X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=199c4e599a9ff1e5cc0cf83a272f668e993b91b1;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=1acc0ca9c0d0ad7c51da2ca25c309da0b900a520;hpb=227daebd9bdf92c83712e077d958a690cdee0f7a;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 1acc0ca..199c4e5 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1,84 +1,114 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, 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.font.LineMetrics; -import java.awt.geom.AffineTransform; -import java.awt.image.*; -import java.util.Hashtable; - -import javax.swing.*; - -import com.stevesoft.pat.Regex; - -import jalview.analysis.AAFrequency; -import jalview.analysis.StructureFrequency; -import jalview.datamodel.*; -import jalview.schemes.ColourSchemeI; +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 MouseListener, - MouseMotionListener, ActionListener, AdjustmentListener +public class AnnotationPanel extends JPanel implements AwtRenderPanelI, + 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"); - final Color HELIX_COLOUR = Color.red.darker(); + public final Color HELIX_COLOUR = Color.red.darker(); - final Color SHEET_COLOUR = Color.green.darker().darker(); + public final Color SHEET_COLOUR = Color.green.darker().darker(); - final Color STEM_COLOUR = Color.blue.darker(); + public final Color STEM_COLOUR = Color.blue.darker(); /** DOCUMENT ME!! */ - AlignViewport av; + public AlignViewport av; AlignmentPanel ap; - int activeRow = -1; + public int activeRow = -1; - BufferedImage image; + public BufferedImage image; - BufferedImage fadedImage; + public volatile BufferedImage fadedImage; Graphics2D gg; - FontMetrics fm; + public FontMetrics fm; - int imgWidth = 0; + public int imgWidth = 0; boolean fastPaint = false; @@ -93,13 +123,15 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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. * @@ -108,9 +140,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public AnnotationPanel(AlignmentPanel ap) { - - MAC = new jalview.util.Platform().isAMac(); - ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -121,22 +150,97 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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(); } public AnnotationPanel(AlignViewport av) { this.av = av; + 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()); } /** @@ -147,7 +251,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public int adjustPanelHeight() { - int height = calcPanelHeight(); + int height = av.calcPanelHeight(); this.setPreferredSize(new Dimension(1, height)); if (ap != null) { @@ -159,73 +263,15 @@ public class AnnotationPanel extends JPanel implements MouseListener, } /** - * 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.alignment.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.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (aa == null) { return; @@ -240,18 +286,22 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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) { @@ -263,19 +313,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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.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. + anot[index] = new Annotation(label, "", ' ', 0); } else { @@ -283,17 +330,18 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } } - 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.colSel.isVisible(index)) + if (!av.getColumnSelection().isVisible(index)) + { continue; + } if (anot[index] == null) { @@ -304,26 +352,27 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } 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) @@ -331,8 +380,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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) { @@ -342,59 +391,87 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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.colSel.isVisible(index)) + 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; + } } + 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 = ""; - 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.colSel.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; } } } @@ -402,13 +479,13 @@ public class AnnotationPanel extends JPanel implements MouseListener, { if (last.length() > 0) { - collatedInput += " "; + collatedInput.append(" "); } - collatedInput += tlabel; + collatedInput.append(tlabel); } } } - return collatedInput; + return collatedInput.toString(); } /** @@ -417,10 +494,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mousePressed(MouseEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (aa == null) { return; @@ -429,6 +507,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, int height = 0; activeRow = -1; + final int y = evt.getY(); for (int i = 0; i < aa.length; i++) { if (aa[i].visible) @@ -436,7 +515,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, height += aa[i].height; } - if (evt.getY() < height) + if (y < height) { if (aa[i].editable) { @@ -446,61 +525,71 @@ public class AnnotationPanel extends JPanel implements MouseListener, { // 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.alignment.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); } /** @@ -509,12 +598,23 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @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()); + } + } /** @@ -523,9 +623,10 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent evt) { - ap.scalePanel.mouseEntered(evt); + ap.getScalePanel().mouseEntered(evt); } /** @@ -534,9 +635,10 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent evt) { - ap.scalePanel.mouseExited(evt); + ap.getScalePanel().mouseExited(evt); } /** @@ -545,15 +647,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent evt) { if (graphStretch > -1) { - av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY + av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY(); - if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0) + if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0) { - av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0; + av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0; } graphStretchY = evt.getY(); adjustPanelHeight(); @@ -561,19 +664,20 @@ public class AnnotationPanel extends JPanel implements MouseListener, } 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.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (aa == null) { @@ -594,7 +698,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (evt.getY() < height) { row = i; - break; } } @@ -605,63 +708,139 @@ public class AnnotationPanel extends JPanel implements MouseListener, return; } - int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + int column = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + + if (av.hasHiddenColumns()) + { + column = av.getColumnSelection().adjustForHiddenColumns(column); + } - if (av.hasHiddenColumns) + AlignmentAnnotation ann = aa[row]; + if (row > -1 && ann.annotations != null + && column < ann.annotations.length) + { + buildToolTip(ann, column, aa); + setStatusMessage(column, ann); + } + else { - res = av.getColumnSelection().adjustForHiddenColumns(res); + 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()); } /** @@ -670,28 +849,24 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseClicked(MouseEvent evt) { - if (activeRow != -1) - { - AlignmentAnnotation[] aa = av.alignment.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) { @@ -699,19 +874,22 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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); @@ -727,14 +905,32 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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) @@ -747,13 +943,20 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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 @@ -761,24 +964,25 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void fastPaint(int horizontal) { - if ((horizontal == 0) || gg == null - || av.alignment.getAlignmentAnnotation() == null - || av.alignment.getAlignmentAnnotation().length < 1 - || av.updatingConsensus || av.updatingConservation) + || av.getAlignment().getAlignmentAnnotation() == null + || av.getAlignment().getAlignmentAnnotation().length < 1 + || av.isCalcInProgress()) { 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) @@ -791,12 +995,21 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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! * @@ -809,18 +1022,23 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ 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()) + 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); @@ -834,15 +1052,22 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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) @@ -850,881 +1075,83 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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 validEnd = false; - boolean labelAllCols = false; - boolean centreColLabels, centreColLabelsDef = av - .getCentreColumnLabels(); - boolean scaleColLabel = false; - boolean[] graphGroupDrawn = new boolean[aa.length]; - int charOffset = 0; // offset for a label - float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a - // column. - Font ofont = g.getFont(); - // \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; - } - centreColLabels = row.centreColLabels || centreColLabelsDef; - labelAllCols = row.showAllColLabels; - scaleColLabel = row.scaleColLabel; - 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; - } + fadedImage = oldFaded; + } + } - if (av.updatingConsensus && aa[i] == av.consensus) - { - y += av.charHeight; + @Override + public FontMetrics getFontMetrics() + { + return fm; + } - 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); + @Override + public Image getFadedImage() + { + return fadedImage; + } - continue; - } - else if (av.updatingConservation - && aa[i].label.equals("Conservation")) - { + @Override + public int getFadedImageWidth() + { + return imgWidth; + } - y += av.charHeight; - g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y - - row.height, imgWidth, y, this); + private int[] bounds = new int[2]; - g.setColor(Color.black); - // g.drawString("Calculating Conservation.....",20, y-row.height/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; + } + } - 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; - } - - // first pass sets up state for drawing continuation from left-hand column - // of startRes - x = (startRes == 0) ? 0 : -1; - 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 (x > -1) - { - 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)) - { - - if (centreColLabels || scaleColLabel) - { - fmWidth = (float) fm.charsWidth( - row.annotations[column].displayCharacter - .toCharArray(), 0, - row.annotations[column].displayCharacter.length()); - - if (scaleColLabel) - { - // justify the label and scale to fit in column - if (fmWidth > av.charWidth) - { - // scale only if the current font isn't already small enough - fmScaling = av.charWidth; - fmScaling /= fmWidth; - g.setFont(ofont.deriveFont(AffineTransform - .getScaleInstance(fmScaling, 1.0))); - // and update the label's width to reflect the scaling. - fmWidth = av.charWidth; - } - } - } - else - { - fmWidth = (float) fm - .charWidth(row.annotations[column].displayCharacter - .charAt(0)); - } - charOffset = (int) ((av.charWidth - fmWidth) / 2f); - - 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 - || (labelAllCols - || !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); - } - g.setFont(ofont); - } - } - if (row.hasIcons) - { - char ss = row.annotations[column].secondaryStructure; - if (ss == 'S') - { - // distinguish between forward/backward base-pairing - if (row.annotations[column].displayCharacter.indexOf(')') > -1) - { - ss = 's'; - } - } - if (!validRes || (ss != lastSS)) - { - if (x > -1) - { - switch (lastSS) - { - case 'H': - drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - - case 'E': - drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - - case 'S': // Stem case for RNA secondary structure - case 's': // and opposite direction - drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - - default: - g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - - lastSSX, 2); - - break; - } - } - if (validRes) - { - lastSS = ss; - } - else - { - lastSS = ' '; - } - if (x > -1) - { - lastSSX = (x * av.charWidth); - } - } - } - - column++; - x++; - } - - if (column >= row.annotations.length) - { - column = row.annotations.length - 1; - validEnd = false; - } - else - { - validEnd = true; - } - - // x ++; - - if (row.hasIcons) - { - switch (lastSS) - { - case 'H': - drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - - case 'E': - drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - case 's': - case 'S': // Stem case for RNA secondary structure - drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - default: - drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - 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; - } - } - } - - private void drawStemAnnot(Graphics g, AlignmentAnnotation row, - int lastSSX, int x, int y, int iconOffset, int startRes, - int column, boolean validRes, boolean validEnd) - { - g.setColor(STEM_COLOUR); - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * av.charWidth); - Regex closeparen = new Regex("(\\))"); - - String dc = column == 0 ? "" - : row.annotations[column - 1].displayCharacter; - - boolean diffupstream = sCol == 0 || row.annotations[sCol - 1] == null - || !dc.equals(row.annotations[sCol - 1].displayCharacter); - boolean diffdownstream = !validRes || !validEnd - || row.annotations[column] == null - || !dc.equals(row.annotations[column].displayCharacter); - // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream); - // If a closing base pair half of the stem, display a backward arrow - if (column > 0 && closeparen.search(dc)) - { - if (diffupstream) - // if (validRes && column>1 && row.annotations[column-2]!=null && - // dc.equals(row.annotations[column-2].displayCharacter)) - { - g.fillPolygon(new int[] - { lastSSX + 5, lastSSX + 5, lastSSX }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3); - x1 += 5; - } - if (diffdownstream) - { - x2 -= 1; - } - } - else - { - // display a forward arrow - if (diffdownstream) - { - g.fillPolygon(new int[] - { x2 - 5, x2 - 5, x2 }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3); - x2 -= 5; - } - if (diffupstream) - { - x1 += 1; - } - } - // draw arrow body - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7); - } - - private void drawGlyphLine(Graphics g, AlignmentAnnotation row, - int lastSSX, int x, int y, int iconOffset, int startRes, - int column, boolean validRes, boolean validEnd) - { - g.setColor(Color.gray); - g - .fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - - lastSSX, 2); - } - - private void drawSheetAnnot(Graphics g, AlignmentAnnotation row, - int lastSSX, int x, int y, int iconOffset, int startRes, - int column, boolean validRes, boolean validEnd) - { - g.setColor(SHEET_COLOUR); - - if (!validEnd || !validRes || row.annotations[column] == null - || row.annotations[column].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); - } - - } - - private void drawHelixAnnot(Graphics g, AlignmentAnnotation row, - int lastSSX, int x, int y, int iconOffset, int startRes, - int column, boolean validRes, boolean validEnd) - { - g.setColor(HELIX_COLOUR); - - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * av.charWidth); - - if (MAC) - { - int ofs = av.charWidth / 2; - // Off by 1 offset when drawing rects and ovals - // to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8); - if (sCol == 0 || row.annotations[sCol - 1] == null - || row.annotations[sCol - 1].secondaryStructure != 'H') - { - } - else - { - // g.setColor(Color.orange); - g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8, - 0, 0); - } - if (!validRes || row.annotations[column] == null - || row.annotations[column].secondaryStructure != 'H') - { - - } - else - { - // g.setColor(Color.magenta); - g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs - + 1, 8, 0, 0); - - } - - return; - } - - 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 (!validRes || 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); - } - - public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, - int eRes, int y, float min, float max, int graphHeight) - { - 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()); - } - } - - public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, - int eRes, float min, float max, int y) - { - ColourSchemeI profcolour = av.getGlobalColourScheme(); - if (profcolour == null) - { - profcolour = new jalview.schemes.ZappoColourScheme(); - } - if (sRes > aa.annotations.length) - { - return; - } - Font ofont = g.getFont(); - 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; - boolean renderHistogram = true, renderProfile = true; - if (aa.autoCalculated && aa.label.startsWith("Consensus")) - { - // TODO: generalise this to have render styles for consensus/profile data - if (aa.groupRef != null) - { - renderHistogram = aa.groupRef.isShowConsensusHistogram(); - renderProfile = aa.groupRef.isShowSequenceLogo(); - } - else - { - renderHistogram = av.isShowConsensusHistogram(); - renderProfile = av.isShowSequenceLogo(); - } - } - 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 (renderHistogram) - { - 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); - } - } - // draw profile if available - if (renderProfile && aa.annotations[column].value != 0) - { - - int profl[] = getProfileFor(aa, column); - // just try to draw the logo if profl is not null - if (profl != null) - { - - /* - * if (profl != null) { - * - * for (int i = 0; i < profl.length; i++) { System.out.print(profl[i] - * + ","); } - * - * } - */ - int ht = y1, htn = y2 - y1;// aa.graphHeight; - float wdth; - double ht2 = 0; - char[] dc; - - /** - * profl.length == 11 indicates that the profile of a secondary - * structure conservation row was accesed. - * Therefore dc gets length 2, to have space for a basepair instead of - * just a single nucleotide - */ - if (profl.length == 22) - { - dc = new char[2]; - } - else - { - dc = new char[1]; - } - - LineMetrics lm; - for (int c = 1; profl != null && c < profl[0];) - { - dc[0] = (char) profl[c++]; - - if (aa.label.startsWith("StrucConsensus")) - { - dc[1] = 'A'; - } - - wdth = av.charWidth; - wdth /= (float) fm.charsWidth(dc, 0, dc.length); - - if (c > 2) - { - ht += (int) ht2; - } - { - // if (aa.annotations[column].value==0) { - // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, - // (ht2=(aa.graphHeight*0.1/av.charHeight))))); - // ht = y2-(int)ht2; - // } else { - g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance( - wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0)) - / av.charHeight))); - lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g); - // htn -=ht2; - // } - g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null) - // ? );// try to get a - // colourscheme for the - // group(aa.groupRef.cs==null) - // ? av.textColour2 : - // cs.findColour(dc)); - // System.out.println(dc[0]); - - g.drawChars(dc, 0, dc.length, x * av.charWidth, - (int) (ht + lm.getHeight())); - - // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent(); - } - } - g.setFont(ofont); - } - } - 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()); - } - } - - private int[] getProfileFor(AlignmentAnnotation aa, int column) - { - if (aa.autoCalculated && aa.label.startsWith("Consensus")) - { - if (aa.groupRef != null && aa.groupRef.consensusData != null - && aa.groupRef.isShowSequenceLogo()) - { - return AAFrequency.extractProfile( - aa.groupRef.consensusData[column], aa.groupRef - .getIgnoreGapsConsensus()); - } - // TODO extend annotation row to enable dynamic and static profile data to - // be stored - if (aa.groupRef == null && aa.sequenceRef == null - && av.isShowSequenceLogo()) - { - return AAFrequency.extractProfile(av.hconsensus[column], av - .getIgnoreGapsConsensus()); - } - } - else - { - if (aa.autoCalculated && aa.label.startsWith("StrucConsensus")) - { - if (aa.groupRef != null && aa.groupRef.consensusData != null - && aa.groupRef.isShowSequenceLogo()) - { - //TODO check what happens for group selections - return StructureFrequency.extractProfile( - aa.groupRef.consensusData[column], aa.groupRef - .getIgnoreGapsConsensus(),column); - } - // TODO extend annotation row to enable dynamic and static profile data - // to - // be stored - if (aa.groupRef == null && aa.sequenceRef == null - && av.isShowSequenceLogo()) - { - return StructureFrequency.extractProfile(av.hStrucConsensus[column], - av.getIgnoreGapsConsensus(),column); - } - } - - } - return null; - } - - // used by overview window - public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, - int y, int sRes, int eRes) + /** + * Try to ensure any references held are nulled + */ + public void dispose() { - 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++) + 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) { - 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; + renderer.dispose(); } } - }