2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.datamodel.AlignmentI;
24 import jalview.datamodel.HiddenColumns;
25 import jalview.datamodel.SearchResultsI;
26 import jalview.datamodel.SequenceGroup;
27 import jalview.datamodel.SequenceI;
28 import jalview.datamodel.VisibleContigsIterator;
29 import jalview.renderer.ScaleRenderer;
30 import jalview.renderer.ScaleRenderer.ScaleMark;
31 import jalview.util.Comparison;
32 import jalview.viewmodel.ViewportListenerI;
33 import jalview.viewmodel.ViewportRanges;
35 import java.awt.BasicStroke;
36 import java.awt.BorderLayout;
37 import java.awt.Color;
38 import java.awt.FontMetrics;
39 import java.awt.Graphics;
40 import java.awt.Graphics2D;
41 import java.awt.RenderingHints;
42 import java.awt.Shape;
43 import java.awt.image.BufferedImage;
44 import java.beans.PropertyChangeEvent;
45 import java.util.Iterator;
46 import java.util.List;
48 import javax.swing.JComponent;
51 * The Swing component on which the alignment sequences, and annotations (if
52 * shown), are drawn. This includes scales above, left and right (if shown) in
53 * Wrapped mode, but not the scale above in Unwrapped mode.
56 public class SeqCanvas extends JComponent implements ViewportListenerI
59 * vertical gap in pixels between sequences and annotations when in wrapped mode
61 static final int SEQS_ANNOTATION_GAP = 3;
63 private static final String ZEROS = "0000000000";
65 final FeatureRenderer fr;
75 private final SequenceRenderer seqRdr;
77 private boolean fastPaint = false;
79 private boolean fastpainting = false;
81 private AnnotationPanel annotations;
84 * measurements for drawing a wrapped alignment
86 private int labelWidthEast; // label right width in pixels if shown
88 private int labelWidthWest; // label left width in pixels if shown
90 int wrappedSpaceAboveAlignment; // gap between widths
92 int wrappedRepeatHeightPx; // height in pixels of wrapped width
94 private int wrappedVisibleWidths; // number of wrapped widths displayed
96 private Graphics2D gg;
99 * Creates a new SeqCanvas object.
103 public SeqCanvas(AlignmentPanel ap)
106 fr = new FeatureRenderer(ap);
107 seqRdr = new SequenceRenderer(av);
108 setLayout(new BorderLayout());
109 PaintRefresher.Register(this, av.getSequenceSetId());
110 setBackground(Color.white);
112 av.getRanges().addPropertyChangeListener(this);
115 public SequenceRenderer getSequenceRenderer()
120 public FeatureRenderer getFeatureRenderer()
126 * Draws the scale above a region of a wrapped alignment, consisting of a
127 * column number every major interval (10 columns).
130 * the graphics context to draw on, positioned at the start (bottom
131 * left) of the line on which to draw any scale marks
133 * start alignment column (0..)
135 * end alignment column (0..)
137 * y offset to draw at
139 private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
141 int charHeight = av.getCharHeight();
142 int charWidth = av.getCharWidth();
145 * white fill the scale space (for the fastPaint case)
147 g.setColor(Color.white);
148 g.fillRect(0, ypos - charHeight - charHeight / 2, getWidth(),
149 charHeight * 3 / 2 + 2);
150 g.setColor(Color.black);
152 List<ScaleMark> marks = new ScaleRenderer().calculateMarks(av, startx,
154 for (ScaleMark mark : marks)
156 int mpos = mark.column; // (i - startx - 1)
161 String mstring = mark.text;
167 g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
171 * draw a tick mark below the column number, centred on the column;
172 * height of tick mark is 4 pixels less than half a character
174 int xpos = (mpos * charWidth) + (charWidth / 2);
175 g.drawLine(xpos, (ypos + 2) - (charHeight / 2), xpos, ypos - 2);
181 * Draw the scale to the left or right of a wrapped alignment
184 * graphics context, positioned at the start of the scale to be drawn
186 * first column of wrapped width (0.. excluding any hidden columns)
188 * last column of wrapped width (0.. excluding any hidden columns)
190 * vertical offset at which to begin the scale
192 * if true, scale is left of residues, if false, scale is right
194 void drawVerticalScale(Graphics g, final int startx, final int endx,
195 final int ypos, final boolean left)
197 int charHeight = av.getCharHeight();
198 int charWidth = av.getCharWidth();
200 int yPos = ypos + charHeight;
204 if (av.hasHiddenColumns())
206 HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
207 startX = hiddenColumns.visibleToAbsoluteColumn(startx);
208 endX = hiddenColumns.visibleToAbsoluteColumn(endx);
210 FontMetrics fm = getFontMetrics(av.getFont());
212 for (int i = 0; i < av.getAlignment().getHeight(); i++)
214 SequenceI seq = av.getAlignment().getSequenceAt(i);
217 * find sequence position of first non-gapped position -
218 * to the right if scale left, to the left if scale right
220 int index = left ? startX : endX;
222 while (index >= startX && index <= endX)
224 if (!Comparison.isGap(seq.getCharAt(index)))
226 value = seq.findPosition(index);
240 * white fill the space for the scale
242 g.setColor(Color.white);
243 int y = (yPos + (i * charHeight)) - (charHeight / 5);
244 // fillRect origin is top left of rectangle
245 g.fillRect(0, y - charHeight, left ? labelWidthWest : labelWidthEast,
251 * draw scale value, right justified within its width less half a
252 * character width padding on the right
254 int labelSpace = left ? labelWidthWest : labelWidthEast;
255 labelSpace -= charWidth / 2; // leave space to the right
256 String valueAsString = String.valueOf(value);
257 int labelLength = fm.stringWidth(valueAsString);
258 int xOffset = labelSpace - labelLength;
259 g.setColor(Color.black);
260 g.drawString(valueAsString, xOffset, y);
266 * Does a fast paint of an alignment in response to a scroll. Most of the
267 * visible region is simply copied and shifted, and then any newly visible
268 * columns or rows are drawn. The scroll may be horizontal or vertical, but
269 * not both at once. Scrolling may be the result of
271 * <li>dragging a scroll bar</li>
272 * <li>clicking in the scroll bar</li>
273 * <li>scrolling by trackpad, middle mouse button, or other device</li>
274 * <li>by moving the box in the Overview window</li>
275 * <li>programmatically to make a highlighted position visible</li>
279 * columns to shift right (positive) or left (negative)
281 * rows to shift down (positive) or up (negative)
283 public void fastPaint(int horizontal, int vertical)
285 if (fastpainting || gg == null || img == null)
294 int charHeight = av.getCharHeight();
295 int charWidth = av.getCharWidth();
297 ViewportRanges ranges = av.getRanges();
298 int startRes = ranges.getStartRes();
299 int endRes = ranges.getEndRes();
300 int startSeq = ranges.getStartSeq();
301 int endSeq = ranges.getEndSeq();
305 gg.copyArea(horizontal * charWidth, vertical * charHeight,
306 img.getWidth(), img.getHeight(), -horizontal * charWidth,
307 -vertical * charHeight);
309 if (horizontal > 0) // scrollbar pulled right, image to the left
311 transX = (endRes - startRes - horizontal) * charWidth;
312 startRes = endRes - horizontal;
314 else if (horizontal < 0)
316 endRes = startRes - horizontal;
319 if (vertical > 0) // scroll down
321 startSeq = endSeq - vertical;
323 if (startSeq < ranges.getStartSeq())
324 { // ie scrolling too fast, more than a page at a time
325 startSeq = ranges.getStartSeq();
329 transY = img.getHeight() - ((vertical + 1) * charHeight);
332 else if (vertical < 0)
334 endSeq = startSeq - vertical;
336 if (endSeq > ranges.getEndSeq())
338 endSeq = ranges.getEndSeq();
342 gg.translate(transX, transY);
343 drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
344 gg.translate(-transX, -transY);
346 // Call repaint on alignment panel so that repaints from other alignment
347 // panel components can be aggregated. Otherwise performance of the
348 // overview window and others may be adversely affected.
349 av.getAlignPanel().repaint();
352 fastpainting = false;
357 public void paintComponent(Graphics g)
359 super.paintComponent(g);
361 int charHeight = av.getCharHeight();
362 int charWidth = av.getCharWidth();
364 ViewportRanges ranges = av.getRanges();
366 int width = getWidth();
367 int height = getHeight();
369 width -= (width % charWidth);
370 height -= (height % charHeight);
372 if ((img != null) && (fastPaint
373 || (getVisibleRect().width != g.getClipBounds().width)
374 || (getVisibleRect().height != g.getClipBounds().height)))
376 g.drawImage(img, 0, 0, this);
378 drawSelectionGroup((Graphics2D) g, ranges.getStartRes(),
379 ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq());
383 else if (width > 0 && height > 0)
386 * img is a cached version of the last view we drew, if any
387 * if we have no img or the size has changed, make a new one
389 if (img == null || width != img.getWidth()
390 || height != img.getHeight())
392 img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
393 gg = (Graphics2D) img.getGraphics();
394 gg.setFont(av.getFont());
399 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
400 RenderingHints.VALUE_ANTIALIAS_ON);
403 gg.setColor(Color.white);
404 gg.fillRect(0, 0, img.getWidth(), img.getHeight());
406 if (av.getWrapAlignment())
408 drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
412 drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
413 ranges.getStartSeq(), ranges.getEndSeq(), 0);
416 drawSelectionGroup(gg, ranges.getStartRes(),
417 ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq());
419 g.drawImage(img, 0, 0, this);
424 drawCursor(g, ranges.getStartRes(), ranges.getEndRes(),
425 ranges.getStartSeq(), ranges.getEndSeq());
430 * Draw an alignment panel for printing
433 * Graphics object to draw with
435 * start residue of print area
437 * end residue of print area
439 * start sequence of print area
441 * end sequence of print area
443 public void drawPanelForPrinting(Graphics g1, int startRes, int endRes,
444 int startSeq, int endSeq)
446 drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
448 drawSelectionGroup((Graphics2D) g1, startRes, endRes,
453 * Draw a wrapped alignment panel for printing
456 * Graphics object to draw with
458 * width of drawing area
459 * @param canvasHeight
460 * height of drawing area
462 * start residue of print area
464 public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth,
465 int canvasHeight, int startRes)
467 drawWrappedPanel(g, canvasWidth, canvasHeight, startRes);
469 SequenceGroup group = av.getSelectionGroup();
472 drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight,
478 * Returns the visible width of the canvas in residues, after allowing for
479 * East or West scales (if shown)
482 * the width in pixels (possibly including scales)
486 public int getWrappedCanvasWidth(int canvasWidth)
488 int charWidth = av.getCharWidth();
490 FontMetrics fm = getFontMetrics(av.getFont());
494 if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
496 labelWidth = getLabelWidth(fm);
499 labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
501 labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
503 return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
507 * Returns a pixel width sufficient to show the largest sequence coordinate
508 * (end position) in the alignment, calculated as the FontMetrics width of
509 * zeroes "0000000" limited to the number of decimal digits to be shown (3 for
510 * 1-10, 4 for 11-99 etc). One character width is added to this, to allow for
511 * half a character width space on either side.
516 protected int getLabelWidth(FontMetrics fm)
519 * find the biggest sequence end position we need to show
520 * (note this is not necessarily the sequence length)
523 AlignmentI alignment = av.getAlignment();
524 for (int i = 0; i < alignment.getHeight(); i++)
526 maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd());
530 for (int i = maxWidth; i > 0; i /= 10)
535 return fm.stringWidth(ZEROS.substring(0, length)) + av.getCharWidth();
539 * Draws as many widths of a wrapped alignment as can fit in the visible
544 * available width in pixels
545 * @param canvasHeight
546 * available height in pixels
548 * the first column (0...) of the alignment to draw
550 public void drawWrappedPanel(Graphics g, int canvasWidth,
551 int canvasHeight, final int startColumn)
553 int wrappedWidthInResidues = calculateWrappedGeometry(canvasWidth,
556 av.setWrappedWidth(wrappedWidthInResidues);
558 ViewportRanges ranges = av.getRanges();
559 ranges.setViewportStartAndWidth(startColumn, wrappedWidthInResidues);
561 // we need to call this again to make sure the startColumn +
562 // wrappedWidthInResidues values are used to calculate wrappedVisibleWidths
564 calculateWrappedGeometry(canvasWidth, canvasHeight);
567 * draw one width at a time (excluding any scales shown),
568 * until we have run out of either alignment or vertical space available
570 int ypos = wrappedSpaceAboveAlignment;
571 int maxWidth = ranges.getVisibleAlignmentWidth();
573 int start = startColumn;
574 int currentWidth = 0;
575 while ((currentWidth < wrappedVisibleWidths) && (start < maxWidth))
578 .min(maxWidth, start + wrappedWidthInResidues - 1);
579 drawWrappedWidth(g, ypos, start, endColumn, canvasHeight);
580 ypos += wrappedRepeatHeightPx;
581 start += wrappedWidthInResidues;
585 drawWrappedDecorators(g, startColumn);
589 * Calculates and saves values needed when rendering a wrapped alignment.
590 * These depend on many factors, including
592 * <li>canvas width and height</li>
593 * <li>number of visible sequences, and height of annotations if shown</li>
594 * <li>font and character width</li>
595 * <li>whether scales are shown left, right or above the alignment</li>
599 * @param canvasHeight
600 * @return the number of residue columns in each width
602 protected int calculateWrappedGeometry(int canvasWidth, int canvasHeight)
604 int charHeight = av.getCharHeight();
607 * vertical space in pixels between wrapped widths of alignment
608 * - one character height, or two if scale above is drawn
610 wrappedSpaceAboveAlignment = charHeight
611 * (av.getScaleAboveWrapped() ? 2 : 1);
614 * compute height in pixels of the wrapped widths
615 * - start with space above plus sequences
617 wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
618 wrappedRepeatHeightPx += av.getAlignment().getHeight()
622 * add annotations panel height if shown
623 * also gap between sequences and annotations
625 if (av.isShowAnnotation())
627 wrappedRepeatHeightPx += getAnnotationHeight();
628 wrappedRepeatHeightPx += SEQS_ANNOTATION_GAP; // 3px
632 * number of visible widths (the last one may be part height),
633 * ensuring a part height includes at least one sequence
635 ViewportRanges ranges = av.getRanges();
636 wrappedVisibleWidths = canvasHeight / wrappedRepeatHeightPx;
637 int remainder = canvasHeight % wrappedRepeatHeightPx;
638 if (remainder >= (wrappedSpaceAboveAlignment + charHeight))
640 wrappedVisibleWidths++;
644 * compute width in residues; this also sets East and West label widths
646 int wrappedWidthInResidues = getWrappedCanvasWidth(canvasWidth);
649 * limit visibleWidths to not exceed width of alignment
651 int xMax = ranges.getVisibleAlignmentWidth();
652 int startToEnd = xMax - ranges.getStartRes();
653 int maxWidths = startToEnd / wrappedWidthInResidues;
654 if (startToEnd % wrappedWidthInResidues > 0)
658 wrappedVisibleWidths = Math.min(wrappedVisibleWidths, maxWidths);
660 return wrappedWidthInResidues;
664 * Draws one width of a wrapped alignment, including sequences and
665 * annnotations, if shown, but not scales or hidden column markers
671 * @param canvasHeight
673 protected void drawWrappedWidth(Graphics g, final int ypos,
674 final int startColumn, final int endColumn,
675 final int canvasHeight)
677 ViewportRanges ranges = av.getRanges();
678 int viewportWidth = ranges.getViewportWidth();
680 int endx = Math.min(startColumn + viewportWidth - 1, endColumn);
683 * move right before drawing by the width of the scale left (if any)
684 * plus column offset from left margin (usually zero, but may be non-zero
685 * when fast painting is drawing just a few columns)
687 int charWidth = av.getCharWidth();
688 int xOffset = labelWidthWest
689 + ((startColumn - ranges.getStartRes()) % viewportWidth)
691 g.translate(xOffset, 0);
693 // When printing we have an extra clipped region,
694 // the Printable page which we need to account for here
695 Shape clip = g.getClip();
699 g.setClip(0, 0, viewportWidth * charWidth, canvasHeight);
703 g.setClip(0, (int) clip.getBounds().getY(),
704 viewportWidth * charWidth, (int) clip.getBounds().getHeight());
708 * white fill the region to be drawn (so incremental fast paint doesn't
709 * scribble over an existing image)
711 g.setColor(Color.white);
712 g.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
713 wrappedRepeatHeightPx);
715 drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1,
718 int cHeight = av.getAlignment().getHeight() * av.getCharHeight();
720 if (av.isShowAnnotation())
722 final int yShift = cHeight + ypos + SEQS_ANNOTATION_GAP;
723 g.translate(0, yShift);
724 if (annotations == null)
726 annotations = new AnnotationPanel(av);
729 annotations.renderer.drawComponent(annotations, av, g, -1,
730 startColumn, endx + 1);
731 g.translate(0, -yShift);
734 g.translate(-xOffset, 0);
738 * Draws scales left, right and above (if shown), and any hidden column
739 * markers, on all widths of the wrapped alignment
744 protected void drawWrappedDecorators(Graphics g, final int startColumn)
746 int charWidth = av.getCharWidth();
748 g.setFont(av.getFont());
749 g.setColor(Color.black);
751 int ypos = wrappedSpaceAboveAlignment;
752 ViewportRanges ranges = av.getRanges();
753 int viewportWidth = ranges.getViewportWidth();
754 int maxWidth = ranges.getVisibleAlignmentWidth();
756 int startCol = startColumn;
758 while (widthsDrawn < wrappedVisibleWidths)
760 int endColumn = Math.min(maxWidth, startCol + viewportWidth - 1);
762 if (av.getScaleLeftWrapped())
764 drawVerticalScale(g, startCol, endColumn - 1, ypos, true);
767 if (av.getScaleRightWrapped())
769 int x = labelWidthWest + viewportWidth * charWidth;
771 drawVerticalScale(g, startCol, endColumn, ypos, false);
776 * white fill region of scale above and hidden column markers
777 * (to support incremental fast paint of image)
779 g.translate(labelWidthWest, 0);
780 g.setColor(Color.white);
781 g.fillRect(0, ypos - wrappedSpaceAboveAlignment, viewportWidth
782 * charWidth + labelWidthWest, wrappedSpaceAboveAlignment);
783 g.setColor(Color.black);
784 g.translate(-labelWidthWest, 0);
786 g.translate(labelWidthWest, 0);
788 if (av.getScaleAboveWrapped())
790 drawNorthScale(g, startCol, endColumn, ypos);
793 if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
795 drawHiddenColumnMarkers(g, ypos, startCol, endColumn);
798 g.translate(-labelWidthWest, 0);
800 ypos += wrappedRepeatHeightPx;
801 startCol += viewportWidth;
807 * Draws markers (triangles) above hidden column positions between startColumn
815 protected void drawHiddenColumnMarkers(Graphics g, int ypos,
816 int startColumn, int endColumn)
818 int charHeight = av.getCharHeight();
819 int charWidth = av.getCharWidth();
821 g.setColor(Color.blue);
823 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
825 Iterator<Integer> it = hidden.getStartRegionIterator(startColumn,
829 res = it.next() - startColumn;
831 if (res < 0 || res > endColumn - startColumn + 1)
837 * draw a downward-pointing triangle at the hidden columns location
838 * (before the following visible column)
840 int xMiddle = res * charWidth;
841 int[] xPoints = new int[] { xMiddle - charHeight / 4,
842 xMiddle + charHeight / 4, xMiddle };
843 int yTop = ypos - (charHeight / 2);
844 int[] yPoints = new int[] { yTop, yTop, yTop + 8 };
845 g.fillPolygon(xPoints, yPoints, 3);
850 * Draw a selection group over a wrapped alignment
852 private void drawWrappedSelection(Graphics2D g, SequenceGroup group,
854 int canvasHeight, int startRes)
856 // chop the wrapped alignment extent up into panel-sized blocks and treat
857 // each block as if it were a block from an unwrapped alignment
858 g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
859 BasicStroke.JOIN_ROUND, 3f, new float[]
861 g.setColor(Color.RED);
863 int charWidth = av.getCharWidth();
864 int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
866 int startx = startRes;
867 int maxwidth = av.getAlignment().getVisibleWidth();
868 int ypos = wrappedSpaceAboveAlignment;
870 while ((ypos <= canvasHeight) && (startx < maxwidth))
872 // set end value to be start + width, or maxwidth, whichever is smaller
873 int endx = startx + cWidth - 1;
880 g.translate(labelWidthWest, 0);
881 drawUnwrappedSelection(g, group, startx, endx, 0,
882 av.getAlignment().getHeight() - 1,
884 g.translate(-labelWidthWest, 0);
886 ypos += wrappedRepeatHeightPx;
890 g.setStroke(new BasicStroke());
894 * Answers zero if annotations are not shown, otherwise recalculates and answers
895 * the total height of all annotation rows in pixels
899 int getAnnotationHeight()
901 if (!av.isShowAnnotation())
906 if (annotations == null)
908 annotations = new AnnotationPanel(av);
911 return annotations.adjustPanelHeight();
915 * Draws the visible region of the alignment on the graphics context. If there
916 * are hidden column markers in the visible region, then each sub-region
917 * between the markers is drawn separately, followed by the hidden column
921 * the graphics context, positioned at the first residue to be drawn
923 * offset of the first column to draw (0..)
925 * offset of the last column to draw (0..)
927 * offset of the first sequence to draw (0..)
929 * offset of the last sequence to draw (0..)
931 * vertical offset at which to draw (for wrapped alignments)
933 public void drawPanel(Graphics g1, final int startRes, final int endRes,
934 final int startSeq, final int endSeq, final int yOffset)
936 int charHeight = av.getCharHeight();
937 int charWidth = av.getCharWidth();
939 if (!av.hasHiddenColumns())
941 draw(g1, startRes, endRes, startSeq, endSeq, yOffset);
949 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
950 VisibleContigsIterator regions = hidden
951 .getVisContigsIterator(startRes, endRes + 1, true);
953 while (regions.hasNext())
955 int[] region = regions.next();
956 blockEnd = region[1];
957 blockStart = region[0];
960 * draw up to just before the next hidden region, or the end of
961 * the visible region, whichever comes first
963 g1.translate(screenY * charWidth, 0);
965 draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
968 * draw the downline of the hidden column marker (ScalePanel draws the
969 * triangle on top) if we reached it
971 if (av.getShowHiddenMarkers()
972 && (regions.hasNext() || regions.endsAtHidden()))
974 g1.setColor(Color.blue);
976 g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
977 0 + yOffset, (blockEnd - blockStart + 1) * charWidth - 1,
978 (endSeq - startSeq + 1) * charHeight + yOffset);
981 g1.translate(-screenY * charWidth, 0);
982 screenY += blockEnd - blockStart + 1;
989 * Draws a region of the visible alignment
993 * offset of the first column in the visible region (0..)
995 * offset of the last column in the visible region (0..)
997 * offset of the first sequence in the visible region (0..)
999 * offset of the last sequence in the visible region (0..)
1001 * vertical offset at which to draw (for wrapped alignments)
1003 private void draw(Graphics g, int startRes, int endRes, int startSeq,
1004 int endSeq, int offset)
1006 int charHeight = av.getCharHeight();
1007 int charWidth = av.getCharWidth();
1009 g.setFont(av.getFont());
1010 seqRdr.prepare(g, av.isRenderGaps());
1014 // / First draw the sequences
1015 // ///////////////////////////
1016 for (int i = startSeq; i <= endSeq; i++)
1018 nextSeq = av.getAlignment().getSequenceAt(i);
1019 if (nextSeq == null)
1021 // occasionally, a race condition occurs such that the alignment row is
1025 seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
1026 startRes, endRes, offset + ((i - startSeq) * charHeight));
1028 if (av.isShowSequenceFeatures())
1030 fr.drawSequence(g, nextSeq, startRes, endRes,
1031 offset + ((i - startSeq) * charHeight), false);
1035 * highlight search Results once sequence has been drawn
1037 if (av.hasSearchResults())
1039 SearchResultsI searchResults = av.getSearchResults();
1040 int[] visibleResults = searchResults.getResults(nextSeq, startRes,
1042 if (visibleResults != null)
1044 for (int r = 0; r < visibleResults.length; r += 2)
1046 seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
1047 visibleResults[r + 1],
1048 (visibleResults[r] - startRes) * charWidth,
1049 offset + ((i - startSeq) * charHeight));
1055 if (av.getSelectionGroup() != null
1056 || av.getAlignment().getGroups().size() > 0)
1058 drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
1064 * Draws the outlines of any groups defined on the alignment (excluding the
1065 * current selection group, if any)
1074 void drawGroupsBoundaries(Graphics g1, int startRes, int endRes,
1075 int startSeq, int endSeq, int offset)
1077 Graphics2D g = (Graphics2D) g1;
1079 SequenceGroup group = null;
1080 int groupIndex = -1;
1082 if (av.getAlignment().getGroups().size() > 0)
1084 group = av.getAlignment().getGroups().get(0);
1092 g.setColor(group.getOutlineColour());
1094 drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
1099 if (groupIndex >= av.getAlignment().getGroups().size())
1104 group = av.getAlignment().getGroups().get(groupIndex);
1106 } while (groupIndex < av.getAlignment().getGroups().size());
1113 * Draws the outline of the current selection group (if any)
1121 private void drawSelectionGroup(Graphics2D g, int startRes, int endRes,
1122 int startSeq, int endSeq)
1124 SequenceGroup group = av.getSelectionGroup();
1130 g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
1131 BasicStroke.JOIN_ROUND, 3f, new float[]
1133 g.setColor(Color.RED);
1134 if (!av.getWrapAlignment())
1136 drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq,
1141 drawWrappedSelection(g, group, getWidth(), getHeight(),
1142 av.getRanges().getStartRes());
1144 g.setStroke(new BasicStroke());
1148 * Draw the cursor as a separate image and overlay
1151 * start residue of area to draw cursor in
1153 * end residue of area to draw cursor in
1155 * start sequence of area to draw cursor in
1157 * end sequence of are to draw cursor in
1158 * @return a transparent image of the same size as the sequence canvas, with
1159 * the cursor drawn on it, if any
1161 private void drawCursor(Graphics g, int startRes, int endRes,
1165 // convert the cursorY into a position on the visible alignment
1166 int cursor_ypos = cursorY;
1168 // don't do work unless we have to
1169 if (cursor_ypos >= startSeq && cursor_ypos <= endSeq)
1173 int startx = startRes;
1176 // convert the cursorX into a position on the visible alignment
1177 int cursor_xpos = av.getAlignment().getHiddenColumns()
1178 .absoluteToVisibleColumn(cursorX);
1180 if (av.getAlignment().getHiddenColumns().isVisible(cursorX))
1183 if (av.getWrapAlignment())
1185 // work out the correct offsets for the cursor
1186 int charHeight = av.getCharHeight();
1187 int charWidth = av.getCharWidth();
1188 int canvasWidth = getWidth();
1189 int canvasHeight = getHeight();
1191 // height gap above each panel
1192 int hgap = charHeight;
1193 if (av.getScaleAboveWrapped())
1198 int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
1200 int cHeight = av.getAlignment().getHeight() * charHeight;
1202 endx = startx + cWidth - 1;
1203 int ypos = hgap; // vertical offset
1205 // iterate down the wrapped panels
1206 while ((ypos <= canvasHeight) && (endx < cursor_xpos))
1208 // update vertical offset
1209 ypos += cHeight + getAnnotationHeight() + hgap;
1211 // update horizontal offset
1213 endx = startx + cWidth - 1;
1216 xoffset = labelWidthWest;
1219 // now check if cursor is within range for x values
1220 if (cursor_xpos >= startx && cursor_xpos <= endx)
1222 // get the character the cursor is drawn at
1223 SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
1224 char s = seq.getCharAt(cursorX);
1226 seqRdr.drawCursor(g, s,
1227 xoffset + (cursor_xpos - startx) * av.getCharWidth(),
1228 yoffset + (cursor_ypos - startSeq) * av.getCharHeight());
1236 * Draw a selection group over an unwrapped alignment
1239 * graphics object to draw with
1243 * start residue of area to draw
1245 * end residue of area to draw
1247 * start sequence of area to draw
1249 * end sequence of area to draw
1251 * vertical offset (used when called from wrapped alignment code)
1253 private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
1254 int startRes, int endRes, int startSeq, int endSeq, int offset)
1256 int charWidth = av.getCharWidth();
1258 if (!av.hasHiddenColumns())
1260 drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
1265 // package into blocks of visible columns
1270 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
1271 VisibleContigsIterator regions = hidden
1272 .getVisContigsIterator(startRes, endRes + 1, true);
1273 while (regions.hasNext())
1275 int[] region = regions.next();
1276 blockEnd = region[1];
1277 blockStart = region[0];
1279 g.translate(screenY * charWidth, 0);
1280 drawPartialGroupOutline(g, group,
1281 blockStart, blockEnd, startSeq, endSeq, offset);
1283 g.translate(-screenY * charWidth, 0);
1284 screenY += blockEnd - blockStart + 1;
1290 * Draws part of a selection group outline
1298 * @param verticalOffset
1300 private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group,
1301 int startRes, int endRes, int startSeq, int endSeq,
1304 int charHeight = av.getCharHeight();
1305 int charWidth = av.getCharWidth();
1306 int visWidth = (endRes - startRes + 1) * charWidth;
1310 boolean inGroup = false;
1315 List<SequenceI> seqs = group.getSequences(null);
1317 // position of start residue of group relative to startRes, in pixels
1318 int sx = (group.getStartRes() - startRes) * charWidth;
1320 // width of group in pixels
1321 int xwidth = (((group.getEndRes() + 1) - group.getStartRes())
1324 if (!(sx + xwidth < 0 || sx > visWidth))
1326 for (i = startSeq; i <= endSeq; i++)
1328 sy = verticalOffset + (i - startSeq) * charHeight;
1330 if ((sx <= (endRes - startRes) * charWidth)
1331 && seqs.contains(av.getAlignment().getSequenceAt(i)))
1334 && !seqs.contains(av.getAlignment().getSequenceAt(i + 1)))
1336 bottom = sy + charHeight;
1341 if (((top == -1) && (i == 0)) || !seqs
1342 .contains(av.getAlignment().getSequenceAt(i - 1)))
1353 drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
1354 drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
1356 // reset top and bottom
1364 sy = verticalOffset + ((i - startSeq) * charHeight);
1365 drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
1366 drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
1372 * Draw horizontal selection group boundaries at top and bottom positions
1375 * graphics object to draw on
1381 * visWidth maximum available width
1383 * position to draw top of group at
1385 * position to draw bottom of group at
1387 private void drawHorizontals(Graphics2D g, int sx, int xwidth,
1388 int visWidth, int top, int bottom)
1398 // don't let width extend beyond current block, or group extent
1400 if (startx + width >= visWidth)
1402 width = visWidth - startx;
1407 g.drawLine(startx, top, startx + width, top);
1412 g.drawLine(startx, bottom - 1, startx + width, bottom - 1);
1417 * Draw vertical lines at sx and sx+xwidth providing they lie within
1421 * graphics object to draw on
1427 * visWidth maximum available width
1433 private void drawVerticals(Graphics2D g, int sx, int xwidth, int visWidth,
1436 // if start position is visible, draw vertical line to left of
1438 if (sx >= 0 && sx < visWidth)
1440 g.drawLine(sx, oldY, sx, sy);
1443 // if end position is visible, draw vertical line to right of
1445 if (sx + xwidth < visWidth)
1447 g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
1452 * Highlights search results in the visible region by rendering as white text
1453 * on a black background. Any previous highlighting is removed. Answers true
1454 * if any highlight was left on the visible alignment (so status bar should be
1455 * set to match), else false.
1457 * Currently fastPaint is not implemented for wrapped alignments. If a wrapped
1458 * alignment had to be scrolled to show the highlighted region, then it should
1459 * be fully redrawn, otherwise a fast paint can be performed. This argument
1460 * could be removed if fast paint of scrolled wrapped alignment is coded in
1461 * future (JAL-2609).
1464 * @param noFastPaint
1467 public boolean highlightSearchResults(SearchResultsI results,
1468 boolean noFastPaint)
1474 boolean wrapped = av.getWrapAlignment();
1477 fastPaint = !noFastPaint;
1478 fastpainting = fastPaint;
1481 * to avoid redrawing the whole visible region, we instead
1482 * redraw just the minimal regions to remove previous highlights
1485 SearchResultsI previous = av.getSearchResults();
1486 av.setSearchResults(results);
1487 boolean redrawn = false;
1488 boolean drawn = false;
1491 redrawn = drawMappedPositionsWrapped(previous);
1492 drawn = drawMappedPositionsWrapped(results);
1497 redrawn = drawMappedPositions(previous);
1498 drawn = drawMappedPositions(results);
1503 * if highlights were either removed or added, repaint
1511 * return true only if highlights were added
1517 fastpainting = false;
1522 * Redraws the minimal rectangle in the visible region (if any) that includes
1523 * mapped positions of the given search results. Whether or not positions are
1524 * highlighted depends on the SearchResults set on the Viewport. This allows
1525 * this method to be called to either clear or set highlighting. Answers true
1526 * if any positions were drawn (in which case a repaint is still required),
1532 protected boolean drawMappedPositions(SearchResultsI results)
1534 if ((results == null) || (gg == null)) // JAL-2784 check gg is not null
1540 * calculate the minimal rectangle to redraw that
1541 * includes both new and existing search results
1543 int firstSeq = Integer.MAX_VALUE;
1545 int firstCol = Integer.MAX_VALUE;
1547 boolean matchFound = false;
1549 ViewportRanges ranges = av.getRanges();
1550 int firstVisibleColumn = ranges.getStartRes();
1551 int lastVisibleColumn = ranges.getEndRes();
1552 AlignmentI alignment = av.getAlignment();
1553 if (av.hasHiddenColumns())
1555 firstVisibleColumn = alignment.getHiddenColumns()
1556 .visibleToAbsoluteColumn(firstVisibleColumn);
1557 lastVisibleColumn = alignment.getHiddenColumns()
1558 .visibleToAbsoluteColumn(lastVisibleColumn);
1561 for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
1562 .getEndSeq(); seqNo++)
1564 SequenceI seq = alignment.getSequenceAt(seqNo);
1566 int[] visibleResults = results.getResults(seq, firstVisibleColumn,
1568 if (visibleResults != null)
1570 for (int i = 0; i < visibleResults.length - 1; i += 2)
1572 int firstMatchedColumn = visibleResults[i];
1573 int lastMatchedColumn = visibleResults[i + 1];
1574 if (firstMatchedColumn <= lastVisibleColumn
1575 && lastMatchedColumn >= firstVisibleColumn)
1578 * found a search results match in the visible region -
1579 * remember the first and last sequence matched, and the first
1580 * and last visible columns in the matched positions
1583 firstSeq = Math.min(firstSeq, seqNo);
1584 lastSeq = Math.max(lastSeq, seqNo);
1585 firstMatchedColumn = Math.max(firstMatchedColumn,
1586 firstVisibleColumn);
1587 lastMatchedColumn = Math.min(lastMatchedColumn,
1589 firstCol = Math.min(firstCol, firstMatchedColumn);
1590 lastCol = Math.max(lastCol, lastMatchedColumn);
1598 if (av.hasHiddenColumns())
1600 firstCol = alignment.getHiddenColumns()
1601 .absoluteToVisibleColumn(firstCol);
1602 lastCol = alignment.getHiddenColumns().absoluteToVisibleColumn(lastCol);
1604 int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
1605 int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
1606 gg.translate(transX, transY);
1607 drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0);
1608 gg.translate(-transX, -transY);
1615 public void propertyChange(PropertyChangeEvent evt)
1617 String eventName = evt.getPropertyName();
1619 if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
1625 else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
1633 if (eventName.equals(ViewportRanges.STARTRES)
1634 || eventName.equals(ViewportRanges.STARTRESANDSEQ))
1636 // Make sure we're not trying to draw a panel
1637 // larger than the visible window
1638 if (eventName.equals(ViewportRanges.STARTRES))
1640 scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
1644 scrollX = ((int[]) evt.getNewValue())[0]
1645 - ((int[]) evt.getOldValue())[0];
1647 ViewportRanges vpRanges = av.getRanges();
1649 int range = vpRanges.getEndRes() - vpRanges.getStartRes() + 1;
1650 if (scrollX > range)
1654 else if (scrollX < -range)
1659 // Both scrolling and resizing change viewport ranges: scrolling changes
1660 // both start and end points, but resize only changes end values.
1661 // Here we only want to fastpaint on a scroll, with resize using a normal
1662 // paint, so scroll events are identified as changes to the horizontal or
1663 // vertical start value.
1664 if (eventName.equals(ViewportRanges.STARTRES))
1666 if (av.getWrapAlignment())
1668 fastPaintWrapped(scrollX);
1672 fastPaint(scrollX, 0);
1675 else if (eventName.equals(ViewportRanges.STARTSEQ))
1678 fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
1680 else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
1682 if (av.getWrapAlignment())
1684 fastPaintWrapped(scrollX);
1688 fastPaint(scrollX, 0);
1691 else if (eventName.equals(ViewportRanges.STARTSEQ))
1694 fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
1696 else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
1698 if (av.getWrapAlignment())
1700 fastPaintWrapped(scrollX);
1706 * Does a minimal update of the image for a scroll movement. This method
1707 * handles scroll movements of up to one width of the wrapped alignment (one
1708 * click in the vertical scrollbar). Larger movements (for example after a
1709 * scroll to highlight a mapped position) trigger a full redraw instead.
1712 * number of positions scrolled (right if positive, left if negative)
1714 protected void fastPaintWrapped(int scrollX)
1716 ViewportRanges ranges = av.getRanges();
1718 if (Math.abs(scrollX) >= ranges.getViewportWidth())
1721 * shift of one view width or more is
1722 * overcomplicated to handle in this method
1729 if (fastpainting || gg == null)
1735 fastpainting = true;
1739 calculateWrappedGeometry(getWidth(), getHeight());
1742 * relocate the regions of the alignment that are still visible
1744 shiftWrappedAlignment(-scrollX);
1747 * add new columns (sequence, annotation)
1748 * - at top left if scrollX < 0
1749 * - at right of last two widths if scrollX > 0
1753 int startRes = ranges.getStartRes();
1754 drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes, startRes
1755 - scrollX - 1, getHeight());
1759 fastPaintWrappedAddRight(scrollX);
1763 * draw all scales (if shown) and hidden column markers
1765 drawWrappedDecorators(gg, ranges.getStartRes());
1770 fastpainting = false;
1775 * Draws the specified number of columns at the 'end' (bottom right) of a
1776 * wrapped alignment view, including sequences and annotations if shown, but
1777 * not scales. Also draws the same number of columns at the right hand end of
1778 * the second last width shown, if the last width is not full height (so
1779 * cannot simply be copied from the graphics image).
1783 protected void fastPaintWrappedAddRight(int columns)
1790 ViewportRanges ranges = av.getRanges();
1791 int viewportWidth = ranges.getViewportWidth();
1792 int charWidth = av.getCharWidth();
1795 * draw full height alignment in the second last row, last columns, if the
1796 * last row was not full height
1798 int visibleWidths = wrappedVisibleWidths;
1799 int canvasHeight = getHeight();
1800 boolean lastWidthPartHeight = (wrappedVisibleWidths * wrappedRepeatHeightPx) > canvasHeight;
1802 if (lastWidthPartHeight)
1804 int widthsAbove = Math.max(0, visibleWidths - 2);
1805 int ypos = wrappedRepeatHeightPx * widthsAbove
1806 + wrappedSpaceAboveAlignment;
1807 int endRes = ranges.getEndRes();
1808 endRes += widthsAbove * viewportWidth;
1809 int startRes = endRes - columns;
1810 int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth)
1814 * white fill first to erase annotations
1816 gg.translate(xOffset, 0);
1817 gg.setColor(Color.white);
1818 gg.fillRect(labelWidthWest, ypos,
1819 (endRes - startRes + 1) * charWidth, wrappedRepeatHeightPx);
1820 gg.translate(-xOffset, 0);
1822 drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
1826 * draw newly visible columns in last wrapped width (none if we
1827 * have reached the end of the alignment)
1828 * y-offset for drawing last width is height of widths above,
1831 int widthsAbove = visibleWidths - 1;
1832 int ypos = wrappedRepeatHeightPx * widthsAbove
1833 + wrappedSpaceAboveAlignment;
1834 int endRes = ranges.getEndRes();
1835 endRes += widthsAbove * viewportWidth;
1836 int startRes = endRes - columns + 1;
1839 * white fill first to erase annotations
1841 int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth)
1843 gg.translate(xOffset, 0);
1844 gg.setColor(Color.white);
1845 int width = viewportWidth * charWidth - xOffset;
1846 gg.fillRect(labelWidthWest, ypos, width, wrappedRepeatHeightPx);
1847 gg.translate(-xOffset, 0);
1849 gg.setFont(av.getFont());
1850 gg.setColor(Color.black);
1852 if (startRes < ranges.getVisibleAlignmentWidth())
1854 drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
1858 * and finally, white fill any space below the visible alignment
1860 int heightBelow = canvasHeight - visibleWidths * wrappedRepeatHeightPx;
1861 if (heightBelow > 0)
1863 gg.setColor(Color.white);
1864 gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow);
1869 * Shifts the visible alignment by the specified number of columns - left if
1870 * negative, right if positive. Copies and moves sequences and annotations (if
1871 * shown). Scales, hidden column markers and any newly visible columns must be
1876 protected void shiftWrappedAlignment(int positions)
1882 int charWidth = av.getCharWidth();
1884 int canvasHeight = getHeight();
1885 ViewportRanges ranges = av.getRanges();
1886 int viewportWidth = ranges.getViewportWidth();
1887 int widthToCopy = (ranges.getViewportWidth() - Math.abs(positions))
1889 int heightToCopy = wrappedRepeatHeightPx - wrappedSpaceAboveAlignment;
1890 int xMax = ranges.getVisibleAlignmentWidth();
1895 * shift right (after scroll left)
1896 * for each wrapped width (starting with the last), copy (width-positions)
1897 * columns from the left margin to the right margin, and copy positions
1898 * columns from the right margin of the row above (if any) to the
1899 * left margin of the current row
1903 * get y-offset of last wrapped width, first row of sequences
1905 int y = canvasHeight / wrappedRepeatHeightPx * wrappedRepeatHeightPx;
1906 y += wrappedSpaceAboveAlignment;
1907 int copyFromLeftStart = labelWidthWest;
1908 int copyFromRightStart = copyFromLeftStart + widthToCopy;
1913 * shift 'widthToCopy' residues by 'positions' places to the right
1915 gg.copyArea(copyFromLeftStart, y, widthToCopy, heightToCopy,
1916 positions * charWidth, 0);
1920 * copy 'positions' residue from the row above (right hand end)
1921 * to this row's left hand end
1923 gg.copyArea(copyFromRightStart, y - wrappedRepeatHeightPx,
1924 positions * charWidth, heightToCopy, -widthToCopy,
1925 wrappedRepeatHeightPx);
1928 y -= wrappedRepeatHeightPx;
1934 * shift left (after scroll right)
1935 * for each wrapped width (starting with the first), copy (width-positions)
1936 * columns from the right margin to the left margin, and copy positions
1937 * columns from the left margin of the row below (if any) to the
1938 * right margin of the current row
1940 int xpos = av.getRanges().getStartRes();
1941 int y = wrappedSpaceAboveAlignment;
1942 int copyFromRightStart = labelWidthWest - positions * charWidth;
1944 while (y < canvasHeight)
1946 gg.copyArea(copyFromRightStart, y, widthToCopy, heightToCopy,
1947 positions * charWidth, 0);
1948 if (y + wrappedRepeatHeightPx < canvasHeight - wrappedRepeatHeightPx
1949 && (xpos + viewportWidth <= xMax))
1951 gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx, -positions
1952 * charWidth, heightToCopy, widthToCopy,
1953 -wrappedRepeatHeightPx);
1956 y += wrappedRepeatHeightPx;
1957 xpos += viewportWidth;
1964 * Redraws any positions in the search results in the visible region of a
1965 * wrapped alignment. Any highlights are drawn depending on the search results
1966 * set on the Viewport, not the <code>results</code> argument. This allows
1967 * this method to be called either to clear highlights (passing the previous
1968 * search results), or to draw new highlights.
1973 protected boolean drawMappedPositionsWrapped(SearchResultsI results)
1975 if ((results == null) || (gg == null)) // JAL-2784 check gg is not null
1979 int charHeight = av.getCharHeight();
1981 boolean matchFound = false;
1983 calculateWrappedGeometry(getWidth(), getHeight());
1984 int wrappedWidth = av.getWrappedWidth();
1985 int wrappedHeight = wrappedRepeatHeightPx;
1987 ViewportRanges ranges = av.getRanges();
1988 int canvasHeight = getHeight();
1989 int repeats = canvasHeight / wrappedHeight;
1990 if (canvasHeight / wrappedHeight > 0)
1995 int firstVisibleColumn = ranges.getStartRes();
1996 int lastVisibleColumn = ranges.getStartRes() + repeats
1997 * ranges.getViewportWidth() - 1;
1999 AlignmentI alignment = av.getAlignment();
2000 if (av.hasHiddenColumns())
2002 firstVisibleColumn = alignment.getHiddenColumns()
2003 .visibleToAbsoluteColumn(firstVisibleColumn);
2004 lastVisibleColumn = alignment.getHiddenColumns()
2005 .visibleToAbsoluteColumn(lastVisibleColumn);
2008 int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
2010 for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
2011 .getEndSeq(); seqNo++)
2013 SequenceI seq = alignment.getSequenceAt(seqNo);
2015 int[] visibleResults = results.getResults(seq, firstVisibleColumn,
2017 if (visibleResults != null)
2019 for (int i = 0; i < visibleResults.length - 1; i += 2)
2021 int firstMatchedColumn = visibleResults[i];
2022 int lastMatchedColumn = visibleResults[i + 1];
2023 if (firstMatchedColumn <= lastVisibleColumn
2024 && lastMatchedColumn >= firstVisibleColumn)
2027 * found a search results match in the visible region
2029 firstMatchedColumn = Math.max(firstMatchedColumn,
2030 firstVisibleColumn);
2031 lastMatchedColumn = Math.min(lastMatchedColumn,
2035 * draw each mapped position separately (as contiguous positions may
2036 * wrap across lines)
2038 for (int mappedPos = firstMatchedColumn; mappedPos <= lastMatchedColumn; mappedPos++)
2040 int displayColumn = mappedPos;
2041 if (av.hasHiddenColumns())
2043 displayColumn = alignment.getHiddenColumns()
2044 .absoluteToVisibleColumn(displayColumn);
2048 * transX: offset from left edge of canvas to residue position
2050 int transX = labelWidthWest
2051 + ((displayColumn - ranges.getStartRes()) % wrappedWidth)
2052 * av.getCharWidth();
2055 * transY: offset from top edge of canvas to residue position
2057 int transY = gapHeight;
2058 transY += (displayColumn - ranges.getStartRes())
2059 / wrappedWidth * wrappedHeight;
2060 transY += (seqNo - ranges.getStartSeq()) * av.getCharHeight();
2063 * yOffset is from graphics origin to start of visible region
2065 int yOffset = 0;// (displayColumn / wrappedWidth) * wrappedHeight;
2066 if (transY < getHeight())
2069 gg.translate(transX, transY);
2070 drawPanel(gg, displayColumn, displayColumn, seqNo, seqNo,
2072 gg.translate(-transX, -transY);
2084 * Answers the width in pixels of the left scale labels (0 if not shown)
2088 int getLabelWidthWest()
2090 return labelWidthWest;