import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
import jalview.util.Comparison;
import java.awt.Shape;
import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
import java.util.List;
import javax.swing.JComponent;
/**
- * DOCUMENT ME!
+ * The Swing component on which the alignment sequences, and annotations (if
+ * shown), are drawn. This includes scales above, left and right (if shown) in
+ * Wrapped mode, but not the scale above in Unwrapped mode.
*
- * @author $author$
- * @version $Revision$
*/
public class SeqCanvas extends JComponent implements ViewportListenerI
{
- private static String ZEROS = "0000000000";
+ private static final String ZEROS = "0000000000";
final FeatureRenderer fr;
- final SequenceRenderer sr;
-
BufferedImage img;
- Graphics2D gg;
-
- int imgWidth;
-
- int imgHeight;
-
AlignViewport av;
- boolean fastPaint = false;
-
- boolean fastpainting = false;
-
int cursorX = 0;
int cursorY = 0;
+ private final SequenceRenderer seqRdr;
+
+ private boolean fastPaint = false;
+
+ private boolean fastpainting = false;
+
private AnnotationPanel annotations;
/*
* measurements for drawing a wrapped alignment
*/
- int labelWidthWest; // label left width in pixels if shown
-
private int labelWidthEast; // label right width in pixels if shown
+ private int labelWidthWest; // label left width in pixels if shown
+
private int wrappedSpaceAboveAlignment; // gap between widths
private int wrappedRepeatHeightPx; // height in pixels of wrapped width
private int wrappedVisibleWidths; // number of wrapped widths displayed
+ private Graphics2D gg;
+
/**
* Creates a new SeqCanvas object.
*
- * @param av
- * DOCUMENT ME!
+ * @param ap
*/
public SeqCanvas(AlignmentPanel ap)
{
this.av = ap.av;
fr = new FeatureRenderer(ap);
- sr = new SequenceRenderer(av);
+ seqRdr = new SequenceRenderer(av);
setLayout(new BorderLayout());
PaintRefresher.Register(this, av.getSequenceSetId());
setBackground(Color.white);
public SequenceRenderer getSequenceRenderer()
{
- return sr;
+ return seqRdr;
}
public FeatureRenderer getFeatureRenderer()
* @param left
* if true, scale is left of residues, if false, scale is right
*/
- void drawVerticalScale(Graphics g, int startx, int endx, int ypos,
- boolean left)
+ void drawVerticalScale(Graphics g, final int startx, final int endx,
+ final int ypos, final boolean left)
{
int charHeight = av.getCharHeight();
int charWidth = av.getCharWidth();
- ypos += charHeight;
+ int yPos = ypos + charHeight;
+ int startX = startx;
+ int endX = endx;
if (av.hasHiddenColumns())
{
HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
- startx = hiddenColumns.adjustForHiddenColumns(startx);
- endx = hiddenColumns.adjustForHiddenColumns(endx);
+ startX = hiddenColumns.visibleToAbsoluteColumn(startx);
+ endX = hiddenColumns.visibleToAbsoluteColumn(endx);
}
FontMetrics fm = getFontMetrics(av.getFont());
* find sequence position of first non-gapped position -
* to the right if scale left, to the left if scale right
*/
- int index = left ? startx : endx;
+ int index = left ? startX : endX;
int value = -1;
- while (index >= startx && index <= endx)
+ while (index >= startX && index <= endX)
{
if (!Comparison.isGap(seq.getCharAt(index)))
{
* white fill the space for the scale
*/
g.setColor(Color.white);
- int y = (ypos + (i * charHeight)) - (charHeight / 5);
+ int y = (yPos + (i * charHeight)) - (charHeight / 5);
// fillRect origin is top left of rectangle
g.fillRect(0, y - charHeight, left ? labelWidthWest : labelWidthEast,
charHeight + 1);
if (value != -1)
{
-
/*
- * draw scale value, right justified, with half a character width
- * separation from the sequence data
+ * draw scale value, right justified within its width less half a
+ * character width padding on the right
*/
+ int labelSpace = left ? labelWidthWest : labelWidthEast;
+ labelSpace -= charWidth / 2; // leave space to the right
String valueAsString = String.valueOf(value);
- int justify = fm.stringWidth(valueAsString) + charWidth;
- int xpos = left ? labelWidthWest - justify + charWidth / 2
- : labelWidthEast - justify + charWidth / 2;
+ int labelLength = fm.stringWidth(valueAsString);
+ int xOffset = labelSpace - labelLength;
g.setColor(Color.black);
- g.drawString(valueAsString, xpos, y);
+ g.drawString(valueAsString, xOffset, y);
}
}
}
*/
public void fastPaint(int horizontal, int vertical)
{
- if (fastpainting || gg == null)
+ if (fastpainting || gg == null || img == null)
{
return;
}
{
int charHeight = av.getCharHeight();
int charWidth = av.getCharWidth();
-
+
ViewportRanges ranges = av.getRanges();
int startRes = ranges.getStartRes();
int endRes = ranges.getEndRes();
int endSeq = ranges.getEndSeq();
int transX = 0;
int transY = 0;
-
- gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
- imgHeight, -horizontal * charWidth, -vertical * charHeight);
+
+ gg.copyArea(horizontal * charWidth, vertical * charHeight,
+ img.getWidth(), img.getHeight(), -horizontal * charWidth,
+ -vertical * charHeight);
if (horizontal > 0) // scrollbar pulled right, image to the left
{
{
endRes = startRes - horizontal;
}
- else if (vertical > 0) // scroll down
+
+ if (vertical > 0) // scroll down
{
startSeq = endSeq - vertical;
}
else
{
- transY = imgHeight - ((vertical + 1) * charHeight);
+ transY = img.getHeight() - ((vertical + 1) * charHeight);
}
}
else if (vertical < 0)
drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
gg.translate(-transX, -transY);
- repaint();
+ // Call repaint on alignment panel so that repaints from other alignment
+ // panel components can be aggregated. Otherwise performance of the
+ // overview window and others may be adversely affected.
+ av.getAlignPanel().repaint();
} finally
{
fastpainting = false;
@Override
public void paintComponent(Graphics g)
{
+ super.paintComponent(g);
+
int charHeight = av.getCharHeight();
int charWidth = av.getCharWidth();
- BufferedImage lcimg = img; // take reference since other threads may null
- // img and call later.
- super.paintComponent(g);
-
- if (lcimg != null && (fastPaint
+
+ ViewportRanges ranges = av.getRanges();
+
+ int width = getWidth();
+ int height = getHeight();
+
+ width -= (width % charWidth);
+ height -= (height % charHeight);
+
+ drawSelectionGroup((Graphics2D) g,
+ ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq());
+
+ if ((img != null) && (fastPaint
|| (getVisibleRect().width != g.getClipBounds().width)
|| (getVisibleRect().height != g.getClipBounds().height)))
{
- g.drawImage(lcimg, 0, 0, this);
- fastPaint = false;
- return;
- }
-
- // this draws the whole of the alignment
- imgWidth = getWidth();
- imgHeight = getHeight();
+ g.drawImage(img, 0, 0, this);
- imgWidth -= (imgWidth % charWidth);
- imgHeight -= (imgHeight % charHeight);
+ drawSelectionGroup((Graphics2D) g, ranges.getStartRes(),
+ ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq());
- if ((imgWidth < 1) || (imgHeight < 1))
- {
- return;
+ fastPaint = false;
}
-
- if (lcimg == null || imgWidth != lcimg.getWidth()
- || imgHeight != lcimg.getHeight())
+ else if (width > 0 && height > 0)
{
- try
+ /*
+ * img is a cached version of the last view we drew, if any
+ * if we have no img or the size has changed, make a new one
+ */
+ if (img == null || width != img.getWidth()
+ || height != img.getHeight())
{
- lcimg = img = new BufferedImage(imgWidth, imgHeight,
- BufferedImage.TYPE_INT_RGB);
+ img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
gg = (Graphics2D) img.getGraphics();
gg.setFont(av.getFont());
- } catch (OutOfMemoryError er)
+ }
+
+ if (av.antiAlias)
{
- System.gc();
- System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
- new OOMWarning("Creating alignment image for display", er);
-
- return;
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
}
+
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, img.getWidth(), img.getHeight());
+
+ if (av.getWrapAlignment())
+ {
+ drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+ }
+ else
+ {
+ drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq(), 0);
+ }
+
+ drawSelectionGroup(gg, ranges.getStartRes(),
+ ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq());
+
+ g.drawImage(img, 0, 0, this);
}
- if (av.antiAlias)
+ if (av.cursorMode)
{
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ drawCursor(g, ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq());
}
+ }
+
+ /**
+ * Draw an alignment panel for printing
+ *
+ * @param g1
+ * Graphics object to draw with
+ * @param startRes
+ * start residue of print area
+ * @param endRes
+ * end residue of print area
+ * @param startSeq
+ * start sequence of print area
+ * @param endSeq
+ * end sequence of print area
+ */
+ public void drawPanelForPrinting(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+ drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
- gg.setColor(Color.white);
- gg.fillRect(0, 0, imgWidth, imgHeight);
+ drawSelectionGroup((Graphics2D) g1, startRes, endRes,
+ startSeq, endSeq);
+ }
- ViewportRanges ranges = av.getRanges();
- if (av.getWrapAlignment())
- {
- drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
- }
- else
+ /**
+ * Draw a wrapped alignment panel for printing
+ *
+ * @param g
+ * Graphics object to draw with
+ * @param canvasWidth
+ * width of drawing area
+ * @param canvasHeight
+ * height of drawing area
+ * @param startRes
+ * start residue of print area
+ */
+ public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth,
+ int canvasHeight, int startRes)
+ {
+ drawWrappedPanel(g, canvasWidth, canvasHeight, startRes);
+
+ SequenceGroup group = av.getSelectionGroup();
+ if (group != null)
{
- drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
- ranges.getStartSeq(), ranges.getEndSeq(), 0);
+ drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight,
+ startRes);
}
-
- g.drawImage(lcimg, 0, 0, this);
-
}
/**
FontMetrics fm = getFontMetrics(av.getFont());
- labelWidthEast = 0;
- labelWidthWest = 0;
-
- if (av.getScaleRightWrapped())
+ int labelWidth = 0;
+
+ if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
{
- labelWidthEast = getLabelWidth(fm);
+ labelWidth = getLabelWidth(fm);
}
- if (av.getScaleLeftWrapped())
- {
- labelWidthWest = labelWidthEast > 0 ? labelWidthEast
- : getLabelWidth(fm);
- }
+ labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
+
+ labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
}
/**
- * Returns a pixel width suitable for showing the largest sequence coordinate
- * (end position) in the alignment. Returns 2 plus the number of decimal
- * digits to be shown (3 for 1-10, 4 for 11-99 etc).
+ * Returns a pixel width sufficient to show the largest sequence coordinate
+ * (end position) in the alignment, calculated as the FontMetrics width of
+ * zeroes "0000000" limited to the number of decimal digits to be shown (3 for
+ * 1-10, 4 for 11-99 etc). One character width is added to this, to allow for
+ * half a character width space on either side.
*
* @param fm
* @return
maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd());
}
- int length = 2;
+ int length = 0;
for (int i = maxWidth; i > 0; i /= 10)
{
length++;
}
- return fm.stringWidth(ZEROS.substring(0, length));
+ return fm.stringWidth(ZEROS.substring(0, length)) + av.getCharWidth();
}
/**
ViewportRanges ranges = av.getRanges();
ranges.setViewportStartAndWidth(startColumn, wrappedWidthInResidues);
+ // we need to call this again to make sure the startColumn +
+ // wrappedWidthInResidues values are used to calculate wrappedVisibleWidths
+ // correctly.
+ calculateWrappedGeometry(canvasWidth, canvasHeight);
+
/*
- * draw one width at a time (including any scales or annotation shown),
+ * draw one width at a time (excluding any scales or annotation shown),
* until we have run out of either alignment or vertical space available
*/
int ypos = wrappedSpaceAboveAlignment;
protected int calculateWrappedGeometry(int canvasWidth, int canvasHeight)
{
int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
-
- /*
- * width of labels in pixels left and right (if shown)
- */
- int labelWidth = 0;
- if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
- {
- FontMetrics fm = getFontMetrics(av.getFont());
- labelWidth = getLabelWidth(fm);
- }
- labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
- labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
/*
* vertical space in pixels between wrapped widths of alignment
*/
wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
// add sequences
- wrappedRepeatHeightPx += av.getRanges().getViewportHeight() * charHeight;
+ wrappedRepeatHeightPx += av.getAlignment().getHeight()
+ * charHeight;
// add annotations panel height if shown
wrappedRepeatHeightPx += getAnnotationHeight();
/*
- * number of residue columns we can show in each row;
- * this is just canvas width less scale left and right (if shown),
- * as a whole multiple of character widths
- */
- int wrappedWidthInResidues = (canvasWidth - labelWidthEast - labelWidthWest)
- / charWidth;
-
- /*
* number of visible widths (the last one may be part height),
* ensuring a part height includes at least one sequence
*/
ViewportRanges ranges = av.getRanges();
- int xMax = ranges.getVisibleAlignmentWidth();
wrappedVisibleWidths = canvasHeight / wrappedRepeatHeightPx;
int remainder = canvasHeight % wrappedRepeatHeightPx;
if (remainder >= (wrappedSpaceAboveAlignment + charHeight))
}
/*
+ * compute width in residues; this also sets East and West label widths
+ */
+ int wrappedWidthInResidues = getWrappedCanvasWidth(canvasWidth);
+
+ /*
* limit visibleWidths to not exceed width of alignment
*/
- int maxWidths = (xMax - ranges.getStartRes()) / wrappedWidthInResidues;
- if (xMax % wrappedWidthInResidues > 0)
+ int xMax = ranges.getVisibleAlignmentWidth();
+ int startToEnd = xMax - ranges.getStartRes();
+ int maxWidths = startToEnd / wrappedWidthInResidues;
+ if (startToEnd % wrappedWidthInResidues > 0)
{
maxWidths++;
}
* @param endColumn
* @param canvasHeight
*/
- protected void drawWrappedWidth(Graphics g, int ypos,
- int startColumn, int endColumn, int canvasHeight)
+ protected void drawWrappedWidth(Graphics g, int ypos, int startColumn,
+ int endColumn, int canvasHeight)
{
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
-
ViewportRanges ranges = av.getRanges();
int viewportWidth = ranges.getViewportWidth();
* plus column offset from left margin (usually zero, but may be non-zero
* when fast painting is drawing just a few columns)
*/
+ int charWidth = av.getCharWidth();
int xOffset = labelWidthWest
+ ((startColumn - ranges.getStartRes()) % viewportWidth)
* charWidth;
* white fill the region to be drawn (so incremental fast paint doesn't
* scribble over an existing image)
*/
- gg.setColor(Color.white);
- gg.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
+ g.setColor(Color.white);
+ g.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
wrappedRepeatHeightPx);
drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1,
ypos);
- int cHeight = av.getAlignment().getHeight() * charHeight;
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight();
if (av.isShowAnnotation())
{
* @param g
* @param startColumn
*/
- protected void drawWrappedDecorators(Graphics g, int startColumn)
+ protected void drawWrappedDecorators(Graphics g, final int startColumn)
{
int charWidth = av.getCharWidth();
int viewportWidth = ranges.getViewportWidth();
int maxWidth = ranges.getVisibleAlignmentWidth();
int widthsDrawn = 0;
+ int startCol = startColumn;
+
while (widthsDrawn < wrappedVisibleWidths)
{
- int endColumn = Math.min(maxWidth, startColumn + viewportWidth - 1);
+ int endColumn = Math.min(maxWidth, startCol + viewportWidth - 1);
if (av.getScaleLeftWrapped())
{
- drawVerticalScale(g, startColumn, endColumn - 1, ypos, true);
+ drawVerticalScale(g, startCol, endColumn - 1, ypos, true);
}
if (av.getScaleRightWrapped())
{
int x = labelWidthWest + viewportWidth * charWidth;
g.translate(x, 0);
- drawVerticalScale(g, startColumn, endColumn, ypos, false);
+ drawVerticalScale(g, startCol, endColumn, ypos, false);
g.translate(-x, 0);
}
* white fill region of scale above and hidden column markers
* (to support incremental fast paint of image)
*/
+ g.translate(labelWidthWest, 0);
g.setColor(Color.white);
g.fillRect(0, ypos - wrappedSpaceAboveAlignment, viewportWidth
* charWidth + labelWidthWest, wrappedSpaceAboveAlignment);
g.setColor(Color.black);
+ g.translate(-labelWidthWest, 0);
g.translate(labelWidthWest, 0);
if (av.getScaleAboveWrapped())
{
- drawNorthScale(g, startColumn, endColumn, ypos);
+ drawNorthScale(g, startCol, endColumn, ypos);
}
if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
{
- drawHiddenColumnMarkers(g, ypos, startColumn, endColumn);
+ drawHiddenColumnMarkers(g, ypos, startCol, endColumn);
}
g.translate(-labelWidthWest, 0);
ypos += wrappedRepeatHeightPx;
- startColumn += viewportWidth;
+ startCol += viewportWidth;
widthsDrawn++;
}
}
/**
+ * Draws markers (triangles) above hidden column positions between startColumn
+ * and endColumn.
+ *
* @param g
* @param ypos
* @param startColumn
int charWidth = av.getCharWidth();
g.setColor(Color.blue);
+ int res;
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- List<Integer> positions = hidden.findHiddenRegionPositions();
- for (int pos : positions)
+
+ Iterator<Integer> it = hidden.getStartRegionIterator(startColumn,
+ endColumn);
+ while (it.hasNext())
{
- int res = pos - startColumn;
+ res = it.next() - startColumn;
- if (res < 0 || res > endColumn - startColumn)
+ if (res < 0 || res > endColumn - startColumn + 1)
{
continue;
}
}
}
+ /*
+ * Draw a selection group over a wrapped alignment
+ */
+ private void drawWrappedSelection(Graphics2D g, SequenceGroup group,
+ int canvasWidth,
+ int canvasHeight, int startRes)
+ {
+ int charHeight = av.getCharHeight();
+ int charWidth = av.getCharWidth();
+
+ // height gap above each panel
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += charHeight;
+ }
+
+ int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
+ / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
+
+ int startx = startRes;
+ int endx;
+ int ypos = hgap; // vertical offset
+ int maxwidth = av.getAlignment().getWidth();
+
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .absoluteToVisibleColumn(maxwidth);
+ }
+
+ // chop the wrapped alignment extent up into panel-sized blocks and treat
+ // each block as if it were a block from an unwrapped alignment
+ g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
+ g.setColor(Color.RED);
+ while ((ypos <= canvasHeight) && (startx < maxwidth))
+ {
+ // set end value to be start + width, or maxwidth, whichever is smaller
+ endx = startx + cWidth - 1;
+
+ if (endx > maxwidth)
+ {
+ endx = maxwidth;
+ }
+
+ g.translate(labelWidthWest, 0);
+
+ drawUnwrappedSelection(g, group, startx, endx, 0,
+ av.getAlignment().getHeight() - 1,
+ ypos);
+
+ g.translate(-labelWidthWest, 0);
+
+ // update vertical offset
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ // update horizontal offset
+ startx += cWidth;
+ }
+ g.setStroke(new BasicStroke());
+ }
+
int getAnnotationHeight()
{
if (!av.isShowAnnotation())
else
{
int screenY = 0;
- final int screenYMax = endRes - startRes;
- int blockStart = startRes;
- int blockEnd = endRes;
+ int blockStart;
+ int blockEnd;
- for (int[] region : av.getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy())
- {
- int hideStart = region[0];
- int hideEnd = region[1];
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ VisibleContigsIterator regions = hidden
+ .getVisContigsIterator(startRes, endRes + 1, true);
- if (hideStart <= blockStart)
- {
- blockStart += (hideEnd - hideStart) + 1;
- continue;
- }
+ while (regions.hasNext())
+ {
+ int[] region = regions.next();
+ blockEnd = region[1];
+ blockStart = region[0];
/*
* draw up to just before the next hidden region, or the end of
* the visible region, whichever comes first
*/
- blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
- - screenY);
-
g1.translate(screenY * charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
* draw the downline of the hidden column marker (ScalePanel draws the
* triangle on top) if we reached it
*/
- if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
+ if (av.getShowHiddenMarkers()
+ && (regions.hasNext() || regions.endsAtHidden()))
{
g1.setColor(Color.blue);
g1.translate(-screenY * charWidth, 0);
screenY += blockEnd - blockStart + 1;
- blockStart = hideEnd + 1;
-
- if (screenY > screenYMax)
- {
- // already rendered last block
- return;
- }
- }
-
- if (screenY <= screenYMax)
- {
- // remaining visible region to render
- blockEnd = blockStart + screenYMax - screenY;
- g1.translate(screenY * charWidth, 0);
- draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
-
- g1.translate(-screenY * charWidth, 0);
}
}
int charWidth = av.getCharWidth();
g.setFont(av.getFont());
- sr.prepare(g, av.isRenderGaps());
+ seqRdr.prepare(g, av.isRenderGaps());
SequenceI nextSeq;
// empty
continue;
}
- sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
+ seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
startRes, endRes, offset + ((i - startSeq) * charHeight));
if (av.isShowSequenceFeatures())
if (av.hasSearchResults())
{
SearchResultsI searchResults = av.getSearchResults();
- int[] visibleResults = searchResults.getResults(nextSeq,
- startRes, endRes);
+ int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+ endRes);
if (visibleResults != null)
{
for (int r = 0; r < visibleResults.length; r += 2)
{
- sr.drawHighlightedText(nextSeq, visibleResults[r],
+ seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
visibleResults[r + 1],
(visibleResults[r] - startRes) * charWidth,
offset + ((i - startSeq) * charHeight));
}
}
}
-
- if (av.cursorMode && cursorY == i && cursorX >= startRes
- && cursorX <= endRes)
- {
- sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
- offset + ((i - startSeq) * charHeight));
- }
}
if (av.getSelectionGroup() != null
}
+ /**
+ * Draws the outlines of any groups defined on the alignment (excluding the
+ * current selection group, if any)
+ *
+ * @param g1
+ * @param startRes
+ * @param endRes
+ * @param startSeq
+ * @param endSeq
+ * @param offset
+ */
void drawGroupsBoundaries(Graphics g1, int startRes, int endRes,
int startSeq, int endSeq, int offset)
{
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
-
Graphics2D g = (Graphics2D) g1;
- //
- // ///////////////////////////////////
- // Now outline any areas if necessary
- // ///////////////////////////////////
- SequenceGroup group = av.getSelectionGroup();
- int sx = -1;
- int sy = -1;
- int ex = -1;
+ SequenceGroup group = null;
int groupIndex = -1;
- int visWidth = (endRes - startRes + 1) * charWidth;
- if ((group == null) && (av.getAlignment().getGroups().size() > 0))
+ if (av.getAlignment().getGroups().size() > 0)
{
group = av.getAlignment().getGroups().get(0);
groupIndex = 0;
if (group != null)
{
+ g.setColor(group.getOutlineColour());
+
do
{
- int oldY = -1;
- int i = 0;
- boolean inGroup = false;
- int top = -1;
- int bottom = -1;
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
+ endSeq, offset);
- for (i = startSeq; i <= endSeq; i++)
- {
- sx = (group.getStartRes() - startRes) * charWidth;
- sy = offset + ((i - startSeq) * charHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
- - 1;
-
- if (sx + ex < 0 || sx > visWidth)
- {
- continue;
- }
+ groupIndex++;
- if ((sx <= (endRes - startRes) * charWidth)
- && group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i)))
- {
- if ((bottom == -1) && !group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i + 1)))
- {
- bottom = sy + charHeight;
- }
+ if (groupIndex >= av.getAlignment().getGroups().size())
+ {
+ break;
+ }
- if (!inGroup)
- {
- if (((top == -1) && (i == 0)) || !group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i - 1)))
- {
- top = sy;
- }
+ group = av.getAlignment().getGroups().get(groupIndex);
- oldY = sy;
- inGroup = true;
+ } while (groupIndex < av.getAlignment().getGroups().size());
- if (group == av.getSelectionGroup())
- {
- g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
- g.setColor(Color.RED);
- }
- else
- {
- g.setStroke(new BasicStroke());
- g.setColor(group.getOutlineColour());
- }
- }
- }
- else
- {
- if (inGroup)
- {
- if (sx >= 0 && sx < visWidth)
- {
- g.drawLine(sx, oldY, sx, sy);
- }
+ }
- if (sx + ex < visWidth)
- {
- g.drawLine(sx + ex, oldY, sx + ex, sy);
- }
+ }
- if (sx < 0)
- {
- ex += sx;
- sx = 0;
- }
+ /**
+ * Draws the outline of the current selection group (if any)
+ *
+ * @param g
+ * @param startRes
+ * @param endRes
+ * @param startSeq
+ * @param endSeq
+ */
+ private void drawSelectionGroup(Graphics2D g, int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+ SequenceGroup group = av.getSelectionGroup();
+ if (group == null)
+ {
+ return;
+ }
- if (sx + ex > visWidth)
- {
- ex = visWidth;
- }
+ g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
+ g.setColor(Color.RED);
+ if (!av.getWrapAlignment())
+ {
+ drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq,
+ 0);
+ }
+ else
+ {
+ drawWrappedSelection(g, group, getWidth(), getHeight(),
+ av.getRanges().getStartRes());
+ }
+ g.setStroke(new BasicStroke());
+ }
- else if (sx + ex >= (endRes - startRes + 1) * charWidth)
- {
- ex = (endRes - startRes + 1) * charWidth;
- }
+ /**
+ * Draw the cursor as a separate image and overlay
+ *
+ * @param startRes
+ * start residue of area to draw cursor in
+ * @param endRes
+ * end residue of area to draw cursor in
+ * @param startSeq
+ * start sequence of area to draw cursor in
+ * @param endSeq
+ * end sequence of are to draw cursor in
+ * @return a transparent image of the same size as the sequence canvas, with
+ * the cursor drawn on it, if any
+ */
+ private void drawCursor(Graphics g, int startRes, int endRes,
+ int startSeq,
+ int endSeq)
+ {
+ // convert the cursorY into a position on the visible alignment
+ int cursor_ypos = cursorY;
- if (top != -1)
- {
- g.drawLine(sx, top, sx + ex, top);
- top = -1;
- }
+ // don't do work unless we have to
+ if (cursor_ypos >= startSeq && cursor_ypos <= endSeq)
+ {
+ int yoffset = 0;
+ int xoffset = 0;
+ int startx = startRes;
+ int endx = endRes;
- if (bottom != -1)
- {
- g.drawLine(sx, bottom, sx + ex, bottom);
- bottom = -1;
- }
+ // convert the cursorX into a position on the visible alignment
+ int cursor_xpos = av.getAlignment().getHiddenColumns()
+ .absoluteToVisibleColumn(cursorX);
- inGroup = false;
- }
- }
- }
+ if (av.getAlignment().getHiddenColumns().isVisible(cursorX))
+ {
- if (inGroup)
+ if (av.getWrapAlignment())
{
- sy = offset + ((i - startSeq) * charHeight);
- if (sx >= 0 && sx < visWidth)
+ // work out the correct offsets for the cursor
+ int charHeight = av.getCharHeight();
+ int charWidth = av.getCharWidth();
+ int canvasWidth = getWidth();
+ int canvasHeight = getHeight();
+
+ // height gap above each panel
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
{
- g.drawLine(sx, oldY, sx, sy);
+ hgap += charHeight;
}
- if (sx + ex < visWidth)
- {
- g.drawLine(sx + ex, oldY, sx + ex, sy);
- }
+ int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
+ / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
- if (sx < 0)
- {
- ex += sx;
- sx = 0;
- }
+ endx = startx + cWidth - 1;
+ int ypos = hgap; // vertical offset
- if (sx + ex > visWidth)
+ // iterate down the wrapped panels
+ while ((ypos <= canvasHeight) && (endx < cursor_xpos))
{
- ex = visWidth;
- }
- else if (sx + ex >= (endRes - startRes + 1) * charWidth)
- {
- ex = (endRes - startRes + 1) * charWidth;
+ // update vertical offset
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ // update horizontal offset
+ startx += cWidth;
+ endx = startx + cWidth - 1;
}
+ yoffset = ypos;
+ xoffset = labelWidthWest;
+ }
+
+ // now check if cursor is within range for x values
+ if (cursor_xpos >= startx && cursor_xpos <= endx)
+ {
+ // get the character the cursor is drawn at
+ SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
+ char s = seq.getCharAt(cursorX);
+
+ seqRdr.drawCursor(g, s,
+ xoffset + (cursor_xpos - startx) * av.getCharWidth(),
+ yoffset + (cursor_ypos - startSeq) * av.getCharHeight());
+ }
+ }
+ }
+ }
+
+
+ /**
+ * Draw a selection group over an unwrapped alignment
+ *
+ * @param g
+ * graphics object to draw with
+ * @param group
+ * selection group
+ * @param startRes
+ * start residue of area to draw
+ * @param endRes
+ * end residue of area to draw
+ * @param startSeq
+ * start sequence of area to draw
+ * @param endSeq
+ * end sequence of area to draw
+ * @param offset
+ * vertical offset (used when called from wrapped alignment code)
+ */
+ private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq, int offset)
+ {
+ int charWidth = av.getCharWidth();
+
+ if (!av.hasHiddenColumns())
+ {
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
+ offset);
+ }
+ else
+ {
+ // package into blocks of visible columns
+ int screenY = 0;
+ int blockStart;
+ int blockEnd;
+
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ VisibleContigsIterator regions = hidden
+ .getVisContigsIterator(startRes, endRes + 1, true);
+ while (regions.hasNext())
+ {
+ int[] region = regions.next();
+ blockEnd = region[1];
+ blockStart = region[0];
+
+ g.translate(screenY * charWidth, 0);
+ drawPartialGroupOutline(g, group,
+ blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g.translate(-screenY * charWidth, 0);
+ screenY += blockEnd - blockStart + 1;
+ }
+ }
+ }
+
+ /**
+ * Draws part of a selection group outline
+ *
+ * @param g
+ * @param group
+ * @param startRes
+ * @param endRes
+ * @param startSeq
+ * @param endSeq
+ * @param verticalOffset
+ */
+ private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq,
+ int verticalOffset)
+ {
+ int charHeight = av.getCharHeight();
+ int charWidth = av.getCharWidth();
+ int visWidth = (endRes - startRes + 1) * charWidth;
+
+ int oldY = -1;
+ int i = 0;
+ boolean inGroup = false;
+ int top = -1;
+ int bottom = -1;
+ int sy = -1;
+
+ List<SequenceI> seqs = group.getSequences(null);
+
+ // position of start residue of group relative to startRes, in pixels
+ int sx = (group.getStartRes() - startRes) * charWidth;
- if (top != -1)
+ // width of group in pixels
+ int xwidth = (((group.getEndRes() + 1) - group.getStartRes())
+ * charWidth) - 1;
+
+ if (!(sx + xwidth < 0 || sx > visWidth))
+ {
+ for (i = startSeq; i <= endSeq; i++)
+ {
+ sy = verticalOffset + (i - startSeq) * charHeight;
+
+ if ((sx <= (endRes - startRes) * charWidth)
+ && seqs.contains(av.getAlignment().getSequenceAt(i)))
+ {
+ if ((bottom == -1)
+ && !seqs.contains(av.getAlignment().getSequenceAt(i + 1)))
{
- g.drawLine(sx, top, sx + ex, top);
- top = -1;
+ bottom = sy + charHeight;
}
- if (bottom != -1)
+ if (!inGroup)
{
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
- bottom = -1;
+ if (((top == -1) && (i == 0)) || !seqs
+ .contains(av.getAlignment().getSequenceAt(i - 1)))
+ {
+ top = sy;
+ }
+
+ oldY = sy;
+ inGroup = true;
}
+ }
+ else if (inGroup)
+ {
+ drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
+ drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
+ // reset top and bottom
+ top = -1;
+ bottom = -1;
inGroup = false;
}
+ }
+ if (inGroup)
+ {
+ sy = verticalOffset + ((i - startSeq) * charHeight);
+ drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
+ drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
+ }
+ }
+ }
- groupIndex++;
-
- g.setStroke(new BasicStroke());
+ /**
+ * Draw horizontal selection group boundaries at top and bottom positions
+ *
+ * @param g
+ * graphics object to draw on
+ * @param sx
+ * start x position
+ * @param xwidth
+ * width of gap
+ * @param visWidth
+ * visWidth maximum available width
+ * @param top
+ * position to draw top of group at
+ * @param bottom
+ * position to draw bottom of group at
+ */
+ private void drawHorizontals(Graphics2D g, int sx, int xwidth,
+ int visWidth, int top, int bottom)
+ {
+ int width = xwidth;
+ int startx = sx;
+ if (startx < 0)
+ {
+ width += startx;
+ startx = 0;
+ }
- if (groupIndex >= av.getAlignment().getGroups().size())
- {
- break;
- }
+ // don't let width extend beyond current block, or group extent
+ // fixes JAL-2672
+ if (startx + width >= visWidth)
+ {
+ width = visWidth - startx;
+ }
- group = av.getAlignment().getGroups().get(groupIndex);
+ if (top != -1)
+ {
+ g.drawLine(startx, top, startx + width, top);
+ }
- } while (groupIndex < av.getAlignment().getGroups().size());
+ if (bottom != -1)
+ {
+ g.drawLine(startx, bottom - 1, startx + width, bottom - 1);
+ }
+ }
+ /**
+ * Draw vertical lines at sx and sx+xwidth providing they lie within
+ * [0,visWidth)
+ *
+ * @param g
+ * graphics object to draw on
+ * @param sx
+ * start x position
+ * @param xwidth
+ * width of gap
+ * @param visWidth
+ * visWidth maximum available width
+ * @param oldY
+ * top y value
+ * @param sy
+ * bottom y value
+ */
+ private void drawVerticals(Graphics2D g, int sx, int xwidth, int visWidth,
+ int oldY, int sy)
+ {
+ // if start position is visible, draw vertical line to left of
+ // group
+ if (sx >= 0 && sx < visWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
}
+ // if end position is visible, draw vertical line to right of
+ // group
+ if (sx + xwidth < visWidth)
+ {
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
+ }
}
-
+
/**
* Highlights search results in the visible region by rendering as white text
* on a black background. Any previous highlighting is removed. Answers true
*/
protected boolean drawMappedPositions(SearchResultsI results)
{
- if (results == null)
+ if ((results == null) || (gg == null)) // JAL-2784 check gg is not null
{
return false;
}
if (av.hasHiddenColumns())
{
firstVisibleColumn = alignment.getHiddenColumns()
- .adjustForHiddenColumns(firstVisibleColumn);
+ .visibleToAbsoluteColumn(firstVisibleColumn);
lastVisibleColumn = alignment.getHiddenColumns()
- .adjustForHiddenColumns(lastVisibleColumn);
+ .visibleToAbsoluteColumn(lastVisibleColumn);
}
for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
if (av.hasHiddenColumns())
{
firstCol = alignment.getHiddenColumns()
- .findColumnPosition(firstCol);
- lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol);
+ .absoluteToVisibleColumn(firstCol);
+ lastCol = alignment.getHiddenColumns().absoluteToVisibleColumn(lastCol);
}
int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
{
String eventName = evt.getPropertyName();
+ if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
+ {
+ fastPaint = true;
+ repaint();
+ return;
+ }
+ else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
+ {
+ fastPaint = false;
+ repaint();
+ return;
+ }
+
int scrollX = 0;
- if (eventName.equals(ViewportRanges.STARTRES))
+ if (eventName.equals(ViewportRanges.STARTRES)
+ || eventName.equals(ViewportRanges.STARTRESANDSEQ))
{
// Make sure we're not trying to draw a panel
// larger than the visible window
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+ }
+ else
+ {
+ scrollX = ((int[]) evt.getNewValue())[0]
+ - ((int[]) evt.getOldValue())[0];
+ }
ViewportRanges vpRanges = av.getRanges();
- scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+
int range = vpRanges.getEndRes() - vpRanges.getStartRes();
if (scrollX > range)
{
scrollX = -range;
}
}
-
- // Both scrolling and resizing change viewport ranges: scrolling changes
- // both start and end points, but resize only changes end values.
- // Here we only want to fastpaint on a scroll, with resize using a normal
- // paint, so scroll events are identified as changes to the horizontal or
- // vertical start value.
- if (eventName.equals(ViewportRanges.STARTRES))
- {
- // scroll - startres and endres both change
- if (av.getWrapAlignment())
+ // Both scrolling and resizing change viewport ranges: scrolling changes
+ // both start and end points, but resize only changes end values.
+ // Here we only want to fastpaint on a scroll, with resize using a normal
+ // paint, so scroll events are identified as changes to the horizontal or
+ // vertical start value.
+ if (eventName.equals(ViewportRanges.STARTRES))
{
- fastPaintWrapped(scrollX);
+ if (av.getWrapAlignment())
+ {
+ fastPaintWrapped(scrollX);
+ }
+ else
+ {
+ fastPaint(scrollX, 0);
+ }
}
- else
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
{
- fastPaint(scrollX, 0);
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
}
+ else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ if (av.getWrapAlignment())
+ {
+ fastPaintWrapped(scrollX);
+ }
+ else
+ {
+ fastPaint(scrollX, 0);
+ }
}
else if (eventName.equals(ViewportRanges.STARTSEQ))
{
+ // scroll
fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
}
+ else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ if (av.getWrapAlignment())
+ {
+ fastPaintWrapped(scrollX);
+ }
+ }
}
/**
}
}
+
/**
* Redraws any positions in the search results in the visible region of a
* wrapped alignment. Any highlights are drawn depending on the search results
*/
protected boolean drawMappedPositionsWrapped(SearchResultsI results)
{
- if (results == null)
+ if ((results == null) || (gg == null)) // JAL-2784 check gg is not null
{
return false;
}
if (av.hasHiddenColumns())
{
firstVisibleColumn = alignment.getHiddenColumns()
- .adjustForHiddenColumns(firstVisibleColumn);
+ .visibleToAbsoluteColumn(firstVisibleColumn);
lastVisibleColumn = alignment.getHiddenColumns()
- .adjustForHiddenColumns(lastVisibleColumn);
+ .visibleToAbsoluteColumn(lastVisibleColumn);
}
int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
if (av.hasHiddenColumns())
{
displayColumn = alignment.getHiddenColumns()
- .findColumnPosition(displayColumn);
+ .absoluteToVisibleColumn(displayColumn);
}
/*
return matchFound;
}
+
+ /**
+ * Answers the width in pixels of the left scale labels (0 if not shown)
+ *
+ * @return
+ */
+ int getLabelWidthWest()
+ {
+ return labelWidthWest;
+ }
}
git://source.jalview.org / jalview.git / blobdiff