2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import java.awt.AlphaComposite;
24 import java.awt.Color;
25 import java.awt.Dimension;
26 import java.awt.FontMetrics;
27 import java.awt.Graphics;
28 import java.awt.Graphics2D;
29 import java.awt.Image;
30 import java.awt.Rectangle;
31 import java.awt.RenderingHints;
32 import java.awt.event.ActionEvent;
33 import java.awt.event.ActionListener;
34 import java.awt.event.AdjustmentEvent;
35 import java.awt.event.AdjustmentListener;
36 import java.awt.event.MouseEvent;
37 import java.awt.event.MouseListener;
38 import java.awt.event.MouseMotionListener;
39 import java.awt.event.MouseWheelEvent;
40 import java.awt.event.MouseWheelListener;
41 import java.awt.image.BufferedImage;
42 import java.beans.PropertyChangeEvent;
43 import java.util.ArrayList;
44 import java.util.Collections;
45 import java.util.List;
47 import javax.swing.JMenuItem;
48 import javax.swing.JPanel;
49 import javax.swing.JPopupMenu;
50 import javax.swing.Scrollable;
51 import javax.swing.ToolTipManager;
53 import jalview.datamodel.AlignmentAnnotation;
54 import jalview.datamodel.AlignmentI;
55 import jalview.datamodel.Annotation;
56 import jalview.datamodel.ColumnSelection;
57 import jalview.datamodel.HiddenColumns;
58 import jalview.datamodel.SequenceI;
59 import jalview.gui.JalviewColourChooser.ColourChooserListener;
60 import jalview.renderer.AnnotationRenderer;
61 import jalview.renderer.AwtRenderPanelI;
62 import jalview.schemes.ResidueProperties;
63 import jalview.util.Comparison;
64 import jalview.util.MessageManager;
65 import jalview.util.Platform;
66 import jalview.viewmodel.ViewportListenerI;
67 import jalview.viewmodel.ViewportRanges;
70 * AnnotationPanel displays visible portion of annotation rows below unwrapped
76 public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
77 MouseListener, MouseWheelListener, MouseMotionListener,
78 ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
82 Select, Resize, Undefined
85 String HELIX = MessageManager.getString("label.helix");
87 String SHEET = MessageManager.getString("label.sheet");
90 * For RNA secondary structure "stems" aka helices
92 String STEM = MessageManager.getString("label.rna_helix");
94 String LABEL = MessageManager.getString("label.label");
96 String REMOVE = MessageManager.getString("label.remove_annotation");
98 String COLOUR = MessageManager.getString("action.colour");
100 public final Color HELIX_COLOUR = Color.red.darker();
102 public final Color SHEET_COLOUR = Color.green.darker().darker();
104 public final Color STEM_COLOUR = Color.blue.darker();
107 public AlignViewport av;
111 public int activeRow = -1;
113 public BufferedImage image;
115 public volatile BufferedImage fadedImage;
117 // private Graphics2D gg;
119 public FontMetrics fm;
121 public int imgWidth = 0;
123 boolean fastPaint = false;
125 // Used For mouse Dragging and resizing graphs
126 int graphStretch = -1;
128 int mouseDragLastX = -1;
130 int mouseDragLastY = -1;
132 DragMode dragMode = DragMode.Undefined;
134 boolean mouseDragging = false;
136 // for editing cursor
141 public final AnnotationRenderer renderer;
143 private MouseWheelListener[] _mwl;
146 * Creates a new AnnotationPanel object.
151 public AnnotationPanel(AlignmentPanel ap)
153 setName("AnnotationPanel");
154 ToolTipManager.sharedInstance().registerComponent(this);
155 ToolTipManager.sharedInstance().setInitialDelay(0);
156 ToolTipManager.sharedInstance().setDismissDelay(10000);
159 this.setLayout(null);
160 addMouseListener(this);
161 addMouseMotionListener(this);
162 ap.annotationScroller.getVerticalScrollBar()
163 .addAdjustmentListener(this);
164 // save any wheel listeners on the scroller, so we can propagate scroll
166 _mwl = ap.annotationScroller.getMouseWheelListeners();
167 // and then set our own listener to consume all mousewheel events
168 ap.annotationScroller.addMouseWheelListener(this);
169 renderer = new AnnotationRenderer();
171 av.getRanges().addPropertyChangeListener(this);
174 public AnnotationPanel(AlignViewport av)
177 renderer = new AnnotationRenderer();
181 public void mouseWheelMoved(MouseWheelEvent e)
186 double wheelRotation = e.getPreciseWheelRotation();
187 if (wheelRotation > 0)
189 av.getRanges().scrollRight(true);
191 else if (wheelRotation < 0)
193 av.getRanges().scrollRight(false);
198 // TODO: find the correct way to let the event bubble up to
199 // ap.annotationScroller
200 for (MouseWheelListener mwl : _mwl)
204 mwl.mouseWheelMoved(e);
215 public Dimension getPreferredScrollableViewportSize()
217 Dimension ps = getPreferredSize();
218 return new Dimension(ps.width, adjustForAlignFrame(false, ps.height));
222 public int getScrollableBlockIncrement(Rectangle visibleRect,
223 int orientation, int direction)
229 public boolean getScrollableTracksViewportHeight()
235 public boolean getScrollableTracksViewportWidth()
241 public int getScrollableUnitIncrement(Rectangle visibleRect,
242 int orientation, int direction)
251 * java.awt.event.AdjustmentListener#adjustmentValueChanged(java.awt.event
255 public void adjustmentValueChanged(AdjustmentEvent evt)
257 // update annotation label display
258 ap.getAlabels().setScrollOffset(-evt.getValue());
262 * Calculates the height of the annotation displayed in the annotation panel.
263 * Callers should normally call the ap.adjustAnnotationHeight method to ensure
264 * all annotation associated components are updated correctly.
267 public int adjustPanelHeight()
269 int height = av.calcPanelHeight();
270 this.setPreferredSize(new Dimension(1, height));
273 // revalidate only when the alignment panel is fully constructed
287 public void actionPerformed(ActionEvent evt)
289 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
294 Annotation[] anot = aa[activeRow].annotations;
296 if (anot.length < av.getColumnSelection().getMax())
298 Annotation[] temp = new Annotation[av.getColumnSelection().getMax()
300 System.arraycopy(anot, 0, temp, 0, anot.length);
302 aa[activeRow].annotations = anot;
305 String action = evt.getActionCommand();
306 if (action.equals(REMOVE))
308 for (int index : av.getColumnSelection().getSelected())
310 if (av.getAlignment().getHiddenColumns().isVisible(index))
316 else if (action.equals(LABEL))
318 String exMesg = collectAnnotVals(anot, LABEL);
319 String label = JvOptionPane.showInputDialog(
320 MessageManager.getString("label.enter_label"), exMesg);
327 if ((label.length() > 0) && !aa[activeRow].hasText)
329 aa[activeRow].hasText = true;
332 for (int index : av.getColumnSelection().getSelected())
334 if (!av.getAlignment().getHiddenColumns().isVisible(index))
339 if (anot[index] == null)
341 anot[index] = new Annotation(label, "", ' ', 0);
345 anot[index].displayCharacter = label;
349 else if (action.equals(COLOUR))
351 final Annotation[] fAnot = anot;
352 String title = MessageManager
353 .getString("label.select_foreground_colour");
354 ColourChooserListener listener = new ColourChooserListener()
357 public void colourSelected(Color c)
359 HiddenColumns hiddenColumns = av.getAlignment()
361 for (int index : av.getColumnSelection().getSelected())
363 if (hiddenColumns.isVisible(index))
365 if (fAnot[index] == null)
367 fAnot[index] = new Annotation("", "", ' ', 0);
369 fAnot[index].colour = c;
374 JalviewColourChooser.showColourChooser(this, title, Color.black,
378 // HELIX, SHEET or STEM
381 String symbol = "\u03B1"; // alpha
383 if (action.equals(HELIX))
387 else if (action.equals(SHEET))
390 symbol = "\u03B2"; // beta
393 // Added by LML to color stems
394 else if (action.equals(STEM))
397 int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
398 symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
401 if (!aa[activeRow].hasIcons)
403 aa[activeRow].hasIcons = true;
406 String label = JvOptionPane.showInputDialog(MessageManager
407 .getString("label.enter_label_for_the_structure"), symbol);
414 if ((label.length() > 0) && !aa[activeRow].hasText)
416 aa[activeRow].hasText = true;
417 if (action.equals(STEM))
419 aa[activeRow].showAllColLabels = true;
422 for (int index : av.getColumnSelection().getSelected())
424 if (!av.getAlignment().getHiddenColumns().isVisible(index))
429 if (anot[index] == null)
431 anot[index] = new Annotation(label, "", type, 0);
434 anot[index].secondaryStructure = type != 'S' ? type
435 : label.length() == 0 ? ' ' : label.charAt(0);
436 anot[index].displayCharacter = label;
441 av.getAlignment().validateAnnotation(aa[activeRow]);
442 ap.alignmentChanged();
443 ap.alignFrame.setMenusForViewport();
451 * Returns any existing annotation concatenated as a string. For each
452 * annotation, takes the description, if any, else the secondary structure
453 * character (if type is HELIX, SHEET or STEM), else the display character (if
460 private String collectAnnotVals(Annotation[] anots, String type)
462 // TODO is this method wanted? why? 'last' is not used
464 StringBuilder collatedInput = new StringBuilder(64);
466 ColumnSelection viscols = av.getColumnSelection();
467 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
470 * the selection list (read-only view) is in selection order, not
471 * column order; make a copy so we can sort it
473 List<Integer> selected = new ArrayList<>(viscols.getSelected());
474 Collections.sort(selected);
475 for (int index : selected)
477 // always check for current display state - just in case
478 if (!hidden.isVisible(index))
482 String tlabel = null;
483 if (anots[index] != null)
484 { // LML added stem code
485 if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
486 || type.equals(LABEL))
488 tlabel = anots[index].description;
489 if (tlabel == null || tlabel.length() < 1)
491 if (type.equals(HELIX) || type.equals(SHEET)
492 || type.equals(STEM))
494 tlabel = "" + anots[index].secondaryStructure;
498 tlabel = "" + anots[index].displayCharacter;
502 if (tlabel != null && !tlabel.equals(last))
504 if (last.length() > 0)
506 collatedInput.append(" ");
508 collatedInput.append(tlabel);
512 return collatedInput.toString();
516 * Action on right mouse pressed on Mac is to show a pop-up menu for the
517 * annotation. Action on left mouse pressed is to find which annotation is
518 * pressed and mark the start of a column selection or graph resize operation.
523 public void mousePressed(MouseEvent evt)
526 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
531 mouseDragLastX = evt.getX();
532 mouseDragLastY = evt.getY();
535 * add visible annotation heights until we reach the y
536 * position, to find which annotation it is in
541 final int y = evt.getY();
542 for (int i = 0; i < aa.length; i++)
546 height += aa[i].height;
555 else if (aa[i].graph > 0)
558 * we have clicked on a resizable graph annotation
567 * isPopupTrigger fires in mousePressed on Mac,
568 * not until mouseRelease on Windows
570 if (evt.isPopupTrigger() && activeRow != -1)
572 showPopupMenu(y, evt.getX());
576 ap.getScalePanel().mousePressed(evt);
580 * Construct and display a context menu at the right-click position
585 void showPopupMenu(final int y, int x)
587 if (av.getColumnSelection() == null
588 || av.getColumnSelection().isEmpty())
593 JPopupMenu pop = new JPopupMenu(
594 MessageManager.getString("label.structure_type"));
597 * Just display the needed structure options
599 if (av.getAlignment().isNucleotide())
601 item = new JMenuItem(STEM);
602 item.addActionListener(this);
607 item = new JMenuItem(HELIX);
608 item.addActionListener(this);
610 item = new JMenuItem(SHEET);
611 item.addActionListener(this);
614 item = new JMenuItem(LABEL);
615 item.addActionListener(this);
617 item = new JMenuItem(COLOUR);
618 item.addActionListener(this);
620 item = new JMenuItem(REMOVE);
621 item.addActionListener(this);
623 pop.show(this, x, y);
627 * Action on mouse up is to clear mouse drag data and call mouseReleased on
628 * ScalePanel, to deal with defining the selection group (if any) defined by
634 public void mouseReleased(MouseEvent evt)
639 mouseDragging = false;
640 dragMode = DragMode.Undefined;
641 ap.getScalePanel().mouseReleased(evt);
644 * isPopupTrigger is set in mouseReleased on Windows
645 * (in mousePressed on Mac)
647 if (evt.isPopupTrigger() && activeRow != -1)
649 showPopupMenu(evt.getY(), evt.getX());
661 public void mouseEntered(MouseEvent evt)
663 this.mouseDragging = false;
664 ap.getScalePanel().mouseEntered(evt);
668 * On leaving the panel, calls ScalePanel.mouseExited to deal with scrolling
669 * with column selection on a mouse drag
674 public void mouseExited(MouseEvent evt)
676 ap.getScalePanel().mouseExited(evt);
686 public void mouseDragged(MouseEvent evt)
689 * todo: if dragMode is Undefined:
690 * - set to Select if dx > dy
691 * - set to Resize if dy > dx
692 * - do nothing if dx == dy
694 final int x = evt.getX();
695 final int y = evt.getY();
696 if (dragMode == DragMode.Undefined)
698 int dx = Math.abs(x - mouseDragLastX);
699 int dy = Math.abs(y - mouseDragLastY);
700 if (graphStretch == -1 || dx > dy)
703 * mostly horizontal drag, or not a graph annotation
705 dragMode = DragMode.Select;
710 * mostly vertical drag
712 dragMode = DragMode.Resize;
716 if (dragMode == DragMode.Undefined)
719 * drag is diagonal - defer deciding whether to
720 * treat as up/down or left/right
726 if (dragMode == DragMode.Resize)
729 * resize graph annotation if mouse was dragged up or down
731 int deltaY = mouseDragLastY - evt.getY();
734 AlignmentAnnotation graphAnnotation = av.getAlignment()
735 .getAlignmentAnnotation()[graphStretch];
736 int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
737 graphAnnotation.graphHeight = newHeight;
740 ap.paintAlignment(false, false);
746 * for mouse drag left or right, delegate to
747 * ScalePanel to adjust the column selection
749 ap.getScalePanel().mouseDragged(evt);
759 * Constructs the tooltip, and constructs and displays a status message, for
760 * the current mouse position
765 public void mouseMoved(MouseEvent evt)
767 int yPos = evt.getY();
768 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
770 int row = getRowIndex(yPos, aa);
774 this.setToolTipText(null);
778 int column = (evt.getX() / av.getCharWidth())
779 + av.getRanges().getStartRes();
780 column = Math.min(column, av.getRanges().getEndRes());
782 if (av.hasHiddenColumns())
784 column = av.getAlignment().getHiddenColumns()
785 .visibleToAbsoluteColumn(column);
788 AlignmentAnnotation ann = aa[row];
789 if (row > -1 && ann.annotations != null
790 && column < ann.annotations.length)
792 String toolTip = buildToolTip(ann, column, aa);
793 setToolTipText(toolTip == null ? null
794 : JvSwingUtils.wrapTooltip(true, toolTip));
795 String msg = getStatusMessage(av.getAlignment(), column, ann);
796 ap.alignFrame.setStatus(msg);
800 this.setToolTipText(null);
801 ap.alignFrame.setStatus(" ");
806 * Answers the index in the annotations array of the visible annotation at the
807 * given y position. This is done by adding the heights of visible annotations
808 * until the y position has been exceeded. Answers -1 if no annotations are
809 * visible, or the y position is below all annotations.
815 static int getRowIndex(int yPos, AlignmentAnnotation[] aa)
824 for (int i = 0; i < aa.length; i++)
828 height += aa[i].height;
841 * Answers a tooltip for the annotation at the current mouse position, not
842 * wrapped in <html> tags (apply if wanted). Answers null if there is no
849 static String buildToolTip(AlignmentAnnotation ann, int column,
850 AlignmentAnnotation[] anns)
852 String tooltip = null;
853 if (ann.graphGroup > -1)
855 StringBuilder tip = new StringBuilder(32);
856 boolean first = true;
857 for (int i = 0; i < anns.length; i++)
859 if (anns[i].graphGroup == ann.graphGroup
860 && anns[i].annotations[column] != null)
867 tip.append(anns[i].label);
868 String description = anns[i].annotations[column].description;
869 if (description != null && description.length() > 0)
871 tip.append(" ").append(description);
875 tooltip = first ? null : tip.toString();
877 else if (column < ann.annotations.length
878 && ann.annotations[column] != null)
880 tooltip = ann.annotations[column].description;
887 * Constructs and returns the status bar message
893 static String getStatusMessage(AlignmentI al, int column,
894 AlignmentAnnotation ann)
897 * show alignment column and annotation description if any
899 StringBuilder text = new StringBuilder(32);
900 text.append(MessageManager.getString("label.column")).append(" ")
903 if (column < ann.annotations.length && ann.annotations[column] != null)
905 String description = ann.annotations[column].description;
906 if (description != null && description.trim().length() > 0)
908 text.append(" ").append(description);
913 * if the annotation is sequence-specific, show the sequence number
914 * in the alignment, and (if not a gap) the residue and position
916 SequenceI seqref = ann.sequenceRef;
919 int seqIndex = al.findIndex(seqref);
922 text.append(", ").append(MessageManager.getString("label.sequence"))
923 .append(" ").append(seqIndex + 1);
924 char residue = seqref.getCharAt(column);
925 if (!Comparison.isGap(residue))
929 if (al.isNucleotide())
931 name = ResidueProperties.nucleotideName
932 .get(String.valueOf(residue));
933 text.append(" Nucleotide: ")
934 .append(name != null ? name : residue);
938 name = 'X' == residue ? "X"
939 : ('*' == residue ? "STOP"
940 : ResidueProperties.aa2Triplet
941 .get(String.valueOf(residue)));
942 text.append(" Residue: ").append(name != null ? name : residue);
944 int residuePos = seqref.findPosition(column);
945 text.append(" (").append(residuePos).append(")");
950 return text.toString();
960 public void mouseClicked(MouseEvent evt)
962 // if (activeRow != -1)
964 // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
965 // AlignmentAnnotation anot = aa[activeRow];
969 // TODO mouseClicked-content and drawCursor are quite experimental!
970 public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
973 int pady = av.getCharHeight() / 5;
975 graphics.setColor(Color.black);
976 graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
978 if (av.validCharWidth)
980 graphics.setColor(Color.white);
982 char s = seq.getCharAt(res);
984 charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
985 graphics.drawString(String.valueOf(s), charOffset + x1,
986 (y1 + av.getCharHeight()) - pady);
991 private volatile boolean imageFresh = false;
993 private Rectangle visibleRect = new Rectangle(),
994 clipBounds = new Rectangle();
1003 public void paintComponent(Graphics g)
1006 // BH: note that this method is generally recommended to
1007 // call super.paintComponent(g). Otherwise, the children of this
1008 // component will not be rendered. That is not needed here
1009 // because AnnotationPanel does not have any children. It is
1010 // just a JPanel contained in a JViewPort.
1012 computeVisibleRect(visibleRect);
1014 g.setColor(Color.white);
1015 g.fillRect(0, 0, visibleRect.width, visibleRect.height);
1017 ViewportRanges ranges = av.getRanges();
1019 if (allowFastPaint && image != null)
1021 // BH 2018 optimizing generation of new Rectangle().
1023 || (visibleRect.width != (clipBounds = g
1024 .getClipBounds(clipBounds)).width)
1025 || (visibleRect.height != clipBounds.height))
1027 g.drawImage(image, 0, 0, this);
1033 imgWidth = (ranges.getEndRes() - ranges.getStartRes() + 1)
1034 * av.getCharWidth();
1042 if (image == null || imgWidth != image.getWidth(this)
1043 || image.getHeight(this) != getHeight())
1047 image = new BufferedImage(imgWidth,
1048 ap.getAnnotationPanel().getHeight(),
1049 BufferedImage.TYPE_INT_RGB);
1050 } catch (OutOfMemoryError oom)
1055 } catch (Exception x)
1060 "Couldn't allocate memory to redraw screen. Please restart Jalview",
1064 gg = (Graphics2D) image.getGraphics();
1068 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
1069 RenderingHints.VALUE_ANTIALIAS_ON);
1072 gg.setFont(av.getFont());
1073 fm = gg.getFontMetrics();
1074 gg.setColor(Color.white);
1075 gg.fillRect(0, 0, imgWidth, image.getHeight());
1080 gg = (Graphics2D) image.getGraphics();
1084 drawComponent(gg, ranges.getStartRes(), av.getRanges().getEndRes() + 1);
1087 g.drawImage(image, 0, 0, this);
1091 * non-Thread safe repaint
1094 * repaint with horizontal shift in alignment
1096 public void fastPaint(int horizontal)
1098 if ((horizontal == 0) || image == null
1099 || av.getAlignment().getAlignmentAnnotation() == null
1100 || av.getAlignment().getAlignmentAnnotation().length < 1
1101 || av.isCalcInProgress())
1107 int sr = av.getRanges().getStartRes();
1108 int er = av.getRanges().getEndRes() + 1;
1117 Graphics2D gg = (Graphics2D) image.getGraphics();
1119 gg.copyArea(0, 0, imgWidth, getHeight(),
1120 -horizontal * av.getCharWidth(), 0);
1122 if (horizontal > 0) // scrollbar pulled right, image to the left
1124 transX = (er - sr - horizontal) * av.getCharWidth();
1125 sr = er - horizontal;
1127 else if (horizontal < 0)
1129 er = sr - horizontal;
1132 gg.translate(transX, 0);
1134 drawComponent(gg, sr, er);
1136 gg.translate(-transX, 0);
1142 // Call repaint on alignment panel so that repaints from other alignment
1143 // panel components can be aggregated. Otherwise performance of the overview
1144 // window and others may be adversely affected.
1145 av.getAlignPanel().repaint();
1148 private volatile boolean lastImageGood = false;
1160 public void drawComponent(Graphics g, int startRes, int endRes)
1162 BufferedImage oldFaded = fadedImage;
1163 if (av.isCalcInProgress())
1167 lastImageGood = false;
1170 // We'll keep a record of the old image,
1171 // and draw a faded image until the calculation
1174 && (fadedImage == null || fadedImage.getWidth() != imgWidth
1175 || fadedImage.getHeight() != image.getHeight()))
1177 // System.err.println("redraw faded image ("+(fadedImage==null ?
1178 // "null image" : "") + " lastGood="+lastImageGood+")");
1179 fadedImage = new BufferedImage(imgWidth, image.getHeight(),
1180 BufferedImage.TYPE_INT_RGB);
1182 Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
1184 fadedG.setColor(Color.white);
1185 fadedG.fillRect(0, 0, imgWidth, image.getHeight());
1187 fadedG.setComposite(
1188 AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f));
1189 fadedG.drawImage(image, 0, 0, this);
1192 // make sure we don't overwrite the last good faded image until all
1193 // calculations have finished
1194 lastImageGood = false;
1199 if (fadedImage != null)
1201 oldFaded = fadedImage;
1206 g.setColor(Color.white);
1207 g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
1209 g.setFont(av.getFont());
1212 fm = g.getFontMetrics();
1215 if ((av.getAlignment().getAlignmentAnnotation() == null)
1216 || (av.getAlignment().getAlignmentAnnotation().length < 1))
1218 g.setColor(Color.white);
1219 g.fillRect(0, 0, getWidth(), getHeight());
1220 g.setColor(Color.black);
1221 if (av.validCharWidth)
1223 g.drawString(MessageManager
1224 .getString("label.alignment_has_no_annotations"), 20, 15);
1229 lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes,
1231 if (!lastImageGood && fadedImage == null)
1233 fadedImage = oldFaded;
1238 public FontMetrics getFontMetrics()
1244 public Image getFadedImage()
1250 public int getFadedImageWidth()
1255 private int[] bounds = new int[2];
1257 private boolean allowFastPaint;
1260 public int[] getVisibleVRange()
1262 if (ap != null && ap.getAlabels() != null)
1264 int sOffset = -ap.getAlabels().getScrollOffset();
1265 int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
1266 bounds[0] = sOffset;
1267 bounds[1] = visHeight;
1277 * Try to ensure any references held are nulled
1279 public void dispose()
1289 * I created the renderer so I will dispose of it
1291 if (renderer != null)
1298 public void propertyChange(PropertyChangeEvent evt)
1300 // Respond to viewport range changes (e.g. alignment panel was scrolled)
1301 // Both scrolling and resizing change viewport ranges: scrolling changes
1302 // both start and end points, but resize only changes end values.
1303 // Here we only want to fastpaint on a scroll, with resize using a normal
1304 // paint, so scroll events are identified as changes to the horizontal or
1305 // vertical start value.
1306 if (evt.getPropertyName().equals(ViewportRanges.STARTRES))
1308 fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
1310 else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
1312 fastPaint(((int[]) evt.getNewValue())[0]
1313 - ((int[]) evt.getOldValue())[0]);
1315 else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
1322 * computes the visible height of the annotation panel
1324 * @param adjustPanelHeight
1325 * - when false, just adjust existing height according to other
1327 * @param annotationHeight
1328 * @return height to use for the ScrollerPreferredVisibleSize
1330 public int adjustForAlignFrame(boolean adjustPanelHeight,
1331 int annotationHeight)
1334 * Estimate available height in the AlignFrame for alignment +
1335 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
1336 * hscroll, status bar, insets.
1338 int stuff = (ap.getViewName() != null ? 30 : 0)
1339 + (Platform.isAMacAndNotJS() ? 120 : 140);
1340 int availableHeight = ap.alignFrame.getHeight() - stuff;
1341 int rowHeight = av.getCharHeight();
1343 if (adjustPanelHeight)
1345 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
1348 * If not enough vertical space, maximize annotation height while keeping
1349 * at least two rows of alignment visible
1351 if (annotationHeight + alignmentHeight > availableHeight)
1353 annotationHeight = Math.min(annotationHeight,
1354 availableHeight - 2 * rowHeight);
1359 // maintain same window layout whilst updating sliders
1360 annotationHeight = Math.min(ap.annotationScroller.getSize().height,
1361 availableHeight - 2 * rowHeight);
1363 return annotationHeight;
1367 * Clears the flag that allows a 'fast paint' on the next repaint, so
1368 * requiring a full repaint
1370 public void setNoFastPaint()
1372 allowFastPaint = false;