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.SequenceI;
27 import jalview.renderer.AnnotationRenderer;
28 import jalview.renderer.AwtRenderPanelI;
29 import jalview.schemes.ResidueProperties;
30 import jalview.util.Comparison;
31 import jalview.util.MessageManager;
33 import java.awt.AlphaComposite;
34 import java.awt.Color;
35 import java.awt.Dimension;
36 import java.awt.FontMetrics;
37 import java.awt.Graphics;
38 import java.awt.Graphics2D;
39 import java.awt.Image;
40 import java.awt.Rectangle;
41 import java.awt.RenderingHints;
42 import java.awt.event.ActionEvent;
43 import java.awt.event.ActionListener;
44 import java.awt.event.AdjustmentEvent;
45 import java.awt.event.AdjustmentListener;
46 import java.awt.event.MouseEvent;
47 import java.awt.event.MouseListener;
48 import java.awt.event.MouseMotionListener;
49 import java.awt.event.MouseWheelEvent;
50 import java.awt.event.MouseWheelListener;
51 import java.awt.image.BufferedImage;
52 import java.util.ArrayList;
53 import java.util.Collections;
54 import java.util.List;
56 import javax.swing.JColorChooser;
57 import javax.swing.JMenuItem;
58 import javax.swing.JOptionPane;
59 import javax.swing.JPanel;
60 import javax.swing.JPopupMenu;
61 import javax.swing.Scrollable;
62 import javax.swing.ToolTipManager;
65 * AnnotationPanel displays visible portion of annotation rows below unwrapped
71 public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
72 MouseListener, MouseWheelListener, MouseMotionListener,
73 ActionListener, AdjustmentListener, Scrollable
75 String HELIX = MessageManager.getString("label.helix");
77 String SHEET = MessageManager.getString("label.sheet");
80 * For RNA secondary structure "stems" aka helices
82 String STEM = MessageManager.getString("label.rna_helix");
84 String LABEL = MessageManager.getString("label.label");
86 String REMOVE = MessageManager.getString("label.remove_annotation");
88 String COLOUR = MessageManager.getString("action.colour");
90 public final Color HELIX_COLOUR = Color.red.darker();
92 public final Color SHEET_COLOUR = Color.green.darker().darker();
94 public final Color STEM_COLOUR = Color.blue.darker();
97 public AlignViewport av;
101 public int activeRow = -1;
103 public BufferedImage image;
105 public volatile BufferedImage fadedImage;
109 public FontMetrics fm;
111 public int imgWidth = 0;
113 boolean fastPaint = false;
115 // Used For mouse Dragging and resizing graphs
116 int graphStretch = -1;
118 int graphStretchY = -1;
120 int min; // used by mouseDragged to see if user
122 int max; // used by mouseDragged to see if user
124 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)
146 MAC = jalview.util.Platform.isAMac();
148 ToolTipManager.sharedInstance().registerComponent(this);
149 ToolTipManager.sharedInstance().setInitialDelay(0);
150 ToolTipManager.sharedInstance().setDismissDelay(10000);
153 this.setLayout(null);
154 addMouseListener(this);
155 addMouseMotionListener(this);
156 ap.annotationScroller.getVerticalScrollBar()
157 .addAdjustmentListener(this);
158 // save any wheel listeners on the scroller, so we can propagate scroll
160 _mwl = ap.annotationScroller.getMouseWheelListeners();
161 // and then set our own listener to consume all mousewheel events
162 ap.annotationScroller.addMouseWheelListener(this);
163 renderer = new AnnotationRenderer();
166 public AnnotationPanel(AlignViewport av)
169 renderer = new AnnotationRenderer();
173 public void mouseWheelMoved(MouseWheelEvent e)
178 if (e.getWheelRotation() > 0)
180 ap.scrollRight(true);
184 ap.scrollRight(false);
189 // TODO: find the correct way to let the event bubble up to
190 // ap.annotationScroller
191 for (MouseWheelListener mwl : _mwl)
195 mwl.mouseWheelMoved(e);
206 public Dimension getPreferredScrollableViewportSize()
208 return getPreferredSize();
212 public int getScrollableBlockIncrement(Rectangle visibleRect,
213 int orientation, int direction)
219 public boolean getScrollableTracksViewportHeight()
225 public boolean getScrollableTracksViewportWidth()
231 public int getScrollableUnitIncrement(Rectangle visibleRect,
232 int orientation, int direction)
241 * java.awt.event.AdjustmentListener#adjustmentValueChanged(java.awt.event
245 public void adjustmentValueChanged(AdjustmentEvent evt)
247 // update annotation label display
248 ap.getAlabels().setScrollOffset(-evt.getValue());
252 * Calculates the height of the annotation displayed in the annotation panel.
253 * Callers should normally call the ap.adjustAnnotationHeight method to ensure
254 * all annotation associated components are updated correctly.
257 public int adjustPanelHeight()
259 int height = av.calcPanelHeight();
260 this.setPreferredSize(new Dimension(1, height));
263 // revalidate only when the alignment panel is fully constructed
277 public void actionPerformed(ActionEvent evt)
279 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
284 Annotation[] anot = aa[activeRow].annotations;
286 if (anot.length < av.getColumnSelection().getMax())
288 Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
289 System.arraycopy(anot, 0, temp, 0, anot.length);
291 aa[activeRow].annotations = anot;
294 String action = evt.getActionCommand();
295 if (action.equals(REMOVE))
297 for (int index : av.getColumnSelection().getSelected())
299 if (av.getColumnSelection().isVisible(index))
305 else if (action.equals(LABEL))
307 String exMesg = collectAnnotVals(anot, LABEL);
308 String label = JOptionPane.showInputDialog(this,
309 MessageManager.getString("label.enter_label"), exMesg);
316 if ((label.length() > 0) && !aa[activeRow].hasText)
318 aa[activeRow].hasText = true;
321 for (int index : av.getColumnSelection().getSelected())
323 if (!av.getColumnSelection().isVisible(index))
328 if (anot[index] == null)
330 anot[index] = new Annotation(label, "", ' ', 0);
334 anot[index].displayCharacter = label;
338 else if (action.equals(COLOUR))
340 Color col = JColorChooser.showDialog(this,
341 MessageManager.getString("label.select_foreground_colour"),
344 for (int index : av.getColumnSelection().getSelected())
346 if (!av.getColumnSelection().isVisible(index))
351 if (anot[index] == null)
353 anot[index] = new Annotation("", "", ' ', 0);
356 anot[index].colour = col;
360 // HELIX, SHEET or STEM
363 String symbol = "\u03B1"; // alpha
365 if (action.equals(HELIX))
369 else if (action.equals(SHEET))
372 symbol = "\u03B2"; // beta
375 // Added by LML to color stems
376 else if (action.equals(STEM))
379 int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
380 symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
383 if (!aa[activeRow].hasIcons)
385 aa[activeRow].hasIcons = true;
388 String label = JOptionPane.showInputDialog(MessageManager
389 .getString("label.enter_label_for_the_structure"), symbol);
396 if ((label.length() > 0) && !aa[activeRow].hasText)
398 aa[activeRow].hasText = true;
399 if (action.equals(STEM))
401 aa[activeRow].showAllColLabels = true;
404 for (int index : av.getColumnSelection().getSelected())
406 if (!av.getColumnSelection().isVisible(index))
411 if (anot[index] == null)
413 anot[index] = new Annotation(label, "", type, 0);
416 anot[index].secondaryStructure = type != 'S' ? type : label
417 .length() == 0 ? ' ' : label.charAt(0);
418 anot[index].displayCharacter = label;
423 av.getAlignment().validateAnnotation(aa[activeRow]);
424 ap.alignmentChanged();
425 ap.alignFrame.setMenusForViewport();
433 * Returns any existing annotation concatenated as a string. For each
434 * annotation, takes the description, if any, else the secondary structure
435 * character (if type is HELIX, SHEET or STEM), else the display character (if
442 private String collectAnnotVals(Annotation[] anots, String type)
444 // TODO is this method wanted? why? 'last' is not used
446 StringBuilder collatedInput = new StringBuilder(64);
448 ColumnSelection viscols = av.getColumnSelection();
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 (!viscols.isVisible(index))
463 String tlabel = null;
464 if (anots[index] != null)
465 { // LML added stem code
466 if (type.equals(HELIX) || type.equals(SHEET)
467 || type.equals(STEM) || 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()) + av.getStartRes();
718 if (av.hasHiddenColumns())
720 column = av.getColumnSelection().adjustForHiddenColumns(column);
723 AlignmentAnnotation ann = aa[row];
724 if (row > -1 && ann.annotations != null
725 && column < ann.annotations.length)
727 buildToolTip(ann, column, aa);
728 setStatusMessage(column, ann);
732 this.setToolTipText(null);
733 ap.alignFrame.statusBar.setText(" ");
738 * Builds a tooltip for the annotation at the current mouse position.
744 void buildToolTip(AlignmentAnnotation ann, int column,
745 AlignmentAnnotation[] anns)
747 if (ann.graphGroup > -1)
749 StringBuilder tip = new StringBuilder(32);
750 tip.append("<html>");
751 for (int i = 0; i < anns.length; i++)
753 if (anns[i].graphGroup == ann.graphGroup
754 && anns[i].annotations[column] != null)
756 tip.append(anns[i].label);
757 String description = anns[i].annotations[column].description;
758 if (description != null && description.length() > 0)
760 tip.append(" ").append(description);
765 if (tip.length() != 6)
767 tip.setLength(tip.length() - 4);
768 this.setToolTipText(tip.toString() + "</html>");
771 else if (ann.annotations[column] != null)
773 String description = ann.annotations[column].description;
774 if (description != null && description.length() > 0)
776 this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
781 // clear the tooltip.
782 this.setToolTipText(null);
787 * Constructs and displays the status bar message
792 void setStatusMessage(int column, AlignmentAnnotation ann)
795 * show alignment column and annotation description if any
797 StringBuilder text = new StringBuilder(32);
798 text.append(MessageManager.getString("label.column")).append(" ")
801 if (ann.annotations[column] != null)
803 String description = ann.annotations[column].description;
804 if (description != null && description.trim().length() > 0)
806 text.append(" ").append(description);
811 * if the annotation is sequence-specific, show the sequence number
812 * in the alignment, and (if not a gap) the residue and position
814 SequenceI seqref = ann.sequenceRef;
817 int seqIndex = av.getAlignment().findIndex(seqref);
821 .append(MessageManager.getString("label.sequence"))
823 .append(seqIndex + 1);
824 char residue = seqref.getCharAt(column);
825 if (!Comparison.isGap(residue))
829 if (av.getAlignment().isNucleotide())
831 name = ResidueProperties.nucleotideName.get(String
833 text.append(" Nucleotide: ").append(
834 name != null ? name : residue);
838 name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
839 : ResidueProperties.aa2Triplet.get(String
841 text.append(" Residue: ").append(name != null ? name : residue);
843 int residuePos = seqref.findPosition(column);
844 text.append(" (").append(residuePos).append(")");
849 ap.alignFrame.statusBar.setText(text.toString());
859 public void mouseClicked(MouseEvent evt)
861 // if (activeRow != -1)
863 // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
864 // AlignmentAnnotation anot = aa[activeRow];
868 // TODO mouseClicked-content and drawCursor are quite experimental!
869 public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
872 int pady = av.getCharHeight() / 5;
874 graphics.setColor(Color.black);
875 graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
877 if (av.validCharWidth)
879 graphics.setColor(Color.white);
881 char s = seq.getCharAt(res);
883 charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
884 graphics.drawString(String.valueOf(s), charOffset + x1,
885 (y1 + av.getCharHeight()) - pady);
890 private volatile boolean imageFresh = false;
899 public void paintComponent(Graphics g)
901 g.setColor(Color.white);
902 g.fillRect(0, 0, getWidth(), getHeight());
906 if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
907 || (getVisibleRect().height != g.getClipBounds().height))
909 g.drawImage(image, 0, 0, this);
914 imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
919 if (image == null || imgWidth != image.getWidth(this)
920 || image.getHeight(this) != getHeight())
924 image = new BufferedImage(imgWidth, ap.getAnnotationPanel()
925 .getHeight(), BufferedImage.TYPE_INT_RGB);
926 } catch (OutOfMemoryError oom)
931 } catch (Exception x)
936 "Couldn't allocate memory to redraw screen. Please restart Jalview",
940 gg = (Graphics2D) image.getGraphics();
944 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
945 RenderingHints.VALUE_ANTIALIAS_ON);
948 gg.setFont(av.getFont());
949 fm = gg.getFontMetrics();
950 gg.setColor(Color.white);
951 gg.fillRect(0, 0, imgWidth, image.getHeight());
955 drawComponent(gg, av.startRes, av.endRes + 1);
957 g.drawImage(image, 0, 0, this);
961 * set true to enable redraw timing debug output on stderr
963 private final boolean debugRedraw = false;
966 * non-Thread safe repaint
969 * repaint with horizontal shift in alignment
971 public void fastPaint(int horizontal)
973 if ((horizontal == 0) || gg == null
974 || av.getAlignment().getAlignmentAnnotation() == null
975 || av.getAlignment().getAlignmentAnnotation().length < 1
976 || av.isCalcInProgress())
981 long stime = System.currentTimeMillis();
982 gg.copyArea(0, 0, imgWidth, getHeight(),
983 -horizontal * av.getCharWidth(), 0);
984 long mtime = System.currentTimeMillis();
985 int sr = av.startRes;
986 int er = av.endRes + 1;
989 if (horizontal > 0) // scrollbar pulled right, image to the left
991 transX = (er - sr - horizontal) * av.getCharWidth();
992 sr = er - horizontal;
994 else if (horizontal < 0)
996 er = sr - horizontal;
999 gg.translate(transX, 0);
1001 drawComponent(gg, sr, er);
1003 gg.translate(-transX, 0);
1004 long dtime = System.currentTimeMillis();
1007 long rtime = System.currentTimeMillis();
1010 System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t"
1011 + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime)
1012 + "\tRepaint call:\t" + (rtime - dtime));
1017 private volatile boolean lastImageGood = false;
1029 public void drawComponent(Graphics g, int startRes, int endRes)
1031 BufferedImage oldFaded = fadedImage;
1032 if (av.isCalcInProgress())
1036 lastImageGood = false;
1039 // We'll keep a record of the old image,
1040 // and draw a faded image until the calculation
1043 && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage
1044 .getHeight() != image.getHeight()))
1046 // System.err.println("redraw faded image ("+(fadedImage==null ?
1047 // "null image" : "") + " lastGood="+lastImageGood+")");
1048 fadedImage = new BufferedImage(imgWidth, image.getHeight(),
1049 BufferedImage.TYPE_INT_RGB);
1051 Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
1053 fadedG.setColor(Color.white);
1054 fadedG.fillRect(0, 0, imgWidth, image.getHeight());
1056 fadedG.setComposite(AlphaComposite.getInstance(
1057 AlphaComposite.SRC_OVER, .3f));
1058 fadedG.drawImage(image, 0, 0, this);
1061 // make sure we don't overwrite the last good faded image until all
1062 // calculations have finished
1063 lastImageGood = false;
1068 if (fadedImage != null)
1070 oldFaded = fadedImage;
1075 g.setColor(Color.white);
1076 g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
1078 g.setFont(av.getFont());
1081 fm = g.getFontMetrics();
1084 if ((av.getAlignment().getAlignmentAnnotation() == null)
1085 || (av.getAlignment().getAlignmentAnnotation().length < 1))
1087 g.setColor(Color.white);
1088 g.fillRect(0, 0, getWidth(), getHeight());
1089 g.setColor(Color.black);
1090 if (av.validCharWidth)
1092 g.drawString(MessageManager
1093 .getString("label.alignment_has_no_annotations"), 20, 15);
1098 lastImageGood = renderer.drawComponent(this, av, g, activeRow,
1100 if (!lastImageGood && fadedImage == null)
1102 fadedImage = oldFaded;
1107 public FontMetrics getFontMetrics()
1113 public Image getFadedImage()
1119 public int getFadedImageWidth()
1124 private int[] bounds = new int[2];
1127 public int[] getVisibleVRange()
1129 if (ap != null && ap.getAlabels() != null)
1131 int sOffset = -ap.getAlabels().getScrollOffset();
1132 int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
1133 bounds[0] = sOffset;
1134 bounds[1] = visHeight;