X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=b18501e4695a5e85e768bf45a3902bca69ee64f3;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=149f432f360dfb54b119ff3acd5505687e18178f;hpb=aa4c2cc89e5b9412f4b0211525b9aa76ea4a1920;p=jalview.git
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 149f432..b18501e 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,80 +1,117 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.awt.*;
import java.awt.event.*;
import java.awt.image.*;
+
import javax.swing.*;
import jalview.datamodel.*;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
+import jalview.util.MessageManager;
/**
- * DOCUMENT ME!
- *
+ * AnnotationPanel displays visible portion of annotation rows below unwrapped
+ * alignment
+ *
* @author $author$
* @version $Revision$
*/
-public class AnnotationPanel
- extends JPanel implements MouseListener,
- MouseMotionListener, ActionListener, AdjustmentListener
+public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
+ MouseListener, MouseWheelListener, MouseMotionListener,
+ ActionListener, AdjustmentListener, Scrollable
{
final String HELIX = "Helix";
+
final String SHEET = "Sheet";
+
+ /**
+ * For RNA secondary structure "stems" aka helices
+ */
+ final String STEM = "RNA Helix";
+
final String LABEL = "Label";
+
final String REMOVE = "Remove Annotation";
+
final String COLOUR = "Colour";
- final Color HELIX_COLOUR = Color.red.darker();
- final Color SHEET_COLOUR = Color.green.darker().darker();
+
+ public final Color HELIX_COLOUR = Color.red.darker();
+
+ public final Color SHEET_COLOUR = Color.green.darker().darker();
+
+ public final Color STEM_COLOUR = Color.blue.darker();
/** DOCUMENT ME!! */
- AlignViewport av;
+ public AlignViewport av;
+
AlignmentPanel ap;
- int activeRow = -1;
- BufferedImage image;
- BufferedImage fadedImage;
+
+ public int activeRow = -1;
+
+ public BufferedImage image;
+
+ public volatile BufferedImage fadedImage;
+
Graphics2D gg;
- FontMetrics fm;
- int imgWidth = 0;
+
+ public FontMetrics fm;
+
+ public int imgWidth = 0;
+
boolean fastPaint = false;
- //Used For mouse Dragging and resizing graphs
+ // Used For mouse Dragging and resizing graphs
int graphStretch = -1;
+
int graphStretchY = -1;
- int min; //used by mouseDragged to see if user
- int max; //used by mouseDragged to see if user
+
+ int min; // used by mouseDragged to see if user
+
+ int max; // used by mouseDragged to see if user
+
boolean mouseDragging = false;
boolean MAC = false;
+ // for editing cursor
+ int cursorX = 0;
+
+ int cursorY = 0;
+
+ public final AnnotationRenderer renderer;
+
+ private MouseWheelListener[] _mwl;
+
/**
* Creates a new AnnotationPanel object.
- *
- * @param ap DOCUMENT ME!
+ *
+ * @param ap
+ * DOCUMENT ME!
*/
public AnnotationPanel(AlignmentPanel ap)
{
- if (System.getProperty("os.name").startsWith("Mac"))
- {
- MAC = true;
- }
+ MAC = new jalview.util.Platform().isAMac();
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
@@ -84,85 +121,134 @@ public class AnnotationPanel
this.setLayout(null);
addMouseListener(this);
addMouseMotionListener(this);
- ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
+ ap.annotationScroller.getVerticalScrollBar()
+ .addAdjustmentListener(this);
+ // save any wheel listeners on the scroller, so we can propagate scroll
+ // events to them.
+ _mwl = ap.annotationScroller.getMouseWheelListeners();
+ // and then set our own listener to consume all mousewheel events
+ ap.annotationScroller.addMouseWheelListener(this);
+ renderer = new AnnotationRenderer();
}
public AnnotationPanel(AlignViewport av)
{
this.av = av;
+ renderer = new AnnotationRenderer();
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
- ap.alabels.setScrollOffset( -evt.getValue());
- }
-
- /**
- * DOCUMENT ME!
- */
- public int adjustPanelHeight()
+ @Override
+ public void mouseWheelMoved(MouseWheelEvent e)
{
- // setHeight of panels
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- int height = 0;
-
- if (aa != null)
+ if (e.isShiftDown())
+ {
+ e.consume();
+ if (e.getWheelRotation() > 0)
+ {
+ ap.scrollRight(true);
+ }
+ else
+ {
+ ap.scrollRight(false);
+ }
+ }
+ else
{
- for (int i = 0; i < aa.length; i++)
+ // TODO: find the correct way to let the event bubble up to
+ // ap.annotationScroller
+ for (MouseWheelListener mwl : _mwl)
{
- if (!aa[i].visible)
+ if (mwl != null)
{
- continue;
+ mwl.mouseWheelMoved(e);
}
-
- aa[i].height = 0;
-
- if (aa[i].hasText)
+ if (e.isConsumed())
{
- aa[i].height += av.charHeight;
+ break;
}
+ }
+ }
+ }
- if (aa[i].hasIcons)
- {
- aa[i].height += 16;
- }
+ @Override
+ public Dimension getPreferredScrollableViewportSize()
+ {
+ return getPreferredSize();
+ }
- if (aa[i].graph > 0)
- {
- aa[i].height += aa[i].graphHeight;
- }
+ @Override
+ public int getScrollableBlockIncrement(Rectangle visibleRect,
+ int orientation, int direction)
+ {
+ return 30;
+ }
- if (aa[i].height == 0)
- {
- aa[i].height = 20;
- }
+ @Override
+ public boolean getScrollableTracksViewportHeight()
+ {
+ return false;
+ }
- height += aa[i].height;
- }
- }
- else
- {
- height = 20;
- }
+ @Override
+ public boolean getScrollableTracksViewportWidth()
+ {
+ return true;
+ }
+
+ @Override
+ public int getScrollableUnitIncrement(Rectangle visibleRect,
+ int orientation, int direction)
+ {
+ return 30;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.AdjustmentListener#adjustmentValueChanged(java.awt.event
+ * .AdjustmentEvent)
+ */
+ @Override
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ // update annotation label display
+ ap.alabels.setScrollOffset(-evt.getValue());
+ }
+ /**
+ * Calculates the height of the annotation displayed in the annotation panel.
+ * Callers should normally call the ap.adjustAnnotationHeight method to ensure
+ * all annotation associated components are updated correctly.
+ *
+ */
+ public int adjustPanelHeight()
+ {
+ int height = av.calcPanelHeight();
this.setPreferredSize(new Dimension(1, height));
+ if (ap != null)
+ {
+ // revalidate only when the alignment panel is fully constructed
+ ap.validate();
+ }
return height;
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void actionPerformed(ActionEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
Annotation[] anot = aa[activeRow].annotations;
if (anot.length < av.getColumnSelection().getMax())
@@ -183,14 +269,15 @@ public class AnnotationPanel
else if (evt.getActionCommand().equals(LABEL))
{
String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL);
- String label = JOptionPane.showInputDialog(this,"Enter label",exMesg);
-
+ String label = JOptionPane.showInputDialog(this, MessageManager.getString("label.enter_label"),
+ exMesg);
+
if (label == null)
{
return;
}
- if ( (label.length() > 0) && !aa[activeRow].hasText)
+ if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
}
@@ -199,13 +286,18 @@ public class AnnotationPanel
{
int index = av.getColumnSelection().columnAt(i);
- if(!av.colSel.isVisible(index))
+ if (!av.getColumnSelection().isVisible(index))
continue;
if (anot[index] == null)
{
- anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that null exceptions aren't raised elsewhere.
- } else {
+ anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
+ // null exceptions
+ // aren't raised
+ // elsewhere.
+ }
+ else
+ {
anot[index].displayCharacter = label;
}
}
@@ -213,14 +305,13 @@ public class AnnotationPanel
else if (evt.getActionCommand().equals(COLOUR))
{
Color col = JColorChooser.showDialog(this,
- "Choose foreground colour",
- Color.black);
+ "Choose foreground colour", Color.black);
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
int index = av.getColumnSelection().columnAt(i);
- if(!av.colSel.isVisible(index))
+ if (!av.getColumnSelection().isVisible(index))
continue;
if (anot[index] == null)
@@ -231,7 +322,8 @@ public class AnnotationPanel
anot[index].colour = col;
}
}
- else // HELIX OR SHEET
+ else
+ // HELIX OR SHEET
{
char type = 0;
String symbol = "\u03B1";
@@ -246,30 +338,39 @@ public class AnnotationPanel
symbol = "\u03B2";
}
+ // Added by LML to color stems
+ else if (evt.getActionCommand().equals(STEM))
+ {
+ type = 'S';
+ symbol = "\u03C3";
+ }
+
if (!aa[activeRow].hasIcons)
{
aa[activeRow].hasIcons = true;
}
String label = JOptionPane.showInputDialog(
- "Enter a label for the structure?",
- symbol);
+ MessageManager.getString("label.enter_label_for_the_structure"), symbol);
if (label == null)
{
return;
}
- if ( (label.length() > 0) && !aa[activeRow].hasText)
+ if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
+ if (evt.getActionCommand().equals(STEM))
+ {
+ aa[activeRow].showAllColLabels=true;
+ }
}
-
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
int index = av.getColumnSelection().columnAt(i);
- if(!av.colSel.isVisible(index))
+ if (!av.getColumnSelection().isVisible(index))
continue;
if (anot[index] == null)
@@ -279,49 +380,58 @@ public class AnnotationPanel
anot[index].secondaryStructure = type;
anot[index].displayCharacter = label;
+
}
}
-
+ av.getAlignment().validateAnnotation(aa[activeRow]);
+ ap.alignmentChanged();
+
adjustPanelHeight();
repaint();
return;
}
- private String collectAnnotVals(Annotation[] anot, ColumnSelection columnSelection,
- String label2)
+ private String collectAnnotVals(Annotation[] anot,
+ ColumnSelection columnSelection, String label2)
{
- String collatedInput="";
- String last="";
+ String collatedInput = "";
+ String last = "";
+ ColumnSelection viscols = av.getColumnSelection();
+ // TODO: refactor and save av.getColumnSelection for efficiency
for (int i = 0; i < columnSelection.size(); i++)
{
int index = columnSelection.columnAt(i);
// always check for current display state - just in case
- if(!av.colSel.isVisible(index))
+ if (!viscols.isVisible(index))
continue;
- String tlabel=null;
+ String tlabel = null;
if (anot[index] != null)
- {
- if (label2.equals(HELIX) || label2.equals(SHEET) || label2.equals(LABEL))
+ { // LML added stem code
+ if (label2.equals(HELIX) || label2.equals(SHEET)
+ || label2.equals(STEM) || label2.equals(LABEL))
{
tlabel = anot[index].description;
- if (tlabel == null)
+ if (tlabel == null || tlabel.length() < 1)
{
- if (label2.equals(HELIX) || label2.equals(SHEET))
+ if (label2.equals(HELIX) || label2.equals(SHEET)
+ || label2.equals(STEM))
+ {
+ tlabel = "" + anot[index].secondaryStructure;
+ }
+ else
{
- tlabel = ""+anot[index].secondaryStructure;
- } else {
- tlabel = ""+anot[index].displayCharacter;
- }
+ tlabel = "" + anot[index].displayCharacter;
+ }
}
}
- if (tlabel!=null && !tlabel.equals(last))
+ if (tlabel != null && !tlabel.equals(last))
{
- if (last.length()>0)
+ if (last.length() > 0)
{
- collatedInput+=" ";
+ collatedInput += " ";
}
- collatedInput+=tlabel;
+ collatedInput += tlabel;
}
}
}
@@ -330,13 +440,15 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void mousePressed(MouseEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
return;
@@ -360,7 +472,7 @@ public class AnnotationPanel
}
else if (aa[i].graph > 0)
{
- //Stretch Graph
+ // Stretch Graph
graphStretch = i;
graphStretchY = evt.getY();
}
@@ -376,13 +488,26 @@ public class AnnotationPanel
return;
}
- JPopupMenu pop = new JPopupMenu("Structure type");
- JMenuItem item = new JMenuItem(HELIX);
- item.addActionListener(this);
- pop.add(item);
- item = new JMenuItem(SHEET);
- item.addActionListener(this);
- pop.add(item);
+ JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.structure_type"));
+ JMenuItem item;
+ /*
+ * Just display the needed structure options
+ */
+ if (av.getAlignment().isNucleotide() == true)
+ {
+ item = new JMenuItem(STEM);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ else
+ {
+ item = new JMenuItem(HELIX);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new JMenuItem(SHEET);
+ item.addActionListener(this);
+ pop.add(item);
+ }
item = new JMenuItem(LABEL);
item.addActionListener(this);
pop.add(item);
@@ -408,9 +533,11 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void mouseReleased(MouseEvent evt)
{
graphStretch = -1;
@@ -421,19 +548,23 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void mouseEntered(MouseEvent evt)
{
- ap.scalePanel.mouseEntered(evt);
+ ap.scalePanel.mouseEntered(evt);
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void mouseExited(MouseEvent evt)
{
ap.scalePanel.mouseExited(evt);
@@ -441,18 +572,20 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (graphStretch > -1)
{
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight +=
- graphStretchY - evt.getY();
- if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+ av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+ - evt.getY();
+ if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
{
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+ av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
}
graphStretchY = evt.getY();
adjustPanelHeight();
@@ -466,12 +599,14 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void mouseMoved(MouseEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
@@ -505,24 +640,24 @@ public class AnnotationPanel
int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
- if (aa[row].annotations != null
- && row > -1
- && res < (int) aa[row].annotations.length)
+ if (row > -1 && aa[row].annotations != null
+ && res < aa[row].annotations.length)
{
if (aa[row].graphGroup > -1)
{
StringBuffer tip = new StringBuffer("");
for (int gg = 0; gg < aa.length; gg++)
{
- if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res] != null)
+ if (aa[gg].graphGroup == aa[row].graphGroup
+ && aa[gg].annotations[res] != null)
{
- tip.append(aa[gg].label + " " + aa[gg].annotations[res].description +
- "
");
+ tip.append(aa[gg].label + " "
+ + aa[gg].annotations[res].description + "
");
}
}
if (tip.length() != 6)
@@ -532,15 +667,21 @@ public class AnnotationPanel
}
}
else if (aa[row].annotations[res] != null
- && aa[row].annotations[res].description != null)
+ && aa[row].annotations[res].description != null
+ && aa[row].annotations[res].description.length() > 0)
+ {
+ this.setToolTipText(""+JvSwingUtils.wrapTooltip(aa[row].annotations[res].description)+"");
+ }
+ else
{
- this.setToolTipText(aa[row].annotations[res].description);
+ // clear the tooltip.
+ this.setToolTipText(null);
}
if (aa[row].annotations[res] != null)
{
- StringBuffer text = new StringBuffer("Sequence position " +
- (res + 1));
+ StringBuffer text = new StringBuffer("Sequence position "
+ + (res + 1));
if (aa[row].annotations[res].description != null)
{
@@ -558,18 +699,51 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void mouseClicked(MouseEvent evt)
{
+// if (activeRow != -1)
+// {
+// AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+// AlignmentAnnotation anot = aa[activeRow];
+// }
}
+ // TODO mouseClicked-content and drawCursor are quite experimental!
+ public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
+ int y1)
+ {
+ int pady = av.charHeight / 5;
+ int charOffset = 0;
+ graphics.setColor(Color.black);
+ graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+
+ if (av.validCharWidth)
+ {
+ graphics.setColor(Color.white);
+
+ char s = seq.getCharAt(res);
+
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s), charOffset + x1,
+ (y1 + av.charHeight) - pady);
+ }
+
+ }
+
+ private volatile boolean imageFresh = false;
+
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g)
{
g.setColor(Color.white);
@@ -577,9 +751,8 @@ public class AnnotationPanel
if (image != null)
{
- if (fastPaint
- || (getVisibleRect().width != g.getClipBounds().width)
- || (getVisibleRect().height != g.getClipBounds().height))
+ if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
+ || (getVisibleRect().height != g.getClipBounds().height))
{
g.drawImage(image, 0, 0, this);
fastPaint = false;
@@ -587,51 +760,71 @@ public class AnnotationPanel
}
}
imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
- if (imgWidth<1)
+ if (imgWidth < 1)
return;
- if (image == null || imgWidth != image.getWidth()
- || image.getHeight(this) != getHeight())
+ if (image == null || imgWidth != image.getWidth(this)
+ || image.getHeight(this) != getHeight())
{
- image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
- BufferedImage.TYPE_INT_RGB);
+ try
+ {
+ image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
+ BufferedImage.TYPE_INT_RGB);
+ } catch (OutOfMemoryError oom)
+ {
+ try
+ {
+ System.gc();
+ } catch (Exception x)
+ {
+ }
+ ;
+ new OOMWarning(
+ "Couldn't allocate memory to redraw screen. Please restart Jalview",
+ oom);
+ return;
+ }
gg = (Graphics2D) image.getGraphics();
if (av.antiAlias)
{
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ RenderingHints.VALUE_ANTIALIAS_ON);
}
gg.setFont(av.getFont());
fm = gg.getFontMetrics();
gg.setColor(Color.white);
gg.fillRect(0, 0, imgWidth, image.getHeight());
+ imageFresh = true;
}
drawComponent(gg, av.startRes, av.endRes + 1);
+ imageFresh = false;
g.drawImage(image, 0, 0, this);
}
-
/**
- * DOCUMENT ME!
- *
- * @param horizontal DOCUMENT ME!
+ * set true to enable redraw timing debug output on stderr
+ */
+ private final boolean debugRedraw = false;
+ /**
+ * non-Thread safe repaint
+ *
+ * @param horizontal
+ * repaint with horizontal shift in alignment
*/
public void fastPaint(int horizontal)
{
- if ( (horizontal == 0)
- || gg == null
- || av.alignment.getAlignmentAnnotation() == null
- || av.alignment.getAlignmentAnnotation().length < 1
- || av.updatingConsensus
- || av.updatingConservation)
+ if ((horizontal == 0) || gg == null
+ || av.getAlignment().getAlignmentAnnotation() == null
+ || av.getAlignment().getAlignmentAnnotation().length < 1
+ || av.isCalcInProgress())
{
repaint();
return;
}
-
+ long stime=System.currentTimeMillis();
gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
-
+ long mtime=System.currentTimeMillis();
int sr = av.startRes;
int er = av.endRes + 1;
int transX = 0;
@@ -650,58 +843,75 @@ public class AnnotationPanel
drawComponent(gg, sr, er);
- gg.translate( -transX, 0);
-
+ gg.translate(-transX, 0);
+ long dtime=System.currentTimeMillis();
fastPaint = true;
-
repaint();
+ long rtime=System.currentTimeMillis();
+ if (debugRedraw) {
+ System.err.println("Scroll:\t"+horizontal+"\tCopyArea:\t"+(mtime-stime)+"\tDraw component:\t"+(dtime-mtime)+"\tRepaint call:\t"+(rtime-dtime));
+ }
}
+ private volatile boolean lastImageGood = false;
+
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param startRes DOCUMENT ME!
- * @param endRes DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ * @param endRes
+ * DOCUMENT ME!
*/
public void drawComponent(Graphics g, int startRes, int endRes)
{
- if (av.updatingConsensus || av.updatingConservation)
+ BufferedImage oldFaded = fadedImage;
+ if (av.isCalcInProgress())
{
if (image == null)
{
+ lastImageGood = false;
return;
}
- //We'll keep a record of the old image,
- //and draw a faded image until the calculation
- //has completed
- if (fadedImage == null
- || fadedImage.getWidth() != imgWidth
- || fadedImage.getHeight() != image.getHeight())
+ // We'll keep a record of the old image,
+ // and draw a faded image until the calculation
+ // has completed
+ if (lastImageGood
+ && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage
+ .getHeight() != image.getHeight()))
{
- fadedImage = new BufferedImage(
- imgWidth, image.getHeight(),
- BufferedImage.TYPE_INT_RGB);
+ // System.err.println("redraw faded image ("+(fadedImage==null ?
+ // "null image" : "") + " lastGood="+lastImageGood+")");
+ fadedImage = new BufferedImage(imgWidth, image.getHeight(),
+ BufferedImage.TYPE_INT_RGB);
Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
fadedG.setColor(Color.white);
fadedG.fillRect(0, 0, imgWidth, image.getHeight());
- fadedG.setComposite(
- AlphaComposite.getInstance(
+ fadedG.setComposite(AlphaComposite.getInstance(
AlphaComposite.SRC_OVER, .3f));
fadedG.drawImage(image, 0, 0, this);
}
+ // make sure we don't overwrite the last good faded image until all
+ // calculations have finished
+ lastImageGood = false;
}
else
{
+ if (fadedImage != null)
+ {
+ oldFaded = fadedImage;
+ }
fadedImage = null;
}
-
+
g.setColor(Color.white);
g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
@@ -711,628 +921,54 @@ public class AnnotationPanel
fm = g.getFontMetrics();
}
- if ( (av.alignment.getAlignmentAnnotation() == null) ||
- (av.alignment.getAlignmentAnnotation().length < 1))
+ if ((av.getAlignment().getAlignmentAnnotation() == null)
+ || (av.getAlignment().getAlignmentAnnotation().length < 1))
{
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
g.setColor(Color.black);
if (av.validCharWidth)
{
- g.drawString("Alignment has no annotations", 20, 15);
+ g.drawString(MessageManager.getString("label.alignment_has_no_annotations"), 20, 15);
}
return;
}
-
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
- int x = 0, y=0;
- int column = 0;
- char lastSS;
- int lastSSX;
- int iconOffset = 0;
- boolean validRes = false;
-
- boolean[] graphGroupDrawn = new boolean[aa.length];
-
- //\u03B2 \u03B1
- for (int i = 0; i < aa.length; i++)
+ lastImageGood = renderer.drawComponent(this, av, g, activeRow,
+ startRes, endRes);
+ if (!lastImageGood && fadedImage == null)
{
- AlignmentAnnotation row = aa[i];
-
- if (!row.visible)
- {
- continue;
- }
-
- lastSS = ' ';
- lastSSX = 0;
-
- if (row.graph > 0)
- {
- if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
- {
- continue;
- }
-
- // this is so that we draw the characters below the graph
- y += row.height;
-
- if (row.hasText)
- {
- iconOffset =av.charHeight -fm.getDescent();
- y -= av.charHeight;
- }
- }
- else if (row.hasText)
- {
- iconOffset = av.charHeight -fm.getDescent();
-
- }
- else
- {
- iconOffset = 0;
- }
-
-
- if (av.updatingConsensus && aa[i] == av.consensus)
- {
- y += av.charHeight;
-
- g.drawImage(fadedImage,
- 0, y - row.height, imgWidth, y,
- 0, y - row.height, imgWidth, y, this);
- g.setColor(Color.black);
- // g.drawString("Calculating Consensus....",20, y-row.height/2);
-
- continue;
- }
- else if (av.updatingConservation && aa[i].label.equals("Conservation"))
- {
-
- y += av.charHeight;
- g.drawImage(fadedImage,
- 0, y - row.height, imgWidth, y,
- 0, y - row.height, imgWidth, y, this);
-
- g.setColor(Color.black);
- // g.drawString("Calculating Conservation.....",20, y-row.height/2);
-
- continue;
- }
- else if (av.updatingConservation && aa[i].label.equals("Quality"))
- {
-
- y += av.charHeight;
- g.drawImage(fadedImage,
- 0, y - row.height, imgWidth, y,
- 0, y - row.height, imgWidth, y, this);
- g.setColor(Color.black);
- /// g.drawString("Calculating Quality....",20, y-row.height/2);
-
- continue;
- }
-
-
-
- x = 0;
- while (x < endRes - startRes)
- {
- if (av.hasHiddenColumns)
- {
- column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);
- if (column > row.annotations.length - 1)
- {
- break;
- }
- }
- else
- {
- column = startRes + x;
- }
-
- if ( (row.annotations==null)
- || (row.annotations.length <= column)
- || (row.annotations[column] == null))
- {
- validRes = false;
- }
- else
- {
- validRes = true;
- }
-
- if (activeRow == i)
- {
- g.setColor(Color.red);
-
- if (av.getColumnSelection() != null)
- {
- for (int n = 0; n < av.getColumnSelection().size(); n++)
- {
- int v = av.getColumnSelection().columnAt(n);
-
- if (v == column)
- {
- g.fillRect(x * av.charWidth, y,
- av.charWidth, av.charHeight);
- }
- }
- }
- }
-
- if (av.validCharWidth && validRes
- && row.annotations[column].displayCharacter != null
- && (row.annotations[column].displayCharacter.length() > 0))
- {
-
- int charOffset = (av.charWidth -
- fm.charWidth(row.annotations[column].
- displayCharacter.charAt(
- 0))) / 2;
-
- if (row.annotations[column].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(row.annotations[column].colour);
-
- if (column == 0 || row.graph > 0)
- {
- g.drawString(row.annotations[column].displayCharacter,
- (x * av.charWidth) + charOffset,
- y + iconOffset);
- }
- else if (
- row.annotations[column - 1] == null
- || (!row.annotations[column].displayCharacter.equals(
- row.annotations[column - 1].displayCharacter)
- ||
- (row.annotations[column].displayCharacter.length() < 2 &&
- row.annotations[column].secondaryStructure == ' ')))
- {
- g.drawString(row.annotations[column].displayCharacter,
- x * av.charWidth + charOffset,
- y + iconOffset);
- }
- }
-
- if (row.hasIcons)
- {
- if (!validRes ||
- (row.annotations[column].secondaryStructure != lastSS))
- {
- switch (lastSS)
- {
- case 'H':
- g.setColor(HELIX_COLOUR);
- if (MAC)
- {
- //Off by 1 offset when drawing rects and ovals
- //to offscreen image on the MAC
- g.fillRoundRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX, 7, 8, 8);
- break;
- }
-
- int sCol = (lastSSX / av.charWidth) + startRes;
- int x1 = lastSSX;
- int x2 = (x * av.charWidth);
-
- if (sCol == 0 ||
- row.annotations[sCol - 1] == null ||
- row.annotations[sCol - 1].secondaryStructure != 'H')
- {
- g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
- 180);
- x1 += av.charWidth / 2;
- }
-
- if (row.annotations[column] == null ||
- row.annotations[column].secondaryStructure != 'H')
- {
- g.fillArc( (x * av.charWidth) - av.charWidth,
- y + 4 + iconOffset, av.charWidth, 8, 270, 180);
- x2 -= av.charWidth / 2;
- }
-
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
- break;
-
- case 'E':
- g.setColor(SHEET_COLOUR);
- g.fillRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX - 4, 7);
- g.fillPolygon(new int[]
- { (x * av.charWidth) - 4,
- (x * av.charWidth) - 4,
- (x * av.charWidth)},
- new int[]
- {
- y + iconOffset, y + 14 + iconOffset,
- y + 8 + iconOffset
- }, 3);
-
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset,
- (x * av.charWidth) - lastSSX, 2);
-
- break;
- }
-
- if (validRes)
- {
- lastSS = row.annotations[column].secondaryStructure;
- }
- else
- {
- lastSS = ' ';
- }
-
- lastSSX = (x * av.charWidth);
- }
- }
-
- column++;
- x++;
- }
-
- if (column >= row.annotations.length)
- {
- column = row.annotations.length - 1;
- }
-
- // x ++;
-
- if (row.hasIcons)
- {
- switch (lastSS)
- {
- case 'H':
- g.setColor(HELIX_COLOUR);
- if (MAC)
- {
- //Off by 1 offset when drawing rects and ovals
- //to offscreen image on the MAC
- g.fillRoundRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX, 7, 8, 8);
- break;
- }
-
- int sCol = (lastSSX / av.charWidth) + startRes;
- int x1 = lastSSX;
- int x2 = (x * av.charWidth);
-
- if (sCol == 0 ||
- row.annotations[sCol - 1] == null ||
- row.annotations[sCol - 1].secondaryStructure != 'H')
- {
- g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);
- x1 += av.charWidth / 2;
- }
-
- if (row.annotations[column] == null ||
- row.annotations[column].secondaryStructure != 'H')
- {
- g.fillArc( (x * av.charWidth) - av.charWidth,
- y + 4 + iconOffset, av.charWidth, 8, 270,
- 180);
- x2 -= av.charWidth / 2;
- }
-
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
-
- break;
-
- case 'E':
- g.setColor(SHEET_COLOUR);
-
- if (row.annotations[endRes] == null
- || row.annotations[endRes].secondaryStructure != 'E')
- {
- g.fillRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX - 4, 7);
- g.fillPolygon(new int[]
- { (x * av.charWidth) - 4,
- (x * av.charWidth) - 4,
- (x * av.charWidth)},
- new int[]
- {
- y + iconOffset, y + 14 + iconOffset,
- y + 7 + iconOffset
- }, 3);
- }
- else
- {
- g.fillRect(lastSSX, y + 4 + iconOffset,
- (x + 1) * av.charWidth - lastSSX, 7);
- }
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset,
- (x * av.charWidth) - lastSSX, 2);
-
- break;
- }
- }
-
- if (row.graph > 0 && row.graphHeight > 0)
- {
- if (row.graph == AlignmentAnnotation.LINE_GRAPH)
- {
- if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
- {
- float groupmax = -999999, groupmin = 9999999;
- for (int gg = 0; gg < aa.length; gg++)
- {
- if (aa[gg].graphGroup != row.graphGroup)
- {
- continue;
- }
-
- if (aa[gg] != row)
- {
- aa[gg].visible = false;
- }
-
- if (aa[gg].graphMax > groupmax)
- {
- groupmax = aa[gg].graphMax;
- }
- if (aa[gg].graphMin < groupmin)
- {
- groupmin = aa[gg].graphMin;
- }
- }
-
- for (int gg = 0; gg < aa.length; gg++)
- {
- if (aa[gg].graphGroup == row.graphGroup)
- {
- drawLineGraph(g, aa[gg], startRes, endRes, y,
- groupmin, groupmax,
- row.graphHeight);
- }
- }
-
- graphGroupDrawn[row.graphGroup] = true;
- }
- else
- {
- drawLineGraph(g, row, startRes, endRes,
- y, row.graphMin, row.graphMax, row.graphHeight);
- }
- }
- else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
- {
- drawBarGraph(g, row, startRes, endRes,
- row.graphMin, row.graphMax, y);
- }
- }
-
- if (row.graph > 0 && row.hasText)
- {
- y += av.charHeight;
- }
-
- if (row.graph == 0)
- {
- y += aa[i].height;
- }
+ fadedImage = oldFaded;
}
}
- public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
- int sRes, int eRes,
- int y,
- float min, float max,
- int graphHeight)
+ @Override
+ public FontMetrics getFontMetrics()
{
- if (sRes > aa.annotations.length)
- {
- return;
- }
-
- int x = 0;
-
- //Adjustment for fastpaint to left
- if (eRes < av.endRes)
- {
- eRes++;
- }
-
- eRes = Math.min(eRes, aa.annotations.length);
-
- if (sRes == 0)
- {
- x++;
- }
-
- int y1 = y, y2 = y;
- float range = max - min;
-
- ////Draw origin
- if (min < 0)
- {
- y2 = y - (int) ( (0 - min / range) * graphHeight);
- }
-
- g.setColor(Color.gray);
- g.drawLine(x - av.charWidth, y2, (eRes - sRes + 1) * av.charWidth, y2);
-
- eRes = Math.min(eRes, aa.annotations.length);
-
- int column;
- int aaMax = aa.annotations.length - 1;
-
- while (x < eRes - sRes)
- {
- column = sRes + x;
- if (av.hasHiddenColumns)
- {
- column = av.getColumnSelection().adjustForHiddenColumns(column);
- }
-
- if (column > aaMax)
- {
- break;
- }
-
- if (aa.annotations[column] == null || aa.annotations[column - 1] == null)
- {
- x++;
- continue;
- }
-
- if (aa.annotations[column].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(aa.annotations[column].colour);
-
- y1 = y -
- (int) ( ( (aa.annotations[column - 1].value - min) / range) * graphHeight);
- y2 = y -
- (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight);
-
- g.drawLine(x * av.charWidth - av.charWidth / 2, y1,
- x * av.charWidth + av.charWidth / 2, y2);
- x++;
- }
-
- if (aa.threshold != null)
- {
- g.setColor(aa.threshold.colour);
- Graphics2D g2 = (Graphics2D) g;
- g2.setStroke(new BasicStroke(1,
- BasicStroke.CAP_SQUARE,
- BasicStroke.JOIN_ROUND, 3f,
- new float[]
- {5f, 3f}, 0f));
-
- y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight);
- g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
- g2.setStroke(new BasicStroke());
- }
+ return fm;
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
- int sRes, int eRes,
- float min, float max,
- int y)
+ @Override
+ public Image getFadedImage()
{
- if (sRes > aa.annotations.length)
- {
- return;
- }
-
- eRes = Math.min(eRes, aa.annotations.length);
-
- int x = 0, y1 = y, y2 = y;
-
- float range = max - min;
-
- if (min < 0)
- {
- y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);
- }
-
- g.setColor(Color.gray);
-
- g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2);
-
- int column;
- int aaMax = aa.annotations.length - 1;
-
- while (x < eRes - sRes)
- {
- column = sRes + x;
- if (av.hasHiddenColumns)
- {
- column = av.getColumnSelection().adjustForHiddenColumns(column);
- }
-
- if (column > aaMax)
- {
- break;
- }
-
- if (aa.annotations[column] == null)
- {
- x++;
- continue;
- }
-
- if (aa.annotations[column].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(aa.annotations[column].colour);
-
- y1 = y -
- (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);
-
- if (y1 - y2 > 0)
- {
- g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
- }
- else
- {
- g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
- }
-
- x++;
-
- }
- if (aa.threshold != null)
- {
- g.setColor(aa.threshold.colour);
- Graphics2D g2 = (Graphics2D) g;
- g2.setStroke(new BasicStroke(1,
- BasicStroke.CAP_SQUARE,
- BasicStroke.JOIN_ROUND, 3f,
- new float[]
- {5f, 3f}, 0f));
-
- y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight);
- g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
- g2.setStroke(new BasicStroke());
- }
+ return fadedImage;
}
- // used by overview window
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y,
- int sRes, int eRes)
+ @Override
+ public int getFadedImageWidth()
{
- eRes = Math.min(eRes, aa.annotations.length);
- g.setColor(Color.white);
- g.fillRect(0, 0, width, y);
- g.setColor(new Color(0, 0, 180));
-
- int x = 0, height;
-
- for (int j = sRes; j < eRes; j++)
+ return imgWidth;
+ }
+ private int[] bounds = new int[2];
+ @Override
+ public int[] getVisibleVRange()
+ {
+ if (ap!=null && ap.alabels!=null)
{
- if (aa.annotations[j] != null)
- {
- if (aa.annotations[j].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(aa.annotations[j].colour);
-
- height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);
- if (height > y)
- {
- height = y;
- }
-
- g.fillRect(x, y - height, av.charWidth, height);
- }
- x += av.charWidth;
- }
+ int sOffset=-ap.alabels.scrollOffset;
+ int visHeight = sOffset+ap.annotationSpaceFillerHolder.getHeight();
+ bounds[0] = sOffset; bounds[1]=visHeight;
+ return bounds;
+ } else return null;
}
-
}