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 if (dragMode == DragMode.Resize)
642 ap.adjustAnnotationHeight();
644 dragMode = DragMode.Undefined;
645 ap.getScalePanel().mouseReleased(evt);
648 * isPopupTrigger is set in mouseReleased on Windows
649 * (in mousePressed on Mac)
651 if (evt.isPopupTrigger() && activeRow != -1)
653 showPopupMenu(evt.getY(), evt.getX());
665 public void mouseEntered(MouseEvent evt)
667 this.mouseDragging = false;
668 ap.getScalePanel().mouseEntered(evt);
672 * On leaving the panel, calls ScalePanel.mouseExited to deal with scrolling
673 * with column selection on a mouse drag
678 public void mouseExited(MouseEvent evt)
680 ap.getScalePanel().mouseExited(evt);
684 * Action on starting or continuing a mouse drag. There are two possible
687 * <li>drag up or down on a graphed annotation increases or decreases the
688 * height of the graph</li>
689 * <li>dragging left or right selects the columns dragged across</li>
691 * A drag on a graph annotation is treated as column selection if it starts
692 * with more horizontal than vertical movement, and as resize if it starts
693 * with more vertical than horizontal movement. Once started, the drag does
699 public void mouseDragged(MouseEvent evt)
702 * if dragMode is Undefined:
703 * - set to Select if dx > dy
704 * - set to Resize if dy > dx
705 * - do nothing if dx == dy
707 final int x = evt.getX();
708 final int y = evt.getY();
709 if (dragMode == DragMode.Undefined)
711 int dx = Math.abs(x - mouseDragLastX);
712 int dy = Math.abs(y - mouseDragLastY);
713 if (graphStretch == -1 || dx > dy)
716 * mostly horizontal drag, or not a graph annotation
718 dragMode = DragMode.Select;
723 * mostly vertical drag
725 dragMode = DragMode.Resize;
729 if (dragMode == DragMode.Undefined)
732 * drag is diagonal - defer deciding whether to
733 * treat as up/down or left/right
739 if (dragMode == DragMode.Resize)
742 * resize graph annotation if mouse was dragged up or down
744 int deltaY = mouseDragLastY - evt.getY();
747 AlignmentAnnotation graphAnnotation = av.getAlignment()
748 .getAlignmentAnnotation()[graphStretch];
749 int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
750 graphAnnotation.graphHeight = newHeight;
753 ap.paintAlignment(false, false);
759 * for mouse drag left or right, delegate to
760 * ScalePanel to adjust the column selection
762 ap.getScalePanel().mouseDragged(evt);
772 * Constructs the tooltip, and constructs and displays a status message, for
773 * the current mouse position
778 public void mouseMoved(MouseEvent evt)
780 int yPos = evt.getY();
781 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
783 int row = getRowIndex(yPos, aa);
787 this.setToolTipText(null);
791 int column = (evt.getX() / av.getCharWidth())
792 + av.getRanges().getStartRes();
793 column = Math.min(column, av.getRanges().getEndRes());
795 if (av.hasHiddenColumns())
797 column = av.getAlignment().getHiddenColumns()
798 .visibleToAbsoluteColumn(column);
801 AlignmentAnnotation ann = aa[row];
802 if (row > -1 && ann.annotations != null
803 && column < ann.annotations.length)
805 String toolTip = buildToolTip(ann, column, aa);
806 setToolTipText(toolTip == null ? null
807 : JvSwingUtils.wrapTooltip(true, toolTip));
808 String msg = getStatusMessage(av.getAlignment(), column, ann);
809 ap.alignFrame.setStatus(msg);
813 this.setToolTipText(null);
814 ap.alignFrame.setStatus(" ");
819 * Answers the index in the annotations array of the visible annotation at the
820 * given y position. This is done by adding the heights of visible annotations
821 * until the y position has been exceeded. Answers -1 if no annotations are
822 * visible, or the y position is below all annotations.
828 static int getRowIndex(int yPos, AlignmentAnnotation[] aa)
837 for (int i = 0; i < aa.length; i++)
841 height += aa[i].height;
854 * Answers a tooltip for the annotation at the current mouse position, not
855 * wrapped in <html> tags (apply if wanted). Answers null if there is no
862 static String buildToolTip(AlignmentAnnotation ann, int column,
863 AlignmentAnnotation[] anns)
865 String tooltip = null;
866 if (ann.graphGroup > -1)
868 StringBuilder tip = new StringBuilder(32);
869 boolean first = true;
870 for (int i = 0; i < anns.length; i++)
872 if (anns[i].graphGroup == ann.graphGroup
873 && anns[i].annotations[column] != null)
880 tip.append(anns[i].label);
881 String description = anns[i].annotations[column].description;
882 if (description != null && description.length() > 0)
884 tip.append(" ").append(description);
888 tooltip = first ? null : tip.toString();
890 else if (column < ann.annotations.length
891 && ann.annotations[column] != null)
893 tooltip = ann.annotations[column].description;
894 if ("".equals(tooltip))
904 * Constructs and returns the status bar message
910 static String getStatusMessage(AlignmentI al, int column,
911 AlignmentAnnotation ann)
914 * show alignment column and annotation description if any
916 StringBuilder text = new StringBuilder(32);
917 text.append(MessageManager.getString("label.column")).append(" ")
920 if (column < ann.annotations.length && ann.annotations[column] != null)
922 String description = ann.annotations[column].description;
923 if (description != null && description.trim().length() > 0)
925 text.append(" ").append(description);
930 * if the annotation is sequence-specific, show the sequence number
931 * in the alignment, and (if not a gap) the residue and position
933 SequenceI seqref = ann.sequenceRef;
936 int seqIndex = al.findIndex(seqref);
939 text.append(", ").append(MessageManager.getString("label.sequence"))
940 .append(" ").append(seqIndex + 1);
941 char residue = seqref.getCharAt(column);
942 if (!Comparison.isGap(residue))
946 if (al.isNucleotide())
948 name = ResidueProperties.nucleotideName
949 .get(String.valueOf(residue));
950 text.append(" Nucleotide: ")
951 .append(name != null ? name : residue);
955 name = 'X' == residue ? "X"
956 : ('*' == residue ? "STOP"
957 : ResidueProperties.aa2Triplet
958 .get(String.valueOf(residue)));
959 text.append(" Residue: ").append(name != null ? name : residue);
961 int residuePos = seqref.findPosition(column);
962 text.append(" (").append(residuePos).append(")");
967 return text.toString();
977 public void mouseClicked(MouseEvent evt)
979 // if (activeRow != -1)
981 // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
982 // AlignmentAnnotation anot = aa[activeRow];
986 // TODO mouseClicked-content and drawCursor are quite experimental!
987 public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
990 int pady = av.getCharHeight() / 5;
992 graphics.setColor(Color.black);
993 graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
995 if (av.validCharWidth)
997 graphics.setColor(Color.white);
999 char s = seq.getCharAt(res);
1001 charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
1002 graphics.drawString(String.valueOf(s), charOffset + x1,
1003 (y1 + av.getCharHeight()) - pady);
1008 private volatile boolean imageFresh = false;
1010 private Rectangle visibleRect = new Rectangle(),
1011 clipBounds = new Rectangle();
1020 public void paintComponent(Graphics g)
1023 // BH: note that this method is generally recommended to
1024 // call super.paintComponent(g). Otherwise, the children of this
1025 // component will not be rendered. That is not needed here
1026 // because AnnotationPanel does not have any children. It is
1027 // just a JPanel contained in a JViewPort.
1029 computeVisibleRect(visibleRect);
1031 g.setColor(Color.white);
1032 g.fillRect(0, 0, visibleRect.width, visibleRect.height);
1034 ViewportRanges ranges = av.getRanges();
1036 if (allowFastPaint && image != null)
1038 // BH 2018 optimizing generation of new Rectangle().
1040 || (visibleRect.width != (clipBounds = g
1041 .getClipBounds(clipBounds)).width)
1042 || (visibleRect.height != clipBounds.height))
1044 g.drawImage(image, 0, 0, this);
1050 imgWidth = (ranges.getEndRes() - ranges.getStartRes() + 1)
1051 * av.getCharWidth();
1059 if (image == null || imgWidth != image.getWidth(this)
1060 || image.getHeight(this) != getHeight())
1064 image = new BufferedImage(imgWidth,
1065 ap.getAnnotationPanel().getHeight(),
1066 BufferedImage.TYPE_INT_RGB);
1067 } catch (OutOfMemoryError oom)
1072 } catch (Exception x)
1077 "Couldn't allocate memory to redraw screen. Please restart Jalview",
1081 gg = (Graphics2D) image.getGraphics();
1085 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
1086 RenderingHints.VALUE_ANTIALIAS_ON);
1089 gg.setFont(av.getFont());
1090 fm = gg.getFontMetrics();
1091 gg.setColor(Color.white);
1092 gg.fillRect(0, 0, imgWidth, image.getHeight());
1097 gg = (Graphics2D) image.getGraphics();
1101 drawComponent(gg, ranges.getStartRes(), av.getRanges().getEndRes() + 1);
1104 g.drawImage(image, 0, 0, this);
1108 * non-Thread safe repaint
1111 * repaint with horizontal shift in alignment
1113 public void fastPaint(int horizontal)
1115 if ((horizontal == 0) || image == null
1116 || av.getAlignment().getAlignmentAnnotation() == null
1117 || av.getAlignment().getAlignmentAnnotation().length < 1
1118 || av.isCalcInProgress())
1124 int sr = av.getRanges().getStartRes();
1125 int er = av.getRanges().getEndRes() + 1;
1134 Graphics2D gg = (Graphics2D) image.getGraphics();
1136 gg.copyArea(0, 0, imgWidth, getHeight(),
1137 -horizontal * av.getCharWidth(), 0);
1139 if (horizontal > 0) // scrollbar pulled right, image to the left
1141 transX = (er - sr - horizontal) * av.getCharWidth();
1142 sr = er - horizontal;
1144 else if (horizontal < 0)
1146 er = sr - horizontal;
1149 gg.translate(transX, 0);
1151 drawComponent(gg, sr, er);
1153 gg.translate(-transX, 0);
1159 // Call repaint on alignment panel so that repaints from other alignment
1160 // panel components can be aggregated. Otherwise performance of the overview
1161 // window and others may be adversely affected.
1162 av.getAlignPanel().repaint();
1165 private volatile boolean lastImageGood = false;
1177 public void drawComponent(Graphics g, int startRes, int endRes)
1179 BufferedImage oldFaded = fadedImage;
1180 if (av.isCalcInProgress())
1184 lastImageGood = false;
1187 // We'll keep a record of the old image,
1188 // and draw a faded image until the calculation
1191 && (fadedImage == null || fadedImage.getWidth() != imgWidth
1192 || fadedImage.getHeight() != image.getHeight()))
1194 // System.err.println("redraw faded image ("+(fadedImage==null ?
1195 // "null image" : "") + " lastGood="+lastImageGood+")");
1196 fadedImage = new BufferedImage(imgWidth, image.getHeight(),
1197 BufferedImage.TYPE_INT_RGB);
1199 Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
1201 fadedG.setColor(Color.white);
1202 fadedG.fillRect(0, 0, imgWidth, image.getHeight());
1204 fadedG.setComposite(
1205 AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f));
1206 fadedG.drawImage(image, 0, 0, this);
1209 // make sure we don't overwrite the last good faded image until all
1210 // calculations have finished
1211 lastImageGood = false;
1216 if (fadedImage != null)
1218 oldFaded = fadedImage;
1223 g.setColor(Color.white);
1224 g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
1226 g.setFont(av.getFont());
1229 fm = g.getFontMetrics();
1232 if ((av.getAlignment().getAlignmentAnnotation() == null)
1233 || (av.getAlignment().getAlignmentAnnotation().length < 1))
1235 g.setColor(Color.white);
1236 g.fillRect(0, 0, getWidth(), getHeight());
1237 g.setColor(Color.black);
1238 if (av.validCharWidth)
1240 g.drawString(MessageManager
1241 .getString("label.alignment_has_no_annotations"), 20, 15);
1246 lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes,
1248 if (!lastImageGood && fadedImage == null)
1250 fadedImage = oldFaded;
1255 public FontMetrics getFontMetrics()
1261 public Image getFadedImage()
1267 public int getFadedImageWidth()
1272 private int[] bounds = new int[2];
1274 private boolean allowFastPaint;
1277 public int[] getVisibleVRange()
1279 if (ap != null && ap.getAlabels() != null)
1281 int sOffset = -ap.getAlabels().getScrollOffset();
1282 int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
1283 bounds[0] = sOffset;
1284 bounds[1] = visHeight;
1294 * Try to ensure any references held are nulled
1296 public void dispose()
1306 * I created the renderer so I will dispose of it
1308 if (renderer != null)
1315 public void propertyChange(PropertyChangeEvent evt)
1317 // Respond to viewport range changes (e.g. alignment panel was scrolled)
1318 // Both scrolling and resizing change viewport ranges: scrolling changes
1319 // both start and end points, but resize only changes end values.
1320 // Here we only want to fastpaint on a scroll, with resize using a normal
1321 // paint, so scroll events are identified as changes to the horizontal or
1322 // vertical start value.
1323 if (evt.getPropertyName().equals(ViewportRanges.STARTRES))
1325 fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
1327 else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
1329 fastPaint(((int[]) evt.getNewValue())[0]
1330 - ((int[]) evt.getOldValue())[0]);
1332 else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
1339 * computes the visible height of the annotation panel
1341 * @param adjustPanelHeight
1342 * - when false, just adjust existing height according to other
1344 * @param annotationHeight
1345 * @return height to use for the ScrollerPreferredVisibleSize
1347 public int adjustForAlignFrame(boolean adjustPanelHeight,
1348 int annotationHeight)
1351 * Estimate available height in the AlignFrame for alignment +
1352 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
1353 * hscroll, status bar, insets.
1355 int stuff = (ap.getViewName() != null ? 30 : 0)
1356 + (Platform.isAMacAndNotJS() ? 120 : 140);
1357 int availableHeight = ap.alignFrame.getHeight() - stuff;
1358 int rowHeight = av.getCharHeight();
1360 if (adjustPanelHeight)
1362 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
1365 * If not enough vertical space, maximize annotation height while keeping
1366 * at least two rows of alignment visible
1368 if (annotationHeight + alignmentHeight > availableHeight)
1370 annotationHeight = Math.min(annotationHeight,
1371 availableHeight - 2 * rowHeight);
1376 // maintain same window layout whilst updating sliders
1377 annotationHeight = Math.min(ap.annotationScroller.getSize().height,
1378 availableHeight - 2 * rowHeight);
1380 return annotationHeight;
1384 * Clears the flag that allows a 'fast paint' on the next repaint, so
1385 * requiring a full repaint
1387 public void setNoFastPaint()
1389 allowFastPaint = false;