*/
package jalview.gui;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-import jalview.renderer.AwtRenderPanelI;
-import jalview.schemes.ResidueProperties;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
import java.awt.AlphaComposite;
import java.awt.Color;
import java.awt.Dimension;
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 javax.swing.JColorChooser;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
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.ContactMatrixI;
+import jalview.datamodel.ContactRange;
+import jalview.datamodel.GraphLine;
+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.Format;
+import jalview.util.MessageManager;
+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
* alignment
{
enum DragMode
{
- Select, Resize, Undefined
+ Select, Resize, Undefined, MatrixSelect
};
String HELIX = MessageManager.getString("label.helix");
public volatile BufferedImage fadedImage;
- Graphics2D gg;
+ // private Graphics2D gg;
public FontMetrics fm;
int mouseDragLastY = -1;
+ int firstDragX = -1;
+
+ int firstDragY = -1;
+
DragMode dragMode = DragMode.Undefined;
boolean mouseDragging = false;
private MouseWheelListener[] _mwl;
+ private boolean notJustOne;
+
/**
* Creates a new AnnotationPanel object.
*
else if (action.equals(LABEL))
{
String exMesg = collectAnnotVals(anot, LABEL);
- String label = JvOptionPane.showInputDialog(this,
+ String label = JvOptionPane.showInputDialog(
MessageManager.getString("label.enter_label"), exMesg);
if (label == null)
}
else if (action.equals(COLOUR))
{
- Color col = JColorChooser.showDialog(this,
- MessageManager.getString("label.select_foreground_colour"),
- Color.black);
-
- for (int index : av.getColumnSelection().getSelected())
+ final Annotation[] fAnot = anot;
+ String title = MessageManager
+ .getString("label.select_foreground_colour");
+ ColourChooserListener listener = new ColourChooserListener()
{
- if (!av.getAlignment().getHiddenColumns().isVisible(index))
- {
- continue;
- }
-
- if (anot[index] == null)
+ @Override
+ public void colourSelected(Color c)
{
- anot[index] = new Annotation("", "", ' ', 0);
- }
-
- anot[index].colour = col;
- }
+ HiddenColumns hiddenColumns = av.getAlignment()
+ .getHiddenColumns();
+ for (int index : av.getColumnSelection().getSelected())
+ {
+ if (hiddenColumns.isVisible(index))
+ {
+ if (fAnot[index] == null)
+ {
+ fAnot[index] = new Annotation("", "", ' ', 0);
+ }
+ fAnot[index].colour = c;
+ }
+ }
+ };
+ };
+ 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.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
+ {
+ // 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[] allAnnotation = av.getAlignment()
+ .getAlignmentAnnotation();
+ if (allAnnotation == null || rowIndex[0] < 0
+ || rowIndex[0] >= allAnnotation.length)
+ {
+ return false;
+ }
+ 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);
+ if (cXci != null)
+ {
+ /**
+ * 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)
+ {
+ // simplest approach is to select all group containing column
+ if (matrix.hasGroups())
+ {
+ SequenceI rseq = clicked.sequenceRef;
+ BitSet grp = new BitSet();
+ grp.or(matrix.getGroupsFor(forCurrentX.getPosition()));
+ // 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();
+ 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);
+ }
+ }
+ }
+ }
+ // 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++;
+
+ }
+ }
+
+ }
+ }
+ }
+ ap.paintAlignment(false, false);
+ PaintRefresher.Refresh(ap, av.getSequenceSetId());
+ av.sendSelection();
+ return true;
}
/**
@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)
+ {
+ ap.adjustAnnotationHeight();
+ }
dragMode = DragMode.Undefined;
- ap.getScalePanel().mouseReleased(evt);
+ if (!matrix_clicked(evt))
+ {
+ ap.getScalePanel().mouseReleased(evt);
+ }
/*
* isPopupTrigger is set in mouseReleased on Windows
@Override
public void mouseEntered(MouseEvent evt)
{
+ this.mouseDragging = false;
ap.getScalePanel().mouseEntered(evt);
}
/**
- * DOCUMENT ME!
+ * On leaving the panel, calls ScalePanel.mouseExited to deal with scrolling
+ * with column selection on a mouse drag
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mouseExited(MouseEvent evt)
}
/**
- * DOCUMENT ME!
+ * Action on starting or continuing a mouse drag. There are two possible
+ * actions:
+ * <ul>
+ * <li>drag up or down on a graphed annotation increases or decreases the
+ * height of the graph</li>
+ * <li>dragging left or right selects the columns dragged across</li>
+ * </ul>
+ * A drag on a graph annotation is treated as column selection if it starts
+ * with more horizontal than vertical movement, and as resize if it starts
+ * with more vertical than horizontal movement. Once started, the drag does
+ * not change mode.
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mouseDragged(MouseEvent evt)
{
/*
- * todo: if dragMode is Undefined:
+ * if dragMode is Undefined:
* - set to Select if dx > dy
* - set to Resize if dy > dx
* - do nothing if dx == dy
* mostly vertical drag
*/
dragMode = DragMode.Resize;
+ notJustOne = evt.isShiftDown();
+
+ /*
+ * but could also be a matrix drag
+ */
+ if ((evt.isAltDown() || evt.isAltGraphDown()) && (av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP))
+ {
+ /*
+ * dragging in a matrix
+ */
+ dragMode = DragMode.MatrixSelect;
+ firstDragX = mouseDragLastX;
+ firstDragY = mouseDragLastY;
+ }
}
}
if (dragMode == DragMode.Undefined)
+
{
/*
* drag is diagonal - defer deciding whether to
AlignmentAnnotation graphAnnotation = av.getAlignment()
.getAlignmentAnnotation()[graphStretch];
int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
- graphAnnotation.graphHeight = newHeight;
+ if (notJustOne)
+ {
+ for (AlignmentAnnotation similar : av.getAlignment()
+ .findAnnotations(null, graphAnnotation.getCalcId(),
+ graphAnnotation.label))
+ {
+ similar.graphHeight = newHeight;
+ }
+
+ }
+ else
+ {
+ graphAnnotation.graphHeight = newHeight;
+ }
adjustPanelHeight();
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)
+ {
+ jalview.bin.Console.trace("Drag out of range. needs to be clipped");
+
+ }
+ if (rowIndex[0] != toRowIndex[0])
+ {
+ jalview.bin.Console
+ .trace("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)
+ {
+ // FIXME will need two ContactGeometry objects when handling contact
+ // matrices with differing numbers of rows at each
+ // column
+ ContactGeometry xcgeom = new ContactGeometry(forFromX,
+ cma.graphHeight);
+ ContactGeometry.contactInterval lastXci = xcgeom.mapFor(rowIndex[1]);
+ ContactGeometry.contactInterval cXci = xcgeom
+ .mapFor(rowIndex[1] + deltaY);
+
+ // mark rectangular region formed by drag
+ 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, cXci.cStart);
+ to = Math.max(lastXci.cEnd, cXci.cEnd);
+ int[] mappedPos = forFromX.getMappedPositionsFor(fr, to);
+ if (mappedPos != 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)
+ {
+ 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 - 1);
+ }
+ }
+ }
+ fr = Math.min(lastX, currentX);
+ to = Math.max(lastX, currentX);
+
+ jalview.bin.Console.trace("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)
{
- setToolTipText(buildToolTip(ann, column, aa));
- String msg = getStatusMessage(av.getAlignment(), column, ann);
+ 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,
+ 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;
}
- int row = -1;
- int height = 0;
+ return getRowIndexAndOffset(yPos, aa)[0];
+ }
+ static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)
+ {
+ int[] res = new int[2];
+ res[0] = -1;
+ res[1] = 0;
+ if (aa == null)
+ {
+ return res;
+ }
+ int row = -1;
+ 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] = yPos - lheight;
break;
}
}
- return row;
+ return res;
}
/**
- * Answers a tooltip for the annotation at the current mouse position
+ * Answers a tooltip for the annotation at the current mouse position, not
+ * wrapped in <html> tags (apply if wanted). Answers null if there is no
+ * tooltip to show.
*
* @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)
{
StringBuilder tip = new StringBuilder(32);
- tip.append("<html>");
+ boolean first = true;
for (int i = 0; i < anns.length; i++)
{
if (anns[i].graphGroup == ann.graphGroup
&& anns[i].annotations[column] != null)
{
+ if (!first)
+ {
+ tip.append("<br>");
+ }
+ first = false;
tip.append(anns[i].label);
String description = anns[i].annotations[column].description;
if (description != null && description.length() > 0)
{
tip.append(" ").append(description);
}
- tip.append("<br>");
}
}
- if (tip.length() != 6)
- {
- tip.setLength(tip.length() - 4);
- tooltip = tip.toString() + "</html>";
- }
+ tooltip = first ? null : tip.toString();
}
else if (column < ann.annotations.length
&& ann.annotations[column] != null)
{
- String description = ann.annotations[column].description;
- if (description != null && description.length() > 0)
+ tooltip = ann.annotations[column].description;
+ }
+ // TODO abstract tooltip generator so different implementations can be built
+ if (ann.graph == AlignmentAnnotation.CONTACT_MAP)
+ {
+ if (rowAndOffset >= ann.graphHeight)
{
- tooltip = JvSwingUtils.wrapTooltip(true, description);
+ return null;
}
- else
+ ContactListI clist = av.getContactList(ann, column);
+ if (clist != null)
{
- tooltip = null; // no tooltip if null or empty description
+ ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight);
+ ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset);
+ ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
+ StringBuilder tooltipb = new StringBuilder();
+ tooltipb.append("Contact from ").append(clist.getPosition())
+ .append(", [").append(ci.cStart).append(" - ")
+ .append(ci.cEnd).append("]").append("<br/>Mean:");
+ Format.appendPercentage(tooltipb, (float) cr.getMean(), 2);
+ tooltip = tooltipb.toString();
+ 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, highlightPos, null);
}
}
- else
- {
- // clear the tooltip.
- tooltip = 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();
+
/**
* DOCUMENT ME!
*
@Override
public void paintComponent(Graphics g)
{
- super.paintComponent(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.
+
+ computeVisibleRect(visibleRect);
g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
+ g.fillRect(0, 0, visibleRect.width, visibleRect.height);
if (image != null)
{
- if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
- || (getVisibleRect().height != g.getClipBounds().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);
fastPaint = false;
return;
}
}
- imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
- + 1) * av.getCharWidth();
+ updateFadedImageWidth();
if (imgWidth < 1)
{
return;
}
+ Graphics2D gg;
if (image == null || imgWidth != image.getWidth(this)
|| image.getHeight(this) != getHeight())
{
- try
- {
- image = new BufferedImage(imgWidth,
- ap.getAnnotationPanel().getHeight(),
- BufferedImage.TYPE_INT_RGB);
- } catch (OutOfMemoryError oom)
+ boolean tried = false;
+ image = null;
+ while (image == null && !tried)
{
try
{
- System.gc();
- } catch (Exception x)
+ image = new BufferedImage(imgWidth,
+ ap.getAnnotationPanel().getHeight(),
+ BufferedImage.TYPE_INT_RGB);
+ tried = true;
+ } catch (IllegalArgumentException exc)
{
+ jalview.bin.Console.errPrintln(
+ "Serious issue with viewport geometry imgWidth requested was "
+ + imgWidth);
+ return;
+ } catch (OutOfMemoryError oom)
+ {
+ try
+ {
+ System.gc();
+ } catch (Exception x)
+ {
+ }
+ ;
+ new OOMWarning(
+ "Couldn't allocate memory to redraw screen. Please restart Jalview",
+ oom);
+ return;
}
- ;
- new OOMWarning(
- "Couldn't allocate memory to redraw screen. Please restart Jalview",
- oom);
- return;
+
}
gg = (Graphics2D) image.getGraphics();
gg.fillRect(0, 0, imgWidth, image.getHeight());
imageFresh = true;
}
-
+ else
+ {
+ gg = (Graphics2D) image.getGraphics();
+
+ }
+
drawComponent(gg, av.getRanges().getStartRes(),
av.getRanges().getEndRes() + 1);
+ gg.dispose();
imageFresh = false;
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
*/
*/
public void fastPaint(int horizontal)
{
- if ((horizontal == 0) || gg == null
+ if ((horizontal == 0) || image == null
|| av.getAlignment().getAlignmentAnnotation() == null
|| av.getAlignment().getAlignmentAnnotation().length < 1
|| av.isCalcInProgress())
int er = av.getRanges().getEndRes() + 1;
int transX = 0;
- gg.copyArea(0, 0, imgWidth, getHeight(),
- -horizontal * av.getCharWidth(), 0);
+ Graphics2D gg = (Graphics2D) image.getGraphics();
- 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 == 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);
{
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
@Override
public int getFadedImageWidth()
{
+ updateFadedImageWidth();
return imgWidth;
}
ap = null;
image = null;
fadedImage = null;
- gg = null;
+ // gg = null;
_mwl = null;
/*
* hscroll, status bar, insets.
*/
int stuff = (ap.getViewName() != null ? 30 : 0)
- + (Platform.isAMac() ? 120 : 140);
+ + (Platform.isAMacAndNotJS() ? 120 : 140);
int availableHeight = ap.alignFrame.getHeight() - stuff;
int rowHeight = av.getCharHeight();
git://source.jalview.org / jalview.git / blobdiff