // just a JPanel contained in a JViewPort.
+
+ // BH: note that this method is generally recommended to
+ // call super.paintComponent(g). Otherwise, the children of this
+ // component will not be rendered. That is not needed here
+ // because AnnotationPanel does not have any children. It is
+ // just a JPanel contained in a JViewPort.
computeVisibleRect(visibleRect);
-
+
g.setColor(Color.white);
g.fillRect(0, 0, visibleRect.width, visibleRect.height);
if (image != null)
{
- // BH 2018 optimizing generation of new Rectangle().
- if (fastPaint || (visibleRect.width != (clipBounds = g.getClipBounds(clipBounds)).width)
- || (visibleRect.height != clipBounds.height))
+ // BH 2018 optimizing generation of new Rectangle().
+ if (fastPaint
+ || (visibleRect.width != (clipBounds = g
+ .getClipBounds(clipBounds)).width)
+ || (visibleRect.height != clipBounds.height))
{
-
- g.drawImage(image, 0, 0, this);
+ g.drawImage(image, 0, 0, this);
fastPaint = false;
return;
}
gg.setColor(Color.white);
gg.fillRect(0, 0, imgWidth, image.getHeight());
imageFresh = true;
- } else {
- gg = (Graphics2D) image.getGraphics();
+ }
+ else
+ {
+ gg = (Graphics2D) image.getGraphics();
}
-
+
drawComponent(gg, av.getRanges().getStartRes(),
av.getRanges().getEndRes() + 1);
gg.dispose();
Graphics2D gg = (Graphics2D) image.getGraphics();
- gg.copyArea(0, 0, imgWidth, getHeight(),
- -horizontal * av.getCharWidth(), 0);
-
- if (horizontal > 0) // scrollbar pulled right, image to the left
- {
- transX = (er - sr - horizontal) * av.getCharWidth();
- sr = er - horizontal;
- }
- else if (horizontal < 0)
+ if (imgWidth > Math.abs(horizontal * av.getCharWidth()))
{
- er = sr - horizontal;
- }
+ // scroll is less than imgWidth away so can re-use buffered graphics
+ gg.copyArea(0, 0, imgWidth, getHeight(),
+ -horizontal * av.getCharWidth(), 0);
+ if (horizontal > 0) // scrollbar pulled right, image to the left
+ {
+ transX = (er - sr - horizontal) * av.getCharWidth();
+ sr = er - horizontal;
+ }
+ else if (horizontal < 0)
+ {
+ er = sr - horizontal;
+ }
+ }
gg.translate(transX, 0);
drawComponent(gg, sr, er);
gg.translate(-transX, 0);
gg.dispose();
-
+
fastPaint = true;
// Call repaint on alignment panel so that repaints from other alignment
{
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
ap = null;
image = null;
fadedImage = null;
-// gg = null;
+ // gg = null;
_mwl = null;
/*
git://source.jalview.org / jalview.git / blobdiff