X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=15adafc7a88938a4ed184aaa825e252a2d73ccee;hb=0751c58086542f9e0466201b624f84d1efd547bb;hp=bd7d5fb78bea6d976e136d7967df91deef49f685;hpb=f5d6c0018555b2c453c2c0354c84cd5d2d81e3b9;p=jalview.git
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index bd7d5fb..15adafc 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -20,21 +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.util.Platform;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
import java.awt.AlphaComposite;
import java.awt.Color;
import java.awt.Dimension;
@@ -65,6 +50,22 @@ import javax.swing.JPopupMenu;
import javax.swing.Scrollable;
import javax.swing.ToolTipManager;
+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.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.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
/**
* AnnotationPanel displays visible portion of annotation rows below unwrapped
* alignment
@@ -149,9 +150,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
*/
public AnnotationPanel(AlignmentPanel ap)
{
-// setBackground(Color.white); // BH 2019
-
- ToolTipManager.sharedInstance().registerComponent(this);
+ setName("AnnotationPanel");
+ ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
this.ap = ap;
@@ -356,7 +356,8 @@ 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))
@@ -367,10 +368,11 @@ 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
@@ -635,6 +637,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
mouseDragLastX = -1;
mouseDragLastY = -1;
mouseDragging = false;
+ if (dragMode == DragMode.Resize)
+ {
+ ap.adjustAnnotationHeight();
+ }
dragMode = DragMode.Undefined;
ap.getScalePanel().mouseReleased(evt);
@@ -675,16 +681,25 @@ 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
@@ -712,14 +727,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
if (dragMode == DragMode.Undefined)
- {
+ {
/*
* drag is diagonal - defer deciding whether to
* treat as up/down or left/right
*/
- return;
- }
-
+ return;
+ }
try
{
if (dragMode == DragMode.Resize)
@@ -735,6 +749,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
graphAnnotation.graphHeight = newHeight;
adjustPanelHeight();
+ setNoFastPaint();
ap.paintAlignment(false, false);
}
}
@@ -762,30 +777,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
@Override
public void mouseMoved(MouseEvent evt)
{
+ int yPos = evt.getY();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
- if (aa == null)
- {
- this.setToolTipText(null);
- return;
- }
-
- int row = -1;
- int height = 0;
-
- for (int i = 0; i < aa.length; i++)
- {
- if (aa[i].visible)
- {
- height += aa[i].height;
- }
-
- if (evt.getY() < height)
- {
- row = i;
- break;
- }
- }
+ int row = getRowIndex(yPos, aa);
if (row == -1)
{
@@ -795,6 +790,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
int column = (evt.getX() / av.getCharWidth())
+ av.getRanges().getStartRes();
+ column = Math.min(column, av.getRanges().getEndRes());
if (av.hasHiddenColumns())
{
@@ -806,8 +802,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
if (row > -1 && ann.annotations != null
&& column < ann.annotations.length)
{
- buildToolTip(ann, column, aa);
- setStatusMessage(column, ann);
+ String toolTip = buildToolTip(ann, column, aa);
+ setToolTipText(toolTip == null ? null
+ : JvSwingUtils.wrapTooltip(true, toolTip));
+ String msg = getStatusMessage(av.getAlignment(), column, ann);
+ ap.alignFrame.setStatus(msg);
}
else
{
@@ -817,65 +816,99 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
/**
- * Builds a tooltip for the annotation at the current mouse position.
+ * 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)
+ {
+ return -1;
+ }
+ int row = -1;
+ int height = 0;
+
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].visible)
+ {
+ height += aa[i].height;
+ }
+
+ if (height > yPos)
+ {
+ row = i;
+ break;
+ }
+ }
+ return row;
+ }
+
+ /**
+ * 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
*/
- void buildToolTip(AlignmentAnnotation ann, int column,
+ static String buildToolTip(AlignmentAnnotation ann, int column,
AlignmentAnnotation[] anns)
{
+ 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
+ tooltip = ann.annotations[column].description;
+ if ("".equals(tooltip))
{
- this.setToolTipText(null); // no tooltip if null or empty description
+ tooltip = null;
}
}
- else
- {
- // clear the tooltip.
- this.setToolTipText(null);
- }
+
+ return tooltip;
}
/**
- * Constructs and displays the status bar message
+ * Constructs and returns the status bar message
*
+ * @param al
* @param column
* @param ann
*/
- void setStatusMessage(int column, AlignmentAnnotation ann)
+ static String getStatusMessage(AlignmentI al, int column,
+ AlignmentAnnotation ann)
{
/*
* show alignment column and annotation description if any
@@ -884,7 +917,7 @@ 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)
@@ -900,7 +933,7 @@ 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"))
@@ -910,7 +943,7 @@ 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));
@@ -931,7 +964,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
}
- ap.alignFrame.setStatus(text.toString());
+ return text.toString();
}
/**
@@ -973,7 +1006,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
private volatile boolean imageFresh = false;
- private Rectangle visibleRect = new Rectangle(), clipBounds = new Rectangle();
+
+ private Rectangle visibleRect = new Rectangle(),
+ clipBounds = new Rectangle();
/**
* DOCUMENT ME!
@@ -984,35 +1019,40 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
@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)
+ ViewportRanges ranges = av.getRanges();
+
+ if (allowFastPaint && 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;
}
}
- imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
- + 1) * av.getCharWidth();
+
+ imgWidth = (ranges.getEndRes() - ranges.getStartRes() + 1)
+ * av.getCharWidth();
+
if (imgWidth < 1)
{
+ fastPaint = false;
return;
}
Graphics2D gg;
@@ -1051,24 +1091,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
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);
+
+ drawComponent(gg, ranges.getStartRes(), av.getRanges().getEndRes() + 1);
gg.dispose();
imageFresh = false;
g.drawImage(image, 0, 0, this);
}
/**
- * set true to enable redraw timing debug output on stderr
- */
- private final boolean debugRedraw = false;
-
- /**
* non-Thread safe repaint
*
* @param horizontal
@@ -1089,6 +1125,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
int er = av.getRanges().getEndRes() + 1;
int transX = 0;
+ if (er == sr + 1)
+ {
+ fastPaint = false;
+ return;
+ }
+
Graphics2D gg = (Graphics2D) image.getGraphics();
gg.copyArea(0, 0, imgWidth, getHeight(),
@@ -1111,7 +1153,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
gg.translate(-transX, 0);
gg.dispose();
-
+
fastPaint = true;
// Call repaint on alignment panel so that repaints from other alignment
@@ -1229,6 +1271,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
private int[] bounds = new int[2];
+ private boolean allowFastPaint;
+
@Override
public int[] getVisibleVRange()
{
@@ -1255,7 +1299,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
ap = null;
image = null;
fadedImage = null;
-// gg = null;
+ // gg = null;
_mwl = null;
/*
@@ -1335,4 +1379,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
return annotationHeight;
}
+
+ /**
+ * Clears the flag that allows a 'fast paint' on the next repaint, so
+ * requiring a full repaint
+ */
+ public void setNoFastPaint()
+ {
+ allowFastPaint = false;
+ }
+
}