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.BitSet;
45 import java.util.Collections;
46 import java.util.List;
48 import javax.swing.JMenuItem;
49 import javax.swing.JPanel;
50 import javax.swing.JPopupMenu;
51 import javax.swing.Scrollable;
52 import javax.swing.ToolTipManager;
54 import jalview.api.AlignViewportI;
55 import jalview.datamodel.AlignmentAnnotation;
56 import jalview.datamodel.AlignmentI;
57 import jalview.datamodel.Annotation;
58 import jalview.datamodel.ColumnSelection;
59 import jalview.datamodel.ContactListI;
60 import jalview.datamodel.ContactMatrixI;
61 import jalview.datamodel.ContactRange;
62 import jalview.datamodel.GraphLine;
63 import jalview.datamodel.HiddenColumns;
64 import jalview.datamodel.SequenceI;
65 import jalview.gui.JalviewColourChooser.ColourChooserListener;
66 import jalview.renderer.AnnotationRenderer;
67 import jalview.renderer.AwtRenderPanelI;
68 import jalview.renderer.ContactGeometry;
69 import jalview.schemes.ResidueProperties;
70 import jalview.util.Comparison;
71 import jalview.util.MessageManager;
72 import jalview.util.Platform;
73 import jalview.viewmodel.ViewportListenerI;
74 import jalview.viewmodel.ViewportRanges;
75 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
78 * AnnotationPanel displays visible portion of annotation rows below unwrapped
84 public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
85 MouseListener, MouseWheelListener, MouseMotionListener,
86 ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
90 Select, Resize, Undefined, MatrixSelect
93 String HELIX = MessageManager.getString("label.helix");
95 String SHEET = MessageManager.getString("label.sheet");
98 * For RNA secondary structure "stems" aka helices
100 String STEM = MessageManager.getString("label.rna_helix");
102 String LABEL = MessageManager.getString("label.label");
104 String REMOVE = MessageManager.getString("label.remove_annotation");
106 String COLOUR = MessageManager.getString("action.colour");
108 public final Color HELIX_COLOUR = Color.red.darker();
110 public final Color SHEET_COLOUR = Color.green.darker().darker();
112 public final Color STEM_COLOUR = Color.blue.darker();
115 public AlignViewport av;
119 public int activeRow = -1;
121 public BufferedImage image;
123 public volatile BufferedImage fadedImage;
125 // private Graphics2D gg;
127 public FontMetrics fm;
129 public int imgWidth = 0;
131 boolean fastPaint = false;
133 // Used For mouse Dragging and resizing graphs
134 int graphStretch = -1;
136 int mouseDragLastX = -1;
138 int mouseDragLastY = -1;
144 DragMode dragMode = DragMode.Undefined;
146 boolean mouseDragging = false;
148 // for editing cursor
153 public final AnnotationRenderer renderer;
155 private MouseWheelListener[] _mwl;
157 private boolean notJustOne;
160 * Creates a new AnnotationPanel object.
165 public AnnotationPanel(AlignmentPanel ap)
167 ToolTipManager.sharedInstance().registerComponent(this);
168 ToolTipManager.sharedInstance().setInitialDelay(0);
169 ToolTipManager.sharedInstance().setDismissDelay(10000);
172 this.setLayout(null);
173 addMouseListener(this);
174 addMouseMotionListener(this);
175 ap.annotationScroller.getVerticalScrollBar()
176 .addAdjustmentListener(this);
177 // save any wheel listeners on the scroller, so we can propagate scroll
179 _mwl = ap.annotationScroller.getMouseWheelListeners();
180 // and then set our own listener to consume all mousewheel events
181 ap.annotationScroller.addMouseWheelListener(this);
182 renderer = new AnnotationRenderer();
184 av.getRanges().addPropertyChangeListener(this);
187 public AnnotationPanel(AlignViewport av)
190 renderer = new AnnotationRenderer();
194 public void mouseWheelMoved(MouseWheelEvent e)
199 double wheelRotation = e.getPreciseWheelRotation();
200 if (wheelRotation > 0)
202 av.getRanges().scrollRight(true);
204 else if (wheelRotation < 0)
206 av.getRanges().scrollRight(false);
211 // TODO: find the correct way to let the event bubble up to
212 // ap.annotationScroller
213 for (MouseWheelListener mwl : _mwl)
217 mwl.mouseWheelMoved(e);
228 public Dimension getPreferredScrollableViewportSize()
230 Dimension ps = getPreferredSize();
231 return new Dimension(ps.width, adjustForAlignFrame(false, ps.height));
235 public int getScrollableBlockIncrement(Rectangle visibleRect,
236 int orientation, int direction)
242 public boolean getScrollableTracksViewportHeight()
248 public boolean getScrollableTracksViewportWidth()
254 public int getScrollableUnitIncrement(Rectangle visibleRect,
255 int orientation, int direction)
264 * java.awt.event.AdjustmentListener#adjustmentValueChanged(java.awt.event
268 public void adjustmentValueChanged(AdjustmentEvent evt)
270 // update annotation label display
271 ap.getAlabels().setScrollOffset(-evt.getValue());
275 * Calculates the height of the annotation displayed in the annotation panel.
276 * Callers should normally call the ap.adjustAnnotationHeight method to ensure
277 * all annotation associated components are updated correctly.
280 public int adjustPanelHeight()
282 int height = av.calcPanelHeight();
283 this.setPreferredSize(new Dimension(1, height));
286 // revalidate only when the alignment panel is fully constructed
300 public void actionPerformed(ActionEvent evt)
302 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
307 Annotation[] anot = aa[activeRow].annotations;
309 if (anot.length < av.getColumnSelection().getMax())
311 Annotation[] temp = new Annotation[av.getColumnSelection().getMax()
313 System.arraycopy(anot, 0, temp, 0, anot.length);
315 aa[activeRow].annotations = anot;
318 String action = evt.getActionCommand();
319 if (action.equals(REMOVE))
321 for (int index : av.getColumnSelection().getSelected())
323 if (av.getAlignment().getHiddenColumns().isVisible(index))
329 else if (action.equals(LABEL))
331 String exMesg = collectAnnotVals(anot, LABEL);
332 String label = JvOptionPane.showInputDialog(
333 MessageManager.getString("label.enter_label"), exMesg);
340 if ((label.length() > 0) && !aa[activeRow].hasText)
342 aa[activeRow].hasText = true;
345 for (int index : av.getColumnSelection().getSelected())
347 if (!av.getAlignment().getHiddenColumns().isVisible(index))
352 if (anot[index] == null)
354 anot[index] = new Annotation(label, "", ' ', 0);
358 anot[index].displayCharacter = label;
362 else if (action.equals(COLOUR))
364 final Annotation[] fAnot = anot;
365 String title = MessageManager
366 .getString("label.select_foreground_colour");
367 ColourChooserListener listener = new ColourChooserListener()
370 public void colourSelected(Color c)
372 HiddenColumns hiddenColumns = av.getAlignment()
374 for (int index : av.getColumnSelection().getSelected())
376 if (hiddenColumns.isVisible(index))
378 if (fAnot[index] == null)
380 fAnot[index] = new Annotation("", "", ' ', 0);
382 fAnot[index].colour = c;
387 JalviewColourChooser.showColourChooser(this, title, Color.black,
391 // HELIX, SHEET or STEM
394 String symbol = "\u03B1"; // alpha
396 if (action.equals(HELIX))
400 else if (action.equals(SHEET))
403 symbol = "\u03B2"; // beta
406 // Added by LML to color stems
407 else if (action.equals(STEM))
410 int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
411 symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
414 if (!aa[activeRow].hasIcons)
416 aa[activeRow].hasIcons = true;
419 String label = JvOptionPane.showInputDialog(MessageManager
420 .getString("label.enter_label_for_the_structure"), symbol);
427 if ((label.length() > 0) && !aa[activeRow].hasText)
429 aa[activeRow].hasText = true;
430 if (action.equals(STEM))
432 aa[activeRow].showAllColLabels = true;
435 for (int index : av.getColumnSelection().getSelected())
437 if (!av.getAlignment().getHiddenColumns().isVisible(index))
442 if (anot[index] == null)
444 anot[index] = new Annotation(label, "", type, 0);
447 anot[index].secondaryStructure = type != 'S' ? type
448 : label.length() == 0 ? ' ' : label.charAt(0);
449 anot[index].displayCharacter = label;
454 av.getAlignment().validateAnnotation(aa[activeRow]);
455 ap.alignmentChanged();
456 ap.alignFrame.setMenusForViewport();
464 * Returns any existing annotation concatenated as a string. For each
465 * annotation, takes the description, if any, else the secondary structure
466 * character (if type is HELIX, SHEET or STEM), else the display character (if
473 private String collectAnnotVals(Annotation[] anots, String type)
475 // TODO is this method wanted? why? 'last' is not used
477 StringBuilder collatedInput = new StringBuilder(64);
479 ColumnSelection viscols = av.getColumnSelection();
480 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
483 * the selection list (read-only view) is in selection order, not
484 * column order; make a copy so we can sort it
486 List<Integer> selected = new ArrayList<>(viscols.getSelected());
487 Collections.sort(selected);
488 for (int index : selected)
490 // always check for current display state - just in case
491 if (!hidden.isVisible(index))
495 String tlabel = null;
496 if (anots[index] != null)
497 { // LML added stem code
498 if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
499 || type.equals(LABEL))
501 tlabel = anots[index].description;
502 if (tlabel == null || tlabel.length() < 1)
504 if (type.equals(HELIX) || type.equals(SHEET)
505 || type.equals(STEM))
507 tlabel = "" + anots[index].secondaryStructure;
511 tlabel = "" + anots[index].displayCharacter;
515 if (tlabel != null && !tlabel.equals(last))
517 if (last.length() > 0)
519 collatedInput.append(" ");
521 collatedInput.append(tlabel);
525 return collatedInput.toString();
529 * Action on right mouse pressed on Mac is to show a pop-up menu for the
530 * annotation. Action on left mouse pressed is to find which annotation is
531 * pressed and mark the start of a column selection or graph resize operation.
536 public void mousePressed(MouseEvent evt)
539 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
544 mouseDragLastX = evt.getX();
545 mouseDragLastY = evt.getY();
548 * add visible annotation heights until we reach the y
549 * position, to find which annotation it is in
554 // todo could reuse getRowIndexAndOffset ?
555 final int y = evt.getY();
557 for (int i = 0; i < aa.length; i++)
561 height += aa[i].height;
570 else if (aa[i].graph != 0)
573 * we have clicked on a resizable graph annotation
576 yOffset = height - y;
583 * isPopupTrigger fires in mousePressed on Mac,
584 * not until mouseRelease on Windows
586 if (evt.isPopupTrigger() && activeRow != -1)
588 showPopupMenu(y, evt.getX());
592 if (graphStretch != -1)
595 if (aa[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP)
597 // data in row has position on y as well as x axis
598 if (evt.isAltDown() || evt.isAltGraphDown())
600 dragMode = DragMode.MatrixSelect;
601 firstDragX = mouseDragLastX;
602 firstDragY = mouseDragLastY;
608 // no row (or row that can be adjusted) was pressed. Simulate a ruler click
609 ap.getScalePanel().mousePressed(evt);
614 * checks whether the annotation row under the mouse click evt's handles the
618 * @return false if evt was not handled
620 boolean matrix_clicked(MouseEvent evt)
622 int[] rowIndex = getRowIndexAndOffset(evt.getY(),
623 av.getAlignment().getAlignmentAnnotation());
624 int yOffset = rowIndex[1];
626 if (rowIndex == null)
628 System.err.println("IMPLEMENTATION ERROR: matrix click out of range.");
630 AlignmentAnnotation clicked = av.getAlignment()
631 .getAlignmentAnnotation()[rowIndex[0]];
632 if (clicked.graph != AlignmentAnnotation.CONTACT_MAP)
637 // TODO - use existing threshold to select related sections of matrix
638 GraphLine thr = clicked.getThreshold();
640 int currentX = getColumnForXPos(evt.getX());
641 ContactListI forCurrentX = av.getContactList(clicked, currentX);
642 if (forCurrentX != null)
644 ContactGeometry cXcgeom = new ContactGeometry(forCurrentX,
645 clicked.graphHeight);
646 ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset,
649 * start and end range corresponding to the row range under the mouse at
653 fr = Math.min(cXci.cStart, cXci.cEnd);
654 to = Math.max(cXci.cStart, cXci.cEnd);
656 if (evt.isControlDown())
658 ContactMatrixI matrix = av.getContactMatrix(clicked);
662 // simplest approach is to select all group containing column
663 if (matrix.hasGroups())
665 SequenceI rseq = clicked.sequenceRef;
666 BitSet grp = matrix.getGroupsFor(currentX);
667 for (int c = fr; c <= to; c++)
669 BitSet additionalGrp = matrix.getGroupsFor(c);
670 grp.or(additionalGrp);
672 HiddenColumns hc = av.getAlignment().getHiddenColumns();
673 for (int p = grp.nextSetBit(0); p >= 0; p = grp
676 int offp = (rseq != null)
677 ? rseq.findIndex(rseq.getStart() - 1 + p)
680 if (!av.hasHiddenColumns() || hc.isVisible(offp))
682 av.getColumnSelection().addElement(offp);
686 // possible alternative for interactive selection - threshold
687 // gives 'ceiling' for forming a cluster
688 // when a row+column is selected, farthest common ancestor less
689 // than thr is used to compute cluster
695 // select corresponding range in segment under mouse
697 for (int c = fr; c <= to; c++)
699 av.getColumnSelection().addElement(c);
701 av.getColumnSelection().addElement(currentX);
704 // and also select everything lower than the max range adjacent
706 if (PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
709 ContactRange cr = forCurrentX.getRangeFor(fr, to);
711 // TODO: could use GraphLine instead of arbitrary picking
712 // TODO: could report mean/median/variance for partitions
713 // (contiguous selected vs unselected regions and inter-contig
715 // controls feathering - what other elements in row/column
717 double thresh = cr.getMean() + (cr.getMax() - cr.getMean()) * .15;
720 cval = forCurrentX.getContactAt(c);
721 if (// cr.getMin() <= cval &&
724 av.getColumnSelection().addElement(c--);
732 while (c < forCurrentX.getContactHeight())
734 cval = forCurrentX.getContactAt(c);
735 if (// cr.getMin() <= cval &&
738 av.getColumnSelection().addElement(c++);
748 ap.paintAlignment(false, false);
753 * Construct and display a context menu at the right-click position
758 void showPopupMenu(final int y, int x)
760 if (av.getColumnSelection() == null
761 || av.getColumnSelection().isEmpty())
766 JPopupMenu pop = new JPopupMenu(
767 MessageManager.getString("label.structure_type"));
770 * Just display the needed structure options
772 if (av.getAlignment().isNucleotide())
774 item = new JMenuItem(STEM);
775 item.addActionListener(this);
780 item = new JMenuItem(HELIX);
781 item.addActionListener(this);
783 item = new JMenuItem(SHEET);
784 item.addActionListener(this);
787 item = new JMenuItem(LABEL);
788 item.addActionListener(this);
790 item = new JMenuItem(COLOUR);
791 item.addActionListener(this);
793 item = new JMenuItem(REMOVE);
794 item.addActionListener(this);
796 pop.show(this, x, y);
800 * Action on mouse up is to clear mouse drag data and call mouseReleased on
801 * ScalePanel, to deal with defining the selection group (if any) defined by
807 public void mouseReleased(MouseEvent evt)
809 if (dragMode == DragMode.MatrixSelect)
811 matrixSelectRange(evt);
818 mouseDragging = false;
819 if (dragMode == DragMode.Resize)
821 ap.adjustAnnotationHeight();
823 dragMode = DragMode.Undefined;
824 if (!matrix_clicked(evt))
826 ap.getScalePanel().mouseReleased(evt);
830 * isPopupTrigger is set in mouseReleased on Windows
831 * (in mousePressed on Mac)
833 if (evt.isPopupTrigger() && activeRow != -1)
835 showPopupMenu(evt.getY(), evt.getX());
847 public void mouseEntered(MouseEvent evt)
849 this.mouseDragging = false;
850 ap.getScalePanel().mouseEntered(evt);
854 * On leaving the panel, calls ScalePanel.mouseExited to deal with scrolling
855 * with column selection on a mouse drag
860 public void mouseExited(MouseEvent evt)
862 ap.getScalePanel().mouseExited(evt);
866 * Action on starting or continuing a mouse drag. There are two possible
869 * <li>drag up or down on a graphed annotation increases or decreases the
870 * height of the graph</li>
871 * <li>dragging left or right selects the columns dragged across</li>
873 * A drag on a graph annotation is treated as column selection if it starts
874 * with more horizontal than vertical movement, and as resize if it starts
875 * with more vertical than horizontal movement. Once started, the drag does
881 public void mouseDragged(MouseEvent evt)
884 * if dragMode is Undefined:
885 * - set to Select if dx > dy
886 * - set to Resize if dy > dx
887 * - do nothing if dx == dy
889 final int x = evt.getX();
890 final int y = evt.getY();
891 if (dragMode == DragMode.Undefined)
893 int dx = Math.abs(x - mouseDragLastX);
894 int dy = Math.abs(y - mouseDragLastY);
895 if (graphStretch == -1 || dx > dy)
898 * mostly horizontal drag, or not a graph annotation
900 dragMode = DragMode.Select;
905 * mostly vertical drag
907 dragMode = DragMode.Resize;
908 notJustOne = evt.isShiftDown();
911 * but could also be a matrix drag
913 if ((evt.isAltDown() || evt.isAltGraphDown()) && (av.getAlignment()
914 .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP))
917 * dragging in a matrix
919 dragMode = DragMode.MatrixSelect;
920 firstDragX = mouseDragLastX;
921 firstDragY = mouseDragLastY;
926 if (dragMode == DragMode.Undefined)
930 * drag is diagonal - defer deciding whether to
931 * treat as up/down or left/right
938 if (dragMode == DragMode.Resize)
941 * resize graph annotation if mouse was dragged up or down
943 int deltaY = mouseDragLastY - evt.getY();
946 AlignmentAnnotation graphAnnotation = av.getAlignment()
947 .getAlignmentAnnotation()[graphStretch];
948 int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
951 for (AlignmentAnnotation similar : av.getAlignment()
952 .findAnnotations(null, graphAnnotation.getCalcId(),
953 graphAnnotation.label))
955 similar.graphHeight = newHeight;
961 graphAnnotation.graphHeight = newHeight;
964 ap.paintAlignment(false, false);
967 else if (dragMode == DragMode.MatrixSelect)
970 * TODO draw a rubber band for range
974 ap.paintAlignment(false, false);
979 * for mouse drag left or right, delegate to
980 * ScalePanel to adjust the column selection
982 ap.getScalePanel().mouseDragged(evt);
991 public void matrixSelectRange(MouseEvent evt)
994 * get geometry of drag
996 int fromY = Math.min(firstDragY, evt.getY());
997 int toY = Math.max(firstDragY, evt.getY());
998 int fromX = Math.min(firstDragX, evt.getX());
999 int toX = Math.max(firstDragX, evt.getX());
1001 int deltaY = toY - fromY;
1002 int deltaX = toX - fromX;
1004 int[] rowIndex = getRowIndexAndOffset(fromY,
1005 av.getAlignment().getAlignmentAnnotation());
1006 int[] toRowIndex = getRowIndexAndOffset(toY,
1007 av.getAlignment().getAlignmentAnnotation());
1009 if (rowIndex == null || toRowIndex == null)
1011 System.out.println("Drag out of range. needs to be clipped");
1014 if (rowIndex[0] != toRowIndex[0])
1016 System.out.println("Drag went to another row. needs to be clipped");
1019 // rectangular selection on matrix style annotation
1020 AlignmentAnnotation cma = av.getAlignment()
1021 .getAlignmentAnnotation()[rowIndex[0]];
1023 int lastX = getColumnForXPos(fromX);
1024 int currentX = getColumnForXPos(toX);
1025 int fromXc = Math.min(lastX, currentX);
1026 int toXc = Math.max(lastX, currentX);
1027 ContactListI forFromX = av.getContactList(cma, fromXc);
1028 ContactListI forToX = av.getContactList(cma, toXc);
1030 if (forFromX != null && forToX != null)
1032 ContactGeometry lastXcgeom = new ContactGeometry(forFromX,
1034 ContactGeometry.contactInterval lastXci = lastXcgeom
1035 .mapFor(rowIndex[1], rowIndex[1] - deltaY);
1037 ContactGeometry cXcgeom = new ContactGeometry(forToX,
1039 ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1],
1040 rowIndex[1] - deltaY);
1042 // mark rectangular region formed by drag
1043 System.err.println("Matrix Selection from last(" + fromXc + ",["
1044 + lastXci.cStart + "," + lastXci.cEnd + "]) to cur(" + toXc
1045 + ",[" + cXci.cStart + "," + cXci.cEnd + "])");
1047 fr = Math.min(lastXci.cStart, lastXci.cEnd);
1048 to = Math.max(lastXci.cStart, lastXci.cEnd);
1049 System.err.println("Marking " + fr + " to " + to);
1050 for (int c = fr; c <= to; c++)
1052 if (cma.sequenceRef != null)
1054 int col = cma.sequenceRef.findIndex(c);
1055 av.getColumnSelection().addElement(col);
1059 av.getColumnSelection().addElement(c);
1062 fr = Math.min(cXci.cStart, cXci.cEnd);
1063 to = Math.max(cXci.cStart, cXci.cEnd);
1064 System.err.println("Marking " + fr + " to " + to);
1065 for (int c = fr; c <= to; c++)
1067 if (cma.sequenceRef != null)
1069 int col = cma.sequenceRef.findIndex(c);
1070 av.getColumnSelection().addElement(col);
1074 av.getColumnSelection().addElement(c);
1077 fr = Math.min(lastX, currentX);
1078 to = Math.max(lastX, currentX);
1080 System.err.println("Marking " + fr + " to " + to);
1081 for (int c = fr; c <= to; c++)
1083 av.getColumnSelection().addElement(c);
1090 * Constructs the tooltip, and constructs and displays a status message, for
1091 * the current mouse position
1096 public void mouseMoved(MouseEvent evt)
1098 int yPos = evt.getY();
1099 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
1100 int rowAndOffset[] = getRowIndexAndOffset(yPos, aa);
1101 int row = rowAndOffset[0];
1105 this.setToolTipText(null);
1109 int column = getColumnForXPos(evt.getX());
1111 AlignmentAnnotation ann = aa[row];
1112 if (row > -1 && ann.annotations != null
1113 && column < ann.annotations.length)
1115 String toolTip = buildToolTip(ann, column, aa, rowAndOffset[1], av,
1117 setToolTipText(toolTip == null ? null
1118 : JvSwingUtils.wrapTooltip(true, toolTip));
1119 String msg = getStatusMessage(av.getAlignment(), column, ann,
1120 rowAndOffset[1], av);
1121 ap.alignFrame.setStatus(msg);
1125 this.setToolTipText(null);
1126 ap.alignFrame.setStatus(" ");
1130 private int getColumnForXPos(int x)
1132 int column = (x / av.getCharWidth()) + av.getRanges().getStartRes();
1133 column = Math.min(column, av.getRanges().getEndRes());
1135 if (av.hasHiddenColumns())
1137 column = av.getAlignment().getHiddenColumns()
1138 .visibleToAbsoluteColumn(column);
1144 * Answers the index in the annotations array of the visible annotation at the
1145 * given y position. This is done by adding the heights of visible annotations
1146 * until the y position has been exceeded. Answers -1 if no annotations are
1147 * visible, or the y position is below all annotations.
1153 static int getRowIndex(int yPos, AlignmentAnnotation[] aa)
1159 return getRowIndexAndOffset(yPos, aa)[0];
1162 static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)
1164 int[] res = new int[2];
1172 int height = 0, lheight = 0;
1173 for (int i = 0; i < aa.length; i++)
1178 height += aa[i].height;
1185 res[1] = height - yPos;
1193 * Answers a tooltip for the annotation at the current mouse position, not
1194 * wrapped in <html> tags (apply if wanted). Answers null if there is no
1200 * @param rowAndOffset
1202 static String buildToolTip(AlignmentAnnotation ann, int column,
1203 AlignmentAnnotation[] anns, int rowAndOffset, AlignViewportI av,
1206 String tooltip = null;
1207 if (ann.graphGroup > -1)
1209 StringBuilder tip = new StringBuilder(32);
1210 boolean first = true;
1211 for (int i = 0; i < anns.length; i++)
1213 if (anns[i].graphGroup == ann.graphGroup
1214 && anns[i].annotations[column] != null)
1221 tip.append(anns[i].label);
1222 String description = anns[i].annotations[column].description;
1223 if (description != null && description.length() > 0)
1225 tip.append(" ").append(description);
1229 tooltip = first ? null : tip.toString();
1231 else if (column < ann.annotations.length
1232 && ann.annotations[column] != null)
1234 tooltip = ann.annotations[column].description;
1236 // TODO abstract tooltip generator so different implementations can be built
1237 if (ann.graph == AlignmentAnnotation.CONTACT_MAP)
1239 ContactListI clist = av.getContactList(ann, column);
1242 ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight);
1243 ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset);
1244 ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
1245 tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
1246 + " - " + ci.cEnd + "]" + "<br/>Mean:" + cr.getMean();
1247 int col = ann.sequenceRef.findPosition(column);
1248 ap.getStructureSelectionManager()
1249 .highlightPositionsOn(ann.sequenceRef, new int[][]
1250 { new int[] { col, col },
1252 { ci.cStart, ci.cEnd } }, null);
1259 * Constructs and returns the status bar message
1264 * @param rowAndOffset
1266 static String getStatusMessage(AlignmentI al, int column,
1267 AlignmentAnnotation ann, int rowAndOffset, AlignViewportI av)
1270 * show alignment column and annotation description if any
1272 StringBuilder text = new StringBuilder(32);
1273 text.append(MessageManager.getString("label.column")).append(" ")
1274 .append(column + 1);
1276 if (column < ann.annotations.length && ann.annotations[column] != null)
1278 String description = ann.annotations[column].description;
1279 if (description != null && description.trim().length() > 0)
1281 text.append(" ").append(description);
1286 * if the annotation is sequence-specific, show the sequence number
1287 * in the alignment, and (if not a gap) the residue and position
1289 SequenceI seqref = ann.sequenceRef;
1292 int seqIndex = al.findIndex(seqref);
1295 text.append(", ").append(MessageManager.getString("label.sequence"))
1296 .append(" ").append(seqIndex + 1);
1297 char residue = seqref.getCharAt(column);
1298 if (!Comparison.isGap(residue))
1302 if (al.isNucleotide())
1304 name = ResidueProperties.nucleotideName
1305 .get(String.valueOf(residue));
1306 text.append(" Nucleotide: ")
1307 .append(name != null ? name : residue);
1311 name = 'X' == residue ? "X"
1312 : ('*' == residue ? "STOP"
1313 : ResidueProperties.aa2Triplet
1314 .get(String.valueOf(residue)));
1315 text.append(" Residue: ").append(name != null ? name : residue);
1317 int residuePos = seqref.findPosition(column);
1318 text.append(" (").append(residuePos).append(")");
1323 return text.toString();
1333 public void mouseClicked(MouseEvent evt)
1335 // if (activeRow != -1)
1337 // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
1338 // AlignmentAnnotation anot = aa[activeRow];
1342 // TODO mouseClicked-content and drawCursor are quite experimental!
1343 public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
1346 int pady = av.getCharHeight() / 5;
1348 graphics.setColor(Color.black);
1349 graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
1351 if (av.validCharWidth)
1353 graphics.setColor(Color.white);
1355 char s = seq.getCharAt(res);
1357 charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
1358 graphics.drawString(String.valueOf(s), charOffset + x1,
1359 (y1 + av.getCharHeight()) - pady);
1364 private volatile boolean imageFresh = false;
1366 private Rectangle visibleRect = new Rectangle(),
1367 clipBounds = new Rectangle();
1376 public void paintComponent(Graphics g)
1379 // BH: note that this method is generally recommended to
1380 // call super.paintComponent(g). Otherwise, the children of this
1381 // component will not be rendered. That is not needed here
1382 // because AnnotationPanel does not have any children. It is
1383 // just a JPanel contained in a JViewPort.
1385 computeVisibleRect(visibleRect);
1387 g.setColor(Color.white);
1388 g.fillRect(0, 0, visibleRect.width, visibleRect.height);
1392 // BH 2018 optimizing generation of new Rectangle().
1394 || (visibleRect.width != (clipBounds = g
1395 .getClipBounds(clipBounds)).width)
1396 || (visibleRect.height != clipBounds.height))
1399 g.drawImage(image, 0, 0, this);
1404 imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
1405 + 1) * av.getCharWidth();
1411 if (image == null || imgWidth != image.getWidth(this)
1412 || image.getHeight(this) != getHeight())
1414 boolean tried = false;
1416 while (image == null && !tried)
1420 image = new BufferedImage(imgWidth,
1421 ap.getAnnotationPanel().getHeight(),
1422 BufferedImage.TYPE_INT_RGB);
1424 } catch (IllegalArgumentException exc)
1427 "Serious issue with viewport geometry imgWidth requested was "
1430 } catch (OutOfMemoryError oom)
1435 } catch (Exception x)
1440 "Couldn't allocate memory to redraw screen. Please restart Jalview",
1446 gg = (Graphics2D) image.getGraphics();
1450 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
1451 RenderingHints.VALUE_ANTIALIAS_ON);
1454 gg.setFont(av.getFont());
1455 fm = gg.getFontMetrics();
1456 gg.setColor(Color.white);
1457 gg.fillRect(0, 0, imgWidth, image.getHeight());
1462 gg = (Graphics2D) image.getGraphics();
1466 drawComponent(gg, av.getRanges().getStartRes(),
1467 av.getRanges().getEndRes() + 1);
1470 g.drawImage(image, 0, 0, this);
1474 * set true to enable redraw timing debug output on stderr
1476 private final boolean debugRedraw = false;
1479 * non-Thread safe repaint
1482 * repaint with horizontal shift in alignment
1484 public void fastPaint(int horizontal)
1486 if ((horizontal == 0) || image == null
1487 || av.getAlignment().getAlignmentAnnotation() == null
1488 || av.getAlignment().getAlignmentAnnotation().length < 1
1489 || av.isCalcInProgress())
1495 int sr = av.getRanges().getStartRes();
1496 int er = av.getRanges().getEndRes() + 1;
1499 Graphics2D gg = (Graphics2D) image.getGraphics();
1501 if (imgWidth > Math.abs(horizontal * av.getCharWidth()))
1503 // scroll is less than imgWidth away so can re-use buffered graphics
1504 gg.copyArea(0, 0, imgWidth, getHeight(),
1505 -horizontal * av.getCharWidth(), 0);
1507 if (horizontal > 0) // scrollbar pulled right, image to the left
1509 transX = (er - sr - horizontal) * av.getCharWidth();
1510 sr = er - horizontal;
1512 else if (horizontal < 0)
1514 er = sr - horizontal;
1517 gg.translate(transX, 0);
1519 drawComponent(gg, sr, er);
1521 gg.translate(-transX, 0);
1527 // Call repaint on alignment panel so that repaints from other alignment
1528 // panel components can be aggregated. Otherwise performance of the overview
1529 // window and others may be adversely affected.
1530 av.getAlignPanel().repaint();
1533 private volatile boolean lastImageGood = false;
1545 public void drawComponent(Graphics g, int startRes, int endRes)
1547 BufferedImage oldFaded = fadedImage;
1548 if (av.isCalcInProgress())
1552 lastImageGood = false;
1555 // We'll keep a record of the old image,
1556 // and draw a faded image until the calculation
1559 && (fadedImage == null || fadedImage.getWidth() != imgWidth
1560 || fadedImage.getHeight() != image.getHeight()))
1562 // System.err.println("redraw faded image ("+(fadedImage==null ?
1563 // "null image" : "") + " lastGood="+lastImageGood+")");
1564 fadedImage = new BufferedImage(imgWidth, image.getHeight(),
1565 BufferedImage.TYPE_INT_RGB);
1567 Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
1569 fadedG.setColor(Color.white);
1570 fadedG.fillRect(0, 0, imgWidth, image.getHeight());
1572 fadedG.setComposite(
1573 AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f));
1574 fadedG.drawImage(image, 0, 0, this);
1577 // make sure we don't overwrite the last good faded image until all
1578 // calculations have finished
1579 lastImageGood = false;
1584 if (fadedImage != null)
1586 oldFaded = fadedImage;
1591 g.setColor(Color.white);
1592 g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
1594 g.setFont(av.getFont());
1597 fm = g.getFontMetrics();
1600 if ((av.getAlignment().getAlignmentAnnotation() == null)
1601 || (av.getAlignment().getAlignmentAnnotation().length < 1))
1603 g.setColor(Color.white);
1604 g.fillRect(0, 0, getWidth(), getHeight());
1605 g.setColor(Color.black);
1606 if (av.validCharWidth)
1608 g.drawString(MessageManager
1609 .getString("label.alignment_has_no_annotations"), 20, 15);
1614 lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes,
1616 if (!lastImageGood && fadedImage == null)
1618 fadedImage = oldFaded;
1620 if (dragMode == DragMode.MatrixSelect)
1622 g.setColor(Color.yellow);
1623 g.drawRect(Math.min(firstDragX, mouseDragLastX),
1624 Math.min(firstDragY, mouseDragLastY),
1625 Math.max(firstDragX, mouseDragLastX)
1626 - Math.min(firstDragX, mouseDragLastX),
1627 Math.max(firstDragY, mouseDragLastY)
1628 - Math.min(firstDragY, mouseDragLastY));
1634 public FontMetrics getFontMetrics()
1640 public Image getFadedImage()
1646 public int getFadedImageWidth()
1651 private int[] bounds = new int[2];
1654 public int[] getVisibleVRange()
1656 if (ap != null && ap.getAlabels() != null)
1658 int sOffset = -ap.getAlabels().getScrollOffset();
1659 int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
1660 bounds[0] = sOffset;
1661 bounds[1] = visHeight;
1671 * Try to ensure any references held are nulled
1673 public void dispose()
1683 * I created the renderer so I will dispose of it
1685 if (renderer != null)
1692 public void propertyChange(PropertyChangeEvent evt)
1694 // Respond to viewport range changes (e.g. alignment panel was scrolled)
1695 // Both scrolling and resizing change viewport ranges: scrolling changes
1696 // both start and end points, but resize only changes end values.
1697 // Here we only want to fastpaint on a scroll, with resize using a normal
1698 // paint, so scroll events are identified as changes to the horizontal or
1699 // vertical start value.
1700 if (evt.getPropertyName().equals(ViewportRanges.STARTRES))
1702 fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
1704 else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
1706 fastPaint(((int[]) evt.getNewValue())[0]
1707 - ((int[]) evt.getOldValue())[0]);
1709 else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
1716 * computes the visible height of the annotation panel
1718 * @param adjustPanelHeight
1719 * - when false, just adjust existing height according to other
1721 * @param annotationHeight
1722 * @return height to use for the ScrollerPreferredVisibleSize
1724 public int adjustForAlignFrame(boolean adjustPanelHeight,
1725 int annotationHeight)
1728 * Estimate available height in the AlignFrame for alignment +
1729 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
1730 * hscroll, status bar, insets.
1732 int stuff = (ap.getViewName() != null ? 30 : 0)
1733 + (Platform.isAMacAndNotJS() ? 120 : 140);
1734 int availableHeight = ap.alignFrame.getHeight() - stuff;
1735 int rowHeight = av.getCharHeight();
1737 if (adjustPanelHeight)
1739 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
1742 * If not enough vertical space, maximize annotation height while keeping
1743 * at least two rows of alignment visible
1745 if (annotationHeight + alignmentHeight > availableHeight)
1747 annotationHeight = Math.min(annotationHeight,
1748 availableHeight - 2 * rowHeight);
1753 // maintain same window layout whilst updating sliders
1754 annotationHeight = Math.min(ap.annotationScroller.getSize().height,
1755 availableHeight - 2 * rowHeight);
1757 return annotationHeight;