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);
343 fastpainting = false;
348 public void paintComponent(Graphics g)
350 super.paintComponent(g);
352 int charHeight = av.getCharHeight();
353 int charWidth = av.getCharWidth();
355 ViewportRanges ranges = av.getRanges();
357 int width = getWidth();
358 int height = getHeight();
360 width -= (width % charWidth);
361 height -= (height % charHeight);
363 // selectImage is the selection group outline image
364 BufferedImage selectImage = drawSelectionGroup(
365 ranges.getStartRes(), ranges.getEndRes(),
366 ranges.getStartSeq(), ranges.getEndSeq());
368 if ((img != null) && (fastPaint
369 || (getVisibleRect().width != g.getClipBounds().width)
370 || (getVisibleRect().height != g.getClipBounds().height)))
372 BufferedImage lcimg = buildLocalImage(selectImage);
373 g.drawImage(lcimg, 0, 0, this);
376 else if ((width > 0) && (height > 0))
378 // img is a cached version of the last view we drew, if any
379 // if we have no img or the size has changed, make a new one
380 if (img == null || width != img.getWidth()
381 || height != img.getHeight())
388 gg = (Graphics2D) img.getGraphics();
389 gg.setFont(av.getFont());
394 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
395 RenderingHints.VALUE_ANTIALIAS_ON);
398 gg.setColor(Color.white);
399 gg.fillRect(0, 0, img.getWidth(), img.getHeight());
401 if (av.getWrapAlignment())
403 drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
407 drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
408 ranges.getStartSeq(), ranges.getEndSeq(), 0);
411 // lcimg is a local *copy* of img which we'll draw selectImage on top of
412 BufferedImage lcimg = buildLocalImage(selectImage);
413 g.drawImage(lcimg, 0, 0, this);
419 drawCursor(g, ranges.getStartRes(), ranges.getEndRes(),
420 ranges.getStartSeq(), ranges.getEndSeq());
425 * Draw an alignment panel for printing
428 * Graphics object to draw with
430 * start residue of print area
432 * end residue of print area
434 * start sequence of print area
436 * end sequence of print area
438 public void drawPanelForPrinting(Graphics g1, int startRes, int endRes,
439 int startSeq, int endSeq)
441 drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
443 BufferedImage selectImage = drawSelectionGroup(startRes, endRes,
445 if (selectImage != null)
447 ((Graphics2D) g1).setComposite(AlphaComposite
448 .getInstance(AlphaComposite.SRC_OVER));
449 g1.drawImage(selectImage, 0, 0, this);
454 * Draw a wrapped alignment panel for printing
457 * Graphics object to draw with
459 * width of drawing area
460 * @param canvasHeight
461 * height of drawing area
463 * start residue of print area
465 public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth,
466 int canvasHeight, int startRes)
468 SequenceGroup group = av.getSelectionGroup();
470 drawWrappedPanel(g, canvasWidth, canvasHeight, startRes);
474 BufferedImage selectImage = null;
477 selectImage = new BufferedImage(canvasWidth, canvasHeight,
478 BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
479 } catch (OutOfMemoryError er)
482 System.err.println("Print image OutOfMemory Error.\n" + er);
483 new OOMWarning("Creating wrapped alignment image for printing", er);
485 if (selectImage != null)
487 Graphics2D g2 = selectImage.createGraphics();
488 setupSelectionGroup(g2, selectImage);
489 drawWrappedSelection(g2, group, canvasWidth, canvasHeight,
493 AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
494 g.drawImage(selectImage, 0, 0, this);
501 * Make a local image by combining the cached image img
504 private BufferedImage buildLocalImage(BufferedImage selectImage)
506 // clone the cached image
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);
526 * Set up a buffered image of the correct height and size for the sequence canvas
528 private BufferedImage setupImage()
530 BufferedImage lcimg = null;
532 int charWidth = av.getCharWidth();
533 int charHeight = av.getCharHeight();
535 int width = getWidth();
536 int height = getHeight();
538 width -= (width % charWidth);
539 height -= (height % charHeight);
541 if ((width < 1) || (height < 1))
548 lcimg = new BufferedImage(width, height,
549 BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
550 } catch (OutOfMemoryError er)
554 "Group image OutOfMemory Redraw Error.\n" + er);
555 new OOMWarning("Creating alignment image for display", er);
564 * Returns the visible width of the canvas in residues, after allowing for
565 * East or West scales (if shown)
568 * the width in pixels (possibly including scales)
572 public int getWrappedCanvasWidth(int canvasWidth)
574 int charWidth = av.getCharWidth();
576 FontMetrics fm = getFontMetrics(av.getFont());
580 if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
582 labelWidth = getLabelWidth(fm);
585 labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
587 labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
589 return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
593 * Returns a pixel width sufficient to show the largest sequence coordinate
594 * (end position) in the alignment, calculated as the FontMetrics width of
595 * zeroes "0000000" limited to the number of decimal digits to be shown (3 for
596 * 1-10, 4 for 11-99 etc). One character width is added to this, to allow for
597 * half a character width space on either side.
602 protected int getLabelWidth(FontMetrics fm)
605 * find the biggest sequence end position we need to show
606 * (note this is not necessarily the sequence length)
609 AlignmentI alignment = av.getAlignment();
610 for (int i = 0; i < alignment.getHeight(); i++)
612 maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd());
616 for (int i = maxWidth; i > 0; i /= 10)
621 return fm.stringWidth(ZEROS.substring(0, length)) + av.getCharWidth();
625 * Draws as many widths of a wrapped alignment as can fit in the visible
630 * available width in pixels
631 * @param canvasHeight
632 * available height in pixels
634 * the first column (0...) of the alignment to draw
636 public void drawWrappedPanel(Graphics g, int canvasWidth,
637 int canvasHeight, final int startColumn)
639 int wrappedWidthInResidues = calculateWrappedGeometry(canvasWidth,
642 av.setWrappedWidth(wrappedWidthInResidues);
644 ViewportRanges ranges = av.getRanges();
645 ranges.setViewportStartAndWidth(startColumn, wrappedWidthInResidues);
648 * draw one width at a time (including any scales or annotation shown),
649 * until we have run out of either alignment or vertical space available
651 int ypos = wrappedSpaceAboveAlignment;
652 int maxWidth = ranges.getVisibleAlignmentWidth();
654 int start = startColumn;
655 int currentWidth = 0;
656 while ((currentWidth < wrappedVisibleWidths) && (start < maxWidth))
659 .min(maxWidth, start + wrappedWidthInResidues - 1);
660 drawWrappedWidth(g, ypos, start, endColumn, canvasHeight);
661 ypos += wrappedRepeatHeightPx;
662 start += wrappedWidthInResidues;
666 drawWrappedDecorators(g, startColumn);
670 * Calculates and saves values needed when rendering a wrapped alignment.
671 * These depend on many factors, including
673 * <li>canvas width and height</li>
674 * <li>number of visible sequences, and height of annotations if shown</li>
675 * <li>font and character width</li>
676 * <li>whether scales are shown left, right or above the alignment</li>
680 * @param canvasHeight
681 * @return the number of residue columns in each width
683 protected int calculateWrappedGeometry(int canvasWidth, int canvasHeight)
685 int charHeight = av.getCharHeight();
688 * vertical space in pixels between wrapped widths of alignment
689 * - one character height, or two if scale above is drawn
691 wrappedSpaceAboveAlignment = charHeight
692 * (av.getScaleAboveWrapped() ? 2 : 1);
695 * height in pixels of the wrapped widths
697 wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
699 wrappedRepeatHeightPx += av.getRanges().getViewportHeight()
701 // add annotations panel height if shown
702 wrappedRepeatHeightPx += getAnnotationHeight();
705 * number of visible widths (the last one may be part height),
706 * ensuring a part height includes at least one sequence
708 ViewportRanges ranges = av.getRanges();
709 wrappedVisibleWidths = canvasHeight / wrappedRepeatHeightPx;
710 int remainder = canvasHeight % wrappedRepeatHeightPx;
711 if (remainder >= (wrappedSpaceAboveAlignment + charHeight))
713 wrappedVisibleWidths++;
717 * compute width in residues; this also sets East and West label widths
719 int wrappedWidthInResidues = getWrappedCanvasWidth(canvasWidth);
722 * limit visibleWidths to not exceed width of alignment
724 int xMax = ranges.getVisibleAlignmentWidth();
725 int startToEnd = xMax - ranges.getStartRes();
726 int maxWidths = startToEnd / wrappedWidthInResidues;
727 if (startToEnd % wrappedWidthInResidues > 0)
731 wrappedVisibleWidths = Math.min(wrappedVisibleWidths, maxWidths);
733 return wrappedWidthInResidues;
737 * Draws one width of a wrapped alignment, including sequences and
738 * annnotations, if shown, but not scales or hidden column markers
744 * @param canvasHeight
746 protected void drawWrappedWidth(Graphics g, int ypos, int startColumn,
747 int endColumn, int canvasHeight)
749 ViewportRanges ranges = av.getRanges();
750 int viewportWidth = ranges.getViewportWidth();
752 int endx = Math.min(startColumn + viewportWidth - 1, endColumn);
755 * move right before drawing by the width of the scale left (if any)
756 * plus column offset from left margin (usually zero, but may be non-zero
757 * when fast painting is drawing just a few columns)
759 int charWidth = av.getCharWidth();
760 int xOffset = labelWidthWest
761 + ((startColumn - ranges.getStartRes()) % viewportWidth)
763 g.translate(xOffset, 0);
765 // When printing we have an extra clipped region,
766 // the Printable page which we need to account for here
767 Shape clip = g.getClip();
771 g.setClip(0, 0, viewportWidth * charWidth, canvasHeight);
775 g.setClip(0, (int) clip.getBounds().getY(),
776 viewportWidth * charWidth, (int) clip.getBounds().getHeight());
780 * white fill the region to be drawn (so incremental fast paint doesn't
781 * scribble over an existing image)
783 gg.setColor(Color.white);
784 gg.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
785 wrappedRepeatHeightPx);
787 drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1,
790 int cHeight = av.getAlignment().getHeight() * av.getCharHeight();
792 if (av.isShowAnnotation())
794 g.translate(0, cHeight + ypos + 3);
795 if (annotations == null)
797 annotations = new AnnotationPanel(av);
800 annotations.renderer.drawComponent(annotations, av, g, -1,
801 startColumn, endx + 1);
802 g.translate(0, -cHeight - ypos - 3);
805 g.translate(-xOffset, 0);
809 * Draws scales left, right and above (if shown), and any hidden column
810 * markers, on all widths of the wrapped alignment
815 protected void drawWrappedDecorators(Graphics g, final int startColumn)
817 int charWidth = av.getCharWidth();
819 g.setFont(av.getFont());
820 g.setColor(Color.black);
822 int ypos = wrappedSpaceAboveAlignment;
823 ViewportRanges ranges = av.getRanges();
824 int viewportWidth = ranges.getViewportWidth();
825 int maxWidth = ranges.getVisibleAlignmentWidth();
827 int startCol = startColumn;
829 while (widthsDrawn < wrappedVisibleWidths)
831 int endColumn = Math.min(maxWidth, startCol + viewportWidth - 1);
833 if (av.getScaleLeftWrapped())
835 drawVerticalScale(g, startCol, endColumn - 1, ypos, true);
838 if (av.getScaleRightWrapped())
840 int x = labelWidthWest + viewportWidth * charWidth;
842 drawVerticalScale(g, startCol, endColumn, ypos, false);
847 * white fill region of scale above and hidden column markers
848 * (to support incremental fast paint of image)
850 g.translate(labelWidthWest, 0);
851 g.setColor(Color.white);
852 g.fillRect(0, ypos - wrappedSpaceAboveAlignment, viewportWidth
853 * charWidth + labelWidthWest, wrappedSpaceAboveAlignment);
854 g.setColor(Color.black);
855 g.translate(-labelWidthWest, 0);
857 g.translate(labelWidthWest, 0);
859 if (av.getScaleAboveWrapped())
861 drawNorthScale(g, startCol, endColumn, ypos);
864 if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
866 drawHiddenColumnMarkers(g, ypos, startCol, endColumn);
869 g.translate(-labelWidthWest, 0);
871 ypos += wrappedRepeatHeightPx;
872 startCol += viewportWidth;
878 * Draws markers (triangles) above hidden column positions between startColumn
886 protected void drawHiddenColumnMarkers(Graphics g, int ypos,
887 int startColumn, int endColumn)
889 int charHeight = av.getCharHeight();
890 int charWidth = av.getCharWidth();
892 g.setColor(Color.blue);
893 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
894 List<Integer> positions = hidden.findHiddenRegionPositions();
895 for (int pos : positions)
897 int res = pos - startColumn;
899 if (res < 0 || res > endColumn - startColumn + 1)
905 * draw a downward-pointing triangle at the hidden columns location
906 * (before the following visible column)
908 int xMiddle = res * charWidth;
909 int[] xPoints = new int[] { xMiddle - charHeight / 4,
910 xMiddle + charHeight / 4, xMiddle };
911 int yTop = ypos - (charHeight / 2);
912 int[] yPoints = new int[] { yTop, yTop, yTop + 8 };
913 g.fillPolygon(xPoints, yPoints, 3);
918 * Draw a selection group over a wrapped alignment
920 private void drawWrappedSelection(Graphics2D g, SequenceGroup group,
922 int canvasHeight, int startRes)
924 int charHeight = av.getCharHeight();
925 int charWidth = av.getCharWidth();
927 // height gap above each panel
928 int hgap = charHeight;
929 if (av.getScaleAboveWrapped())
934 int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
936 int cHeight = av.getAlignment().getHeight() * charHeight;
938 int startx = startRes;
940 int ypos = hgap; // vertical offset
941 int maxwidth = av.getAlignment().getWidth();
943 if (av.hasHiddenColumns())
945 maxwidth = av.getAlignment().getHiddenColumns()
946 .findColumnPosition(maxwidth);
949 // chop the wrapped alignment extent up into panel-sized blocks and treat
950 // each block as if it were a block from an unwrapped alignment
951 while ((ypos <= canvasHeight) && (startx < maxwidth))
953 // set end value to be start + width, or maxwidth, whichever is smaller
954 endx = startx + cWidth - 1;
961 g.translate(labelWidthWest, 0);
963 drawUnwrappedSelection(g, group, startx, endx, 0,
964 av.getAlignment().getHeight() - 1,
967 g.translate(-labelWidthWest, 0);
969 // update vertical offset
970 ypos += cHeight + getAnnotationHeight() + hgap;
972 // update horizontal offset
977 int getAnnotationHeight()
979 if (!av.isShowAnnotation())
984 if (annotations == null)
986 annotations = new AnnotationPanel(av);
989 return annotations.adjustPanelHeight();
993 * Draws the visible region of the alignment on the graphics context. If there
994 * are hidden column markers in the visible region, then each sub-region
995 * between the markers is drawn separately, followed by the hidden column
999 * the graphics context, positioned at the first residue to be drawn
1001 * offset of the first column to draw (0..)
1003 * offset of the last column to draw (0..)
1005 * offset of the first sequence to draw (0..)
1007 * offset of the last sequence to draw (0..)
1009 * vertical offset at which to draw (for wrapped alignments)
1011 public void drawPanel(Graphics g1, final int startRes, final int endRes,
1012 final int startSeq, final int endSeq, final int yOffset)
1014 int charHeight = av.getCharHeight();
1015 int charWidth = av.getCharWidth();
1017 if (!av.hasHiddenColumns())
1019 draw(g1, startRes, endRes, startSeq, endSeq, yOffset);
1024 final int screenYMax = endRes - startRes;
1025 int blockStart = startRes;
1026 int blockEnd = endRes;
1028 for (int[] region : av.getAlignment().getHiddenColumns()
1029 .getHiddenColumnsCopy())
1031 int hideStart = region[0];
1032 int hideEnd = region[1];
1034 if (hideStart <= blockStart)
1036 blockStart += (hideEnd - hideStart) + 1;
1041 * draw up to just before the next hidden region, or the end of
1042 * the visible region, whichever comes first
1044 blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
1047 g1.translate(screenY * charWidth, 0);
1049 draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
1052 * draw the downline of the hidden column marker (ScalePanel draws the
1053 * triangle on top) if we reached it
1055 if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
1057 g1.setColor(Color.blue);
1059 g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
1060 0 + yOffset, (blockEnd - blockStart + 1) * charWidth - 1,
1061 (endSeq - startSeq + 1) * charHeight + yOffset);
1064 g1.translate(-screenY * charWidth, 0);
1065 screenY += blockEnd - blockStart + 1;
1066 blockStart = hideEnd + 1;
1068 if (screenY > screenYMax)
1070 // already rendered last block
1075 if (screenY <= screenYMax)
1077 // remaining visible region to render
1078 blockEnd = blockStart + screenYMax - screenY;
1079 g1.translate(screenY * charWidth, 0);
1080 draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
1082 g1.translate(-screenY * charWidth, 0);
1089 * Draws a region of the visible alignment
1093 * offset of the first column in the visible region (0..)
1095 * offset of the last column in the visible region (0..)
1097 * offset of the first sequence in the visible region (0..)
1099 * offset of the last sequence in the visible region (0..)
1101 * vertical offset at which to draw (for wrapped alignments)
1103 private void draw(Graphics g, int startRes, int endRes, int startSeq,
1104 int endSeq, int offset)
1106 int charHeight = av.getCharHeight();
1107 int charWidth = av.getCharWidth();
1109 g.setFont(av.getFont());
1110 seqRdr.prepare(g, av.isRenderGaps());
1114 // / First draw the sequences
1115 // ///////////////////////////
1116 for (int i = startSeq; i <= endSeq; i++)
1118 nextSeq = av.getAlignment().getSequenceAt(i);
1119 if (nextSeq == null)
1121 // occasionally, a race condition occurs such that the alignment row is
1125 seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
1126 startRes, endRes, offset + ((i - startSeq) * charHeight));
1128 if (av.isShowSequenceFeatures())
1130 fr.drawSequence(g, nextSeq, startRes, endRes,
1131 offset + ((i - startSeq) * charHeight), false);
1135 * highlight search Results once sequence has been drawn
1137 if (av.hasSearchResults())
1139 SearchResultsI searchResults = av.getSearchResults();
1140 int[] visibleResults = searchResults.getResults(nextSeq,
1142 if (visibleResults != null)
1144 for (int r = 0; r < visibleResults.length; r += 2)
1146 seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
1147 visibleResults[r + 1], (visibleResults[r] - startRes)
1149 + ((i - startSeq) * charHeight));
1155 if (av.getSelectionGroup() != null
1156 || av.getAlignment().getGroups().size() > 0)
1158 drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
1163 void drawGroupsBoundaries(Graphics g1, int startRes, int endRes,
1164 int startSeq, int endSeq, int offset)
1166 Graphics2D g = (Graphics2D) g1;
1168 // ///////////////////////////////////
1169 // Now outline any areas if necessary
1170 // ///////////////////////////////////
1172 SequenceGroup group = null;
1173 int groupIndex = -1;
1175 if (av.getAlignment().getGroups().size() > 0)
1177 group = av.getAlignment().getGroups().get(0);
1183 g.setStroke(new BasicStroke());
1184 g.setColor(group.getOutlineColour());
1188 drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
1193 g.setStroke(new BasicStroke());
1195 if (groupIndex >= av.getAlignment().getGroups().size())
1200 group = av.getAlignment().getGroups().get(groupIndex);
1202 } while (groupIndex < av.getAlignment().getGroups().size());
1210 * Draw the selection group as a separate image and overlay
1212 private BufferedImage drawSelectionGroup(int startRes, int endRes,
1213 int startSeq, int endSeq)
1215 // get a new image of the correct size
1216 BufferedImage selectionImage = setupImage();
1218 if (selectionImage == null)
1223 SequenceGroup group = av.getSelectionGroup();
1230 // set up drawing colour
1231 Graphics2D g = (Graphics2D) selectionImage.getGraphics();
1233 setupSelectionGroup(g, selectionImage);
1235 if (!av.getWrapAlignment())
1237 drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq,
1242 drawWrappedSelection(g, group, getWidth(), getHeight(),
1243 av.getRanges().getStartRes());
1247 return selectionImage;
1251 * Draw the cursor as a separate image and overlay
1254 * start residue of area to draw cursor in
1256 * end residue of area to draw cursor in
1258 * start sequence of area to draw cursor in
1260 * end sequence of are to draw cursor in
1261 * @return a transparent image of the same size as the sequence canvas, with
1262 * the cursor drawn on it, if any
1264 private void drawCursor(Graphics g, int startRes, int endRes,
1268 // convert the cursorY into a position on the visible alignment
1269 int cursor_ypos = av.getAlignment().getHiddenSequences()
1270 .findIndexWithoutHiddenSeqs(cursorY);
1272 // don't do work unless we have to
1273 if (cursor_ypos >= startSeq && cursor_ypos <= endSeq)
1277 int startx = startRes;
1280 // convert the cursorX into a position on the visible alignment
1281 int cursor_xpos = av.getAlignment().getHiddenColumns()
1282 .findColumnPosition(cursorX);
1284 if (av.getWrapAlignment())
1286 // work out the correct offsets for the cursor
1287 int charHeight = av.getCharHeight();
1288 int charWidth = av.getCharWidth();
1289 int canvasWidth = getWidth();
1290 int canvasHeight = getHeight();
1292 // height gap above each panel
1293 int hgap = charHeight;
1294 if (av.getScaleAboveWrapped())
1299 int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
1301 int cHeight = av.getAlignment().getHeight() * charHeight;
1303 endx = startx + cWidth - 1;
1304 int ypos = hgap; // vertical offset
1306 // iterate down the wrapped panels
1307 while ((ypos <= canvasHeight) && (endx < cursor_xpos))
1309 // update vertical offset
1310 ypos += cHeight + getAnnotationHeight() + hgap;
1312 // update horizontal offset
1314 endx = startx + cWidth - 1;
1317 xoffset = labelWidthWest;
1320 // now check if cursor is within range for x values
1321 if (cursor_xpos >= startx && cursor_xpos <= endx)
1323 // get the character the cursor is drawn at
1324 SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
1325 char s = seq.getCharAt(cursorX);
1327 seqRdr.drawCursor(g, s,
1328 xoffset + (cursor_xpos - startx) * av.getCharWidth(),
1329 yoffset + (cursor_ypos - startSeq) * av.getCharHeight());
1336 * Set up graphics for selection group
1338 private void setupSelectionGroup(Graphics2D g,
1339 BufferedImage selectionImage)
1341 // set background to transparent
1342 g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
1343 g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
1345 // set up foreground to draw red dashed line
1346 g.setComposite(AlphaComposite.Src);
1347 g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
1348 BasicStroke.JOIN_ROUND, 3f, new float[]
1350 g.setColor(Color.RED);
1354 * Draw a selection group over an unwrapped alignment
1355 * @param g graphics object to draw with
1356 * @param group selection group
1357 * @param startRes start residue of area to draw
1358 * @param endRes end residue of area to draw
1359 * @param startSeq start sequence of area to draw
1360 * @param endSeq end sequence of area to draw
1361 * @param offset vertical offset (used when called from wrapped alignment code)
1363 private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
1364 int startRes, int endRes, int startSeq, int endSeq, int offset)
1366 int charWidth = av.getCharWidth();
1368 if (!av.hasHiddenColumns())
1370 drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
1375 // package into blocks of visible columns
1377 int blockStart = startRes;
1378 int blockEnd = endRes;
1380 for (int[] region : av.getAlignment().getHiddenColumns()
1381 .getHiddenColumnsCopy())
1383 int hideStart = region[0];
1384 int hideEnd = region[1];
1386 if (hideStart <= blockStart)
1388 blockStart += (hideEnd - hideStart) + 1;
1392 blockEnd = hideStart - 1;
1394 g.translate(screenY * charWidth, 0);
1395 drawPartialGroupOutline(g, group,
1396 blockStart, blockEnd, startSeq, endSeq, offset);
1398 g.translate(-screenY * charWidth, 0);
1399 screenY += blockEnd - blockStart + 1;
1400 blockStart = hideEnd + 1;
1402 if (screenY > (endRes - startRes))
1404 // already rendered last block
1409 if (screenY <= (endRes - startRes))
1411 // remaining visible region to render
1412 blockEnd = blockStart + (endRes - startRes) - screenY;
1413 g.translate(screenY * charWidth, 0);
1414 drawPartialGroupOutline(g, group,
1415 blockStart, blockEnd, startSeq, endSeq, offset);
1417 g.translate(-screenY * charWidth, 0);
1423 * Draw the selection group as a separate image and overlay
1425 private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group,
1426 int startRes, int endRes, int startSeq, int endSeq,
1429 int charHeight = av.getCharHeight();
1430 int charWidth = av.getCharWidth();
1432 int visWidth = (endRes - startRes + 1) * charWidth;
1436 boolean inGroup = false;
1444 for (i = startSeq; i <= endSeq; i++)
1446 // position of start residue of group relative to startRes, in pixels
1447 sx = (group.getStartRes() - startRes) * charWidth;
1449 // width of group in pixels
1450 xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
1453 sy = verticalOffset + (i - startSeq) * charHeight;
1455 if (sx + xwidth < 0 || sx > visWidth)
1460 if ((sx <= (endRes - startRes) * charWidth)
1461 && group.getSequences(null)
1462 .contains(av.getAlignment().getSequenceAt(i)))
1464 if ((bottom == -1) && !group.getSequences(null)
1465 .contains(av.getAlignment().getSequenceAt(i + 1)))
1467 bottom = sy + charHeight;
1472 if (((top == -1) && (i == 0)) || !group.getSequences(null)
1473 .contains(av.getAlignment().getSequenceAt(i - 1)))
1486 // if start position is visible, draw vertical line to left of
1488 if (sx >= 0 && sx < visWidth)
1490 g.drawLine(sx, oldY, sx, sy);
1493 // if end position is visible, draw vertical line to right of
1495 if (sx + xwidth < visWidth)
1497 g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
1506 // don't let width extend beyond current block, or group extent
1508 if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
1510 xwidth = (endRes - startRes + 1) * charWidth - sx;
1513 // draw horizontal line at top of group
1516 g.drawLine(sx, top, sx + xwidth, top);
1520 // draw horizontal line at bottom of group
1523 g.drawLine(sx, bottom, sx + xwidth, bottom);
1534 sy = verticalOffset + ((i - startSeq) * charHeight);
1535 if (sx >= 0 && sx < visWidth)
1537 g.drawLine(sx, oldY, sx, sy);
1540 if (sx + xwidth < visWidth)
1542 g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
1551 if (sx + xwidth > visWidth)
1555 else if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
1557 xwidth = (endRes - startRes + 1) * charWidth;
1562 g.drawLine(sx, top, sx + xwidth, top);
1568 g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1);
1577 * Highlights search results in the visible region by rendering as white text
1578 * on a black background. Any previous highlighting is removed. Answers true
1579 * if any highlight was left on the visible alignment (so status bar should be
1580 * set to match), else false.
1582 * Currently fastPaint is not implemented for wrapped alignments. If a wrapped
1583 * alignment had to be scrolled to show the highlighted region, then it should
1584 * be fully redrawn, otherwise a fast paint can be performed. This argument
1585 * could be removed if fast paint of scrolled wrapped alignment is coded in
1586 * future (JAL-2609).
1589 * @param noFastPaint
1592 public boolean highlightSearchResults(SearchResultsI results,
1593 boolean noFastPaint)
1599 boolean wrapped = av.getWrapAlignment();
1602 fastPaint = !noFastPaint;
1603 fastpainting = fastPaint;
1606 * to avoid redrawing the whole visible region, we instead
1607 * redraw just the minimal regions to remove previous highlights
1610 SearchResultsI previous = av.getSearchResults();
1611 av.setSearchResults(results);
1612 boolean redrawn = false;
1613 boolean drawn = false;
1616 redrawn = drawMappedPositionsWrapped(previous);
1617 drawn = drawMappedPositionsWrapped(results);
1622 redrawn = drawMappedPositions(previous);
1623 drawn = drawMappedPositions(results);
1628 * if highlights were either removed or added, repaint
1636 * return true only if highlights were added
1642 fastpainting = false;
1647 * Redraws the minimal rectangle in the visible region (if any) that includes
1648 * mapped positions of the given search results. Whether or not positions are
1649 * highlighted depends on the SearchResults set on the Viewport. This allows
1650 * this method to be called to either clear or set highlighting. Answers true
1651 * if any positions were drawn (in which case a repaint is still required),
1657 protected boolean drawMappedPositions(SearchResultsI results)
1659 if (results == null)
1665 * calculate the minimal rectangle to redraw that
1666 * includes both new and existing search results
1668 int firstSeq = Integer.MAX_VALUE;
1670 int firstCol = Integer.MAX_VALUE;
1672 boolean matchFound = false;
1674 ViewportRanges ranges = av.getRanges();
1675 int firstVisibleColumn = ranges.getStartRes();
1676 int lastVisibleColumn = ranges.getEndRes();
1677 AlignmentI alignment = av.getAlignment();
1678 if (av.hasHiddenColumns())
1680 firstVisibleColumn = alignment.getHiddenColumns()
1681 .adjustForHiddenColumns(firstVisibleColumn);
1682 lastVisibleColumn = alignment.getHiddenColumns()
1683 .adjustForHiddenColumns(lastVisibleColumn);
1686 for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
1687 .getEndSeq(); seqNo++)
1689 SequenceI seq = alignment.getSequenceAt(seqNo);
1691 int[] visibleResults = results.getResults(seq, firstVisibleColumn,
1693 if (visibleResults != null)
1695 for (int i = 0; i < visibleResults.length - 1; i += 2)
1697 int firstMatchedColumn = visibleResults[i];
1698 int lastMatchedColumn = visibleResults[i + 1];
1699 if (firstMatchedColumn <= lastVisibleColumn
1700 && lastMatchedColumn >= firstVisibleColumn)
1703 * found a search results match in the visible region -
1704 * remember the first and last sequence matched, and the first
1705 * and last visible columns in the matched positions
1708 firstSeq = Math.min(firstSeq, seqNo);
1709 lastSeq = Math.max(lastSeq, seqNo);
1710 firstMatchedColumn = Math.max(firstMatchedColumn,
1711 firstVisibleColumn);
1712 lastMatchedColumn = Math.min(lastMatchedColumn,
1714 firstCol = Math.min(firstCol, firstMatchedColumn);
1715 lastCol = Math.max(lastCol, lastMatchedColumn);
1723 if (av.hasHiddenColumns())
1725 firstCol = alignment.getHiddenColumns()
1726 .findColumnPosition(firstCol);
1727 lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol);
1729 int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
1730 int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
1731 gg.translate(transX, transY);
1732 drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0);
1733 gg.translate(-transX, -transY);
1740 public void propertyChange(PropertyChangeEvent evt)
1742 String eventName = evt.getPropertyName();
1744 if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
1750 else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
1758 if (eventName.equals(ViewportRanges.STARTRES)
1759 || eventName.equals(ViewportRanges.STARTRESANDSEQ))
1761 // Make sure we're not trying to draw a panel
1762 // larger than the visible window
1763 if (eventName.equals(ViewportRanges.STARTRES))
1765 scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
1769 scrollX = ((int[]) evt.getNewValue())[0]
1770 - ((int[]) evt.getOldValue())[0];
1772 ViewportRanges vpRanges = av.getRanges();
1774 int range = vpRanges.getEndRes() - vpRanges.getStartRes();
1775 if (scrollX > range)
1779 else if (scrollX < -range)
1784 // Both scrolling and resizing change viewport ranges: scrolling changes
1785 // both start and end points, but resize only changes end values.
1786 // Here we only want to fastpaint on a scroll, with resize using a normal
1787 // paint, so scroll events are identified as changes to the horizontal or
1788 // vertical start value.
1789 if (eventName.equals(ViewportRanges.STARTRES))
1791 if (av.getWrapAlignment())
1793 fastPaintWrapped(scrollX);
1797 fastPaint(scrollX, 0);
1800 else if (eventName.equals(ViewportRanges.STARTSEQ))
1803 fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
1805 else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
1807 if (av.getWrapAlignment())
1809 fastPaintWrapped(scrollX);
1813 fastPaint(scrollX, 0);
1815 // bizarrely, we only need to scroll on the x value here as fastpaint
1816 // copies the full height of the image anyway. Passing in the y value
1817 // causes nasty repaint artefacts, which only disappear on a full
1824 * Does a minimal update of the image for a scroll movement. This method
1825 * handles scroll movements of up to one width of the wrapped alignment (one
1826 * click in the vertical scrollbar). Larger movements (for example after a
1827 * scroll to highlight a mapped position) trigger a full redraw instead.
1830 * number of positions scrolled (right if positive, left if negative)
1832 protected void fastPaintWrapped(int scrollX)
1834 ViewportRanges ranges = av.getRanges();
1836 if (Math.abs(scrollX) > ranges.getViewportWidth())
1839 * shift of more than one view width is
1840 * overcomplicated to handle in this method
1847 if (fastpainting || gg == null)
1853 fastpainting = true;
1857 calculateWrappedGeometry(getWidth(), getHeight());
1860 * relocate the regions of the alignment that are still visible
1862 shiftWrappedAlignment(-scrollX);
1865 * add new columns (sequence, annotation)
1866 * - at top left if scrollX < 0
1867 * - at right of last two widths if scrollX > 0
1871 int startRes = ranges.getStartRes();
1872 drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes, startRes
1873 - scrollX - 1, getHeight());
1877 fastPaintWrappedAddRight(scrollX);
1881 * draw all scales (if shown) and hidden column markers
1883 drawWrappedDecorators(gg, ranges.getStartRes());
1888 fastpainting = false;
1893 * Draws the specified number of columns at the 'end' (bottom right) of a
1894 * wrapped alignment view, including sequences and annotations if shown, but
1895 * not scales. Also draws the same number of columns at the right hand end of
1896 * the second last width shown, if the last width is not full height (so
1897 * cannot simply be copied from the graphics image).
1901 protected void fastPaintWrappedAddRight(int columns)
1908 ViewportRanges ranges = av.getRanges();
1909 int viewportWidth = ranges.getViewportWidth();
1910 int charWidth = av.getCharWidth();
1913 * draw full height alignment in the second last row, last columns, if the
1914 * last row was not full height
1916 int visibleWidths = wrappedVisibleWidths;
1917 int canvasHeight = getHeight();
1918 boolean lastWidthPartHeight = (wrappedVisibleWidths * wrappedRepeatHeightPx) > canvasHeight;
1920 if (lastWidthPartHeight)
1922 int widthsAbove = Math.max(0, visibleWidths - 2);
1923 int ypos = wrappedRepeatHeightPx * widthsAbove
1924 + wrappedSpaceAboveAlignment;
1925 int endRes = ranges.getEndRes();
1926 endRes += widthsAbove * viewportWidth;
1927 int startRes = endRes - columns;
1928 int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth)
1932 * white fill first to erase annotations
1934 gg.translate(xOffset, 0);
1935 gg.setColor(Color.white);
1936 gg.fillRect(labelWidthWest, ypos,
1937 (endRes - startRes + 1) * charWidth, wrappedRepeatHeightPx);
1938 gg.translate(-xOffset, 0);
1940 drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
1944 * draw newly visible columns in last wrapped width (none if we
1945 * have reached the end of the alignment)
1946 * y-offset for drawing last width is height of widths above,
1949 int widthsAbove = visibleWidths - 1;
1950 int ypos = wrappedRepeatHeightPx * widthsAbove
1951 + wrappedSpaceAboveAlignment;
1952 int endRes = ranges.getEndRes();
1953 endRes += widthsAbove * viewportWidth;
1954 int startRes = endRes - columns + 1;
1957 * white fill first to erase annotations
1959 int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth)
1961 gg.translate(xOffset, 0);
1962 gg.setColor(Color.white);
1963 int width = viewportWidth * charWidth - xOffset;
1964 gg.fillRect(labelWidthWest, ypos, width, wrappedRepeatHeightPx);
1965 gg.translate(-xOffset, 0);
1967 gg.setFont(av.getFont());
1968 gg.setColor(Color.black);
1970 if (startRes < ranges.getVisibleAlignmentWidth())
1972 drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
1976 * and finally, white fill any space below the visible alignment
1978 int heightBelow = canvasHeight - visibleWidths * wrappedRepeatHeightPx;
1979 if (heightBelow > 0)
1981 gg.setColor(Color.white);
1982 gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow);
1987 * Shifts the visible alignment by the specified number of columns - left if
1988 * negative, right if positive. Copies and moves sequences and annotations (if
1989 * shown). Scales, hidden column markers and any newly visible columns must be
1994 protected void shiftWrappedAlignment(int positions)
2000 int charWidth = av.getCharWidth();
2002 int canvasHeight = getHeight();
2003 ViewportRanges ranges = av.getRanges();
2004 int viewportWidth = ranges.getViewportWidth();
2005 int widthToCopy = (ranges.getViewportWidth() - Math.abs(positions))
2007 int heightToCopy = wrappedRepeatHeightPx - wrappedSpaceAboveAlignment;
2008 int xMax = ranges.getVisibleAlignmentWidth();
2013 * shift right (after scroll left)
2014 * for each wrapped width (starting with the last), copy (width-positions)
2015 * columns from the left margin to the right margin, and copy positions
2016 * columns from the right margin of the row above (if any) to the
2017 * left margin of the current row
2021 * get y-offset of last wrapped width, first row of sequences
2023 int y = canvasHeight / wrappedRepeatHeightPx * wrappedRepeatHeightPx;
2024 y += wrappedSpaceAboveAlignment;
2025 int copyFromLeftStart = labelWidthWest;
2026 int copyFromRightStart = copyFromLeftStart + widthToCopy;
2030 gg.copyArea(copyFromLeftStart, y, widthToCopy, heightToCopy,
2031 positions * charWidth, 0);
2034 gg.copyArea(copyFromRightStart, y - wrappedRepeatHeightPx,
2035 positions * charWidth, heightToCopy, -widthToCopy,
2036 wrappedRepeatHeightPx);
2039 y -= wrappedRepeatHeightPx;
2045 * shift left (after scroll right)
2046 * for each wrapped width (starting with the first), copy (width-positions)
2047 * columns from the right margin to the left margin, and copy positions
2048 * columns from the left margin of the row below (if any) to the
2049 * right margin of the current row
2051 int xpos = av.getRanges().getStartRes();
2052 int y = wrappedSpaceAboveAlignment;
2053 int copyFromRightStart = labelWidthWest - positions * charWidth;
2055 while (y < canvasHeight)
2057 gg.copyArea(copyFromRightStart, y, widthToCopy, heightToCopy,
2058 positions * charWidth, 0);
2059 if (y + wrappedRepeatHeightPx < canvasHeight - wrappedRepeatHeightPx
2060 && (xpos + viewportWidth <= xMax))
2062 gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx, -positions
2063 * charWidth, heightToCopy, widthToCopy,
2064 -wrappedRepeatHeightPx);
2067 y += wrappedRepeatHeightPx;
2068 xpos += viewportWidth;
2075 * Redraws any positions in the search results in the visible region of a
2076 * wrapped alignment. Any highlights are drawn depending on the search results
2077 * set on the Viewport, not the <code>results</code> argument. This allows
2078 * this method to be called either to clear highlights (passing the previous
2079 * search results), or to draw new highlights.
2084 protected boolean drawMappedPositionsWrapped(SearchResultsI results)
2086 if (results == null)
2090 int charHeight = av.getCharHeight();
2092 boolean matchFound = false;
2094 calculateWrappedGeometry(getWidth(), getHeight());
2095 int wrappedWidth = av.getWrappedWidth();
2096 int wrappedHeight = wrappedRepeatHeightPx;
2098 ViewportRanges ranges = av.getRanges();
2099 int canvasHeight = getHeight();
2100 int repeats = canvasHeight / wrappedHeight;
2101 if (canvasHeight / wrappedHeight > 0)
2106 int firstVisibleColumn = ranges.getStartRes();
2107 int lastVisibleColumn = ranges.getStartRes() + repeats
2108 * ranges.getViewportWidth() - 1;
2110 AlignmentI alignment = av.getAlignment();
2111 if (av.hasHiddenColumns())
2113 firstVisibleColumn = alignment.getHiddenColumns()
2114 .adjustForHiddenColumns(firstVisibleColumn);
2115 lastVisibleColumn = alignment.getHiddenColumns()
2116 .adjustForHiddenColumns(lastVisibleColumn);
2119 int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
2121 for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
2122 .getEndSeq(); seqNo++)
2124 SequenceI seq = alignment.getSequenceAt(seqNo);
2126 int[] visibleResults = results.getResults(seq, firstVisibleColumn,
2128 if (visibleResults != null)
2130 for (int i = 0; i < visibleResults.length - 1; i += 2)
2132 int firstMatchedColumn = visibleResults[i];
2133 int lastMatchedColumn = visibleResults[i + 1];
2134 if (firstMatchedColumn <= lastVisibleColumn
2135 && lastMatchedColumn >= firstVisibleColumn)
2138 * found a search results match in the visible region
2140 firstMatchedColumn = Math.max(firstMatchedColumn,
2141 firstVisibleColumn);
2142 lastMatchedColumn = Math.min(lastMatchedColumn,
2146 * draw each mapped position separately (as contiguous positions may
2147 * wrap across lines)
2149 for (int mappedPos = firstMatchedColumn; mappedPos <= lastMatchedColumn; mappedPos++)
2151 int displayColumn = mappedPos;
2152 if (av.hasHiddenColumns())
2154 displayColumn = alignment.getHiddenColumns()
2155 .findColumnPosition(displayColumn);
2159 * transX: offset from left edge of canvas to residue position
2161 int transX = labelWidthWest
2162 + ((displayColumn - ranges.getStartRes()) % wrappedWidth)
2163 * av.getCharWidth();
2166 * transY: offset from top edge of canvas to residue position
2168 int transY = gapHeight;
2169 transY += (displayColumn - ranges.getStartRes())
2170 / wrappedWidth * wrappedHeight;
2171 transY += (seqNo - ranges.getStartSeq()) * av.getCharHeight();
2174 * yOffset is from graphics origin to start of visible region
2176 int yOffset = 0;// (displayColumn / wrappedWidth) * wrappedHeight;
2177 if (transY < getHeight())
2180 gg.translate(transX, transY);
2181 drawPanel(gg, displayColumn, displayColumn, seqNo, seqNo,
2183 gg.translate(-transX, -transY);
2195 * Answers the width in pixels of the left scale labels (0 if not shown)
2199 int getLabelWidthWest()
2201 return labelWidthWest;