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;
34 import jalview.viewmodel.ViewportRanges;
36 import java.awt.AlphaComposite;
37 import java.awt.Color;
38 import java.awt.Dimension;
39 import java.awt.FontMetrics;
40 import java.awt.Graphics;
41 import java.awt.Graphics2D;
42 import java.awt.Image;
43 import java.awt.Rectangle;
44 import java.awt.RenderingHints;
45 import java.awt.event.ActionEvent;
46 import java.awt.event.ActionListener;
47 import java.awt.event.AdjustmentEvent;
48 import java.awt.event.AdjustmentListener;
49 import java.awt.event.MouseEvent;
50 import java.awt.event.MouseListener;
51 import java.awt.event.MouseMotionListener;
52 import java.awt.event.MouseWheelEvent;
53 import java.awt.event.MouseWheelListener;
54 import java.awt.image.BufferedImage;
55 import java.beans.PropertyChangeEvent;
56 import java.util.ArrayList;
57 import java.util.Collections;
58 import java.util.List;
60 import javax.swing.JColorChooser;
61 import javax.swing.JMenuItem;
62 import javax.swing.JPanel;
63 import javax.swing.JPopupMenu;
64 import javax.swing.Scrollable;
65 import javax.swing.ToolTipManager;
68 * AnnotationPanel displays visible portion of annotation rows below unwrapped
74 public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
75 MouseListener, MouseWheelListener, MouseMotionListener,
76 ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
78 String HELIX = MessageManager.getString("label.helix");
80 String SHEET = MessageManager.getString("label.sheet");
83 * For RNA secondary structure "stems" aka helices
85 String STEM = MessageManager.getString("label.rna_helix");
87 String LABEL = MessageManager.getString("label.label");
89 String REMOVE = MessageManager.getString("label.remove_annotation");
91 String COLOUR = MessageManager.getString("action.colour");
93 public final Color HELIX_COLOUR = Color.red.darker();
95 public final Color SHEET_COLOUR = Color.green.darker().darker();
97 public final Color STEM_COLOUR = Color.blue.darker();
100 public AlignViewport av;
104 public int activeRow = -1;
106 public BufferedImage image;
108 public volatile BufferedImage fadedImage;
112 public FontMetrics fm;
114 public int imgWidth = 0;
116 boolean fastPaint = false;
118 // Used For mouse Dragging and resizing graphs
119 int graphStretch = -1;
121 int graphStretchY = -1;
123 int min; // used by mouseDragged to see if user
125 int max; // used by mouseDragged to see if user
127 boolean mouseDragging = false;
129 // for editing cursor
134 public final AnnotationRenderer renderer;
136 private MouseWheelListener[] _mwl;
139 * Creates a new AnnotationPanel object.
144 public AnnotationPanel(AlignmentPanel ap)
146 ToolTipManager.sharedInstance().registerComponent(this);
147 ToolTipManager.sharedInstance().setInitialDelay(0);
148 ToolTipManager.sharedInstance().setDismissDelay(10000);
151 this.setLayout(null);
152 addMouseListener(this);
153 addMouseMotionListener(this);
154 ap.annotationScroller.getVerticalScrollBar()
155 .addAdjustmentListener(this);
156 // save any wheel listeners on the scroller, so we can propagate scroll
158 _mwl = ap.annotationScroller.getMouseWheelListeners();
159 // and then set our own listener to consume all mousewheel events
160 ap.annotationScroller.addMouseWheelListener(this);
161 renderer = new AnnotationRenderer();
163 av.getRanges().addPropertyChangeListener(this);
166 public AnnotationPanel(AlignViewport av)
169 renderer = new AnnotationRenderer();
173 public void mouseWheelMoved(MouseWheelEvent e)
178 double wheelRotation = e.getPreciseWheelRotation();
179 if (wheelRotation > 0)
181 av.getRanges().scrollRight(true);
183 else if (wheelRotation < 0)
185 av.getRanges().scrollRight(false);
190 // TODO: find the correct way to let the event bubble up to
191 // ap.annotationScroller
192 for (MouseWheelListener mwl : _mwl)
196 mwl.mouseWheelMoved(e);
207 public Dimension getPreferredScrollableViewportSize()
209 return getPreferredSize();
213 public int getScrollableBlockIncrement(Rectangle visibleRect,
214 int orientation, int direction)
220 public boolean getScrollableTracksViewportHeight()
226 public boolean getScrollableTracksViewportWidth()
232 public int getScrollableUnitIncrement(Rectangle visibleRect,
233 int orientation, int direction)
242 * java.awt.event.AdjustmentListener#adjustmentValueChanged(java.awt.event
246 public void adjustmentValueChanged(AdjustmentEvent evt)
248 // update annotation label display
249 ap.getAlabels().setScrollOffset(-evt.getValue());
253 * Calculates the height of the annotation displayed in the annotation panel.
254 * Callers should normally call the ap.adjustAnnotationHeight method to ensure
255 * all annotation associated components are updated correctly.
258 public int adjustPanelHeight()
260 int height = av.calcPanelHeight();
261 this.setPreferredSize(new Dimension(1, height));
264 // revalidate only when the alignment panel is fully constructed
278 public void actionPerformed(ActionEvent evt)
280 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
285 Annotation[] anot = aa[activeRow].annotations;
287 if (anot.length < av.getColumnSelection().getMax())
289 Annotation[] temp = new Annotation[av.getColumnSelection().getMax()
291 System.arraycopy(anot, 0, temp, 0, anot.length);
293 aa[activeRow].annotations = anot;
296 String action = evt.getActionCommand();
297 if (action.equals(REMOVE))
299 for (int index : av.getColumnSelection().getSelected())
301 if (av.getAlignment().getHiddenColumns().isVisible(index))
307 else if (action.equals(LABEL))
309 String exMesg = collectAnnotVals(anot, LABEL);
310 String label = JvOptionPane.showInputDialog(this,
311 MessageManager.getString("label.enter_label"), exMesg);
318 if ((label.length() > 0) && !aa[activeRow].hasText)
320 aa[activeRow].hasText = true;
323 for (int index : av.getColumnSelection().getSelected())
325 if (!av.getAlignment().getHiddenColumns().isVisible(index))
330 if (anot[index] == null)
332 anot[index] = new Annotation(label, "", ' ', 0);
336 anot[index].displayCharacter = label;
340 else if (action.equals(COLOUR))
342 Color col = JColorChooser.showDialog(this,
343 MessageManager.getString("label.select_foreground_colour"),
346 for (int index : av.getColumnSelection().getSelected())
348 if (!av.getAlignment().getHiddenColumns().isVisible(index))
353 if (anot[index] == null)
355 anot[index] = new Annotation("", "", ' ', 0);
358 anot[index].colour = col;
362 // HELIX, SHEET or STEM
365 String symbol = "\u03B1"; // alpha
367 if (action.equals(HELIX))
371 else if (action.equals(SHEET))
374 symbol = "\u03B2"; // beta
377 // Added by LML to color stems
378 else if (action.equals(STEM))
381 int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
382 symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
385 if (!aa[activeRow].hasIcons)
387 aa[activeRow].hasIcons = true;
390 String label = JvOptionPane.showInputDialog(MessageManager
391 .getString("label.enter_label_for_the_structure"), symbol);
398 if ((label.length() > 0) && !aa[activeRow].hasText)
400 aa[activeRow].hasText = true;
401 if (action.equals(STEM))
403 aa[activeRow].showAllColLabels = true;
406 for (int index : av.getColumnSelection().getSelected())
408 if (!av.getAlignment().getHiddenColumns().isVisible(index))
413 if (anot[index] == null)
415 anot[index] = new Annotation(label, "", type, 0);
418 anot[index].secondaryStructure = type != 'S' ? type
419 : label.length() == 0 ? ' ' : label.charAt(0);
420 anot[index].displayCharacter = label;
425 av.getAlignment().validateAnnotation(aa[activeRow]);
426 ap.alignmentChanged();
427 ap.alignFrame.setMenusForViewport();
435 * Returns any existing annotation concatenated as a string. For each
436 * annotation, takes the description, if any, else the secondary structure
437 * character (if type is HELIX, SHEET or STEM), else the display character (if
444 private String collectAnnotVals(Annotation[] anots, String type)
446 // TODO is this method wanted? why? 'last' is not used
448 StringBuilder collatedInput = new StringBuilder(64);
450 ColumnSelection viscols = av.getColumnSelection();
451 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
454 * the selection list (read-only view) is in selection order, not
455 * column order; make a copy so we can sort it
457 List<Integer> selected = new ArrayList<>(viscols.getSelected());
458 Collections.sort(selected);
459 for (int index : selected)
461 // always check for current display state - just in case
462 if (!hidden.isVisible(index))
466 String tlabel = null;
467 if (anots[index] != null)
468 { // LML added stem code
469 if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
470 || type.equals(LABEL))
472 tlabel = anots[index].description;
473 if (tlabel == null || tlabel.length() < 1)
475 if (type.equals(HELIX) || type.equals(SHEET)
476 || type.equals(STEM))
478 tlabel = "" + anots[index].secondaryStructure;
482 tlabel = "" + anots[index].displayCharacter;
486 if (tlabel != null && !tlabel.equals(last))
488 if (last.length() > 0)
490 collatedInput.append(" ");
492 collatedInput.append(tlabel);
496 return collatedInput.toString();
506 public void mousePressed(MouseEvent evt)
509 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
518 final int y = evt.getY();
519 for (int i = 0; i < aa.length; i++)
523 height += aa[i].height;
532 else if (aa[i].graph > 0)
544 * isPopupTrigger fires in mousePressed on Mac,
545 * not until mouseRelease on Windows
547 if (evt.isPopupTrigger() && activeRow != -1)
549 showPopupMenu(y, evt.getX());
553 ap.getScalePanel().mousePressed(evt);
557 * Construct and display a context menu at the right-click position
562 void showPopupMenu(final int y, int x)
564 if (av.getColumnSelection() == null
565 || av.getColumnSelection().isEmpty())
570 JPopupMenu pop = new JPopupMenu(
571 MessageManager.getString("label.structure_type"));
574 * Just display the needed structure options
576 if (av.getAlignment().isNucleotide())
578 item = new JMenuItem(STEM);
579 item.addActionListener(this);
584 item = new JMenuItem(HELIX);
585 item.addActionListener(this);
587 item = new JMenuItem(SHEET);
588 item.addActionListener(this);
591 item = new JMenuItem(LABEL);
592 item.addActionListener(this);
594 item = new JMenuItem(COLOUR);
595 item.addActionListener(this);
597 item = new JMenuItem(REMOVE);
598 item.addActionListener(this);
600 pop.show(this, x, y);
610 public void mouseReleased(MouseEvent evt)
614 mouseDragging = false;
615 ap.getScalePanel().mouseReleased(evt);
618 * isPopupTrigger is set in mouseReleased on Windows
619 * (in mousePressed on Mac)
621 if (evt.isPopupTrigger() && activeRow != -1)
623 showPopupMenu(evt.getY(), evt.getX());
635 public void mouseEntered(MouseEvent evt)
637 ap.getScalePanel().mouseEntered(evt);
647 public void mouseExited(MouseEvent evt)
649 ap.getScalePanel().mouseExited(evt);
659 public void mouseDragged(MouseEvent evt)
661 if (graphStretch > -1)
664 .getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
666 if (av.getAlignment()
667 .getAlignmentAnnotation()[graphStretch].graphHeight < 0)
670 .getAlignmentAnnotation()[graphStretch].graphHeight = 0;
672 graphStretchY = evt.getY();
674 ap.paintAlignment(false, false);
678 ap.getScalePanel().mouseDragged(evt);
683 * Constructs the tooltip, and constructs and displays a status message, for
684 * the current mouse position
689 public void mouseMoved(MouseEvent evt)
691 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
695 this.setToolTipText(null);
702 for (int i = 0; i < aa.length; i++)
706 height += aa[i].height;
709 if (evt.getY() < height)
718 this.setToolTipText(null);
722 int column = (evt.getX() / av.getCharWidth())
723 + av.getRanges().getStartRes();
725 if (av.hasHiddenColumns())
727 column = av.getAlignment().getHiddenColumns()
728 .visibleToAbsoluteColumn(column);
731 AlignmentAnnotation ann = aa[row];
732 if (row > -1 && ann.annotations != null
733 && column < ann.annotations.length)
735 buildToolTip(ann, column, aa);
736 setStatusMessage(column, ann);
740 this.setToolTipText(null);
741 ap.alignFrame.statusBar.setText(" ");
746 * Builds a tooltip for the annotation at the current mouse position.
752 void buildToolTip(AlignmentAnnotation ann, int column,
753 AlignmentAnnotation[] anns)
755 if (ann.graphGroup > -1)
757 StringBuilder tip = new StringBuilder(32);
758 tip.append("<html>");
759 for (int i = 0; i < anns.length; i++)
761 if (anns[i].graphGroup == ann.graphGroup
762 && anns[i].annotations[column] != null)
764 tip.append(anns[i].label);
765 String description = anns[i].annotations[column].description;
766 if (description != null && description.length() > 0)
768 tip.append(" ").append(description);
773 if (tip.length() != 6)
775 tip.setLength(tip.length() - 4);
776 this.setToolTipText(tip.toString() + "</html>");
779 else if (ann.annotations[column] != null)
781 String description = ann.annotations[column].description;
782 if (description != null && description.length() > 0)
784 this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
788 this.setToolTipText(null); // no tooltip if null or empty description
793 // clear the tooltip.
794 this.setToolTipText(null);
799 * Constructs and displays the status bar message
804 void setStatusMessage(int column, AlignmentAnnotation ann)
807 * show alignment column and annotation description if any
809 StringBuilder text = new StringBuilder(32);
810 text.append(MessageManager.getString("label.column")).append(" ")
813 if (ann.annotations[column] != null)
815 String description = ann.annotations[column].description;
816 if (description != null && description.trim().length() > 0)
818 text.append(" ").append(description);
823 * if the annotation is sequence-specific, show the sequence number
824 * in the alignment, and (if not a gap) the residue and position
826 SequenceI seqref = ann.sequenceRef;
829 int seqIndex = av.getAlignment().findIndex(seqref);
832 text.append(", ").append(MessageManager.getString("label.sequence"))
833 .append(" ").append(seqIndex + 1);
834 char residue = seqref.getCharAt(column);
835 if (!Comparison.isGap(residue))
839 if (av.getAlignment().isNucleotide())
841 name = ResidueProperties.nucleotideName
842 .get(String.valueOf(residue));
843 text.append(" Nucleotide: ")
844 .append(name != null ? name : residue);
848 name = 'X' == residue ? "X"
849 : ('*' == residue ? "STOP"
850 : ResidueProperties.aa2Triplet
851 .get(String.valueOf(residue)));
852 text.append(" Residue: ").append(name != null ? name : residue);
854 int residuePos = seqref.findPosition(column);
855 text.append(" (").append(residuePos).append(")");
860 ap.alignFrame.statusBar.setText(text.toString());
870 public void mouseClicked(MouseEvent evt)
872 // if (activeRow != -1)
874 // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
875 // AlignmentAnnotation anot = aa[activeRow];
879 // TODO mouseClicked-content and drawCursor are quite experimental!
880 public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
883 int pady = av.getCharHeight() / 5;
885 graphics.setColor(Color.black);
886 graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
888 if (av.validCharWidth)
890 graphics.setColor(Color.white);
892 char s = seq.getCharAt(res);
894 charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
895 graphics.drawString(String.valueOf(s), charOffset + x1,
896 (y1 + av.getCharHeight()) - pady);
901 private volatile boolean imageFresh = false;
910 public void paintComponent(Graphics g)
912 super.paintComponent(g);
914 g.setColor(Color.white);
915 g.fillRect(0, 0, getWidth(), getHeight());
919 if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
920 || (getVisibleRect().height != g.getClipBounds().height))
922 g.drawImage(image, 0, 0, this);
927 imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
928 + 1) * av.getCharWidth();
933 if (image == null || imgWidth != image.getWidth(this)
934 || image.getHeight(this) != getHeight())
938 image = new BufferedImage(imgWidth,
939 ap.getAnnotationPanel().getHeight(),
940 BufferedImage.TYPE_INT_RGB);
941 } catch (OutOfMemoryError oom)
946 } catch (Exception x)
951 "Couldn't allocate memory to redraw screen. Please restart Jalview",
955 gg = (Graphics2D) image.getGraphics();
959 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
960 RenderingHints.VALUE_ANTIALIAS_ON);
963 gg.setFont(av.getFont());
964 fm = gg.getFontMetrics();
965 gg.setColor(Color.white);
966 gg.fillRect(0, 0, imgWidth, image.getHeight());
970 drawComponent(gg, av.getRanges().getStartRes(),
971 av.getRanges().getEndRes() + 1);
973 g.drawImage(image, 0, 0, this);
977 * set true to enable redraw timing debug output on stderr
979 private final boolean debugRedraw = false;
982 * non-Thread safe repaint
985 * repaint with horizontal shift in alignment
987 public void fastPaint(int horizontal)
989 if ((horizontal == 0) || gg == null
990 || av.getAlignment().getAlignmentAnnotation() == null
991 || av.getAlignment().getAlignmentAnnotation().length < 1
992 || av.isCalcInProgress())
998 int sr = av.getRanges().getStartRes();
999 int er = av.getRanges().getEndRes() + 1;
1002 gg.copyArea(0, 0, imgWidth, getHeight(),
1003 -horizontal * av.getCharWidth(), 0);
1005 if (horizontal > 0) // scrollbar pulled right, image to the left
1007 transX = (er - sr - horizontal) * av.getCharWidth();
1008 sr = er - horizontal;
1010 else if (horizontal < 0)
1012 er = sr - horizontal;
1015 gg.translate(transX, 0);
1017 drawComponent(gg, sr, er);
1019 gg.translate(-transX, 0);
1023 // Call repaint on alignment panel so that repaints from other alignment
1024 // panel components can be aggregated. Otherwise performance of the overview
1025 // window and others may be adversely affected.
1026 av.getAlignPanel().repaint();
1029 private volatile boolean lastImageGood = false;
1041 public void drawComponent(Graphics g, int startRes, int endRes)
1043 BufferedImage oldFaded = fadedImage;
1044 if (av.isCalcInProgress())
1048 lastImageGood = false;
1051 // We'll keep a record of the old image,
1052 // and draw a faded image until the calculation
1055 && (fadedImage == null || fadedImage.getWidth() != imgWidth
1056 || fadedImage.getHeight() != image.getHeight()))
1058 // System.err.println("redraw faded image ("+(fadedImage==null ?
1059 // "null image" : "") + " lastGood="+lastImageGood+")");
1060 fadedImage = new BufferedImage(imgWidth, image.getHeight(),
1061 BufferedImage.TYPE_INT_RGB);
1063 Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
1065 fadedG.setColor(Color.white);
1066 fadedG.fillRect(0, 0, imgWidth, image.getHeight());
1068 fadedG.setComposite(
1069 AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f));
1070 fadedG.drawImage(image, 0, 0, this);
1073 // make sure we don't overwrite the last good faded image until all
1074 // calculations have finished
1075 lastImageGood = false;
1080 if (fadedImage != null)
1082 oldFaded = fadedImage;
1087 g.setColor(Color.white);
1088 g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
1090 g.setFont(av.getFont());
1093 fm = g.getFontMetrics();
1096 if ((av.getAlignment().getAlignmentAnnotation() == null)
1097 || (av.getAlignment().getAlignmentAnnotation().length < 1))
1099 g.setColor(Color.white);
1100 g.fillRect(0, 0, getWidth(), getHeight());
1101 g.setColor(Color.black);
1102 if (av.validCharWidth)
1104 g.drawString(MessageManager
1105 .getString("label.alignment_has_no_annotations"), 20, 15);
1110 lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes,
1112 if (!lastImageGood && fadedImage == null)
1114 fadedImage = oldFaded;
1119 public FontMetrics getFontMetrics()
1125 public Image getFadedImage()
1131 public int getFadedImageWidth()
1136 private int[] bounds = new int[2];
1139 public int[] getVisibleVRange()
1141 if (ap != null && ap.getAlabels() != null)
1143 int sOffset = -ap.getAlabels().getScrollOffset();
1144 int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
1145 bounds[0] = sOffset;
1146 bounds[1] = visHeight;
1156 * Try to ensure any references held are nulled
1158 public void dispose()
1168 * I created the renderer so I will dispose of it
1170 if (renderer != null)
1177 public void propertyChange(PropertyChangeEvent evt)
1179 // Respond to viewport range changes (e.g. alignment panel was scrolled)
1180 // Both scrolling and resizing change viewport ranges: scrolling changes
1181 // both start and end points, but resize only changes end values.
1182 // Here we only want to fastpaint on a scroll, with resize using a normal
1183 // paint, so scroll events are identified as changes to the horizontal or
1184 // vertical start value.
1185 if (evt.getPropertyName().equals(ViewportRanges.STARTRES))
1187 fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
1189 else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
1191 fastPaint(((int[]) evt.getNewValue())[0]
1192 - ((int[]) evt.getOldValue())[0]);
1194 else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))