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.renderer.ScaleRenderer;
29 import jalview.renderer.ScaleRenderer.ScaleMark;
30 import jalview.util.Comparison;
31 import jalview.viewmodel.ViewportListenerI;
32 import jalview.viewmodel.ViewportRanges;
34 import java.awt.AlphaComposite;
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.List;
47 import javax.swing.JComponent;
50 * The Swing component on which the alignment sequences, and annotations (if
51 * shown), are drawn. This includes scales above, left and right (if shown) in
52 * Wrapped mode, but not the scale above in Unwrapped mode.
55 public class SeqCanvas extends JComponent implements ViewportListenerI
57 private static final String ZEROS = "0000000000";
59 final FeatureRenderer fr;
69 private final SequenceRenderer seqRdr;
71 private boolean fastPaint = false;
73 private boolean fastpainting = false;
75 private AnnotationPanel annotations;
78 * measurements for drawing a wrapped alignment
80 private int labelWidthEast; // label right width in pixels if shown
82 private int labelWidthWest; // label left width in pixels if shown
84 private int wrappedSpaceAboveAlignment; // gap between widths
86 private int wrappedRepeatHeightPx; // height in pixels of wrapped width
88 private int wrappedVisibleWidths; // number of wrapped widths displayed
90 private Graphics2D gg;
93 * Creates a new SeqCanvas object.
97 public SeqCanvas(AlignmentPanel ap)
100 fr = new FeatureRenderer(ap);
101 seqRdr = new SequenceRenderer(av);
102 setLayout(new BorderLayout());
103 PaintRefresher.Register(this, av.getSequenceSetId());
104 setBackground(Color.white);
106 av.getRanges().addPropertyChangeListener(this);
109 public SequenceRenderer getSequenceRenderer()
114 public FeatureRenderer getFeatureRenderer()
120 * Draws the scale above a region of a wrapped alignment, consisting of a
121 * column number every major interval (10 columns).
124 * the graphics context to draw on, positioned at the start (bottom
125 * left) of the line on which to draw any scale marks
127 * start alignment column (0..)
129 * end alignment column (0..)
131 * y offset to draw at
133 private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
135 int charHeight = av.getCharHeight();
136 int charWidth = av.getCharWidth();
139 * white fill the scale space (for the fastPaint case)
141 g.setColor(Color.white);
142 g.fillRect(0, ypos - charHeight - charHeight / 2, getWidth(),
143 charHeight * 3 / 2 + 2);
144 g.setColor(Color.black);
146 List<ScaleMark> marks = new ScaleRenderer().calculateMarks(av, startx,
148 for (ScaleMark mark : marks)
150 int mpos = mark.column; // (i - startx - 1)
155 String mstring = mark.text;
161 g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
165 * draw a tick mark below the column number, centred on the column;
166 * height of tick mark is 4 pixels less than half a character
168 int xpos = (mpos * charWidth) + (charWidth / 2);
169 g.drawLine(xpos, (ypos + 2) - (charHeight / 2), xpos, ypos - 2);
175 * Draw the scale to the left or right of a wrapped alignment
178 * graphics context, positioned at the start of the scale to be drawn
180 * first column of wrapped width (0.. excluding any hidden columns)
182 * last column of wrapped width (0.. excluding any hidden columns)
184 * vertical offset at which to begin the scale
186 * if true, scale is left of residues, if false, scale is right
188 void drawVerticalScale(Graphics g, final int startx, final int endx,
189 final int ypos, final boolean left)
191 int charHeight = av.getCharHeight();
192 int charWidth = av.getCharWidth();
194 int yPos = ypos + charHeight;
198 if (av.hasHiddenColumns())
200 HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
201 startX = hiddenColumns.adjustForHiddenColumns(startx);
202 endX = hiddenColumns.adjustForHiddenColumns(endx);
204 FontMetrics fm = getFontMetrics(av.getFont());
206 for (int i = 0; i < av.getAlignment().getHeight(); i++)
208 SequenceI seq = av.getAlignment().getSequenceAt(i);
211 * find sequence position of first non-gapped position -
212 * to the right if scale left, to the left if scale right
214 int index = left ? startX : endX;
216 while (index >= startX && index <= endX)
218 if (!Comparison.isGap(seq.getCharAt(index)))
220 value = seq.findPosition(index);
234 * white fill the space for the scale
236 g.setColor(Color.white);
237 int y = (yPos + (i * charHeight)) - (charHeight / 5);
238 // fillRect origin is top left of rectangle
239 g.fillRect(0, y - charHeight, left ? labelWidthWest : labelWidthEast,
245 * draw scale value, right justified within its width less half a
246 * character width padding on the right
248 int labelSpace = left ? labelWidthWest : labelWidthEast;
249 labelSpace -= charWidth / 2; // leave space to the right
250 String valueAsString = String.valueOf(value);
251 int labelLength = fm.stringWidth(valueAsString);
252 int xOffset = labelSpace - labelLength;
253 g.setColor(Color.black);
254 g.drawString(valueAsString, xOffset, y);
260 * Does a fast paint of an alignment in response to a scroll. Most of the
261 * visible region is simply copied and shifted, and then any newly visible
262 * columns or rows are drawn. The scroll may be horizontal or vertical, but
263 * not both at once. Scrolling may be the result of
265 * <li>dragging a scroll bar</li>
266 * <li>clicking in the scroll bar</li>
267 * <li>scrolling by trackpad, middle mouse button, or other device</li>
268 * <li>by moving the box in the Overview window</li>
269 * <li>programmatically to make a highlighted position visible</li>
273 * columns to shift right (positive) or left (negative)
275 * rows to shift down (positive) or up (negative)
277 public void fastPaint(int horizontal, int vertical)
279 if (fastpainting || gg == null || img == null)
288 int charHeight = av.getCharHeight();
289 int charWidth = av.getCharWidth();
291 ViewportRanges ranges = av.getRanges();
292 int startRes = ranges.getStartRes();
293 int endRes = ranges.getEndRes();
294 int startSeq = ranges.getStartSeq();
295 int endSeq = ranges.getEndSeq();
299 gg.copyArea(horizontal * charWidth, vertical * charHeight,
300 img.getWidth(), img.getHeight(), -horizontal * charWidth,
301 -vertical * charHeight);
303 if (horizontal > 0) // scrollbar pulled right, image to the left
305 transX = (endRes - startRes - horizontal) * charWidth;
306 startRes = endRes - horizontal;
308 else if (horizontal < 0)
310 endRes = startRes - horizontal;
313 if (vertical > 0) // scroll down
315 startSeq = endSeq - vertical;
317 if (startSeq < ranges.getStartSeq())
318 { // ie scrolling too fast, more than a page at a time
319 startSeq = ranges.getStartSeq();
323 transY = img.getHeight() - ((vertical + 1) * charHeight);
326 else if (vertical < 0)
328 endSeq = startSeq - vertical;
330 if (endSeq > ranges.getEndSeq())
332 endSeq = ranges.getEndSeq();
336 gg.translate(transX, transY);
337 drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
338 gg.translate(-transX, -transY);
340 // Call repaint on alignment panel so that repaints from other alignment
341 // panel components can be aggregated. Otherwise performance of the
343 // window and others may be adversely affected.
344 av.getAlignPanel().repaint();
347 fastpainting = false;
352 public void paintComponent(Graphics g)
354 super.paintComponent(g);
356 int charHeight = av.getCharHeight();
357 int charWidth = av.getCharWidth();
359 ViewportRanges ranges = av.getRanges();
361 int width = getWidth();
362 int height = getHeight();
364 width -= (width % charWidth);
365 height -= (height % charHeight);
367 // selectImage is the selection group outline image
368 BufferedImage selectImage = drawSelectionGroup(
369 ranges.getStartRes(), ranges.getEndRes(),
370 ranges.getStartSeq(), ranges.getEndSeq());
372 if ((img != null) && (fastPaint
373 || (getVisibleRect().width != g.getClipBounds().width)
374 || (getVisibleRect().height != g.getClipBounds().height)))
376 BufferedImage lcimg = buildLocalImage(selectImage);
377 g.drawImage(lcimg, 0, 0, this);
380 else if ((width > 0) && (height > 0))
382 // img is a cached version of the last view we drew, if any
383 // if we have no img or the size has changed, make a new one
384 if (img == null || width != img.getWidth()
385 || height != img.getHeight())
392 gg = (Graphics2D) img.getGraphics();
393 gg.setFont(av.getFont());
398 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
399 RenderingHints.VALUE_ANTIALIAS_ON);
402 gg.setColor(Color.white);
403 gg.fillRect(0, 0, img.getWidth(), img.getHeight());
405 if (av.getWrapAlignment())
407 drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
411 drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
412 ranges.getStartSeq(), ranges.getEndSeq(), 0);
415 // lcimg is a local *copy* of img which we'll draw selectImage on top of
416 BufferedImage lcimg = buildLocalImage(selectImage);
417 g.drawImage(lcimg, 0, 0, this);
422 * Draw an alignment panel for printing
425 * Graphics object to draw with
427 * start residue of print area
429 * end residue of print area
431 * start sequence of print area
433 * end sequence of print area
435 public void drawPanelForPrinting(Graphics g1, int startRes, int endRes,
436 int startSeq, int endSeq)
438 drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
440 BufferedImage selectImage = drawSelectionGroup(startRes, endRes,
442 if (selectImage != null)
444 ((Graphics2D) g1).setComposite(AlphaComposite
445 .getInstance(AlphaComposite.SRC_OVER));
446 g1.drawImage(selectImage, 0, 0, this);
451 * Draw a wrapped alignment panel for printing
454 * Graphics object to draw with
456 * width of drawing area
457 * @param canvasHeight
458 * height of drawing area
460 * start residue of print area
462 public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth,
463 int canvasHeight, int startRes)
465 SequenceGroup group = av.getSelectionGroup();
467 drawWrappedPanel(g, canvasWidth, canvasHeight, startRes);
471 BufferedImage selectImage = null;
474 selectImage = new BufferedImage(canvasWidth, canvasHeight,
475 BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
476 } catch (OutOfMemoryError er)
479 System.err.println("Print image OutOfMemory Error.\n" + er);
480 new OOMWarning("Creating wrapped alignment image for printing", er);
482 if (selectImage != null)
484 Graphics2D g2 = selectImage.createGraphics();
485 setupSelectionGroup(g2, selectImage);
486 drawWrappedSelection(g2, group, canvasWidth, canvasHeight,
490 AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
491 g.drawImage(selectImage, 0, 0, this);
498 * Make a local image by combining the cached image img
501 private BufferedImage buildLocalImage(BufferedImage selectImage)
503 // clone the cached image
504 BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
507 // BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
509 Graphics2D g2d = lcimg.createGraphics();
510 g2d.drawImage(img, 0, 0, null);
512 // overlay selection group on lcimg
513 if (selectImage != null)
516 AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
517 g2d.drawImage(selectImage, 0, 0, this);
525 * Set up a buffered image of the correct height and size for the sequence canvas
527 private BufferedImage setupImage()
529 BufferedImage lcimg = null;
531 int charWidth = av.getCharWidth();
532 int charHeight = av.getCharHeight();
534 int width = getWidth();
535 int height = getHeight();
537 width -= (width % charWidth);
538 height -= (height % charHeight);
540 if ((width < 1) || (height < 1))
547 lcimg = new BufferedImage(width, height,
548 BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
549 } catch (OutOfMemoryError er)
553 "Group image OutOfMemory Redraw Error.\n" + er);
554 new OOMWarning("Creating alignment image for display", er);
563 * Returns the visible width of the canvas in residues, after allowing for
564 * East or West scales (if shown)
567 * the width in pixels (possibly including scales)
571 public int getWrappedCanvasWidth(int canvasWidth)
573 int charWidth = av.getCharWidth();
575 FontMetrics fm = getFontMetrics(av.getFont());
579 if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
581 labelWidth = getLabelWidth(fm);
584 labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
586 labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
588 return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
592 * Returns a pixel width sufficient to show the largest sequence coordinate
593 * (end position) in the alignment, calculated as the FontMetrics width of
594 * zeroes "0000000" limited to the number of decimal digits to be shown (3 for
595 * 1-10, 4 for 11-99 etc). One character width is added to this, to allow for
596 * half a character width space on either side.
601 protected int getLabelWidth(FontMetrics fm)
604 * find the biggest sequence end position we need to show
605 * (note this is not necessarily the sequence length)
608 AlignmentI alignment = av.getAlignment();
609 for (int i = 0; i < alignment.getHeight(); i++)
611 maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd());
615 for (int i = maxWidth; i > 0; i /= 10)
620 return fm.stringWidth(ZEROS.substring(0, length)) + av.getCharWidth();
624 * Draws as many widths of a wrapped alignment as can fit in the visible
629 * available width in pixels
630 * @param canvasHeight
631 * available height in pixels
633 * the first column (0...) of the alignment to draw
635 public void drawWrappedPanel(Graphics g, int canvasWidth,
636 int canvasHeight, final int startColumn)
638 int wrappedWidthInResidues = calculateWrappedGeometry(canvasWidth,
641 av.setWrappedWidth(wrappedWidthInResidues);
643 ViewportRanges ranges = av.getRanges();
644 ranges.setViewportStartAndWidth(startColumn, wrappedWidthInResidues);
647 * draw one width at a time (including any scales or annotation shown),
648 * until we have run out of either alignment or vertical space available
650 int ypos = wrappedSpaceAboveAlignment;
651 int maxWidth = ranges.getVisibleAlignmentWidth();
653 int start = startColumn;
654 int currentWidth = 0;
655 while ((currentWidth < wrappedVisibleWidths) && (start < maxWidth))
658 .min(maxWidth, start + wrappedWidthInResidues - 1);
659 drawWrappedWidth(g, ypos, start, endColumn, canvasHeight);
660 ypos += wrappedRepeatHeightPx;
661 start += wrappedWidthInResidues;
665 drawWrappedDecorators(g, startColumn);
669 * Calculates and saves values needed when rendering a wrapped alignment.
670 * These depend on many factors, including
672 * <li>canvas width and height</li>
673 * <li>number of visible sequences, and height of annotations if shown</li>
674 * <li>font and character width</li>
675 * <li>whether scales are shown left, right or above the alignment</li>
679 * @param canvasHeight
680 * @return the number of residue columns in each width
682 protected int calculateWrappedGeometry(int canvasWidth, int canvasHeight)
684 int charHeight = av.getCharHeight();
687 * vertical space in pixels between wrapped widths of alignment
688 * - one character height, or two if scale above is drawn
690 wrappedSpaceAboveAlignment = charHeight
691 * (av.getScaleAboveWrapped() ? 2 : 1);
694 * height in pixels of the wrapped widths
696 wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
698 wrappedRepeatHeightPx += av.getRanges().getViewportHeight()
700 // add annotations panel height if shown
701 wrappedRepeatHeightPx += getAnnotationHeight();
704 * number of visible widths (the last one may be part height),
705 * ensuring a part height includes at least one sequence
707 ViewportRanges ranges = av.getRanges();
708 wrappedVisibleWidths = canvasHeight / wrappedRepeatHeightPx;
709 int remainder = canvasHeight % wrappedRepeatHeightPx;
710 if (remainder >= (wrappedSpaceAboveAlignment + charHeight))
712 wrappedVisibleWidths++;
716 * compute width in residues; this also sets East and West label widths
718 int wrappedWidthInResidues = getWrappedCanvasWidth(canvasWidth);
721 * limit visibleWidths to not exceed width of alignment
723 int xMax = ranges.getVisibleAlignmentWidth();
724 int startToEnd = xMax - ranges.getStartRes();
725 int maxWidths = startToEnd / wrappedWidthInResidues;
726 if (startToEnd % wrappedWidthInResidues > 0)
730 wrappedVisibleWidths = Math.min(wrappedVisibleWidths, maxWidths);
732 return wrappedWidthInResidues;
736 * Draws one width of a wrapped alignment, including sequences and
737 * annnotations, if shown, but not scales or hidden column markers
743 * @param canvasHeight
745 protected void drawWrappedWidth(Graphics g, int ypos, int startColumn,
746 int endColumn, int canvasHeight)
748 ViewportRanges ranges = av.getRanges();
749 int viewportWidth = ranges.getViewportWidth();
751 int endx = Math.min(startColumn + viewportWidth - 1, endColumn);
754 * move right before drawing by the width of the scale left (if any)
755 * plus column offset from left margin (usually zero, but may be non-zero
756 * when fast painting is drawing just a few columns)
758 int charWidth = av.getCharWidth();
759 int xOffset = labelWidthWest
760 + ((startColumn - ranges.getStartRes()) % viewportWidth)
762 g.translate(xOffset, 0);
764 // When printing we have an extra clipped region,
765 // the Printable page which we need to account for here
766 Shape clip = g.getClip();
770 g.setClip(0, 0, viewportWidth * charWidth, canvasHeight);
774 g.setClip(0, (int) clip.getBounds().getY(),
775 viewportWidth * charWidth, (int) clip.getBounds().getHeight());
779 * white fill the region to be drawn (so incremental fast paint doesn't
780 * scribble over an existing image)
782 gg.setColor(Color.white);
783 gg.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
784 wrappedRepeatHeightPx);
786 drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1,
789 int cHeight = av.getAlignment().getHeight() * av.getCharHeight();
791 if (av.isShowAnnotation())
793 g.translate(0, cHeight + ypos + 3);
794 if (annotations == null)
796 annotations = new AnnotationPanel(av);
799 annotations.renderer.drawComponent(annotations, av, g, -1,
800 startColumn, endx + 1);
801 g.translate(0, -cHeight - ypos - 3);
804 g.translate(-xOffset, 0);
808 * Draws scales left, right and above (if shown), and any hidden column
809 * markers, on all widths of the wrapped alignment
814 protected void drawWrappedDecorators(Graphics g, final int startColumn)
816 int charWidth = av.getCharWidth();
818 g.setFont(av.getFont());
819 g.setColor(Color.black);
821 int ypos = wrappedSpaceAboveAlignment;
822 ViewportRanges ranges = av.getRanges();
823 int viewportWidth = ranges.getViewportWidth();
824 int maxWidth = ranges.getVisibleAlignmentWidth();
826 int startCol = startColumn;
828 while (widthsDrawn < wrappedVisibleWidths)
830 int endColumn = Math.min(maxWidth, startCol + viewportWidth - 1);
832 if (av.getScaleLeftWrapped())
834 drawVerticalScale(g, startCol, endColumn - 1, ypos, true);
837 if (av.getScaleRightWrapped())
839 int x = labelWidthWest + viewportWidth * charWidth;
841 drawVerticalScale(g, startCol, endColumn, ypos, false);
846 * white fill region of scale above and hidden column markers
847 * (to support incremental fast paint of image)
849 g.translate(labelWidthWest, 0);
850 g.setColor(Color.white);
851 g.fillRect(0, ypos - wrappedSpaceAboveAlignment, viewportWidth
852 * charWidth + labelWidthWest, wrappedSpaceAboveAlignment);
853 g.setColor(Color.black);
854 g.translate(-labelWidthWest, 0);
856 g.translate(labelWidthWest, 0);
858 if (av.getScaleAboveWrapped())
860 drawNorthScale(g, startCol, endColumn, ypos);
863 if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
865 drawHiddenColumnMarkers(g, ypos, startCol, endColumn);
868 g.translate(-labelWidthWest, 0);
870 ypos += wrappedRepeatHeightPx;
871 startCol += viewportWidth;
877 * Draws markers (triangles) above hidden column positions between startColumn
885 protected void drawHiddenColumnMarkers(Graphics g, int ypos,
886 int startColumn, int endColumn)
888 int charHeight = av.getCharHeight();
889 int charWidth = av.getCharWidth();
891 g.setColor(Color.blue);
892 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
893 List<Integer> positions = hidden.findHiddenRegionPositions();
894 for (int pos : positions)
896 int res = pos - startColumn;
898 if (res < 0 || res > endColumn - startColumn + 1)
904 * draw a downward-pointing triangle at the hidden columns location
905 * (before the following visible column)
907 int xMiddle = res * charWidth;
908 int[] xPoints = new int[] { xMiddle - charHeight / 4,
909 xMiddle + charHeight / 4, xMiddle };
910 int yTop = ypos - (charHeight / 2);
911 int[] yPoints = new int[] { yTop, yTop, yTop + 8 };
912 g.fillPolygon(xPoints, yPoints, 3);
917 * Draw a selection group over a wrapped alignment
919 private void drawWrappedSelection(Graphics2D g, SequenceGroup group,
921 int canvasHeight, int startRes)
923 int charHeight = av.getCharHeight();
924 int charWidth = av.getCharWidth();
926 // height gap above each panel
927 int hgap = charHeight;
928 if (av.getScaleAboveWrapped())
933 int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
935 int cHeight = av.getAlignment().getHeight() * charHeight;
937 int startx = startRes;
939 int ypos = hgap; // vertical offset
940 int maxwidth = av.getAlignment().getWidth();
942 if (av.hasHiddenColumns())
944 maxwidth = av.getAlignment().getHiddenColumns()
945 .findColumnPosition(maxwidth);
948 // chop the wrapped alignment extent up into panel-sized blocks and treat
949 // each block as if it were a block from an unwrapped alignment
950 while ((ypos <= canvasHeight) && (startx < maxwidth))
952 // set end value to be start + width, or maxwidth, whichever is smaller
953 endx = startx + cWidth - 1;
960 g.translate(labelWidthWest, 0);
962 drawUnwrappedSelection(g, group, startx, endx, 0,
963 av.getAlignment().getHeight() - 1,
966 g.translate(-labelWidthWest, 0);
968 // update vertical offset
969 ypos += cHeight + getAnnotationHeight() + hgap;
971 // update horizontal offset
976 int getAnnotationHeight()
978 if (!av.isShowAnnotation())
983 if (annotations == null)
985 annotations = new AnnotationPanel(av);
988 return annotations.adjustPanelHeight();
992 * Draws the visible region of the alignment on the graphics context. If there
993 * are hidden column markers in the visible region, then each sub-region
994 * between the markers is drawn separately, followed by the hidden column
998 * the graphics context, positioned at the first residue to be drawn
1000 * offset of the first column to draw (0..)
1002 * offset of the last column to draw (0..)
1004 * offset of the first sequence to draw (0..)
1006 * offset of the last sequence to draw (0..)
1008 * vertical offset at which to draw (for wrapped alignments)
1010 public void drawPanel(Graphics g1, final int startRes, final int endRes,
1011 final int startSeq, final int endSeq, final int yOffset)
1013 int charHeight = av.getCharHeight();
1014 int charWidth = av.getCharWidth();
1016 if (!av.hasHiddenColumns())
1018 draw(g1, startRes, endRes, startSeq, endSeq, yOffset);
1023 final int screenYMax = endRes - startRes;
1024 int blockStart = startRes;
1025 int blockEnd = endRes;
1027 for (int[] region : av.getAlignment().getHiddenColumns()
1028 .getHiddenColumnsCopy())
1030 int hideStart = region[0];
1031 int hideEnd = region[1];
1033 if (hideStart <= blockStart)
1035 blockStart += (hideEnd - hideStart) + 1;
1040 * draw up to just before the next hidden region, or the end of
1041 * the visible region, whichever comes first
1043 blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
1046 g1.translate(screenY * charWidth, 0);
1048 draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
1051 * draw the downline of the hidden column marker (ScalePanel draws the
1052 * triangle on top) if we reached it
1054 if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
1056 g1.setColor(Color.blue);
1058 g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
1059 0 + yOffset, (blockEnd - blockStart + 1) * charWidth - 1,
1060 (endSeq - startSeq + 1) * charHeight + yOffset);
1063 g1.translate(-screenY * charWidth, 0);
1064 screenY += blockEnd - blockStart + 1;
1065 blockStart = hideEnd + 1;
1067 if (screenY > screenYMax)
1069 // already rendered last block
1074 if (screenY <= screenYMax)
1076 // remaining visible region to render
1077 blockEnd = blockStart + screenYMax - screenY;
1078 g1.translate(screenY * charWidth, 0);
1079 draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
1081 g1.translate(-screenY * charWidth, 0);
1088 * Draws a region of the visible alignment
1092 * offset of the first column in the visible region (0..)
1094 * offset of the last column in the visible region (0..)
1096 * offset of the first sequence in the visible region (0..)
1098 * offset of the last sequence in the visible region (0..)
1100 * vertical offset at which to draw (for wrapped alignments)
1102 private void draw(Graphics g, int startRes, int endRes, int startSeq,
1103 int endSeq, int offset)
1105 int charHeight = av.getCharHeight();
1106 int charWidth = av.getCharWidth();
1108 g.setFont(av.getFont());
1109 seqRdr.prepare(g, av.isRenderGaps());
1113 // / First draw the sequences
1114 // ///////////////////////////
1115 for (int i = startSeq; i <= endSeq; i++)
1117 nextSeq = av.getAlignment().getSequenceAt(i);
1118 if (nextSeq == null)
1120 // occasionally, a race condition occurs such that the alignment row is
1124 seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
1125 startRes, endRes, offset + ((i - startSeq) * charHeight));
1127 if (av.isShowSequenceFeatures())
1129 fr.drawSequence(g, nextSeq, startRes, endRes,
1130 offset + ((i - startSeq) * charHeight), false);
1134 * highlight search Results once sequence has been drawn
1136 if (av.hasSearchResults())
1138 SearchResultsI searchResults = av.getSearchResults();
1139 int[] visibleResults = searchResults.getResults(nextSeq,
1141 if (visibleResults != null)
1143 for (int r = 0; r < visibleResults.length; r += 2)
1145 seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
1146 visibleResults[r + 1], (visibleResults[r] - startRes)
1148 + ((i - startSeq) * charHeight));
1153 if (av.cursorMode && cursorY == i && cursorX >= startRes
1154 && cursorX <= endRes)
1156 seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
1157 offset + ((i - startSeq) * charHeight));
1161 if (av.getSelectionGroup() != null
1162 || av.getAlignment().getGroups().size() > 0)
1164 drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
1169 void drawGroupsBoundaries(Graphics g1, int startRes, int endRes,
1170 int startSeq, int endSeq, int offset)
1172 Graphics2D g = (Graphics2D) g1;
1174 // ///////////////////////////////////
1175 // Now outline any areas if necessary
1176 // ///////////////////////////////////
1178 SequenceGroup group = null;
1179 int groupIndex = -1;
1181 if (av.getAlignment().getGroups().size() > 0)
1183 group = av.getAlignment().getGroups().get(0);
1189 g.setStroke(new BasicStroke());
1190 g.setColor(group.getOutlineColour());
1194 drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
1199 g.setStroke(new BasicStroke());
1201 if (groupIndex >= av.getAlignment().getGroups().size())
1206 group = av.getAlignment().getGroups().get(groupIndex);
1208 } while (groupIndex < av.getAlignment().getGroups().size());
1216 * Draw the selection group as a separate image and overlay
1218 private BufferedImage drawSelectionGroup(int startRes, int endRes,
1219 int startSeq, int endSeq)
1221 // get a new image of the correct size
1222 BufferedImage selectionImage = setupImage();
1224 if (selectionImage == null)
1229 SequenceGroup group = av.getSelectionGroup();
1236 // set up drawing colour
1237 Graphics2D g = (Graphics2D) selectionImage.getGraphics();
1239 setupSelectionGroup(g, selectionImage);
1241 if (!av.getWrapAlignment())
1243 drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq,
1248 drawWrappedSelection(g, group, getWidth(), getHeight(),
1249 av.getRanges().getStartRes());
1253 return selectionImage;
1257 * Set up graphics for selection group
1259 private void setupSelectionGroup(Graphics2D g,
1260 BufferedImage selectionImage)
1262 // set background to transparent
1263 g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
1264 g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
1266 // set up foreground to draw red dashed line
1267 g.setComposite(AlphaComposite.Src);
1268 g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
1269 BasicStroke.JOIN_ROUND, 3f, new float[]
1271 g.setColor(Color.RED);
1275 * Draw a selection group over an unwrapped alignment
1276 * @param g graphics object to draw with
1277 * @param group selection group
1278 * @param startRes start residue of area to draw
1279 * @param endRes end residue of area to draw
1280 * @param startSeq start sequence of area to draw
1281 * @param endSeq end sequence of area to draw
1282 * @param offset vertical offset (used when called from wrapped alignment code)
1284 private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
1285 int startRes, int endRes, int startSeq, int endSeq, int offset)
1287 int charWidth = av.getCharWidth();
1289 if (!av.hasHiddenColumns())
1291 drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
1296 // package into blocks of visible columns
1298 int blockStart = startRes;
1299 int blockEnd = endRes;
1301 for (int[] region : av.getAlignment().getHiddenColumns()
1302 .getHiddenColumnsCopy())
1304 int hideStart = region[0];
1305 int hideEnd = region[1];
1307 if (hideStart <= blockStart)
1309 blockStart += (hideEnd - hideStart) + 1;
1313 blockEnd = hideStart - 1;
1315 g.translate(screenY * charWidth, 0);
1316 drawPartialGroupOutline(g, group,
1317 blockStart, blockEnd, startSeq, endSeq, offset);
1319 g.translate(-screenY * charWidth, 0);
1320 screenY += blockEnd - blockStart + 1;
1321 blockStart = hideEnd + 1;
1323 if (screenY > (endRes - startRes))
1325 // already rendered last block
1330 if (screenY <= (endRes - startRes))
1332 // remaining visible region to render
1333 blockEnd = blockStart + (endRes - startRes) - screenY;
1334 g.translate(screenY * charWidth, 0);
1335 drawPartialGroupOutline(g, group,
1336 blockStart, blockEnd, startSeq, endSeq, offset);
1338 g.translate(-screenY * charWidth, 0);
1344 * Draw the selection group as a separate image and overlay
1346 private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group,
1347 int startRes, int endRes, int startSeq, int endSeq,
1350 int charHeight = av.getCharHeight();
1351 int charWidth = av.getCharWidth();
1353 int visWidth = (endRes - startRes + 1) * charWidth;
1357 boolean inGroup = false;
1365 for (i = startSeq; i <= endSeq; i++)
1367 // position of start residue of group relative to startRes, in pixels
1368 sx = (group.getStartRes() - startRes) * charWidth;
1370 // width of group in pixels
1371 xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
1374 sy = verticalOffset + (i - startSeq) * charHeight;
1376 if (sx + xwidth < 0 || sx > visWidth)
1381 if ((sx <= (endRes - startRes) * charWidth)
1382 && group.getSequences(null)
1383 .contains(av.getAlignment().getSequenceAt(i)))
1385 if ((bottom == -1) && !group.getSequences(null)
1386 .contains(av.getAlignment().getSequenceAt(i + 1)))
1388 bottom = sy + charHeight;
1393 if (((top == -1) && (i == 0)) || !group.getSequences(null)
1394 .contains(av.getAlignment().getSequenceAt(i - 1)))
1407 // if start position is visible, draw vertical line to left of
1409 if (sx >= 0 && sx < visWidth)
1411 g.drawLine(sx, oldY, sx, sy);
1414 // if end position is visible, draw vertical line to right of
1416 if (sx + xwidth < visWidth)
1418 g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
1427 // don't let width extend beyond current block, or group extent
1429 if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
1431 xwidth = (endRes - startRes + 1) * charWidth - sx;
1434 // draw horizontal line at top of group
1437 g.drawLine(sx, top, sx + xwidth, top);
1441 // draw horizontal line at bottom of group
1444 g.drawLine(sx, bottom, sx + xwidth, bottom);
1455 sy = verticalOffset + ((i - startSeq) * charHeight);
1456 if (sx >= 0 && sx < visWidth)
1458 g.drawLine(sx, oldY, sx, sy);
1461 if (sx + xwidth < visWidth)
1463 g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
1472 if (sx + xwidth > visWidth)
1476 else if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
1478 xwidth = (endRes - startRes + 1) * charWidth;
1483 g.drawLine(sx, top, sx + xwidth, top);
1489 g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1);
1498 * Highlights search results in the visible region by rendering as white text
1499 * on a black background. Any previous highlighting is removed. Answers true
1500 * if any highlight was left on the visible alignment (so status bar should be
1501 * set to match), else false.
1503 * Currently fastPaint is not implemented for wrapped alignments. If a wrapped
1504 * alignment had to be scrolled to show the highlighted region, then it should
1505 * be fully redrawn, otherwise a fast paint can be performed. This argument
1506 * could be removed if fast paint of scrolled wrapped alignment is coded in
1507 * future (JAL-2609).
1510 * @param noFastPaint
1513 public boolean highlightSearchResults(SearchResultsI results,
1514 boolean noFastPaint)
1520 boolean wrapped = av.getWrapAlignment();
1523 fastPaint = !noFastPaint;
1524 fastpainting = fastPaint;
1527 * to avoid redrawing the whole visible region, we instead
1528 * redraw just the minimal regions to remove previous highlights
1531 SearchResultsI previous = av.getSearchResults();
1532 av.setSearchResults(results);
1533 boolean redrawn = false;
1534 boolean drawn = false;
1537 redrawn = drawMappedPositionsWrapped(previous);
1538 drawn = drawMappedPositionsWrapped(results);
1543 redrawn = drawMappedPositions(previous);
1544 drawn = drawMappedPositions(results);
1549 * if highlights were either removed or added, repaint
1557 * return true only if highlights were added
1563 fastpainting = false;
1568 * Redraws the minimal rectangle in the visible region (if any) that includes
1569 * mapped positions of the given search results. Whether or not positions are
1570 * highlighted depends on the SearchResults set on the Viewport. This allows
1571 * this method to be called to either clear or set highlighting. Answers true
1572 * if any positions were drawn (in which case a repaint is still required),
1578 protected boolean drawMappedPositions(SearchResultsI results)
1580 if (results == null)
1586 * calculate the minimal rectangle to redraw that
1587 * includes both new and existing search results
1589 int firstSeq = Integer.MAX_VALUE;
1591 int firstCol = Integer.MAX_VALUE;
1593 boolean matchFound = false;
1595 ViewportRanges ranges = av.getRanges();
1596 int firstVisibleColumn = ranges.getStartRes();
1597 int lastVisibleColumn = ranges.getEndRes();
1598 AlignmentI alignment = av.getAlignment();
1599 if (av.hasHiddenColumns())
1601 firstVisibleColumn = alignment.getHiddenColumns()
1602 .adjustForHiddenColumns(firstVisibleColumn);
1603 lastVisibleColumn = alignment.getHiddenColumns()
1604 .adjustForHiddenColumns(lastVisibleColumn);
1607 for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
1608 .getEndSeq(); seqNo++)
1610 SequenceI seq = alignment.getSequenceAt(seqNo);
1612 int[] visibleResults = results.getResults(seq, firstVisibleColumn,
1614 if (visibleResults != null)
1616 for (int i = 0; i < visibleResults.length - 1; i += 2)
1618 int firstMatchedColumn = visibleResults[i];
1619 int lastMatchedColumn = visibleResults[i + 1];
1620 if (firstMatchedColumn <= lastVisibleColumn
1621 && lastMatchedColumn >= firstVisibleColumn)
1624 * found a search results match in the visible region -
1625 * remember the first and last sequence matched, and the first
1626 * and last visible columns in the matched positions
1629 firstSeq = Math.min(firstSeq, seqNo);
1630 lastSeq = Math.max(lastSeq, seqNo);
1631 firstMatchedColumn = Math.max(firstMatchedColumn,
1632 firstVisibleColumn);
1633 lastMatchedColumn = Math.min(lastMatchedColumn,
1635 firstCol = Math.min(firstCol, firstMatchedColumn);
1636 lastCol = Math.max(lastCol, lastMatchedColumn);
1644 if (av.hasHiddenColumns())
1646 firstCol = alignment.getHiddenColumns()
1647 .findColumnPosition(firstCol);
1648 lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol);
1650 int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
1651 int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
1652 gg.translate(transX, transY);
1653 drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0);
1654 gg.translate(-transX, -transY);
1661 public void propertyChange(PropertyChangeEvent evt)
1663 String eventName = evt.getPropertyName();
1665 if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
1673 if (eventName.equals(ViewportRanges.STARTRES)
1674 || eventName.equals(ViewportRanges.STARTRESANDSEQ))
1676 // Make sure we're not trying to draw a panel
1677 // larger than the visible window
1678 if (eventName.equals(ViewportRanges.STARTRES))
1680 scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
1684 scrollX = ((int[]) evt.getNewValue())[0]
1685 - ((int[]) evt.getOldValue())[0];
1687 ViewportRanges vpRanges = av.getRanges();
1689 int range = vpRanges.getEndRes() - vpRanges.getStartRes();
1690 if (scrollX > range)
1694 else if (scrollX < -range)
1700 // Both scrolling and resizing change viewport ranges: scrolling changes
1701 // both start and end points, but resize only changes end values.
1702 // Here we only want to fastpaint on a scroll, with resize using a normal
1703 // paint, so scroll events are identified as changes to the horizontal or
1704 // vertical start value.
1705 if (eventName.equals(ViewportRanges.STARTRES))
1707 if (av.getWrapAlignment())
1709 fastPaintWrapped(scrollX);
1713 fastPaint(scrollX, 0);
1716 else if (eventName.equals(ViewportRanges.STARTSEQ))
1719 fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
1721 else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
1723 fastPaint(scrollX, 0);
1724 // bizarrely, we only need to scroll on the x value here as fastpaint
1725 // copies the full height of the image anyway. Passing in the y value
1726 // causes nasty repaint artefacts, which only disappear on a full
1732 * Does a minimal update of the image for a scroll movement. This method
1733 * handles scroll movements of up to one width of the wrapped alignment (one
1734 * click in the vertical scrollbar). Larger movements (for example after a
1735 * scroll to highlight a mapped position) trigger a full redraw instead.
1738 * number of positions scrolled (right if positive, left if negative)
1740 protected void fastPaintWrapped(int scrollX)
1742 ViewportRanges ranges = av.getRanges();
1744 if (Math.abs(scrollX) > ranges.getViewportWidth())
1747 * shift of more than one view width is
1748 * overcomplicated to handle in this method
1755 if (fastpainting || gg == null)
1761 fastpainting = true;
1765 calculateWrappedGeometry(getWidth(), getHeight());
1768 * relocate the regions of the alignment that are still visible
1770 shiftWrappedAlignment(-scrollX);
1773 * add new columns (sequence, annotation)
1774 * - at top left if scrollX < 0
1775 * - at right of last two widths if scrollX > 0
1779 int startRes = ranges.getStartRes();
1780 drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes, startRes
1781 - scrollX - 1, getHeight());
1785 fastPaintWrappedAddRight(scrollX);
1789 * draw all scales (if shown) and hidden column markers
1791 drawWrappedDecorators(gg, ranges.getStartRes());
1796 fastpainting = false;
1801 * Draws the specified number of columns at the 'end' (bottom right) of a
1802 * wrapped alignment view, including sequences and annotations if shown, but
1803 * not scales. Also draws the same number of columns at the right hand end of
1804 * the second last width shown, if the last width is not full height (so
1805 * cannot simply be copied from the graphics image).
1809 protected void fastPaintWrappedAddRight(int columns)
1816 ViewportRanges ranges = av.getRanges();
1817 int viewportWidth = ranges.getViewportWidth();
1818 int charWidth = av.getCharWidth();
1821 * draw full height alignment in the second last row, last columns, if the
1822 * last row was not full height
1824 int visibleWidths = wrappedVisibleWidths;
1825 int canvasHeight = getHeight();
1826 boolean lastWidthPartHeight = (wrappedVisibleWidths * wrappedRepeatHeightPx) > canvasHeight;
1828 if (lastWidthPartHeight)
1830 int widthsAbove = Math.max(0, visibleWidths - 2);
1831 int ypos = wrappedRepeatHeightPx * widthsAbove
1832 + wrappedSpaceAboveAlignment;
1833 int endRes = ranges.getEndRes();
1834 endRes += widthsAbove * viewportWidth;
1835 int startRes = endRes - columns;
1836 int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth)
1840 * white fill first to erase annotations
1842 gg.translate(xOffset, 0);
1843 gg.setColor(Color.white);
1844 gg.fillRect(labelWidthWest, ypos,
1845 (endRes - startRes + 1) * charWidth, wrappedRepeatHeightPx);
1846 gg.translate(-xOffset, 0);
1848 drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
1852 * draw newly visible columns in last wrapped width (none if we
1853 * have reached the end of the alignment)
1854 * y-offset for drawing last width is height of widths above,
1857 int widthsAbove = visibleWidths - 1;
1858 int ypos = wrappedRepeatHeightPx * widthsAbove
1859 + wrappedSpaceAboveAlignment;
1860 int endRes = ranges.getEndRes();
1861 endRes += widthsAbove * viewportWidth;
1862 int startRes = endRes - columns + 1;
1865 * white fill first to erase annotations
1867 int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth)
1869 gg.translate(xOffset, 0);
1870 gg.setColor(Color.white);
1871 int width = viewportWidth * charWidth - xOffset;
1872 gg.fillRect(labelWidthWest, ypos, width, wrappedRepeatHeightPx);
1873 gg.translate(-xOffset, 0);
1875 gg.setFont(av.getFont());
1876 gg.setColor(Color.black);
1878 if (startRes < ranges.getVisibleAlignmentWidth())
1880 drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
1884 * and finally, white fill any space below the visible alignment
1886 int heightBelow = canvasHeight - visibleWidths * wrappedRepeatHeightPx;
1887 if (heightBelow > 0)
1889 gg.setColor(Color.white);
1890 gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow);
1895 * Shifts the visible alignment by the specified number of columns - left if
1896 * negative, right if positive. Copies and moves sequences and annotations (if
1897 * shown). Scales, hidden column markers and any newly visible columns must be
1902 protected void shiftWrappedAlignment(int positions)
1908 int charWidth = av.getCharWidth();
1910 int canvasHeight = getHeight();
1911 ViewportRanges ranges = av.getRanges();
1912 int viewportWidth = ranges.getViewportWidth();
1913 int widthToCopy = (ranges.getViewportWidth() - Math.abs(positions))
1915 int heightToCopy = wrappedRepeatHeightPx - wrappedSpaceAboveAlignment;
1916 int xMax = ranges.getVisibleAlignmentWidth();
1921 * shift right (after scroll left)
1922 * for each wrapped width (starting with the last), copy (width-positions)
1923 * columns from the left margin to the right margin, and copy positions
1924 * columns from the right margin of the row above (if any) to the
1925 * left margin of the current row
1929 * get y-offset of last wrapped width, first row of sequences
1931 int y = canvasHeight / wrappedRepeatHeightPx * wrappedRepeatHeightPx;
1932 y += wrappedSpaceAboveAlignment;
1933 int copyFromLeftStart = labelWidthWest;
1934 int copyFromRightStart = copyFromLeftStart + widthToCopy;
1938 gg.copyArea(copyFromLeftStart, y, widthToCopy, heightToCopy,
1939 positions * charWidth, 0);
1942 gg.copyArea(copyFromRightStart, y - wrappedRepeatHeightPx,
1943 positions * charWidth, heightToCopy, -widthToCopy,
1944 wrappedRepeatHeightPx);
1947 y -= wrappedRepeatHeightPx;
1953 * shift left (after scroll right)
1954 * for each wrapped width (starting with the first), copy (width-positions)
1955 * columns from the right margin to the left margin, and copy positions
1956 * columns from the left margin of the row below (if any) to the
1957 * right margin of the current row
1959 int xpos = av.getRanges().getStartRes();
1960 int y = wrappedSpaceAboveAlignment;
1961 int copyFromRightStart = labelWidthWest - positions * charWidth;
1963 while (y < canvasHeight)
1965 gg.copyArea(copyFromRightStart, y, widthToCopy, heightToCopy,
1966 positions * charWidth, 0);
1967 if (y + wrappedRepeatHeightPx < canvasHeight - wrappedRepeatHeightPx
1968 && (xpos + viewportWidth <= xMax))
1970 gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx, -positions
1971 * charWidth, heightToCopy, widthToCopy,
1972 -wrappedRepeatHeightPx);
1975 y += wrappedRepeatHeightPx;
1976 xpos += viewportWidth;
1983 * Redraws any positions in the search results in the visible region of a
1984 * wrapped alignment. Any highlights are drawn depending on the search results
1985 * set on the Viewport, not the <code>results</code> argument. This allows
1986 * this method to be called either to clear highlights (passing the previous
1987 * search results), or to draw new highlights.
1992 protected boolean drawMappedPositionsWrapped(SearchResultsI results)
1994 if (results == null)
1998 int charHeight = av.getCharHeight();
2000 boolean matchFound = false;
2002 calculateWrappedGeometry(getWidth(), getHeight());
2003 int wrappedWidth = av.getWrappedWidth();
2004 int wrappedHeight = wrappedRepeatHeightPx;
2006 ViewportRanges ranges = av.getRanges();
2007 int canvasHeight = getHeight();
2008 int repeats = canvasHeight / wrappedHeight;
2009 if (canvasHeight / wrappedHeight > 0)
2014 int firstVisibleColumn = ranges.getStartRes();
2015 int lastVisibleColumn = ranges.getStartRes() + repeats
2016 * ranges.getViewportWidth() - 1;
2018 AlignmentI alignment = av.getAlignment();
2019 if (av.hasHiddenColumns())
2021 firstVisibleColumn = alignment.getHiddenColumns()
2022 .adjustForHiddenColumns(firstVisibleColumn);
2023 lastVisibleColumn = alignment.getHiddenColumns()
2024 .adjustForHiddenColumns(lastVisibleColumn);
2027 int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
2029 for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
2030 .getEndSeq(); seqNo++)
2032 SequenceI seq = alignment.getSequenceAt(seqNo);
2034 int[] visibleResults = results.getResults(seq, firstVisibleColumn,
2036 if (visibleResults != null)
2038 for (int i = 0; i < visibleResults.length - 1; i += 2)
2040 int firstMatchedColumn = visibleResults[i];
2041 int lastMatchedColumn = visibleResults[i + 1];
2042 if (firstMatchedColumn <= lastVisibleColumn
2043 && lastMatchedColumn >= firstVisibleColumn)
2046 * found a search results match in the visible region
2048 firstMatchedColumn = Math.max(firstMatchedColumn,
2049 firstVisibleColumn);
2050 lastMatchedColumn = Math.min(lastMatchedColumn,
2054 * draw each mapped position separately (as contiguous positions may
2055 * wrap across lines)
2057 for (int mappedPos = firstMatchedColumn; mappedPos <= lastMatchedColumn; mappedPos++)
2059 int displayColumn = mappedPos;
2060 if (av.hasHiddenColumns())
2062 displayColumn = alignment.getHiddenColumns()
2063 .findColumnPosition(displayColumn);
2067 * transX: offset from left edge of canvas to residue position
2069 int transX = labelWidthWest
2070 + ((displayColumn - ranges.getStartRes()) % wrappedWidth)
2071 * av.getCharWidth();
2074 * transY: offset from top edge of canvas to residue position
2076 int transY = gapHeight;
2077 transY += (displayColumn - ranges.getStartRes())
2078 / wrappedWidth * wrappedHeight;
2079 transY += (seqNo - ranges.getStartSeq()) * av.getCharHeight();
2082 * yOffset is from graphics origin to start of visible region
2084 int yOffset = 0;// (displayColumn / wrappedWidth) * wrappedHeight;
2085 if (transY < getHeight())
2088 gg.translate(transX, transY);
2089 drawPanel(gg, displayColumn, displayColumn, seqNo, seqNo,
2091 gg.translate(-transX, -transY);
2103 * Answers the width in pixels of the left scale labels (0 if not shown)
2107 int getLabelWidthWest()
2109 return labelWidthWest;