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.Collections;
53 import java.util.List;
55 import javax.swing.JColorChooser;
56 import javax.swing.JMenuItem;
57 import javax.swing.JOptionPane;
58 import javax.swing.JPanel;
59 import javax.swing.JPopupMenu;
60 import javax.swing.Scrollable;
61 import javax.swing.ToolTipManager;
64 * AnnotationPanel displays visible portion of annotation rows below unwrapped
70 public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
71 MouseListener, MouseWheelListener, MouseMotionListener,
72 ActionListener, AdjustmentListener, Scrollable
74 String HELIX = MessageManager.getString("label.helix");
76 String SHEET = MessageManager.getString("label.sheet");
79 * For RNA secondary structure "stems" aka helices
81 String STEM = MessageManager.getString("label.rna_helix");
83 String LABEL = MessageManager.getString("label.label");
85 String REMOVE = MessageManager.getString("label.remove_annotation");
87 String COLOUR = MessageManager.getString("action.colour");
89 public final Color HELIX_COLOUR = Color.red.darker();
91 public final Color SHEET_COLOUR = Color.green.darker().darker();
93 public final Color STEM_COLOUR = Color.blue.darker();
96 public AlignViewport av;
100 public int activeRow = -1;
102 public BufferedImage image;
104 public volatile BufferedImage fadedImage;
108 public FontMetrics fm;
110 public int imgWidth = 0;
112 boolean fastPaint = false;
114 // Used For mouse Dragging and resizing graphs
115 int graphStretch = -1;
117 int graphStretchY = -1;
119 int min; // used by mouseDragged to see if user
121 int max; // used by mouseDragged to see if user
123 boolean mouseDragging = false;
127 // for editing cursor
132 public final AnnotationRenderer renderer;
134 private MouseWheelListener[] _mwl;
137 * Creates a new AnnotationPanel object.
142 public AnnotationPanel(AlignmentPanel ap)
145 MAC = jalview.util.Platform.isAMac();
147 ToolTipManager.sharedInstance().registerComponent(this);
148 ToolTipManager.sharedInstance().setInitialDelay(0);
149 ToolTipManager.sharedInstance().setDismissDelay(10000);
152 this.setLayout(null);
153 addMouseListener(this);
154 addMouseMotionListener(this);
155 ap.annotationScroller.getVerticalScrollBar()
156 .addAdjustmentListener(this);
157 // save any wheel listeners on the scroller, so we can propagate scroll
159 _mwl = ap.annotationScroller.getMouseWheelListeners();
160 // and then set our own listener to consume all mousewheel events
161 ap.annotationScroller.addMouseWheelListener(this);
162 renderer = new AnnotationRenderer();
165 public AnnotationPanel(AlignViewport av)
168 renderer = new AnnotationRenderer();
172 public void mouseWheelMoved(MouseWheelEvent e)
177 if (e.getWheelRotation() > 0)
179 ap.scrollRight(true);
183 ap.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 if (evt.getActionCommand().equals(REMOVE))
295 for (int index : av.getColumnSelection().getSelected())
297 if (av.getColumnSelection().isVisible(index))
303 else if (evt.getActionCommand().equals(LABEL))
305 String exMesg = collectAnnotVals(anot, LABEL);
306 String label = JOptionPane.showInputDialog(this,
307 MessageManager.getString("label.enter_label"), exMesg);
314 if ((label.length() > 0) && !aa[activeRow].hasText)
316 aa[activeRow].hasText = true;
319 for (int index : av.getColumnSelection().getSelected())
321 if (!av.getColumnSelection().isVisible(index))
326 if (anot[index] == null)
328 anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
335 anot[index].displayCharacter = label;
339 else if (evt.getActionCommand().equals(COLOUR))
341 Color col = JColorChooser.showDialog(this,
342 MessageManager.getString("label.select_foreground_colour"),
345 for (int index : av.getColumnSelection().getSelected())
347 if (!av.getColumnSelection().isVisible(index))
352 if (anot[index] == null)
354 anot[index] = new Annotation("", "", ' ', 0);
357 anot[index].colour = col;
361 // HELIX, SHEET or STEM
364 String symbol = "\u03B1";
366 if (evt.getActionCommand().equals(HELIX))
370 else if (evt.getActionCommand().equals(SHEET))
376 // Added by LML to color stems
377 else if (evt.getActionCommand().equals(STEM))
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 (evt.getActionCommand().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();
449 // TODO: refactor and save av.getColumnSelection for efficiency
450 List<Integer> selected = viscols.getSelected();
451 Collections.sort(selected);
452 for (int index : selected)
454 // always check for current display state - just in case
455 if (!viscols.isVisible(index))
459 String tlabel = null;
460 if (anots[index] != null)
461 { // LML added stem code
462 if (type.equals(HELIX) || type.equals(SHEET)
463 || type.equals(STEM) || type.equals(LABEL))
465 tlabel = anots[index].description;
466 if (tlabel == null || tlabel.length() < 1)
468 if (type.equals(HELIX) || type.equals(SHEET)
469 || type.equals(STEM))
471 tlabel = "" + anots[index].secondaryStructure;
475 tlabel = "" + anots[index].displayCharacter;
479 if (tlabel != null && !tlabel.equals(last))
481 if (last.length() > 0)
483 collatedInput.append(" ");
485 collatedInput.append(tlabel);
489 return collatedInput.toString();
499 public void mousePressed(MouseEvent evt)
502 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
511 for (int i = 0; i < aa.length; i++)
515 height += aa[i].height;
518 if (evt.getY() < height)
524 else if (aa[i].graph > 0)
528 graphStretchY = evt.getY();
535 if (evt.isPopupTrigger() && activeRow != -1)
537 if (av.getColumnSelection() == null)
542 JPopupMenu pop = new JPopupMenu(
543 MessageManager.getString("label.structure_type"));
546 * Just display the needed structure options
548 if (av.getAlignment().isNucleotide() == true)
550 item = new JMenuItem(STEM);
551 item.addActionListener(this);
556 item = new JMenuItem(HELIX);
557 item.addActionListener(this);
559 item = new JMenuItem(SHEET);
560 item.addActionListener(this);
563 item = new JMenuItem(LABEL);
564 item.addActionListener(this);
566 item = new JMenuItem(COLOUR);
567 item.addActionListener(this);
569 item = new JMenuItem(REMOVE);
570 item.addActionListener(this);
572 pop.show(this, evt.getX(), evt.getY());
582 ap.getScalePanel().mousePressed(evt);
593 public void mouseReleased(MouseEvent evt)
597 mouseDragging = false;
598 ap.getScalePanel().mouseReleased(evt);
608 public void mouseEntered(MouseEvent evt)
610 ap.getScalePanel().mouseEntered(evt);
620 public void mouseExited(MouseEvent evt)
622 ap.getScalePanel().mouseExited(evt);
632 public void mouseDragged(MouseEvent evt)
634 if (graphStretch > -1)
636 av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
638 if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
640 av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
642 graphStretchY = evt.getY();
644 ap.paintAlignment(true);
648 ap.getScalePanel().mouseDragged(evt);
653 * Constructs the tooltip, and constructs and displays a status message, for
654 * the current mouse position
659 public void mouseMoved(MouseEvent evt)
661 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
665 this.setToolTipText(null);
672 for (int i = 0; i < aa.length; i++)
676 height += aa[i].height;
679 if (evt.getY() < height)
688 this.setToolTipText(null);
692 int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
694 if (av.hasHiddenColumns())
696 column = av.getColumnSelection().adjustForHiddenColumns(column);
699 AlignmentAnnotation ann = aa[row];
700 if (row > -1 && ann.annotations != null
701 && column < ann.annotations.length)
703 buildToolTip(ann, column, aa);
704 setStatusMessage(column, ann);
708 this.setToolTipText(null);
709 ap.alignFrame.statusBar.setText(" ");
714 * Builds a tooltip for the annotation at the current mouse position.
720 void buildToolTip(AlignmentAnnotation ann, int column,
721 AlignmentAnnotation[] anns)
723 if (ann.graphGroup > -1)
725 StringBuilder tip = new StringBuilder(32);
726 tip.append("<html>");
727 for (int i = 0; i < anns.length; i++)
729 if (anns[i].graphGroup == ann.graphGroup
730 && anns[i].annotations[column] != null)
732 tip.append(anns[i].label);
733 String description = anns[i].annotations[column].description;
734 if (description != null && description.length() > 0)
736 tip.append(" ").append(description);
741 if (tip.length() != 6)
743 tip.setLength(tip.length() - 4);
744 this.setToolTipText(tip.toString() + "</html>");
747 else if (ann.annotations[column] != null)
749 String description = ann.annotations[column].description;
750 if (description != null && description.length() > 0)
752 this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
757 // clear the tooltip.
758 this.setToolTipText(null);
763 * Constructs and displays the status bar message
768 void setStatusMessage(int column, AlignmentAnnotation ann)
771 * show alignment column and annotation description if any
773 StringBuilder text = new StringBuilder(32);
774 text.append(MessageManager.getString("label.column")).append(" ")
777 if (ann.annotations[column] != null)
779 String description = ann.annotations[column].description;
780 if (description != null && description.trim().length() > 0)
782 text.append(" ").append(description);
787 * if the annotation is sequence-specific, show the sequence number
788 * in the alignment, and (if not a gap) the residue and position
790 SequenceI seqref = ann.sequenceRef;
793 int seqIndex = av.getAlignment().findIndex(seqref);
797 .append(MessageManager.getString("label.sequence"))
799 .append(seqIndex + 1);
800 char residue = seqref.getCharAt(column);
801 if (!Comparison.isGap(residue))
805 if (av.getAlignment().isNucleotide())
807 name = ResidueProperties.nucleotideName.get(String
809 text.append(" Nucleotide: ").append(
810 name != null ? name : residue);
814 name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
815 : ResidueProperties.aa2Triplet.get(String
817 text.append(" Residue: ").append(name != null ? name : residue);
819 int residuePos = seqref.findPosition(column);
820 text.append(" (").append(residuePos).append(")");
825 ap.alignFrame.statusBar.setText(text.toString());
835 public void mouseClicked(MouseEvent evt)
837 // if (activeRow != -1)
839 // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
840 // AlignmentAnnotation anot = aa[activeRow];
844 // TODO mouseClicked-content and drawCursor are quite experimental!
845 public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
848 int pady = av.getCharHeight() / 5;
850 graphics.setColor(Color.black);
851 graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
853 if (av.validCharWidth)
855 graphics.setColor(Color.white);
857 char s = seq.getCharAt(res);
859 charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
860 graphics.drawString(String.valueOf(s), charOffset + x1,
861 (y1 + av.getCharHeight()) - pady);
866 private volatile boolean imageFresh = false;
875 public void paintComponent(Graphics g)
877 g.setColor(Color.white);
878 g.fillRect(0, 0, getWidth(), getHeight());
882 if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
883 || (getVisibleRect().height != g.getClipBounds().height))
885 g.drawImage(image, 0, 0, this);
890 imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
895 if (image == null || imgWidth != image.getWidth(this)
896 || image.getHeight(this) != getHeight())
900 image = new BufferedImage(imgWidth, ap.getAnnotationPanel()
901 .getHeight(), BufferedImage.TYPE_INT_RGB);
902 } catch (OutOfMemoryError oom)
907 } catch (Exception x)
912 "Couldn't allocate memory to redraw screen. Please restart Jalview",
916 gg = (Graphics2D) image.getGraphics();
920 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
921 RenderingHints.VALUE_ANTIALIAS_ON);
924 gg.setFont(av.getFont());
925 fm = gg.getFontMetrics();
926 gg.setColor(Color.white);
927 gg.fillRect(0, 0, imgWidth, image.getHeight());
931 drawComponent(gg, av.startRes, av.endRes + 1);
933 g.drawImage(image, 0, 0, this);
937 * set true to enable redraw timing debug output on stderr
939 private final boolean debugRedraw = false;
942 * non-Thread safe repaint
945 * repaint with horizontal shift in alignment
947 public void fastPaint(int horizontal)
949 if ((horizontal == 0) || gg == null
950 || av.getAlignment().getAlignmentAnnotation() == null
951 || av.getAlignment().getAlignmentAnnotation().length < 1
952 || av.isCalcInProgress())
957 long stime = System.currentTimeMillis();
958 gg.copyArea(0, 0, imgWidth, getHeight(),
959 -horizontal * av.getCharWidth(), 0);
960 long mtime = System.currentTimeMillis();
961 int sr = av.startRes;
962 int er = av.endRes + 1;
965 if (horizontal > 0) // scrollbar pulled right, image to the left
967 transX = (er - sr - horizontal) * av.getCharWidth();
968 sr = er - horizontal;
970 else if (horizontal < 0)
972 er = sr - horizontal;
975 gg.translate(transX, 0);
977 drawComponent(gg, sr, er);
979 gg.translate(-transX, 0);
980 long dtime = System.currentTimeMillis();
983 long rtime = System.currentTimeMillis();
986 System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t"
987 + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime)
988 + "\tRepaint call:\t" + (rtime - dtime));
993 private volatile boolean lastImageGood = false;
1005 public void drawComponent(Graphics g, int startRes, int endRes)
1007 BufferedImage oldFaded = fadedImage;
1008 if (av.isCalcInProgress())
1012 lastImageGood = false;
1015 // We'll keep a record of the old image,
1016 // and draw a faded image until the calculation
1019 && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage
1020 .getHeight() != image.getHeight()))
1022 // System.err.println("redraw faded image ("+(fadedImage==null ?
1023 // "null image" : "") + " lastGood="+lastImageGood+")");
1024 fadedImage = new BufferedImage(imgWidth, image.getHeight(),
1025 BufferedImage.TYPE_INT_RGB);
1027 Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
1029 fadedG.setColor(Color.white);
1030 fadedG.fillRect(0, 0, imgWidth, image.getHeight());
1032 fadedG.setComposite(AlphaComposite.getInstance(
1033 AlphaComposite.SRC_OVER, .3f));
1034 fadedG.drawImage(image, 0, 0, this);
1037 // make sure we don't overwrite the last good faded image until all
1038 // calculations have finished
1039 lastImageGood = false;
1044 if (fadedImage != null)
1046 oldFaded = fadedImage;
1051 g.setColor(Color.white);
1052 g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
1054 g.setFont(av.getFont());
1057 fm = g.getFontMetrics();
1060 if ((av.getAlignment().getAlignmentAnnotation() == null)
1061 || (av.getAlignment().getAlignmentAnnotation().length < 1))
1063 g.setColor(Color.white);
1064 g.fillRect(0, 0, getWidth(), getHeight());
1065 g.setColor(Color.black);
1066 if (av.validCharWidth)
1068 g.drawString(MessageManager
1069 .getString("label.alignment_has_no_annotations"), 20, 15);
1074 lastImageGood = renderer.drawComponent(this, av, g, activeRow,
1076 if (!lastImageGood && fadedImage == null)
1078 fadedImage = oldFaded;
1083 public FontMetrics getFontMetrics()
1089 public Image getFadedImage()
1095 public int getFadedImageWidth()
1100 private int[] bounds = new int[2];
1103 public int[] getVisibleVRange()
1105 if (ap != null && ap.getAlabels() != null)
1107 int sOffset = -ap.getAlabels().getScrollOffset();
1108 int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
1109 bounds[0] = sOffset;
1110 bounds[1] = visHeight;