import jalview.datamodel.AlignmentAnnotation;
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.viewmodel.ViewportListenerI;
import java.awt.AlphaComposite;
import java.awt.Color;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
+import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.Scrollable;
*/
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
MouseListener, MouseWheelListener, MouseMotionListener,
- ActionListener, AdjustmentListener, Scrollable
+ ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
{
String HELIX = MessageManager.getString("label.helix");
boolean mouseDragging = false;
- boolean MAC = false;
-
// for editing cursor
int cursorX = 0;
*/
public AnnotationPanel(AlignmentPanel ap)
{
-
- MAC = jalview.util.Platform.isAMac();
-
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
// and then set our own listener to consume all mousewheel events
ap.annotationScroller.addMouseWheelListener(this);
renderer = new AnnotationRenderer();
+
+ av.getRanges().addPropertyChangeListener(this);
}
public AnnotationPanel(AlignViewport av)
e.consume();
if (e.getWheelRotation() > 0)
{
- ap.scrollRight(true);
+ av.getRanges().scrollRight(true);
}
else
{
- ap.scrollRight(false);
+ av.getRanges().scrollRight(false);
}
}
else
{
for (int index : av.getColumnSelection().getSelected())
{
- if (av.getColumnSelection().isVisible(index))
+ if (av.getAlignment().getHiddenColumns().isVisible(index))
{
anot[index] = null;
}
else if (action.equals(LABEL))
{
String exMesg = collectAnnotVals(anot, LABEL);
- String label = JOptionPane.showInputDialog(this,
+ String label = JvOptionPane.showInputDialog(this,
MessageManager.getString("label.enter_label"), exMesg);
if (label == null)
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
aa[activeRow].hasIcons = true;
}
- String label = JOptionPane.showInputDialog(MessageManager
+ String label = JvOptionPane.showInputDialog(MessageManager
.getString("label.enter_label_for_the_structure"), symbol);
if (label == null)
}
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
StringBuilder collatedInput = new StringBuilder(64);
String last = "";
ColumnSelection viscols = av.getColumnSelection();
- // TODO: refactor and save av.getColumnSelection for efficiency
- List<Integer> selected = viscols.getSelected();
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+
+ /*
+ * the selection list (read-only view) is in selection order, not
+ * column order; make a copy so we can sort it
+ */
+ List<Integer> selected = new ArrayList<>(viscols.getSelected());
Collections.sort(selected);
for (int index : selected)
{
// always check for current display state - just in case
- if (!viscols.isVisible(index))
+ if (!hidden.isVisible(index))
{
continue;
}
String tlabel = null;
if (anots[index] != null)
{ // LML added stem code
- if (type.equals(HELIX) || type.equals(SHEET)
- || type.equals(STEM) || type.equals(LABEL))
+ if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
+ || type.equals(LABEL))
{
tlabel = anots[index].description;
if (tlabel == null || tlabel.length() < 1)
}
ap.getScalePanel().mousePressed(evt);
-
}
/**
mouseDragging = false;
ap.getScalePanel().mouseReleased(evt);
+ /*
+ * isPopupTrigger is set in mouseReleased on Windows
+ * (in mousePressed on Mac)
+ */
if (evt.isPopupTrigger() && activeRow != -1)
{
showPopupMenu(evt.getY(), evt.getX());
return;
}
- int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+ int column = (evt.getX() / av.getCharWidth())
+ + av.getRanges().getStartRes();
if (av.hasHiddenColumns())
{
- column = av.getColumnSelection().adjustForHiddenColumns(column);
+ column = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(column);
}
AlignmentAnnotation ann = aa[row];
{
text.append(", ")
.append(MessageManager.getString("label.sequence"))
- .append(" ")
- .append(seqIndex + 1);
+ .append(" ").append(seqIndex + 1);
char residue = seqref.getCharAt(column);
if (!Comparison.isGap(residue))
{
return;
}
}
- imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
+ imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + 1)
+ * av.getCharWidth();
if (imgWidth < 1)
{
return;
imageFresh = true;
}
- drawComponent(gg, av.startRes, av.endRes + 1);
+ drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
+ .getEndRes() + 1);
imageFresh = false;
g.drawImage(image, 0, 0, this);
}
* @param horizontal
* repaint with horizontal shift in alignment
*/
- public void fastPaint(int horizontal)
+ public void fastPaint(int horizontal, boolean isresize)
{
if ((horizontal == 0) || gg == null
|| av.getAlignment().getAlignmentAnnotation() == null
repaint();
return;
}
- long stime = System.currentTimeMillis();
- gg.copyArea(0, 0, imgWidth, getHeight(),
- -horizontal * av.getCharWidth(), 0);
- long mtime = System.currentTimeMillis();
- int sr = av.startRes;
- int er = av.endRes + 1;
+
+ int sr = av.getRanges().getStartRes();
+ int er = av.getRanges().getEndRes() + 1;
int transX = 0;
+ long stime;
+ long mtime;
- if (horizontal > 0) // scrollbar pulled right, image to the left
+ if (isresize)
{
- transX = (er - sr - horizontal) * av.getCharWidth();
- sr = er - horizontal;
+ imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
+ + 1) * av.getCharWidth();
+
+ BufferedImage newimage = new BufferedImage(imgWidth,
+ ap.getAnnotationPanel().getHeight(),
+ BufferedImage.TYPE_INT_ARGB);
+
+ gg = (Graphics2D) newimage.getGraphics();
+ gg.setFont(av.getFont());
+ gg.drawImage(image, null, 0, 0);
+ image = newimage;
+
+ transX = (er - horizontal - sr) * av.getCharWidth();
+ sr = er - horizontal - sr;
}
- else if (horizontal < 0)
+ else
{
- er = sr - horizontal;
+ stime = System.currentTimeMillis();
+ gg.copyArea(0, 0, imgWidth, getHeight(),
+ -horizontal * av.getCharWidth(), 0);
+ mtime = System.currentTimeMillis();
+
+ 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);
return null;
}
}
+
+ /**
+ * Try to ensure any references held are nulled
+ */
+ public void dispose()
+ {
+ av = null;
+ ap = null;
+ image = null;
+ fadedImage = null;
+ gg = null;
+ _mwl = null;
+
+ /*
+ * I created the renderer so I will dispose of it
+ */
+ if (renderer != null)
+ {
+ renderer.dispose();
+ }
+ }
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // Respond to viewport range changes (e.g. alignment panel was scrolled)
+ if (evt.getPropertyName().equals("startres"))
+ {
+ fastPaint((int) evt.getNewValue() - (int) evt.getOldValue(), false);
+ }
+ else if (evt.getPropertyName().equals("endres"))
+ {
+ // resize
+ fastPaint((int) evt.getNewValue() - (int) evt.getOldValue(), true);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff