X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=199c4e599a9ff1e5cc0cf83a272f668e993b91b1;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=20d4d295acb2e6ff1d289fe904088724ef9a7db9;hpb=bb3f28791ddb1a4f55e78a3bcd2ff4a591ebe95d;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 20d4d29..199c4e5 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1,59 +1,91 @@ /* - * 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. - * + * 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 . + * 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 java.util.Hashtable; - -import javax.swing.*; - -import jalview.analysis.AAFrequency; -import jalview.analysis.StructureFrequency; -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(); @@ -70,7 +102,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public BufferedImage image; - public BufferedImage fadedImage; + public volatile BufferedImage fadedImage; Graphics2D gg; @@ -91,8 +123,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, boolean mouseDragging = false; - boolean MAC = false; - // for editing cursor int cursorX = 0; @@ -100,6 +130,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public final AnnotationRenderer renderer; + private MouseWheelListener[] _mwl; + /** * Creates a new AnnotationPanel object. * @@ -108,9 +140,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, */ public AnnotationPanel(AlignmentPanel ap) { - - MAC = new jalview.util.Platform().isAMac(); - ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -121,6 +150,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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(); } @@ -130,15 +164,83 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, renderer = new AnnotationRenderer(); } - /** - * 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) * - * @param evt - * DOCUMENT ME! + * @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()); } /** @@ -149,7 +251,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, */ public int adjustPanelHeight() { - int height = calcPanelHeight(); + int height = av.calcPanelHeight(); this.setPreferredSize(new Dimension(1, height)); if (ap != null) { @@ -161,70 +263,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } /** - * 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! */ + @Override public void actionPerformed(ActionEvent evt) { AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); @@ -242,18 +286,22 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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) { @@ -265,19 +313,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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 { @@ -285,17 +330,18 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } } - 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) { @@ -306,26 +352,27 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } 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) @@ -333,8 +380,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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) { @@ -344,61 +391,87 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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(); + 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 = ""; - // 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 selected = new ArrayList(viscols.getSelected()); + Collections.sort(selected); + for (int index : selected) { - int index = columnSelection.columnAt(i); // always check for current display state - just in case - if (!av.getColumnSelection().isVisible(index)) + 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; } } } @@ -406,13 +479,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { if (last.length() > 0) { - collatedInput += " "; + collatedInput.append(" "); } - collatedInput += tlabel; + collatedInput.append(tlabel); } } } - return collatedInput; + return collatedInput.toString(); } /** @@ -421,6 +494,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * @param evt * DOCUMENT ME! */ + @Override public void mousePressed(MouseEvent evt) { @@ -433,6 +507,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, int height = 0; activeRow = -1; + final int y = evt.getY(); for (int i = 0; i < aa.length; i++) { if (aa[i].visible) @@ -440,7 +515,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, height += aa[i].height; } - if (evt.getY() < height) + if (y < height) { if (aa[i].editable) { @@ -450,61 +525,71 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { // 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); } /** @@ -513,12 +598,23 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * @param evt * DOCUMENT ME! */ + @Override public void mouseReleased(MouseEvent evt) { 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()); + } + } /** @@ -527,9 +623,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * @param evt * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent evt) { - ap.scalePanel.mouseEntered(evt); + ap.getScalePanel().mouseEntered(evt); } /** @@ -538,9 +635,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * @param evt * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent evt) { - ap.scalePanel.mouseExited(evt); + ap.getScalePanel().mouseExited(evt); } /** @@ -549,6 +647,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * @param evt * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent evt) { if (graphStretch > -1) @@ -565,16 +664,17 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } 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) { AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); @@ -598,7 +698,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (evt.getY() < height) { row = i; - break; } } @@ -609,63 +708,139 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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); + } + + AlignmentAnnotation ann = aa[row]; + if (row > -1 && ann.annotations != null + && column < ann.annotations.length) + { + buildToolTip(ann, column, aa); + setStatusMessage(column, ann); + } + else + { + this.setToolTipText(null); + ap.alignFrame.statusBar.setText(" "); } + } - if (row > -1 && aa[row].annotations != null - && res < (int) aa[row].annotations.length) + /** + * 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) { - if (aa[row].graphGroup > -1) + StringBuilder tip = new StringBuilder(32); + tip.append(""); + for (int i = 0; i < anns.length; i++) { - StringBuffer tip = new StringBuffer(""); - 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 + "
"); + tip.append(" ").append(description); } - } - if (tip.length() != 6) - { - tip.setLength(tip.length() - 4); - this.setToolTipText(tip.toString() + ""); + tip.append("
"); } } - 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() + ""); } - 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()); } /** @@ -674,28 +849,24 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, * @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) { @@ -703,19 +874,22 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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; + /** * DOCUMENT ME! * * @param g * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { g.setColor(Color.white); @@ -731,14 +905,32 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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) @@ -751,13 +943,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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); } /** + * set true to enable redraw timing debug output on stderr + */ + private final boolean debugRedraw = false; + + /** * non-Thread safe repaint * * @param horizontal @@ -765,7 +964,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, */ public void fastPaint(int horizontal) { - if ((horizontal == 0) || gg == null || av.getAlignment().getAlignmentAnnotation() == null || av.getAlignment().getAlignmentAnnotation().length < 1 @@ -774,15 +972,17 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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) @@ -795,12 +995,21 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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; + /** * DOCUMENT ME! * @@ -813,18 +1022,23 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, */ public void drawComponent(Graphics g, int startRes, int endRes) { + 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()) + if (lastImageGood + && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage + .getHeight() != image.getHeight())) { + // System.err.println("redraw faded image ("+(fadedImage==null ? + // "null image" : "") + " lastGood="+lastImageGood+")"); fadedImage = new BufferedImage(imgWidth, image.getHeight(), BufferedImage.TYPE_INT_RGB); @@ -838,15 +1052,22 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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()); + g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight()); g.setFont(av.getFont()); if (fm == null) @@ -862,12 +1083,18 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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; } - renderer.drawComponent(this, av, g, activeRow, startRes, endRes); + lastImageGood = renderer.drawComponent(this, av, g, activeRow, + startRes, endRes); + if (!lastImageGood && fadedImage == null) + { + fadedImage = oldFaded; + } } @Override @@ -887,4 +1114,44 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { 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(); + } + } }