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);
894 ContactGeometry cXcgeom = new ContactGeometry(forToX,
896 ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1],
897 rowIndex[1] - deltaY);
899 // mark rectangular region formed by drag
900 System.err.println("Matrix Selection from last(" + fromXc + ",["
901 + lastXci.cStart + "," + lastXci.cEnd + "]) to cur(" + toXc
902 + ",[" + cXci.cStart + "," + cXci.cEnd + "])");
904 fr = Math.min(lastXci.cStart, lastXci.cEnd);
905 to = Math.max(lastXci.cStart, lastXci.cEnd);
906 System.err.println("Marking " + fr + " to " + to);
907 for (int c = fr; c <= to; c++)
909 if (cma.sequenceRef != null)
911 int col = cma.sequenceRef.findIndex(c);
912 av.getColumnSelection().addElement(col);
916 av.getColumnSelection().addElement(c);
919 fr = Math.min(cXci.cStart, cXci.cEnd);
920 to = Math.max(cXci.cStart, cXci.cEnd);
921 System.err.println("Marking " + fr + " to " + to);
922 for (int c = fr; c <= to; c++)
924 if (cma.sequenceRef != null)
926 int col = cma.sequenceRef.findIndex(c);
927 av.getColumnSelection().addElement(col);
931 av.getColumnSelection().addElement(c);
934 fr = Math.min(lastX, currentX);
935 to = Math.max(lastX, currentX);
937 System.err.println("Marking " + fr + " to " + to);
938 for (int c = fr; c <= to; c++)
940 av.getColumnSelection().addElement(c);
947 * Constructs the tooltip, and constructs and displays a status message, for
948 * the current mouse position
953 public void mouseMoved(MouseEvent evt)
955 int yPos = evt.getY();
956 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
957 int rowAndOffset[] = getRowIndexAndOffset(yPos, aa);
958 int row = rowAndOffset[0];
962 this.setToolTipText(null);
966 int column = getColumnForXPos(evt.getX());
968 AlignmentAnnotation ann = aa[row];
969 if (row > -1 && ann.annotations != null
970 && column < ann.annotations.length)
972 String toolTip = buildToolTip(ann, column, aa, rowAndOffset[1], av,
974 setToolTipText(toolTip == null ? null
975 : JvSwingUtils.wrapTooltip(true, toolTip));
976 String msg = getStatusMessage(av.getAlignment(), column, ann,
977 rowAndOffset[1], av);
978 ap.alignFrame.setStatus(msg);
982 this.setToolTipText(null);
983 ap.alignFrame.setStatus(" ");
987 private int getColumnForXPos(int x)
989 int column = (x / av.getCharWidth()) + av.getRanges().getStartRes();
990 column = Math.min(column, av.getRanges().getEndRes());
992 if (av.hasHiddenColumns())
994 column = av.getAlignment().getHiddenColumns()
995 .visibleToAbsoluteColumn(column);
1001 * Answers the index in the annotations array of the visible annotation at the
1002 * given y position. This is done by adding the heights of visible annotations
1003 * until the y position has been exceeded. Answers -1 if no annotations are
1004 * visible, or the y position is below all annotations.
1010 static int getRowIndex(int yPos, AlignmentAnnotation[] aa)
1016 return getRowIndexAndOffset(yPos, aa)[0];
1019 static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)
1021 int[] res = new int[2];
1029 int height = 0, lheight = 0;
1031 for (int i = 0; i < aa.length; i++)
1036 height += aa[i].height;
1043 res[1] = height - yPos;
1051 * Answers a tooltip for the annotation at the current mouse position, not
1052 * wrapped in <html> tags (apply if wanted). Answers null if there is no
1058 * @param rowAndOffset
1060 static String buildToolTip(AlignmentAnnotation ann, int column,
1061 AlignmentAnnotation[] anns, int rowAndOffset, AlignViewportI av,
1064 String tooltip = null;
1065 if (ann.graphGroup > -1)
1067 StringBuilder tip = new StringBuilder(32);
1068 boolean first = true;
1069 for (int i = 0; i < anns.length; i++)
1071 if (anns[i].graphGroup == ann.graphGroup
1072 && anns[i].annotations[column] != null)
1079 tip.append(anns[i].label);
1080 String description = anns[i].annotations[column].description;
1081 if (description != null && description.length() > 0)
1083 tip.append(" ").append(description);
1087 tooltip = first ? null : tip.toString();
1089 else if (column < ann.annotations.length
1090 && ann.annotations[column] != null)
1092 tooltip = ann.annotations[column].description;
1094 // TODO abstract tooltip generator so different implementations can be built
1095 if (ann.graph == AlignmentAnnotation.CUSTOMRENDERER)
1097 ContactListI clist = av.getContactList(ann, column);
1100 ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight);
1101 ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset,
1103 ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
1104 tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
1105 + " - " + ci.cEnd + "]" + "<br/>Mean:" + cr.getMean();
1107 // ap.getStructureSelectionManager().mouseOverSequence(ann.sequenceRef,
1108 // new int[] {column, ci.cStart,ci.cEnd}, -1, null)
1115 * Constructs and returns the status bar message
1120 * @param rowAndOffset
1122 static String getStatusMessage(AlignmentI al, int column,
1123 AlignmentAnnotation ann, int rowAndOffset, AlignViewportI av)
1126 * show alignment column and annotation description if any
1128 StringBuilder text = new StringBuilder(32);
1129 text.append(MessageManager.getString("label.column")).append(" ")
1130 .append(column + 1);
1132 if (column < ann.annotations.length && ann.annotations[column] != null)
1134 String description = ann.annotations[column].description;
1135 if (description != null && description.trim().length() > 0)
1137 text.append(" ").append(description);
1142 * if the annotation is sequence-specific, show the sequence number
1143 * in the alignment, and (if not a gap) the residue and position
1145 SequenceI seqref = ann.sequenceRef;
1148 int seqIndex = al.findIndex(seqref);
1151 text.append(", ").append(MessageManager.getString("label.sequence"))
1152 .append(" ").append(seqIndex + 1);
1153 char residue = seqref.getCharAt(column);
1154 if (!Comparison.isGap(residue))
1158 if (al.isNucleotide())
1160 name = ResidueProperties.nucleotideName
1161 .get(String.valueOf(residue));
1162 text.append(" Nucleotide: ")
1163 .append(name != null ? name : residue);
1167 name = 'X' == residue ? "X"
1168 : ('*' == residue ? "STOP"
1169 : ResidueProperties.aa2Triplet
1170 .get(String.valueOf(residue)));
1171 text.append(" Residue: ").append(name != null ? name : residue);
1173 int residuePos = seqref.findPosition(column);
1174 text.append(" (").append(residuePos).append(")");
1179 return text.toString();
1189 public void mouseClicked(MouseEvent evt)
1191 // if (activeRow != -1)
1193 // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
1194 // AlignmentAnnotation anot = aa[activeRow];
1198 // TODO mouseClicked-content and drawCursor are quite experimental!
1199 public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
1202 int pady = av.getCharHeight() / 5;
1204 graphics.setColor(Color.black);
1205 graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
1207 if (av.validCharWidth)
1209 graphics.setColor(Color.white);
1211 char s = seq.getCharAt(res);
1213 charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
1214 graphics.drawString(String.valueOf(s), charOffset + x1,
1215 (y1 + av.getCharHeight()) - pady);
1220 private volatile boolean imageFresh = false;
1222 private Rectangle visibleRect = new Rectangle(),
1223 clipBounds = new Rectangle();
1232 public void paintComponent(Graphics g)
1235 // BH: note that this method is generally recommended to
1236 // call super.paintComponent(g). Otherwise, the children of this
1237 // component will not be rendered. That is not needed here
1238 // because AnnotationPanel does not have any children. It is
1239 // just a JPanel contained in a JViewPort.
1241 computeVisibleRect(visibleRect);
1243 g.setColor(Color.white);
1244 g.fillRect(0, 0, visibleRect.width, visibleRect.height);
1248 // BH 2018 optimizing generation of new Rectangle().
1250 || (visibleRect.width != (clipBounds = g
1251 .getClipBounds(clipBounds)).width)
1252 || (visibleRect.height != clipBounds.height))
1255 g.drawImage(image, 0, 0, this);
1260 imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
1261 + 1) * av.getCharWidth();
1267 if (image == null || imgWidth != image.getWidth(this)
1268 || image.getHeight(this) != getHeight())
1272 image = new BufferedImage(imgWidth,
1273 ap.getAnnotationPanel().getHeight(),
1274 BufferedImage.TYPE_INT_RGB);
1275 } catch (OutOfMemoryError oom)
1280 } catch (Exception x)
1285 "Couldn't allocate memory to redraw screen. Please restart Jalview",
1289 gg = (Graphics2D) image.getGraphics();
1293 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
1294 RenderingHints.VALUE_ANTIALIAS_ON);
1297 gg.setFont(av.getFont());
1298 fm = gg.getFontMetrics();
1299 gg.setColor(Color.white);
1300 gg.fillRect(0, 0, imgWidth, image.getHeight());
1305 gg = (Graphics2D) image.getGraphics();
1309 drawComponent(gg, av.getRanges().getStartRes(),
1310 av.getRanges().getEndRes() + 1);
1313 g.drawImage(image, 0, 0, this);
1317 * set true to enable redraw timing debug output on stderr
1319 private final boolean debugRedraw = false;
1322 * non-Thread safe repaint
1325 * repaint with horizontal shift in alignment
1327 public void fastPaint(int horizontal)
1329 if ((horizontal == 0) || image == null
1330 || av.getAlignment().getAlignmentAnnotation() == null
1331 || av.getAlignment().getAlignmentAnnotation().length < 1
1332 || av.isCalcInProgress())
1338 int sr = av.getRanges().getStartRes();
1339 int er = av.getRanges().getEndRes() + 1;
1342 Graphics2D gg = (Graphics2D) image.getGraphics();
1344 if (imgWidth > Math.abs(horizontal * av.getCharWidth()))
1346 // scroll is less than imgWidth away so can re-use buffered graphics
1347 gg.copyArea(0, 0, imgWidth, getHeight(),
1348 -horizontal * av.getCharWidth(), 0);
1350 if (horizontal > 0) // scrollbar pulled right, image to the left
1352 transX = (er - sr - horizontal) * av.getCharWidth();
1353 sr = er - horizontal;
1355 else if (horizontal < 0)
1357 er = sr - horizontal;
1360 gg.translate(transX, 0);
1362 drawComponent(gg, sr, er);
1364 gg.translate(-transX, 0);
1370 // Call repaint on alignment panel so that repaints from other alignment
1371 // panel components can be aggregated. Otherwise performance of the overview
1372 // window and others may be adversely affected.
1373 av.getAlignPanel().repaint();
1376 private volatile boolean lastImageGood = false;
1388 public void drawComponent(Graphics g, int startRes, int endRes)
1390 BufferedImage oldFaded = fadedImage;
1391 if (av.isCalcInProgress())
1395 lastImageGood = false;
1398 // We'll keep a record of the old image,
1399 // and draw a faded image until the calculation
1402 && (fadedImage == null || fadedImage.getWidth() != imgWidth
1403 || fadedImage.getHeight() != image.getHeight()))
1405 // System.err.println("redraw faded image ("+(fadedImage==null ?
1406 // "null image" : "") + " lastGood="+lastImageGood+")");
1407 fadedImage = new BufferedImage(imgWidth, image.getHeight(),
1408 BufferedImage.TYPE_INT_RGB);
1410 Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
1412 fadedG.setColor(Color.white);
1413 fadedG.fillRect(0, 0, imgWidth, image.getHeight());
1415 fadedG.setComposite(
1416 AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f));
1417 fadedG.drawImage(image, 0, 0, this);
1420 // make sure we don't overwrite the last good faded image until all
1421 // calculations have finished
1422 lastImageGood = false;
1427 if (fadedImage != null)
1429 oldFaded = fadedImage;
1434 g.setColor(Color.white);
1435 g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
1437 g.setFont(av.getFont());
1440 fm = g.getFontMetrics();
1443 if ((av.getAlignment().getAlignmentAnnotation() == null)
1444 || (av.getAlignment().getAlignmentAnnotation().length < 1))
1446 g.setColor(Color.white);
1447 g.fillRect(0, 0, getWidth(), getHeight());
1448 g.setColor(Color.black);
1449 if (av.validCharWidth)
1451 g.drawString(MessageManager
1452 .getString("label.alignment_has_no_annotations"), 20, 15);
1457 lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes,
1459 if (!lastImageGood && fadedImage == null)
1461 fadedImage = oldFaded;
1463 if (dragMode == DragMode.MatrixSelect)
1465 g.setColor(Color.yellow);
1466 g.drawRect(Math.min(firstDragX, mouseDragLastX),
1467 Math.min(firstDragY, mouseDragLastY),
1468 Math.max(firstDragX, mouseDragLastX)
1469 - Math.min(firstDragX, mouseDragLastX),
1470 Math.max(firstDragY, mouseDragLastY)
1471 - Math.min(firstDragY, mouseDragLastY));
1477 public FontMetrics getFontMetrics()
1483 public Image getFadedImage()
1489 public int getFadedImageWidth()
1494 private int[] bounds = new int[2];
1497 public int[] getVisibleVRange()
1499 if (ap != null && ap.getAlabels() != null)
1501 int sOffset = -ap.getAlabels().getScrollOffset();
1502 int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
1503 bounds[0] = sOffset;
1504 bounds[1] = visHeight;
1514 * Try to ensure any references held are nulled
1516 public void dispose()
1526 * I created the renderer so I will dispose of it
1528 if (renderer != null)
1535 public void propertyChange(PropertyChangeEvent evt)
1537 // Respond to viewport range changes (e.g. alignment panel was scrolled)
1538 // Both scrolling and resizing change viewport ranges: scrolling changes
1539 // both start and end points, but resize only changes end values.
1540 // Here we only want to fastpaint on a scroll, with resize using a normal
1541 // paint, so scroll events are identified as changes to the horizontal or
1542 // vertical start value.
1543 if (evt.getPropertyName().equals(ViewportRanges.STARTRES))
1545 fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
1547 else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
1549 fastPaint(((int[]) evt.getNewValue())[0]
1550 - ((int[]) evt.getOldValue())[0]);
1552 else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
1559 * computes the visible height of the annotation panel
1561 * @param adjustPanelHeight
1562 * - when false, just adjust existing height according to other
1564 * @param annotationHeight
1565 * @return height to use for the ScrollerPreferredVisibleSize
1567 public int adjustForAlignFrame(boolean adjustPanelHeight,
1568 int annotationHeight)
1571 * Estimate available height in the AlignFrame for alignment +
1572 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
1573 * hscroll, status bar, insets.
1575 int stuff = (ap.getViewName() != null ? 30 : 0)
1576 + (Platform.isAMacAndNotJS() ? 120 : 140);
1577 int availableHeight = ap.alignFrame.getHeight() - stuff;
1578 int rowHeight = av.getCharHeight();
1580 if (adjustPanelHeight)
1582 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
1585 * If not enough vertical space, maximize annotation height while keeping
1586 * at least two rows of alignment visible
1588 if (annotationHeight + alignmentHeight > availableHeight)
1590 annotationHeight = Math.min(annotationHeight,
1591 availableHeight - 2 * rowHeight);
1596 // maintain same window layout whilst updating sliders
1597 annotationHeight = Math.min(ap.annotationScroller.getSize().height,
1598 availableHeight - 2 * rowHeight);
1600 return annotationHeight;