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 jalview.datamodel.AlignmentAnnotation;
24 import jalview.datamodel.Annotation;
25 import jalview.datamodel.ColumnSelection;
26 import jalview.datamodel.HiddenColumns;
27 import jalview.datamodel.SequenceI;
28 import jalview.renderer.AnnotationRenderer;
29 import jalview.renderer.AwtRenderPanelI;
30 import jalview.schemes.ResidueProperties;
31 import jalview.util.Comparison;
32 import jalview.util.MessageManager;
33 import jalview.viewmodel.ViewportListenerI;
35 import java.awt.AlphaComposite;
36 import java.awt.Color;
37 import java.awt.Dimension;
38 import java.awt.FontMetrics;
39 import java.awt.Graphics;
40 import java.awt.Graphics2D;
41 import java.awt.Image;
42 import java.awt.Rectangle;
43 import java.awt.RenderingHints;
44 import java.awt.event.ActionEvent;
45 import java.awt.event.ActionListener;
46 import java.awt.event.AdjustmentEvent;
47 import java.awt.event.AdjustmentListener;
48 import java.awt.event.MouseEvent;
49 import java.awt.event.MouseListener;
50 import java.awt.event.MouseMotionListener;
51 import java.awt.event.MouseWheelEvent;
52 import java.awt.event.MouseWheelListener;
53 import java.awt.image.BufferedImage;
54 import java.beans.PropertyChangeEvent;
55 import java.util.ArrayList;
56 import java.util.Collections;
57 import java.util.List;
59 import javax.swing.JColorChooser;
60 import javax.swing.JMenuItem;
61 import javax.swing.JPanel;
62 import javax.swing.JPopupMenu;
63 import javax.swing.Scrollable;
64 import javax.swing.ToolTipManager;
67 * AnnotationPanel displays visible portion of annotation rows below unwrapped
73 public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
74 MouseListener, MouseWheelListener, MouseMotionListener,
75 ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
77 String HELIX = MessageManager.getString("label.helix");
79 String SHEET = MessageManager.getString("label.sheet");
82 * For RNA secondary structure "stems" aka helices
84 String STEM = MessageManager.getString("label.rna_helix");
86 String LABEL = MessageManager.getString("label.label");
88 String REMOVE = MessageManager.getString("label.remove_annotation");
90 String COLOUR = MessageManager.getString("action.colour");
92 public final Color HELIX_COLOUR = Color.red.darker();
94 public final Color SHEET_COLOUR = Color.green.darker().darker();
96 public final Color STEM_COLOUR = Color.blue.darker();
99 public AlignViewport av;
103 public int activeRow = -1;
105 public BufferedImage image;
107 public volatile BufferedImage fadedImage;
111 public FontMetrics fm;
113 public int imgWidth = 0;
115 boolean fastPaint = false;
117 // Used For mouse Dragging and resizing graphs
118 int graphStretch = -1;
120 int graphStretchY = -1;
122 int min; // used by mouseDragged to see if user
124 int max; // used by mouseDragged to see if user
126 boolean mouseDragging = false;
128 // for editing cursor
133 public final AnnotationRenderer renderer;
135 private MouseWheelListener[] _mwl;
138 * Creates a new AnnotationPanel object.
143 public AnnotationPanel(AlignmentPanel ap)
145 ToolTipManager.sharedInstance().registerComponent(this);
146 ToolTipManager.sharedInstance().setInitialDelay(0);
147 ToolTipManager.sharedInstance().setDismissDelay(10000);
150 this.setLayout(null);
151 addMouseListener(this);
152 addMouseMotionListener(this);
153 ap.annotationScroller.getVerticalScrollBar()
154 .addAdjustmentListener(this);
155 // save any wheel listeners on the scroller, so we can propagate scroll
157 _mwl = ap.annotationScroller.getMouseWheelListeners();
158 // and then set our own listener to consume all mousewheel events
159 ap.annotationScroller.addMouseWheelListener(this);
160 renderer = new AnnotationRenderer();
162 av.getRanges().addPropertyChangeListener(this);
165 public AnnotationPanel(AlignViewport av)
168 renderer = new AnnotationRenderer();
172 public void mouseWheelMoved(MouseWheelEvent e)
177 if (e.getWheelRotation() > 0)
179 av.getRanges().scrollRight(true);
183 av.getRanges().scrollRight(false);
188 // TODO: find the correct way to let the event bubble up to
189 // ap.annotationScroller
190 for (MouseWheelListener mwl : _mwl)
194 mwl.mouseWheelMoved(e);
205 public Dimension getPreferredScrollableViewportSize()
207 return getPreferredSize();
211 public int getScrollableBlockIncrement(Rectangle visibleRect,
212 int orientation, int direction)
218 public boolean getScrollableTracksViewportHeight()
224 public boolean getScrollableTracksViewportWidth()
230 public int getScrollableUnitIncrement(Rectangle visibleRect,
231 int orientation, int direction)
240 * java.awt.event.AdjustmentListener#adjustmentValueChanged(java.awt.event
244 public void adjustmentValueChanged(AdjustmentEvent evt)
246 // update annotation label display
247 ap.getAlabels().setScrollOffset(-evt.getValue());
251 * Calculates the height of the annotation displayed in the annotation panel.
252 * Callers should normally call the ap.adjustAnnotationHeight method to ensure
253 * all annotation associated components are updated correctly.
256 public int adjustPanelHeight()
258 int height = av.calcPanelHeight();
259 this.setPreferredSize(new Dimension(1, height));
262 // revalidate only when the alignment panel is fully constructed
276 public void actionPerformed(ActionEvent evt)
278 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
283 Annotation[] anot = aa[activeRow].annotations;
285 if (anot.length < av.getColumnSelection().getMax())
287 Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
288 System.arraycopy(anot, 0, temp, 0, anot.length);
290 aa[activeRow].annotations = anot;
293 String action = evt.getActionCommand();
294 if (action.equals(REMOVE))
296 for (int index : av.getColumnSelection().getSelected())
298 if (av.getAlignment().getHiddenColumns().isVisible(index))
304 else if (action.equals(LABEL))
306 String exMesg = collectAnnotVals(anot, LABEL);
307 String label = JvOptionPane.showInputDialog(this,
308 MessageManager.getString("label.enter_label"), exMesg);
315 if ((label.length() > 0) && !aa[activeRow].hasText)
317 aa[activeRow].hasText = true;
320 for (int index : av.getColumnSelection().getSelected())
322 if (!av.getAlignment().getHiddenColumns().isVisible(index))
327 if (anot[index] == null)
329 anot[index] = new Annotation(label, "", ' ', 0);
333 anot[index].displayCharacter = label;
337 else if (action.equals(COLOUR))
339 Color col = JColorChooser.showDialog(this,
340 MessageManager.getString("label.select_foreground_colour"),
343 for (int index : av.getColumnSelection().getSelected())
345 if (!av.getAlignment().getHiddenColumns().isVisible(index))
350 if (anot[index] == null)
352 anot[index] = new Annotation("", "", ' ', 0);
355 anot[index].colour = col;
359 // HELIX, SHEET or STEM
362 String symbol = "\u03B1"; // alpha
364 if (action.equals(HELIX))
368 else if (action.equals(SHEET))
371 symbol = "\u03B2"; // beta
374 // Added by LML to color stems
375 else if (action.equals(STEM))
378 int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
379 symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
382 if (!aa[activeRow].hasIcons)
384 aa[activeRow].hasIcons = true;
387 String label = JvOptionPane.showInputDialog(MessageManager
388 .getString("label.enter_label_for_the_structure"), symbol);
395 if ((label.length() > 0) && !aa[activeRow].hasText)
397 aa[activeRow].hasText = true;
398 if (action.equals(STEM))
400 aa[activeRow].showAllColLabels = true;
403 for (int index : av.getColumnSelection().getSelected())
405 if (!av.getAlignment().getHiddenColumns().isVisible(index))
410 if (anot[index] == null)
412 anot[index] = new Annotation(label, "", type, 0);
415 anot[index].secondaryStructure = type != 'S' ? type : label
416 .length() == 0 ? ' ' : label.charAt(0);
417 anot[index].displayCharacter = label;
422 av.getAlignment().validateAnnotation(aa[activeRow]);
423 ap.alignmentChanged();
424 ap.alignFrame.setMenusForViewport();
432 * Returns any existing annotation concatenated as a string. For each
433 * annotation, takes the description, if any, else the secondary structure
434 * character (if type is HELIX, SHEET or STEM), else the display character (if
441 private String collectAnnotVals(Annotation[] anots, String type)
443 // TODO is this method wanted? why? 'last' is not used
445 StringBuilder collatedInput = new StringBuilder(64);
447 ColumnSelection viscols = av.getColumnSelection();
448 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
451 * the selection list (read-only view) is in selection order, not
452 * column order; make a copy so we can sort it
454 List<Integer> selected = new ArrayList<Integer>(viscols.getSelected());
455 Collections.sort(selected);
456 for (int index : selected)
458 // always check for current display state - just in case
459 if (!hidden.isVisible(index))
463 String tlabel = null;
464 if (anots[index] != null)
465 { // LML added stem code
466 if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
467 || type.equals(LABEL))
469 tlabel = anots[index].description;
470 if (tlabel == null || tlabel.length() < 1)
472 if (type.equals(HELIX) || type.equals(SHEET)
473 || type.equals(STEM))
475 tlabel = "" + anots[index].secondaryStructure;
479 tlabel = "" + anots[index].displayCharacter;
483 if (tlabel != null && !tlabel.equals(last))
485 if (last.length() > 0)
487 collatedInput.append(" ");
489 collatedInput.append(tlabel);
493 return collatedInput.toString();
503 public void mousePressed(MouseEvent evt)
506 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
515 final int y = evt.getY();
516 for (int i = 0; i < aa.length; i++)
520 height += aa[i].height;
529 else if (aa[i].graph > 0)
541 * isPopupTrigger fires in mousePressed on Mac,
542 * not until mouseRelease on Windows
544 if (evt.isPopupTrigger() && activeRow != -1)
546 showPopupMenu(y, evt.getX());
550 ap.getScalePanel().mousePressed(evt);
554 * Construct and display a context menu at the right-click position
559 void showPopupMenu(final int y, int x)
561 if (av.getColumnSelection() == null
562 || av.getColumnSelection().isEmpty())
567 JPopupMenu pop = new JPopupMenu(
568 MessageManager.getString("label.structure_type"));
571 * Just display the needed structure options
573 if (av.getAlignment().isNucleotide())
575 item = new JMenuItem(STEM);
576 item.addActionListener(this);
581 item = new JMenuItem(HELIX);
582 item.addActionListener(this);
584 item = new JMenuItem(SHEET);
585 item.addActionListener(this);
588 item = new JMenuItem(LABEL);
589 item.addActionListener(this);
591 item = new JMenuItem(COLOUR);
592 item.addActionListener(this);
594 item = new JMenuItem(REMOVE);
595 item.addActionListener(this);
597 pop.show(this, x, y);
607 public void mouseReleased(MouseEvent evt)
611 mouseDragging = false;
612 ap.getScalePanel().mouseReleased(evt);
615 * isPopupTrigger is set in mouseReleased on Windows
616 * (in mousePressed on Mac)
618 if (evt.isPopupTrigger() && activeRow != -1)
620 showPopupMenu(evt.getY(), evt.getX());
632 public void mouseEntered(MouseEvent evt)
634 ap.getScalePanel().mouseEntered(evt);
644 public void mouseExited(MouseEvent evt)
646 ap.getScalePanel().mouseExited(evt);
656 public void mouseDragged(MouseEvent evt)
658 if (graphStretch > -1)
660 av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
662 if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
664 av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
666 graphStretchY = evt.getY();
668 ap.paintAlignment(true);
672 ap.getScalePanel().mouseDragged(evt);
677 * Constructs the tooltip, and constructs and displays a status message, for
678 * the current mouse position
683 public void mouseMoved(MouseEvent evt)
685 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
689 this.setToolTipText(null);
696 for (int i = 0; i < aa.length; i++)
700 height += aa[i].height;
703 if (evt.getY() < height)
712 this.setToolTipText(null);
716 int column = (evt.getX() / av.getCharWidth())
717 + av.getRanges().getStartRes();
719 if (av.hasHiddenColumns())
721 column = av.getAlignment().getHiddenColumns()
722 .adjustForHiddenColumns(column);
725 AlignmentAnnotation ann = aa[row];
726 if (row > -1 && ann.annotations != null
727 && column < ann.annotations.length)
729 buildToolTip(ann, column, aa);
730 setStatusMessage(column, ann);
734 this.setToolTipText(null);
735 ap.alignFrame.statusBar.setText(" ");
740 * Builds a tooltip for the annotation at the current mouse position.
746 void buildToolTip(AlignmentAnnotation ann, int column,
747 AlignmentAnnotation[] anns)
749 if (ann.graphGroup > -1)
751 StringBuilder tip = new StringBuilder(32);
752 tip.append("<html>");
753 for (int i = 0; i < anns.length; i++)
755 if (anns[i].graphGroup == ann.graphGroup
756 && anns[i].annotations[column] != null)
758 tip.append(anns[i].label);
759 String description = anns[i].annotations[column].description;
760 if (description != null && description.length() > 0)
762 tip.append(" ").append(description);
767 if (tip.length() != 6)
769 tip.setLength(tip.length() - 4);
770 this.setToolTipText(tip.toString() + "</html>");
773 else if (ann.annotations[column] != null)
775 String description = ann.annotations[column].description;
776 if (description != null && description.length() > 0)
778 this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
783 // clear the tooltip.
784 this.setToolTipText(null);
789 * Constructs and displays the status bar message
794 void setStatusMessage(int column, AlignmentAnnotation ann)
797 * show alignment column and annotation description if any
799 StringBuilder text = new StringBuilder(32);
800 text.append(MessageManager.getString("label.column")).append(" ")
803 if (ann.annotations[column] != null)
805 String description = ann.annotations[column].description;
806 if (description != null && description.trim().length() > 0)
808 text.append(" ").append(description);
813 * if the annotation is sequence-specific, show the sequence number
814 * in the alignment, and (if not a gap) the residue and position
816 SequenceI seqref = ann.sequenceRef;
819 int seqIndex = av.getAlignment().findIndex(seqref);
823 .append(MessageManager.getString("label.sequence"))
824 .append(" ").append(seqIndex + 1);
825 char residue = seqref.getCharAt(column);
826 if (!Comparison.isGap(residue))
830 if (av.getAlignment().isNucleotide())
832 name = ResidueProperties.nucleotideName.get(String
834 text.append(" Nucleotide: ").append(
835 name != null ? name : residue);
839 name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
840 : ResidueProperties.aa2Triplet.get(String
842 text.append(" Residue: ").append(name != null ? name : residue);
844 int residuePos = seqref.findPosition(column);
845 text.append(" (").append(residuePos).append(")");
850 ap.alignFrame.statusBar.setText(text.toString());
860 public void mouseClicked(MouseEvent evt)
862 // if (activeRow != -1)
864 // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
865 // AlignmentAnnotation anot = aa[activeRow];
869 // TODO mouseClicked-content and drawCursor are quite experimental!
870 public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
873 int pady = av.getCharHeight() / 5;
875 graphics.setColor(Color.black);
876 graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
878 if (av.validCharWidth)
880 graphics.setColor(Color.white);
882 char s = seq.getCharAt(res);
884 charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
885 graphics.drawString(String.valueOf(s), charOffset + x1,
886 (y1 + av.getCharHeight()) - pady);
891 private volatile boolean imageFresh = false;
900 public void paintComponent(Graphics g)
902 g.setColor(Color.white);
903 g.fillRect(0, 0, getWidth(), getHeight());
907 if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
908 || (getVisibleRect().height != g.getClipBounds().height))
910 g.drawImage(image, 0, 0, this);
915 imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + 1)
921 if (image == null || imgWidth != image.getWidth(this)
922 || image.getHeight(this) != getHeight())
926 image = new BufferedImage(imgWidth, ap.getAnnotationPanel()
927 .getHeight(), BufferedImage.TYPE_INT_RGB);
928 } catch (OutOfMemoryError oom)
933 } catch (Exception x)
938 "Couldn't allocate memory to redraw screen. Please restart Jalview",
942 gg = (Graphics2D) image.getGraphics();
946 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
947 RenderingHints.VALUE_ANTIALIAS_ON);
950 gg.setFont(av.getFont());
951 fm = gg.getFontMetrics();
952 gg.setColor(Color.white);
953 gg.fillRect(0, 0, imgWidth, image.getHeight());
957 drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
960 g.drawImage(image, 0, 0, this);
964 * set true to enable redraw timing debug output on stderr
966 private final boolean debugRedraw = false;
969 * non-Thread safe repaint
972 * repaint with horizontal shift in alignment
974 public void fastPaint(int horizontal)
976 if ((horizontal == 0) || gg == null
977 || av.getAlignment().getAlignmentAnnotation() == null
978 || av.getAlignment().getAlignmentAnnotation().length < 1
979 || av.isCalcInProgress())
984 long stime = System.currentTimeMillis();
985 gg.copyArea(0, 0, imgWidth, getHeight(),
986 -horizontal * av.getCharWidth(), 0);
987 long mtime = System.currentTimeMillis();
988 int sr = av.getRanges().getStartRes();
989 int er = av.getRanges().getEndRes() + 1;
992 if (horizontal > 0) // scrollbar pulled right, image to the left
994 transX = (er - sr - horizontal) * av.getCharWidth();
995 sr = er - horizontal;
997 else if (horizontal < 0)
999 er = sr - horizontal;
1002 gg.translate(transX, 0);
1004 drawComponent(gg, sr, er);
1006 gg.translate(-transX, 0);
1007 long dtime = System.currentTimeMillis();
1010 long rtime = System.currentTimeMillis();
1013 System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t"
1014 + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime)
1015 + "\tRepaint call:\t" + (rtime - dtime));
1020 private volatile boolean lastImageGood = false;
1032 public void drawComponent(Graphics g, int startRes, int endRes)
1034 BufferedImage oldFaded = fadedImage;
1035 if (av.isCalcInProgress())
1039 lastImageGood = false;
1042 // We'll keep a record of the old image,
1043 // and draw a faded image until the calculation
1046 && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage
1047 .getHeight() != image.getHeight()))
1049 // System.err.println("redraw faded image ("+(fadedImage==null ?
1050 // "null image" : "") + " lastGood="+lastImageGood+")");
1051 fadedImage = new BufferedImage(imgWidth, image.getHeight(),
1052 BufferedImage.TYPE_INT_RGB);
1054 Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
1056 fadedG.setColor(Color.white);
1057 fadedG.fillRect(0, 0, imgWidth, image.getHeight());
1059 fadedG.setComposite(AlphaComposite.getInstance(
1060 AlphaComposite.SRC_OVER, .3f));
1061 fadedG.drawImage(image, 0, 0, this);
1064 // make sure we don't overwrite the last good faded image until all
1065 // calculations have finished
1066 lastImageGood = false;
1071 if (fadedImage != null)
1073 oldFaded = fadedImage;
1078 g.setColor(Color.white);
1079 g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
1081 g.setFont(av.getFont());
1084 fm = g.getFontMetrics();
1087 if ((av.getAlignment().getAlignmentAnnotation() == null)
1088 || (av.getAlignment().getAlignmentAnnotation().length < 1))
1090 g.setColor(Color.white);
1091 g.fillRect(0, 0, getWidth(), getHeight());
1092 g.setColor(Color.black);
1093 if (av.validCharWidth)
1095 g.drawString(MessageManager
1096 .getString("label.alignment_has_no_annotations"), 20, 15);
1101 lastImageGood = renderer.drawComponent(this, av, g, activeRow,
1103 if (!lastImageGood && fadedImage == null)
1105 fadedImage = oldFaded;
1110 public FontMetrics getFontMetrics()
1116 public Image getFadedImage()
1122 public int getFadedImageWidth()
1127 private int[] bounds = new int[2];
1130 public int[] getVisibleVRange()
1132 if (ap != null && ap.getAlabels() != null)
1134 int sOffset = -ap.getAlabels().getScrollOffset();
1135 int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
1136 bounds[0] = sOffset;
1137 bounds[1] = visHeight;
1147 * Try to ensure any references held are nulled
1149 public void dispose()
1159 * I created the renderer so I will dispose of it
1161 if (renderer != null)
1168 public void propertyChange(PropertyChangeEvent evt)
1170 // Respond to viewport range changes (e.g. alignment panel was scrolled)
1171 if (evt.getPropertyName().equals("startres")
1172 || evt.getPropertyName().equals("endres"))
1174 fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());