/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+ * 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 <http://www.gnu.org/licenses/>.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+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 java.awt.AlphaComposite;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.awt.image.BufferedImage;
+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;
+import javax.swing.ToolTipManager;
/**
- * DOCUMENT ME!
- *
+ * AnnotationPanel displays visible portion of annotation rows below unwrapped
+ * alignment
+ *
* @author $author$
* @version $Revision$
*/
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
- MouseListener, MouseMotionListener, ActionListener,
- AdjustmentListener
+ MouseListener, MouseWheelListener, MouseMotionListener,
+ ActionListener, AdjustmentListener, Scrollable
{
- final String HELIX = "Helix";
+ String HELIX = MessageManager.getString("label.helix");
- final String SHEET = "Sheet";
+ String SHEET = MessageManager.getString("label.sheet");
/**
* For RNA secondary structure "stems" aka helices
*/
- final String STEM = "RNA Helix";
+ String STEM = MessageManager.getString("label.rna_helix");
- final String LABEL = "Label";
+ String LABEL = MessageManager.getString("label.label");
- final String REMOVE = "Remove Annotation";
+ String REMOVE = MessageManager.getString("label.remove_annotation");
- final String COLOUR = "Colour";
+ String COLOUR = MessageManager.getString("action.colour");
public final Color HELIX_COLOUR = Color.red.darker();
boolean mouseDragging = false;
- boolean MAC = false;
-
// for editing cursor
int cursorX = 0;
public final AnnotationRenderer renderer;
+ private MouseWheelListener[] _mwl;
+
/**
* Creates a new AnnotationPanel object.
- *
+ *
* @param ap
* DOCUMENT ME!
*/
public AnnotationPanel(AlignmentPanel ap)
{
-
- MAC = new jalview.util.Platform().isAMac();
-
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
addMouseMotionListener(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();
}
renderer = new AnnotationRenderer();
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
+ @Override
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ if (e.isShiftDown())
+ {
+ e.consume();
+ if (e.getWheelRotation() > 0)
+ {
+ ap.scrollRight(true);
+ }
+ else
+ {
+ ap.scrollRight(false);
+ }
+ }
+ else
+ {
+ // TODO: find the correct way to let the event bubble up to
+ // ap.annotationScroller
+ for (MouseWheelListener mwl : _mwl)
+ {
+ if (mwl != null)
+ {
+ mwl.mouseWheelMoved(e);
+ }
+ if (e.isConsumed())
+ {
+ break;
+ }
+ }
+ }
+ }
+
+ @Override
+ public Dimension getPreferredScrollableViewportSize()
+ {
+ return getPreferredSize();
+ }
+
+ @Override
+ public int getScrollableBlockIncrement(Rectangle visibleRect,
+ int orientation, int direction)
+ {
+ return 30;
+ }
+
+ @Override
+ public boolean getScrollableTracksViewportHeight()
+ {
+ return false;
+ }
+
+ @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)
{
- ap.alabels.setScrollOffset(-evt.getValue());
+ // update annotation label display
+ ap.getAlabels().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 = calcPanelHeight();
+ int height = av.calcPanelHeight();
this.setPreferredSize(new Dimension(1, height));
if (ap != null)
{
}
/**
- * calculate the height for visible annotation, revalidating bounds where
- * necessary ABSTRACT GUI METHOD
- *
- * @return total height of annotation
- */
- public int calcPanelHeight()
- {
- // setHeight of panels
- AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
- int height = 0;
-
- if (aa != null)
- {
- for (int i = 0; i < aa.length; i++)
- {
- if (aa[i] == null)
- {
- System.err.println("Null annotation row: ignoring.");
- continue;
- }
- if (!aa[i].visible)
- {
- continue;
- }
-
- aa[i].height = 0;
-
- if (aa[i].hasText)
- {
- aa[i].height += av.charHeight;
- }
-
- if (aa[i].hasIcons)
- {
- aa[i].height += 16;
- }
-
- if (aa[i].graph > 0)
- {
- aa[i].height += aa[i].graphHeight;
- }
-
- if (aa[i].height == 0)
- {
- aa[i].height = 20;
- }
-
- height += aa[i].height;
- }
- }
- if (height == 0)
- {
- // set minimum
- height = 20;
- }
- return height;
- }
-
- /**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
aa[activeRow].annotations = anot;
}
- if (evt.getActionCommand().equals(REMOVE))
+ String action = evt.getActionCommand();
+ if (action.equals(REMOVE))
{
- for (int i = 0; i < av.getColumnSelection().size(); i++)
+ for (int index : av.getColumnSelection().getSelected())
{
- anot[av.getColumnSelection().columnAt(i)] = null;
+ if (av.getColumnSelection().isVisible(index))
+ {
+ anot[index] = null;
+ }
}
}
- else if (evt.getActionCommand().equals(LABEL))
+ else if (action.equals(LABEL))
{
- String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL);
- String label = JOptionPane.showInputDialog(this, "Enter label",
- exMesg);
+ String exMesg = collectAnnotVals(anot, LABEL);
+ String label = JOptionPane.showInputDialog(this,
+ MessageManager.getString("label.enter_label"), exMesg);
if (label == null)
{
aa[activeRow].hasText = true;
}
- for (int i = 0; i < av.getColumnSelection().size(); i++)
+ for (int index : av.getColumnSelection().getSelected())
{
- int index = av.getColumnSelection().columnAt(i);
-
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.
+ anot[index] = new Annotation(label, "", ' ', 0);
}
else
{
}
}
}
- else if (evt.getActionCommand().equals(COLOUR))
+ else if (action.equals(COLOUR))
{
Color col = JColorChooser.showDialog(this,
- "Choose foreground colour", Color.black);
+ MessageManager.getString("label.select_foreground_colour"),
+ Color.black);
- for (int i = 0; i < av.getColumnSelection().size(); i++)
+ for (int index : av.getColumnSelection().getSelected())
{
- int index = av.getColumnSelection().columnAt(i);
-
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
}
}
else
- // HELIX OR SHEET
+ // HELIX, SHEET or STEM
{
char type = 0;
- String symbol = "\u03B1";
+ String symbol = "\u03B1"; // alpha
- if (evt.getActionCommand().equals(HELIX))
+ if (action.equals(HELIX))
{
type = 'H';
}
- else if (evt.getActionCommand().equals(SHEET))
+ else if (action.equals(SHEET))
{
type = 'E';
- symbol = "\u03B2";
+ symbol = "\u03B2"; // beta
}
// Added by LML to color stems
- else if (evt.getActionCommand().equals(STEM))
+ else if (action.equals(STEM))
{
type = 'S';
- symbol = "\u03C3";
+ int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+ symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
}
if (!aa[activeRow].hasIcons)
aa[activeRow].hasIcons = true;
}
- String label = JOptionPane.showInputDialog(
- "Enter a label for the structure?", symbol);
+ String label = JOptionPane.showInputDialog(MessageManager
+ .getString("label.enter_label_for_the_structure"), symbol);
if (label == null)
{
if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
+ if (action.equals(STEM))
+ {
+ aa[activeRow].showAllColLabels = true;
+ }
}
-
- for (int i = 0; i < av.getColumnSelection().size(); i++)
+ for (int index : av.getColumnSelection().getSelected())
{
- int index = av.getColumnSelection().columnAt(i);
-
if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
anot[index] = new Annotation(label, "", type, 0);
}
- anot[index].secondaryStructure = type;
+ anot[index].secondaryStructure = type != 'S' ? type : label
+ .length() == 0 ? ' ' : label.charAt(0);
anot[index].displayCharacter = label;
+
}
}
- aa[activeRow].validateRangeAndDisplay();
- adjustPanelHeight();
+ av.getAlignment().validateAnnotation(aa[activeRow]);
ap.alignmentChanged();
+ ap.alignFrame.setMenusForViewport();
+ adjustPanelHeight();
repaint();
return;
}
- private String collectAnnotVals(Annotation[] anot,
- ColumnSelection columnSelection, String label2)
+ /**
+ * Returns any existing annotation concatenated as a string. For each
+ * annotation, takes the description, if any, else the secondary structure
+ * character (if type is HELIX, SHEET or STEM), else the display character (if
+ * type is LABEL).
+ *
+ * @param anots
+ * @param type
+ * @return
+ */
+ private String collectAnnotVals(Annotation[] anots, String type)
{
- String collatedInput = "";
+ // TODO is this method wanted? why? 'last' is not used
+
+ StringBuilder collatedInput = new StringBuilder(64);
String last = "";
- ColumnSelection viscols=av.getColumnSelection();
- // TODO: refactor and save av.getColumnSelection for efficiency
- for (int i = 0; i < columnSelection.size(); i++)
+ ColumnSelection viscols = av.getColumnSelection();
+
+ /*
+ * 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<Integer>(viscols.getSelected());
+ Collections.sort(selected);
+ for (int index : selected)
{
- int index = columnSelection.columnAt(i);
// always check for current display state - just in case
if (!viscols.isVisible(index))
+ {
continue;
+ }
String tlabel = null;
- if (anot[index] != null)
+ if (anots[index] != null)
{ // LML added stem code
- if (label2.equals(HELIX) || label2.equals(SHEET)
- || label2.equals(STEM) || label2.equals(LABEL))
+ if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
+ || type.equals(LABEL))
{
- tlabel = anot[index].description;
+ tlabel = anots[index].description;
if (tlabel == null || tlabel.length() < 1)
{
- if (label2.equals(HELIX) || label2.equals(SHEET)
- || label2.equals(STEM))
+ if (type.equals(HELIX) || type.equals(SHEET)
+ || type.equals(STEM))
{
- tlabel = "" + anot[index].secondaryStructure;
+ tlabel = "" + anots[index].secondaryStructure;
}
else
{
- tlabel = "" + anot[index].displayCharacter;
+ tlabel = "" + anots[index].displayCharacter;
}
}
}
{
if (last.length() > 0)
{
- collatedInput += " ";
+ collatedInput.append(" ");
}
- collatedInput += tlabel;
+ collatedInput.append(tlabel);
}
}
}
- return collatedInput;
+ return collatedInput.toString();
}
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
int height = 0;
activeRow = -1;
+ final int y = evt.getY();
for (int i = 0; i < aa.length; i++)
{
if (aa[i].visible)
height += aa[i].height;
}
- if (evt.getY() < height)
+ if (y < height)
{
if (aa[i].editable)
{
{
// Stretch Graph
graphStretch = i;
- graphStretchY = evt.getY();
+ graphStretchY = y;
}
break;
}
}
- if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1)
+ /*
+ * isPopupTrigger fires in mousePressed on Mac,
+ * not until mouseRelease on Windows
+ */
+ if (evt.isPopupTrigger() && activeRow != -1)
{
- if (av.getColumnSelection() == null)
- {
- return;
- }
+ showPopupMenu(y, evt.getX());
+ return;
+ }
- JPopupMenu pop = new JPopupMenu("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);
+ ap.getScalePanel().mousePressed(evt);
+ }
+
+ /**
+ * Construct and display a context menu at the right-click position
+ *
+ * @param y
+ * @param x
+ */
+ void showPopupMenu(final int y, int x)
+ {
+ if (av.getColumnSelection() == null
+ || av.getColumnSelection().isEmpty())
+ {
+ return;
+ }
+
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.structure_type"));
+ JMenuItem item;
+ /*
+ * Just display the needed structure options
+ */
+ if (av.getAlignment().isNucleotide())
+ {
+ item = new JMenuItem(STEM);
item.addActionListener(this);
pop.add(item);
- item = new JMenuItem(COLOUR);
+ }
+ else
+ {
+ item = new JMenuItem(HELIX);
item.addActionListener(this);
pop.add(item);
- item = new JMenuItem(REMOVE);
+ item = new JMenuItem(SHEET);
item.addActionListener(this);
pop.add(item);
- pop.show(this, evt.getX(), evt.getY());
-
- return;
- }
-
- if (aa == null)
- {
- return;
}
-
- ap.scalePanel.mousePressed(evt);
-
+ item = new JMenuItem(LABEL);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new JMenuItem(COLOUR);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new JMenuItem(REMOVE);
+ item.addActionListener(this);
+ pop.add(item);
+ pop.show(this, x, y);
}
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
graphStretch = -1;
graphStretchY = -1;
mouseDragging = false;
- ap.scalePanel.mouseReleased(evt);
+ 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());
+ }
+
}
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
@Override
public void mouseEntered(MouseEvent evt)
{
- ap.scalePanel.mouseEntered(evt);
+ ap.getScalePanel().mouseEntered(evt);
}
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
@Override
public void mouseExited(MouseEvent evt)
{
- ap.scalePanel.mouseExited(evt);
+ ap.getScalePanel().mouseExited(evt);
}
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
}
else
{
- ap.scalePanel.mouseDragged(evt);
+ ap.getScalePanel().mouseDragged(evt);
}
}
/**
- * DOCUMENT ME!
- *
+ * Constructs the tooltip, and constructs and displays a status message, for
+ * the current mouse position
+ *
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mouseMoved(MouseEvent evt)
if (evt.getY() < height)
{
row = i;
-
break;
}
}
return;
}
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+ int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ column = av.getColumnSelection().adjustForHiddenColumns(column);
}
- if (row > -1 && aa[row].annotations != null
- && res < aa[row].annotations.length)
+ AlignmentAnnotation ann = aa[row];
+ if (row > -1 && ann.annotations != null
+ && column < ann.annotations.length)
+ {
+ buildToolTip(ann, column, aa);
+ setStatusMessage(column, ann);
+ }
+ else
{
- if (aa[row].graphGroup > -1)
+ this.setToolTipText(null);
+ ap.alignFrame.statusBar.setText(" ");
+ }
+ }
+
+ /**
+ * Builds a tooltip for the annotation at the current mouse position.
+ *
+ * @param ann
+ * @param column
+ * @param anns
+ */
+ void buildToolTip(AlignmentAnnotation ann, int column,
+ AlignmentAnnotation[] anns)
+ {
+ if (ann.graphGroup > -1)
+ {
+ StringBuilder tip = new StringBuilder(32);
+ tip.append("<html>");
+ for (int i = 0; i < anns.length; i++)
{
- StringBuffer tip = new StringBuffer("<html>");
- for (int gg = 0; gg < aa.length; gg++)
+ if (anns[i].graphGroup == ann.graphGroup
+ && anns[i].annotations[column] != null)
{
- if (aa[gg].graphGroup == aa[row].graphGroup
- && aa[gg].annotations[res] != null)
+ tip.append(anns[i].label);
+ String description = anns[i].annotations[column].description;
+ if (description != null && description.length() > 0)
{
- tip.append(aa[gg].label + " "
- + aa[gg].annotations[res].description + "<br>");
+ tip.append(" ").append(description);
}
- }
- if (tip.length() != 6)
- {
- tip.setLength(tip.length() - 4);
- this.setToolTipText(tip.toString() + "</html>");
+ tip.append("<br>");
}
}
- else if (aa[row].annotations[res] != null
- && aa[row].annotations[res].description != null
- && aa[row].annotations[res].description.length() > 0)
+ if (tip.length() != 6)
{
- this.setToolTipText(aa[row].annotations[res].description);
+ tip.setLength(tip.length() - 4);
+ this.setToolTipText(tip.toString() + "</html>");
}
- else
+ }
+ else if (ann.annotations[column] != null)
+ {
+ String description = ann.annotations[column].description;
+ if (description != null && description.length() > 0)
{
- // clear the tooltip.
- this.setToolTipText(null);
+ this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
}
+ }
+ else
+ {
+ // clear the tooltip.
+ this.setToolTipText(null);
+ }
+ }
- if (aa[row].annotations[res] != null)
+ /**
+ * Constructs and displays the status bar message
+ *
+ * @param column
+ * @param ann
+ */
+ void setStatusMessage(int column, AlignmentAnnotation ann)
+ {
+ /*
+ * show alignment column and annotation description if any
+ */
+ StringBuilder text = new StringBuilder(32);
+ text.append(MessageManager.getString("label.column")).append(" ")
+ .append(column + 1);
+
+ if (ann.annotations[column] != null)
+ {
+ String description = ann.annotations[column].description;
+ if (description != null && description.trim().length() > 0)
{
- StringBuffer text = new StringBuffer("Sequence position "
- + (res + 1));
+ text.append(" ").append(description);
+ }
+ }
- if (aa[row].annotations[res].description != null)
+ /*
+ * if the annotation is sequence-specific, show the sequence number
+ * in the alignment, and (if not a gap) the residue and position
+ */
+ SequenceI seqref = ann.sequenceRef;
+ if (seqref != null)
+ {
+ int seqIndex = av.getAlignment().findIndex(seqref);
+ if (seqIndex != -1)
+ {
+ text.append(", ")
+ .append(MessageManager.getString("label.sequence"))
+ .append(" ").append(seqIndex + 1);
+ char residue = seqref.getCharAt(column);
+ if (!Comparison.isGap(residue))
{
- text.append(" " + aa[row].annotations[res].description);
+ text.append(" ");
+ String name;
+ if (av.getAlignment().isNucleotide())
+ {
+ name = ResidueProperties.nucleotideName.get(String
+ .valueOf(residue));
+ text.append(" Nucleotide: ").append(
+ name != null ? name : residue);
+ }
+ else
+ {
+ name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
+ : ResidueProperties.aa2Triplet.get(String
+ .valueOf(residue)));
+ text.append(" Residue: ").append(name != null ? name : residue);
+ }
+ int residuePos = seqref.findPosition(column);
+ text.append(" (").append(residuePos).append(")");
}
-
- ap.alignFrame.statusBar.setText(text.toString());
}
}
- else
- {
- this.setToolTipText(null);
- }
+
+ ap.alignFrame.statusBar.setText(text.toString());
}
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
@Override
public void mouseClicked(MouseEvent evt)
{
- if (activeRow != -1)
- {
- AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
- AlignmentAnnotation anot = aa[activeRow];
-
- if (anot.description.equals("secondary structure"))
- {
- // System.out.println(anot.description+" "+anot.getRNAStruc());
- }
- }
+ // 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 pady = av.getCharHeight() / 5;
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+ graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
if (av.validCharWidth)
{
char s = seq.getCharAt(res);
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + x1,
- (y1 + av.charHeight) - pady);
+ (y1 + av.getCharHeight()) - pady);
}
}
- private volatile boolean imageFresh=false;
+
+ private volatile boolean imageFresh = false;
+
/**
* DOCUMENT ME!
- *
+ *
* @param g
* DOCUMENT ME!
*/
return;
}
}
- imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
+ imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
if (imgWidth < 1)
+ {
return;
- if (image == null || imgWidth != image.getWidth()
+ }
+ 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.getAnnotationPanel()
+ .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)
fm = gg.getFontMetrics();
gg.setColor(Color.white);
gg.fillRect(0, 0, imgWidth, image.getHeight());
- imageFresh=true;
+ imageFresh = true;
}
drawComponent(gg, av.startRes, av.endRes + 1);
- imageFresh=false;
+ 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
* repaint with horizontal shift in alignment
*/
public void fastPaint(int horizontal)
{
-
if ((horizontal == 0) || gg == null
|| av.getAlignment().getAlignmentAnnotation() == null
|| av.getAlignment().getAlignmentAnnotation().length < 1
repaint();
return;
}
- gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
-
+ 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 transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
- transX = (er - sr - horizontal) * av.charWidth;
+ transX = (er - sr - horizontal) * av.getCharWidth();
sr = er - horizontal;
}
else if (horizontal < 0)
drawComponent(gg, sr, er);
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;
+
+ private volatile boolean lastImageGood = false;
+
/**
* DOCUMENT ME!
- *
+ *
* @param g
* DOCUMENT ME!
* @param startRes
*/
public void drawComponent(Graphics g, int startRes, int endRes)
{
- BufferedImage oldFaded=fadedImage;
+ BufferedImage oldFaded = fadedImage;
if (av.isCalcInProgress())
{
if (image == null)
{
- lastImageGood=false;
+ lastImageGood = false;
return;
}
// 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()))
+ if (lastImageGood
+ && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage
+ .getHeight() != image.getHeight()))
{
-// System.err.println("redraw faded image ("+(fadedImage==null ? "null image" : "") + " lastGood="+lastImageGood+")");
+ // System.err.println("redraw faded image ("+(fadedImage==null ?
+ // "null image" : "") + " lastGood="+lastImageGood+")");
fadedImage = new BufferedImage(imgWidth, image.getHeight(),
BufferedImage.TYPE_INT_RGB);
fadedG.drawImage(image, 0, 0, this);
}
- // make sure we don't overwrite the last good faded image until all calculations have finished
- lastImageGood=false;
+ // make sure we don't overwrite the last good faded image until all
+ // calculations have finished
+ lastImageGood = false;
}
else
{
- if (fadedImage!=null)
+ if (fadedImage != null)
{
- oldFaded=fadedImage;
+ oldFaded = fadedImage;
}
fadedImage = null;
}
g.setColor(Color.white);
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
+ g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
g.setFont(av.getFont());
if (fm == null)
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;
}
- lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes, endRes);
- if (!lastImageGood && fadedImage==null)
+ lastImageGood = renderer.drawComponent(this, av, g, activeRow,
+ startRes, endRes);
+ if (!lastImageGood && fadedImage == null)
{
- fadedImage=oldFaded;
+ fadedImage = oldFaded;
}
}
{
return imgWidth;
}
+
+ private int[] bounds = new int[2];
+
+ @Override
+ public int[] getVisibleVRange()
+ {
+ if (ap != null && ap.getAlabels() != null)
+ {
+ int sOffset = -ap.getAlabels().getScrollOffset();
+ int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
+ bounds[0] = sOffset;
+ bounds[1] = visHeight;
+ return bounds;
+ }
+ else
+ {
+ 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();
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff