X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=ccc086ccc5d589670203d7d571d35ef14e63f84c;hb=0d326d33340305d0eaa539cbf903f778001ebeb7;hp=1460985bc5fbef24665f5d6559b028347b661668;hpb=2639d90e2b52d49cf586c0b602bc606033c9b8ae;p=jalview.git
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 1460985..ccc086c 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -20,20 +20,6 @@
*/
package jalview.gui;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JalviewColourChooser.ColourChooserListener;
-import jalview.renderer.AnnotationRenderer;
-import jalview.renderer.AwtRenderPanelI;
-import jalview.schemes.ResidueProperties;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
import java.awt.AlphaComposite;
import java.awt.Color;
import java.awt.Dimension;
@@ -64,6 +50,26 @@ 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.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;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
/**
* AnnotationPanel displays visible portion of annotation rows below unwrapped
* alignment
@@ -77,7 +83,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
{
enum DragMode
{
- Select, Resize, Undefined
+ Select, Resize, Undefined, MatrixSelect
};
String HELIX = MessageManager.getString("label.helix");
@@ -112,7 +118,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
public volatile BufferedImage fadedImage;
- Graphics2D gg;
+ // private Graphics2D gg;
public FontMetrics fm;
@@ -127,6 +133,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
int mouseDragLastY = -1;
+ int firstDragX = -1;
+
+ int firstDragY = -1;
+
DragMode dragMode = DragMode.Undefined;
boolean mouseDragging = false;
@@ -211,7 +221,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
@Override
public Dimension getPreferredScrollableViewportSize()
{
- return getPreferredSize();
+ Dimension ps = getPreferredSize();
+ return new Dimension(ps.width, adjustForAlignFrame(false, ps.height));
}
@Override
@@ -312,7 +323,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
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)
@@ -352,7 +363,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
@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))
@@ -363,10 +375,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
fAnot[index].colour = c;
}
- }};
+ }
+ };
};
- JalviewColourChooser.showColourChooser(this,
- title, Color.black, listener);
+ JalviewColourChooser.showColourChooser(this, title, Color.black,
+ listener);
}
else
// HELIX, SHEET or STEM
@@ -531,8 +544,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
*/
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)
@@ -546,12 +561,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
{
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;
}
@@ -567,7 +583,44 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
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);
+ }
}
/**
@@ -627,10 +680,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
@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);
@@ -671,16 +734,25 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
/**
- * DOCUMENT ME!
+ * Action on starting or continuing a mouse drag. There are two possible
+ * actions:
+ *
+ * - drag up or down on a graphed annotation increases or decreases the
+ * height of the graph
+ * - dragging left or right selects the columns dragged across
+ *
+ * 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
@@ -704,10 +776,25 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
* 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
@@ -734,6 +821,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
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
{
/*
@@ -749,6 +845,82 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
}
+ 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
@@ -758,120 +930,173 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
@Override
public void mouseMoved(MouseEvent evt)
{
+ int yPos = evt.getY();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ int rowAndOffset[] = getRowIndexAndOffset(yPos, aa);
+ int row = rowAndOffset[0];
- if (aa == null)
+ if (row == -1)
{
this.setToolTipText(null);
return;
}
- int row = -1;
- int height = 0;
+ int column = getColumnForXPos(evt.getX());
- for (int i = 0; i < aa.length; i++)
+ AlignmentAnnotation ann = aa[row];
+ if (row > -1 && ann.annotations != null
+ && column < ann.annotations.length)
{
- if (aa[i].visible)
- {
- height += aa[i].height;
- }
-
- if (evt.getY() < height)
- {
- row = i;
- break;
- }
+ 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);
}
-
- if (row == -1)
+ else
{
this.setToolTipText(null);
- return;
+ ap.alignFrame.setStatus(" ");
}
+ }
- int column = (evt.getX() / av.getCharWidth())
- + av.getRanges().getStartRes();
+ 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;
+ }
- AlignmentAnnotation ann = aa[row];
- if (row > -1 && ann.annotations != null
- && column < ann.annotations.length)
+ /**
+ * 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
+ * until the y position has been exceeded. Answers -1 if no annotations are
+ * visible, or the y position is below all annotations.
+ *
+ * @param yPos
+ * @param aa
+ * @return
+ */
+ static int getRowIndex(int yPos, AlignmentAnnotation[] aa)
+ {
+ if (aa == null)
{
- buildToolTip(ann, column, aa);
- setStatusMessage(column, ann);
+ return -1;
}
- else
+ return getRowIndexAndOffset(yPos, aa)[0];
+ }
+
+ static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)
+ {
+ int[] res = new int[2];
+ if (aa == null)
{
- this.setToolTipText(null);
- ap.alignFrame.statusBar.setText(" ");
+ 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)
+ {
+ lheight = height;
+ height += aa[i].height;
+ }
+
+ if (height > yPos)
+ {
+ row = i;
+ res[0] = row;
+ res[1] = height - yPos;
+ break;
+ }
+ }
+ return res;
}
/**
- * Builds 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
*/
- void buildToolTip(AlignmentAnnotation ann, int column,
- AlignmentAnnotation[] anns)
+ static String buildToolTip(AlignmentAnnotation ann, int column,
+ AlignmentAnnotation[] anns, int rowAndOffset, AlignViewportI av,
+ AlignmentPanel ap)
{
+ String tooltip = null;
if (ann.graphGroup > -1)
{
StringBuilder tip = new StringBuilder(32);
- tip.append("");
+ 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("
");
+ }
+ 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("
");
}
}
- if (tip.length() != 6)
- {
- tip.setLength(tip.length() - 4);
- this.setToolTipText(tip.toString() + "");
- }
+ tooltip = first ? null : tip.toString();
}
- else if (ann.annotations[column] != null)
+ else if (column < ann.annotations.length
+ && ann.annotations[column] != null)
{
- String description = ann.annotations[column].description;
- if (description != null && description.length() > 0)
- {
- this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
- }
- else
- {
- this.setToolTipText(null); // no tooltip if null or empty description
- }
+ tooltip = ann.annotations[column].description;
}
- else
+ // TODO abstract tooltip generator so different implementations can be built
+ if (ann.graph == AlignmentAnnotation.CUSTOMRENDERER)
{
- // clear the tooltip.
- this.setToolTipText(null);
+ 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;
}
/**
- * Constructs and displays the status bar message
+ * Constructs and returns the status bar message
*
+ * @param al
* @param column
* @param ann
+ * @param rowAndOffset
*/
- void setStatusMessage(int column, AlignmentAnnotation ann)
+ static String getStatusMessage(AlignmentI al, int column,
+ AlignmentAnnotation ann, int rowAndOffset, AlignViewportI av)
{
/*
* show alignment column and annotation description if any
@@ -880,7 +1105,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
text.append(MessageManager.getString("label.column")).append(" ")
.append(column + 1);
- if (ann.annotations[column] != null)
+ if (column < ann.annotations.length && ann.annotations[column] != null)
{
String description = ann.annotations[column].description;
if (description != null && description.trim().length() > 0)
@@ -896,7 +1121,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
SequenceI seqref = ann.sequenceRef;
if (seqref != null)
{
- int seqIndex = av.getAlignment().findIndex(seqref);
+ int seqIndex = al.findIndex(seqref);
if (seqIndex != -1)
{
text.append(", ").append(MessageManager.getString("label.sequence"))
@@ -906,7 +1131,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
{
text.append(" ");
String name;
- if (av.getAlignment().isNucleotide())
+ if (al.isNucleotide())
{
name = ResidueProperties.nucleotideName
.get(String.valueOf(residue));
@@ -927,7 +1152,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
}
- ap.alignFrame.statusBar.setText(text.toString());
+ return text.toString();
}
/**
@@ -970,6 +1195,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
private volatile boolean imageFresh = false;
+ private Rectangle visibleRect = new Rectangle(),
+ clipBounds = new Rectangle();
+
/**
* DOCUMENT ME!
*
@@ -979,16 +1207,27 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
@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;
@@ -1000,6 +1239,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
{
return;
}
+ Graphics2D gg;
if (image == null || imgWidth != image.getWidth(this)
|| image.getHeight(this) != getHeight())
{
@@ -1036,9 +1276,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
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);
}
@@ -1056,7 +1302,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
*/
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())
@@ -1069,25 +1315,32 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
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
+ if (imgWidth > Math.abs(horizontal * av.getCharWidth()))
{
- transX = (er - sr - horizontal) * av.getCharWidth();
- sr = er - horizontal;
- }
- else if (horizontal < 0)
- {
- 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
@@ -1183,6 +1436,17 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
{
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
@@ -1231,7 +1495,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
ap = null;
image = null;
fadedImage = null;
- gg = null;
+ // gg = null;
_mwl = null;
/*
@@ -1266,4 +1530,49 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
repaint();
}
}
+
+ /**
+ * computes the visible height of the annotation panel
+ *
+ * @param adjustPanelHeight
+ * - when false, just adjust existing height according to other
+ * windows
+ * @param annotationHeight
+ * @return height to use for the ScrollerPreferredVisibleSize
+ */
+ public int adjustForAlignFrame(boolean adjustPanelHeight,
+ int annotationHeight)
+ {
+ /*
+ * Estimate available height in the AlignFrame for alignment +
+ * annotations. Deduct an estimate for title bar, menu bar, scale panel,
+ * hscroll, status bar, insets.
+ */
+ int stuff = (ap.getViewName() != null ? 30 : 0)
+ + (Platform.isAMacAndNotJS() ? 120 : 140);
+ int availableHeight = ap.alignFrame.getHeight() - stuff;
+ int rowHeight = av.getCharHeight();
+
+ if (adjustPanelHeight)
+ {
+ int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+
+ /*
+ * If not enough vertical space, maximize annotation height while keeping
+ * at least two rows of alignment visible
+ */
+ if (annotationHeight + alignmentHeight > availableHeight)
+ {
+ annotationHeight = Math.min(annotationHeight,
+ availableHeight - 2 * rowHeight);
+ }
+ }
+ else
+ {
+ // maintain same window layout whilst updating sliders
+ annotationHeight = Math.min(ap.annotationScroller.getSize().height,
+ availableHeight - 2 * rowHeight);
+ }
+ return annotationHeight;
+ }
}