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.api.AlignViewportI;
54 import jalview.datamodel.AlignmentAnnotation;
55 import jalview.datamodel.AlignmentI;
56 import jalview.datamodel.Annotation;
57 import jalview.datamodel.ColumnSelection;
58 import jalview.datamodel.ContactListI;
59 import jalview.datamodel.ContactRange;
60 import jalview.datamodel.HiddenColumns;
61 import jalview.datamodel.SequenceI;
62 import jalview.gui.JalviewColourChooser.ColourChooserListener;
63 import jalview.renderer.AnnotationRenderer;
64 import jalview.renderer.AwtRenderPanelI;
65 import jalview.renderer.ContactGeometry;
66 import jalview.schemes.ResidueProperties;
67 import jalview.util.Comparison;
68 import jalview.util.MessageManager;
69 import jalview.util.Platform;
70 import jalview.viewmodel.ViewportListenerI;
71 import jalview.viewmodel.ViewportRanges;
74 * AnnotationPanel displays visible portion of annotation rows below unwrapped
80 public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
81 MouseListener, MouseWheelListener, MouseMotionListener,
82 ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
86 Select, Resize, Undefined, MatrixSelect
89 String HELIX = MessageManager.getString("label.helix");
91 String SHEET = MessageManager.getString("label.sheet");
94 * For RNA secondary structure "stems" aka helices
96 String STEM = MessageManager.getString("label.rna_helix");
98 String LABEL = MessageManager.getString("label.label");
100 String REMOVE = MessageManager.getString("label.remove_annotation");
102 String COLOUR = MessageManager.getString("action.colour");
104 public final Color HELIX_COLOUR = Color.red.darker();
106 public final Color SHEET_COLOUR = Color.green.darker().darker();
108 public final Color STEM_COLOUR = Color.blue.darker();
111 public AlignViewport av;
115 public int activeRow = -1;
117 public BufferedImage image;
119 public volatile BufferedImage fadedImage;
121 // private Graphics2D gg;
123 public FontMetrics fm;
125 public int imgWidth = 0;
127 boolean fastPaint = false;
129 // Used For mouse Dragging and resizing graphs
130 int graphStretch = -1;
132 int mouseDragLastX = -1;
134 int mouseDragLastY = -1;
140 DragMode dragMode = DragMode.Undefined;
142 boolean mouseDragging = false;
144 // for editing cursor
149 public final AnnotationRenderer renderer;
151 private MouseWheelListener[] _mwl;
154 * Creates a new AnnotationPanel object.
159 public AnnotationPanel(AlignmentPanel ap)
161 ToolTipManager.sharedInstance().registerComponent(this);
162 ToolTipManager.sharedInstance().setInitialDelay(0);
163 ToolTipManager.sharedInstance().setDismissDelay(10000);
166 this.setLayout(null);
167 addMouseListener(this);
168 addMouseMotionListener(this);
169 ap.annotationScroller.getVerticalScrollBar()
170 .addAdjustmentListener(this);
171 // save any wheel listeners on the scroller, so we can propagate scroll
173 _mwl = ap.annotationScroller.getMouseWheelListeners();
174 // and then set our own listener to consume all mousewheel events
175 ap.annotationScroller.addMouseWheelListener(this);
176 renderer = new AnnotationRenderer();
178 av.getRanges().addPropertyChangeListener(this);
181 public AnnotationPanel(AlignViewport av)
184 renderer = new AnnotationRenderer();
188 public void mouseWheelMoved(MouseWheelEvent e)
193 double wheelRotation = e.getPreciseWheelRotation();
194 if (wheelRotation > 0)
196 av.getRanges().scrollRight(true);
198 else if (wheelRotation < 0)
200 av.getRanges().scrollRight(false);
205 // TODO: find the correct way to let the event bubble up to
206 // ap.annotationScroller
207 for (MouseWheelListener mwl : _mwl)
211 mwl.mouseWheelMoved(e);
222 public Dimension getPreferredScrollableViewportSize()
224 Dimension ps = getPreferredSize();
225 return new Dimension(ps.width, adjustForAlignFrame(false, ps.height));
229 public int getScrollableBlockIncrement(Rectangle visibleRect,
230 int orientation, int direction)
236 public boolean getScrollableTracksViewportHeight()
242 public boolean getScrollableTracksViewportWidth()
248 public int getScrollableUnitIncrement(Rectangle visibleRect,
249 int orientation, int direction)
258 * java.awt.event.AdjustmentListener#adjustmentValueChanged(java.awt.event
262 public void adjustmentValueChanged(AdjustmentEvent evt)
264 // update annotation label display
265 ap.getAlabels().setScrollOffset(-evt.getValue());
269 * Calculates the height of the annotation displayed in the annotation panel.
270 * Callers should normally call the ap.adjustAnnotationHeight method to ensure
271 * all annotation associated components are updated correctly.
274 public int adjustPanelHeight()
276 int height = av.calcPanelHeight();
277 this.setPreferredSize(new Dimension(1, height));
280 // revalidate only when the alignment panel is fully constructed
294 public void actionPerformed(ActionEvent evt)
296 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
301 Annotation[] anot = aa[activeRow].annotations;
303 if (anot.length < av.getColumnSelection().getMax())
305 Annotation[] temp = new Annotation[av.getColumnSelection().getMax()
307 System.arraycopy(anot, 0, temp, 0, anot.length);
309 aa[activeRow].annotations = anot;
312 String action = evt.getActionCommand();
313 if (action.equals(REMOVE))
315 for (int index : av.getColumnSelection().getSelected())
317 if (av.getAlignment().getHiddenColumns().isVisible(index))
323 else if (action.equals(LABEL))
325 String exMesg = collectAnnotVals(anot, LABEL);
326 String label = JvOptionPane.showInputDialog(
327 MessageManager.getString("label.enter_label"), exMesg);
334 if ((label.length() > 0) && !aa[activeRow].hasText)
336 aa[activeRow].hasText = true;
339 for (int index : av.getColumnSelection().getSelected())
341 if (!av.getAlignment().getHiddenColumns().isVisible(index))
346 if (anot[index] == null)
348 anot[index] = new Annotation(label, "", ' ', 0);
352 anot[index].displayCharacter = label;
356 else if (action.equals(COLOUR))
358 final Annotation[] fAnot = anot;
359 String title = MessageManager
360 .getString("label.select_foreground_colour");
361 ColourChooserListener listener = new ColourChooserListener()
364 public void colourSelected(Color c)
366 HiddenColumns hiddenColumns = av.getAlignment()
368 for (int index : av.getColumnSelection().getSelected())
370 if (hiddenColumns.isVisible(index))
372 if (fAnot[index] == null)
374 fAnot[index] = new Annotation("", "", ' ', 0);
376 fAnot[index].colour = c;
381 JalviewColourChooser.showColourChooser(this, title, Color.black,
385 // HELIX, SHEET or STEM
388 String symbol = "\u03B1"; // alpha
390 if (action.equals(HELIX))
394 else if (action.equals(SHEET))
397 symbol = "\u03B2"; // beta
400 // Added by LML to color stems
401 else if (action.equals(STEM))
404 int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
405 symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
408 if (!aa[activeRow].hasIcons)
410 aa[activeRow].hasIcons = true;
413 String label = JvOptionPane.showInputDialog(MessageManager
414 .getString("label.enter_label_for_the_structure"), symbol);
421 if ((label.length() > 0) && !aa[activeRow].hasText)
423 aa[activeRow].hasText = true;
424 if (action.equals(STEM))
426 aa[activeRow].showAllColLabels = true;
429 for (int index : av.getColumnSelection().getSelected())
431 if (!av.getAlignment().getHiddenColumns().isVisible(index))
436 if (anot[index] == null)
438 anot[index] = new Annotation(label, "", type, 0);
441 anot[index].secondaryStructure = type != 'S' ? type
442 : label.length() == 0 ? ' ' : label.charAt(0);
443 anot[index].displayCharacter = label;
448 av.getAlignment().validateAnnotation(aa[activeRow]);
449 ap.alignmentChanged();
450 ap.alignFrame.setMenusForViewport();
458 * Returns any existing annotation concatenated as a string. For each
459 * annotation, takes the description, if any, else the secondary structure
460 * character (if type is HELIX, SHEET or STEM), else the display character (if
467 private String collectAnnotVals(Annotation[] anots, String type)
469 // TODO is this method wanted? why? 'last' is not used
471 StringBuilder collatedInput = new StringBuilder(64);
473 ColumnSelection viscols = av.getColumnSelection();
474 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
477 * the selection list (read-only view) is in selection order, not
478 * column order; make a copy so we can sort it
480 List<Integer> selected = new ArrayList<>(viscols.getSelected());
481 Collections.sort(selected);
482 for (int index : selected)
484 // always check for current display state - just in case
485 if (!hidden.isVisible(index))
489 String tlabel = null;
490 if (anots[index] != null)
491 { // LML added stem code
492 if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
493 || type.equals(LABEL))
495 tlabel = anots[index].description;
496 if (tlabel == null || tlabel.length() < 1)
498 if (type.equals(HELIX) || type.equals(SHEET)
499 || type.equals(STEM))
501 tlabel = "" + anots[index].secondaryStructure;
505 tlabel = "" + anots[index].displayCharacter;
509 if (tlabel != null && !tlabel.equals(last))
511 if (last.length() > 0)
513 collatedInput.append(" ");
515 collatedInput.append(tlabel);
519 return collatedInput.toString();
523 * Action on right mouse pressed on Mac is to show a pop-up menu for the
524 * annotation. Action on left mouse pressed is to find which annotation is
525 * pressed and mark the start of a column selection or graph resize operation.
530 public void mousePressed(MouseEvent evt)
533 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
538 mouseDragLastX = evt.getX();
539 mouseDragLastY = evt.getY();
542 * add visible annotation heights until we reach the y
543 * position, to find which annotation it is in
548 // todo could reuse getRowIndexAndOffset ?
549 final int y = evt.getY();
551 for (int i = 0; i < aa.length; i++)
555 height += aa[i].height;
564 else if (aa[i].graph != 0)
567 * we have clicked on a resizable graph annotation
570 yOffset = height - y;
577 * isPopupTrigger fires in mousePressed on Mac,
578 * not until mouseRelease on Windows
580 if (evt.isPopupTrigger() && activeRow != -1)
582 showPopupMenu(y, evt.getX());
586 if (graphStretch != -1)
589 if (aa[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER)
591 if (evt.isAltDown() || evt.isAltGraphDown())
593 dragMode = DragMode.MatrixSelect;
594 firstDragX = mouseDragLastX;
595 firstDragY = mouseDragLastY;
599 int currentX = getColumnForXPos(evt.getX());
600 ContactListI forCurrentX = av.getContactList(aa[graphStretch],
602 if (forCurrentX != null)
604 ContactGeometry cXcgeom = new ContactGeometry(forCurrentX,
605 aa[graphStretch].graphHeight);
606 ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset,
609 fr = Math.min(cXci.cStart, cXci.cEnd);
610 to = Math.max(cXci.cStart, cXci.cEnd);
611 for (int c = fr; c <= to; c++)
613 av.getColumnSelection().addElement(c);
615 av.getColumnSelection().addElement(currentX);
622 ap.getScalePanel().mousePressed(evt);
627 * Construct and display a context menu at the right-click position
632 void showPopupMenu(final int y, int x)
634 if (av.getColumnSelection() == null
635 || av.getColumnSelection().isEmpty())
640 JPopupMenu pop = new JPopupMenu(
641 MessageManager.getString("label.structure_type"));
644 * Just display the needed structure options
646 if (av.getAlignment().isNucleotide())
648 item = new JMenuItem(STEM);
649 item.addActionListener(this);
654 item = new JMenuItem(HELIX);
655 item.addActionListener(this);
657 item = new JMenuItem(SHEET);
658 item.addActionListener(this);
661 item = new JMenuItem(LABEL);
662 item.addActionListener(this);
664 item = new JMenuItem(COLOUR);
665 item.addActionListener(this);
667 item = new JMenuItem(REMOVE);
668 item.addActionListener(this);
670 pop.show(this, x, y);
674 * Action on mouse up is to clear mouse drag data and call mouseReleased on
675 * ScalePanel, to deal with defining the selection group (if any) defined by
681 public void mouseReleased(MouseEvent evt)
683 if (dragMode == DragMode.MatrixSelect)
685 matrixSelectRange(evt);
692 mouseDragging = false;
693 if (dragMode == DragMode.Resize)
695 ap.adjustAnnotationHeight();
697 dragMode = DragMode.Undefined;
698 ap.getScalePanel().mouseReleased(evt);
701 * isPopupTrigger is set in mouseReleased on Windows
702 * (in mousePressed on Mac)
704 if (evt.isPopupTrigger() && activeRow != -1)
706 showPopupMenu(evt.getY(), evt.getX());
718 public void mouseEntered(MouseEvent evt)
720 this.mouseDragging = false;
721 ap.getScalePanel().mouseEntered(evt);
725 * On leaving the panel, calls ScalePanel.mouseExited to deal with scrolling
726 * with column selection on a mouse drag
731 public void mouseExited(MouseEvent evt)
733 ap.getScalePanel().mouseExited(evt);
737 * Action on starting or continuing a mouse drag. There are two possible
740 * <li>drag up or down on a graphed annotation increases or decreases the
741 * height of the graph</li>
742 * <li>dragging left or right selects the columns dragged across</li>
744 * A drag on a graph annotation is treated as column selection if it starts
745 * with more horizontal than vertical movement, and as resize if it starts
746 * with more vertical than horizontal movement. Once started, the drag does
752 public void mouseDragged(MouseEvent evt)
755 * if dragMode is Undefined:
756 * - set to Select if dx > dy
757 * - set to Resize if dy > dx
758 * - do nothing if dx == dy
760 final int x = evt.getX();
761 final int y = evt.getY();
762 if (dragMode == DragMode.Undefined)
764 int dx = Math.abs(x - mouseDragLastX);
765 int dy = Math.abs(y - mouseDragLastY);
766 if (graphStretch == -1 || dx > dy)
769 * mostly horizontal drag, or not a graph annotation
771 dragMode = DragMode.Select;
776 * mostly vertical drag
778 dragMode = DragMode.Resize;
781 * but could also be a matrix drag
783 if ((evt.isAltDown() || evt.isAltGraphDown()) && (av.getAlignment()
784 .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER))
787 * dragging in a matrix
789 dragMode = DragMode.MatrixSelect;
790 firstDragX = mouseDragLastX;
791 firstDragY = mouseDragLastY;
796 if (dragMode == DragMode.Undefined)
800 * drag is diagonal - defer deciding whether to
801 * treat as up/down or left/right
808 if (dragMode == DragMode.Resize)
811 * resize graph annotation if mouse was dragged up or down
813 int deltaY = mouseDragLastY - evt.getY();
816 AlignmentAnnotation graphAnnotation = av.getAlignment()
817 .getAlignmentAnnotation()[graphStretch];
818 int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
819 graphAnnotation.graphHeight = newHeight;
821 ap.paintAlignment(false, false);
824 else if (dragMode == DragMode.MatrixSelect)
827 * TODO draw a rubber band for range
831 ap.paintAlignment(false, false);
836 * for mouse drag left or right, delegate to
837 * ScalePanel to adjust the column selection
839 ap.getScalePanel().mouseDragged(evt);
848 public void matrixSelectRange(MouseEvent evt)
851 * get geometry of drag
853 int fromY = Math.min(firstDragY, evt.getY());
854 int toY = Math.max(firstDragY, evt.getY());
855 int fromX = Math.min(firstDragX, evt.getX());
856 int toX = Math.max(firstDragX, evt.getX());
858 int deltaY = toY - fromY;
859 int deltaX = toX - fromX;
861 int[] rowIndex = getRowIndexAndOffset(fromY,
862 av.getAlignment().getAlignmentAnnotation());
863 int[] toRowIndex = getRowIndexAndOffset(toY,
864 av.getAlignment().getAlignmentAnnotation());
866 if (rowIndex == null || toRowIndex == null)
868 System.out.println("Drag out of range. needs to be clipped");
871 if (rowIndex[0] != toRowIndex[0])
873 System.out.println("Drag went to another row. needs to be clipped");
876 // rectangular selection on matrix style annotation
877 AlignmentAnnotation cma = av.getAlignment()
878 .getAlignmentAnnotation()[rowIndex[0]];
880 int lastX = getColumnForXPos(fromX);
881 int currentX = getColumnForXPos(toX);
882 int fromXc = Math.min(lastX, currentX);
883 int toXc = Math.max(lastX, currentX);
884 ContactListI forFromX = av.getContactList(cma, fromXc);
885 ContactListI forToX = av.getContactList(cma, toXc);
887 if (forFromX != null && forToX != null)
889 ContactGeometry lastXcgeom = new ContactGeometry(forFromX,
891 ContactGeometry.contactInterval lastXci = lastXcgeom
892 .mapFor(rowIndex[1], rowIndex[1] + deltaY);
893 ContactGeometry cXcgeom = new ContactGeometry(forToX,
895 ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1],
896 rowIndex[1] + deltaY);
897 // mark rectangular region formed by drag
898 System.err.println("Matrix Selection from last(" + lastXci.cStart
899 + "," + lastXci.cEnd + ") to cur(" + cXci.cStart + ","
902 fr = Math.min(lastXci.cStart, lastXci.cEnd);
903 to = Math.max(lastXci.cStart, lastXci.cEnd);
904 System.err.println("Marking " + fr + " to " + to);
905 for (int c = fr; c <= to; c++)
907 av.getColumnSelection().addElement(c);
909 fr = Math.min(cXci.cStart, cXci.cEnd);
910 to = Math.max(cXci.cStart, cXci.cEnd);
911 System.err.println("Marking " + fr + " to " + to);
912 for (int c = fr; c <= to; c++)
914 av.getColumnSelection().addElement(c);
916 fr = Math.min(lastX, currentX);
917 to = Math.max(lastX, currentX);
919 System.err.println("Marking " + fr + " to " + to);
920 for (int c = fr; c <= to; c++)
922 av.getColumnSelection().addElement(c);
929 * Constructs the tooltip, and constructs and displays a status message, for
930 * the current mouse position
935 public void mouseMoved(MouseEvent evt)
937 int yPos = evt.getY();
938 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
939 int rowAndOffset[] = getRowIndexAndOffset(yPos, aa);
940 int row = rowAndOffset[0];
944 this.setToolTipText(null);
948 int column = getColumnForXPos(evt.getX());
950 AlignmentAnnotation ann = aa[row];
951 if (row > -1 && ann.annotations != null
952 && column < ann.annotations.length)
954 String toolTip = buildToolTip(ann, column, aa, rowAndOffset[1], av,
956 setToolTipText(toolTip == null ? null
957 : JvSwingUtils.wrapTooltip(true, toolTip));
958 String msg = getStatusMessage(av.getAlignment(), column, ann,
959 rowAndOffset[1], av);
960 ap.alignFrame.setStatus(msg);
964 this.setToolTipText(null);
965 ap.alignFrame.setStatus(" ");
969 private int getColumnForXPos(int x)
971 int column = (x / av.getCharWidth()) + av.getRanges().getStartRes();
972 column = Math.min(column, av.getRanges().getEndRes());
974 if (av.hasHiddenColumns())
976 column = av.getAlignment().getHiddenColumns()
977 .visibleToAbsoluteColumn(column);
983 * Answers the index in the annotations array of the visible annotation at the
984 * given y position. This is done by adding the heights of visible annotations
985 * until the y position has been exceeded. Answers -1 if no annotations are
986 * visible, or the y position is below all annotations.
992 static int getRowIndex(int yPos, AlignmentAnnotation[] aa)
998 return getRowIndexAndOffset(yPos, aa)[0];
1001 static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)
1003 int[] res = new int[2];
1011 int height = 0, lheight = 0;
1013 for (int i = 0; i < aa.length; i++)
1018 height += aa[i].height;
1025 res[1] = height - yPos;
1033 * Answers a tooltip for the annotation at the current mouse position, not
1034 * wrapped in <html> tags (apply if wanted). Answers null if there is no
1040 * @param rowAndOffset
1042 static String buildToolTip(AlignmentAnnotation ann, int column,
1043 AlignmentAnnotation[] anns, int rowAndOffset, AlignViewportI av,
1046 String tooltip = null;
1047 if (ann.graphGroup > -1)
1049 StringBuilder tip = new StringBuilder(32);
1050 boolean first = true;
1051 for (int i = 0; i < anns.length; i++)
1053 if (anns[i].graphGroup == ann.graphGroup
1054 && anns[i].annotations[column] != null)
1061 tip.append(anns[i].label);
1062 String description = anns[i].annotations[column].description;
1063 if (description != null && description.length() > 0)
1065 tip.append(" ").append(description);
1069 tooltip = first ? null : tip.toString();
1071 else if (column < ann.annotations.length
1072 && ann.annotations[column] != null)
1074 tooltip = ann.annotations[column].description;
1076 // TODO abstract tooltip generator so different implementations can be built
1077 if (ann.graph == AlignmentAnnotation.CUSTOMRENDERER)
1079 ContactListI clist = av.getContactList(ann, column);
1082 ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight);
1083 ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset,
1085 ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
1086 tooltip = "Contact from " + ci.cStart + " to " + ci.cEnd
1087 + "<br/>Mean:" + cr.getMean();
1089 // ap.getStructureSelectionManager().mouseOverSequence(ann.sequenceRef,
1090 // new int[] {column, ci.cStart,ci.cEnd}, -1, null)
1097 * Constructs and returns the status bar message
1102 * @param rowAndOffset
1104 static String getStatusMessage(AlignmentI al, int column,
1105 AlignmentAnnotation ann, int rowAndOffset, AlignViewportI av)
1108 * show alignment column and annotation description if any
1110 StringBuilder text = new StringBuilder(32);
1111 text.append(MessageManager.getString("label.column")).append(" ")
1112 .append(column + 1);
1114 if (column < ann.annotations.length && ann.annotations[column] != null)
1116 String description = ann.annotations[column].description;
1117 if (description != null && description.trim().length() > 0)
1119 text.append(" ").append(description);
1124 * if the annotation is sequence-specific, show the sequence number
1125 * in the alignment, and (if not a gap) the residue and position
1127 SequenceI seqref = ann.sequenceRef;
1130 int seqIndex = al.findIndex(seqref);
1133 text.append(", ").append(MessageManager.getString("label.sequence"))
1134 .append(" ").append(seqIndex + 1);
1135 char residue = seqref.getCharAt(column);
1136 if (!Comparison.isGap(residue))
1140 if (al.isNucleotide())
1142 name = ResidueProperties.nucleotideName
1143 .get(String.valueOf(residue));
1144 text.append(" Nucleotide: ")
1145 .append(name != null ? name : residue);
1149 name = 'X' == residue ? "X"
1150 : ('*' == residue ? "STOP"
1151 : ResidueProperties.aa2Triplet
1152 .get(String.valueOf(residue)));
1153 text.append(" Residue: ").append(name != null ? name : residue);
1155 int residuePos = seqref.findPosition(column);
1156 text.append(" (").append(residuePos).append(")");
1161 return text.toString();
1171 public void mouseClicked(MouseEvent evt)
1173 // if (activeRow != -1)
1175 // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
1176 // AlignmentAnnotation anot = aa[activeRow];
1180 // TODO mouseClicked-content and drawCursor are quite experimental!
1181 public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
1184 int pady = av.getCharHeight() / 5;
1186 graphics.setColor(Color.black);
1187 graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
1189 if (av.validCharWidth)
1191 graphics.setColor(Color.white);
1193 char s = seq.getCharAt(res);
1195 charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
1196 graphics.drawString(String.valueOf(s), charOffset + x1,
1197 (y1 + av.getCharHeight()) - pady);
1202 private volatile boolean imageFresh = false;
1204 private Rectangle visibleRect = new Rectangle(),
1205 clipBounds = new Rectangle();
1214 public void paintComponent(Graphics g)
1217 // BH: note that this method is generally recommended to
1218 // call super.paintComponent(g). Otherwise, the children of this
1219 // component will not be rendered. That is not needed here
1220 // because AnnotationPanel does not have any children. It is
1221 // just a JPanel contained in a JViewPort.
1223 computeVisibleRect(visibleRect);
1225 g.setColor(Color.white);
1226 g.fillRect(0, 0, visibleRect.width, visibleRect.height);
1230 // BH 2018 optimizing generation of new Rectangle().
1232 || (visibleRect.width != (clipBounds = g
1233 .getClipBounds(clipBounds)).width)
1234 || (visibleRect.height != clipBounds.height))
1237 g.drawImage(image, 0, 0, this);
1242 imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
1243 + 1) * av.getCharWidth();
1249 if (image == null || imgWidth != image.getWidth(this)
1250 || image.getHeight(this) != getHeight())
1254 image = new BufferedImage(imgWidth,
1255 ap.getAnnotationPanel().getHeight(),
1256 BufferedImage.TYPE_INT_RGB);
1257 } catch (OutOfMemoryError oom)
1262 } catch (Exception x)
1267 "Couldn't allocate memory to redraw screen. Please restart Jalview",
1271 gg = (Graphics2D) image.getGraphics();
1275 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
1276 RenderingHints.VALUE_ANTIALIAS_ON);
1279 gg.setFont(av.getFont());
1280 fm = gg.getFontMetrics();
1281 gg.setColor(Color.white);
1282 gg.fillRect(0, 0, imgWidth, image.getHeight());
1287 gg = (Graphics2D) image.getGraphics();
1291 drawComponent(gg, av.getRanges().getStartRes(),
1292 av.getRanges().getEndRes() + 1);
1295 g.drawImage(image, 0, 0, this);
1299 * set true to enable redraw timing debug output on stderr
1301 private final boolean debugRedraw = false;
1304 * non-Thread safe repaint
1307 * repaint with horizontal shift in alignment
1309 public void fastPaint(int horizontal)
1311 if ((horizontal == 0) || image == null
1312 || av.getAlignment().getAlignmentAnnotation() == null
1313 || av.getAlignment().getAlignmentAnnotation().length < 1
1314 || av.isCalcInProgress())
1320 int sr = av.getRanges().getStartRes();
1321 int er = av.getRanges().getEndRes() + 1;
1324 Graphics2D gg = (Graphics2D) image.getGraphics();
1326 if (imgWidth > Math.abs(horizontal * av.getCharWidth()))
1328 // scroll is less than imgWidth away so can re-use buffered graphics
1329 gg.copyArea(0, 0, imgWidth, getHeight(),
1330 -horizontal * av.getCharWidth(), 0);
1332 if (horizontal > 0) // scrollbar pulled right, image to the left
1334 transX = (er - sr - horizontal) * av.getCharWidth();
1335 sr = er - horizontal;
1337 else if (horizontal < 0)
1339 er = sr - horizontal;
1342 gg.translate(transX, 0);
1344 drawComponent(gg, sr, er);
1346 gg.translate(-transX, 0);
1352 // Call repaint on alignment panel so that repaints from other alignment
1353 // panel components can be aggregated. Otherwise performance of the overview
1354 // window and others may be adversely affected.
1355 av.getAlignPanel().repaint();
1358 private volatile boolean lastImageGood = false;
1370 public void drawComponent(Graphics g, int startRes, int endRes)
1372 BufferedImage oldFaded = fadedImage;
1373 if (av.isCalcInProgress())
1377 lastImageGood = false;
1380 // We'll keep a record of the old image,
1381 // and draw a faded image until the calculation
1384 && (fadedImage == null || fadedImage.getWidth() != imgWidth
1385 || fadedImage.getHeight() != image.getHeight()))
1387 // System.err.println("redraw faded image ("+(fadedImage==null ?
1388 // "null image" : "") + " lastGood="+lastImageGood+")");
1389 fadedImage = new BufferedImage(imgWidth, image.getHeight(),
1390 BufferedImage.TYPE_INT_RGB);
1392 Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
1394 fadedG.setColor(Color.white);
1395 fadedG.fillRect(0, 0, imgWidth, image.getHeight());
1397 fadedG.setComposite(
1398 AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f));
1399 fadedG.drawImage(image, 0, 0, this);
1402 // make sure we don't overwrite the last good faded image until all
1403 // calculations have finished
1404 lastImageGood = false;
1409 if (fadedImage != null)
1411 oldFaded = fadedImage;
1416 g.setColor(Color.white);
1417 g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
1419 g.setFont(av.getFont());
1422 fm = g.getFontMetrics();
1425 if ((av.getAlignment().getAlignmentAnnotation() == null)
1426 || (av.getAlignment().getAlignmentAnnotation().length < 1))
1428 g.setColor(Color.white);
1429 g.fillRect(0, 0, getWidth(), getHeight());
1430 g.setColor(Color.black);
1431 if (av.validCharWidth)
1433 g.drawString(MessageManager
1434 .getString("label.alignment_has_no_annotations"), 20, 15);
1439 lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes,
1441 if (!lastImageGood && fadedImage == null)
1443 fadedImage = oldFaded;
1445 if (dragMode == DragMode.MatrixSelect)
1447 g.setColor(Color.yellow);
1448 g.drawRect(Math.min(firstDragX, mouseDragLastX),
1449 Math.min(firstDragY, mouseDragLastY),
1450 Math.max(firstDragX, mouseDragLastX)
1451 - Math.min(firstDragX, mouseDragLastX),
1452 Math.max(firstDragY, mouseDragLastY)
1453 - Math.min(firstDragY, mouseDragLastY));
1459 public FontMetrics getFontMetrics()
1465 public Image getFadedImage()
1471 public int getFadedImageWidth()
1476 private int[] bounds = new int[2];
1479 public int[] getVisibleVRange()
1481 if (ap != null && ap.getAlabels() != null)
1483 int sOffset = -ap.getAlabels().getScrollOffset();
1484 int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
1485 bounds[0] = sOffset;
1486 bounds[1] = visHeight;
1496 * Try to ensure any references held are nulled
1498 public void dispose()
1508 * I created the renderer so I will dispose of it
1510 if (renderer != null)
1517 public void propertyChange(PropertyChangeEvent evt)
1519 // Respond to viewport range changes (e.g. alignment panel was scrolled)
1520 // Both scrolling and resizing change viewport ranges: scrolling changes
1521 // both start and end points, but resize only changes end values.
1522 // Here we only want to fastpaint on a scroll, with resize using a normal
1523 // paint, so scroll events are identified as changes to the horizontal or
1524 // vertical start value.
1525 if (evt.getPropertyName().equals(ViewportRanges.STARTRES))
1527 fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
1529 else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
1531 fastPaint(((int[]) evt.getNewValue())[0]
1532 - ((int[]) evt.getOldValue())[0]);
1534 else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
1541 * computes the visible height of the annotation panel
1543 * @param adjustPanelHeight
1544 * - when false, just adjust existing height according to other
1546 * @param annotationHeight
1547 * @return height to use for the ScrollerPreferredVisibleSize
1549 public int adjustForAlignFrame(boolean adjustPanelHeight,
1550 int annotationHeight)
1553 * Estimate available height in the AlignFrame for alignment +
1554 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
1555 * hscroll, status bar, insets.
1557 int stuff = (ap.getViewName() != null ? 30 : 0)
1558 + (Platform.isAMacAndNotJS() ? 120 : 140);
1559 int availableHeight = ap.alignFrame.getHeight() - stuff;
1560 int rowHeight = av.getCharHeight();
1562 if (adjustPanelHeight)
1564 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
1567 * If not enough vertical space, maximize annotation height while keeping
1568 * at least two rows of alignment visible
1570 if (annotationHeight + alignmentHeight > availableHeight)
1572 annotationHeight = Math.min(annotationHeight,
1573 availableHeight - 2 * rowHeight);
1578 // maintain same window layout whilst updating sliders
1579 annotationHeight = Math.min(ap.annotationScroller.getSize().height,
1580 availableHeight - 2 * rowHeight);
1582 return annotationHeight;