import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
-import java.awt.AlphaComposite; // ok
+import java.awt.AlphaComposite;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
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 seqRdr; //ok
-
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);
- seqRdr = new SequenceRenderer(av); //ok
+ seqRdr = new SequenceRenderer(av);
setLayout(new BorderLayout());
PaintRefresher.Register(this, av.getSequenceSetId());
setBackground(Color.white);
public SequenceRenderer getSequenceRenderer()
{
- return seqRdr; //ok
+ 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.adjustForHiddenColumns(startx);
+ endX = hiddenColumns.adjustForHiddenColumns(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);
}
}
}
- //ok
/**
* Does a fast paint of an alignment in response to a scroll. Most of the
* visible region is simply copied and shifted, and then any newly visible
*/
public void fastPaint(int horizontal, int vertical)
{
- if (fastpainting || gg == null || img == null) //ok
+ if (fastpainting || gg == null || img == null)
{
return;
}
int transX = 0;
int transY = 0;
- gg.copyArea(horizontal * charWidth, vertical * charHeight,
- img.getWidth(), img.getHeight(), -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
- {
- transX = (endRes - startRes - horizontal) * charWidth;
- startRes = endRes - horizontal;
- }
- else if (horizontal < 0)
- {
- endRes = startRes - horizontal;
- }
- else if (vertical > 0) // scroll down
- {
- startSeq = endSeq - vertical;
-
- if (startSeq < ranges.getStartSeq())
- { // ie scrolling too fast, more than a page at a time
- startSeq = ranges.getStartSeq();
+ if (horizontal > 0) // scrollbar pulled right, image to the left
+ {
+ transX = (endRes - startRes - horizontal) * charWidth;
+ startRes = endRes - horizontal;
}
- else
+ else if (horizontal < 0)
{
- transY = img.getHeight() - ((vertical + 1) * charHeight);
+ endRes = startRes - horizontal;
}
- }
- else if (vertical < 0)
- {
- endSeq = startSeq - vertical;
- if (endSeq > ranges.getEndSeq())
+ if (vertical > 0) // scroll down
{
- endSeq = ranges.getEndSeq();
+ startSeq = endSeq - vertical;
+
+ if (startSeq < ranges.getStartSeq())
+ { // ie scrolling too fast, more than a page at a time
+ startSeq = ranges.getStartSeq();
+ }
+ else
+ {
+ transY = img.getHeight() - ((vertical + 1) * charHeight);
+ }
}
- }
+ else if (vertical < 0)
+ {
+ endSeq = startSeq - vertical;
- gg.translate(transX, transY);
- drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
- gg.translate(-transX, -transY);
+ if (endSeq > ranges.getEndSeq())
+ {
+ endSeq = ranges.getEndSeq();
+ }
+ }
- repaint();
+ gg.translate(transX, transY);
+ drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
+ gg.translate(-transX, -transY);
+
+ repaint();
} finally
{
fastpainting = false;
}
}
- //ok
- //ok
@Override
public void paintComponent(Graphics g)
{
// lcimg is a local *copy* of img which we'll draw selectImage on top of
BufferedImage lcimg = buildLocalImage(selectImage);
g.drawImage(lcimg, 0, 0, this);
+
+ }
+
+ if (av.cursorMode)
+ {
+ drawCursor(g, ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq());
}
}
-//ok
/**
* Draw an alignment panel for printing
AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
g2d.drawImage(selectImage, 0, 0, this);
}
+
g2d.dispose();
return lcimg;
{
BufferedImage lcimg = null;
+ int charWidth = av.getCharWidth();
+ int charHeight = av.getCharHeight();
+
int width = getWidth();
int height = getHeight();
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();
}
/**
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 += 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++;
}
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;
+ * charWidth;
g.translate(xOffset, 0);
// When printing we have an extra clipped region,
}
else
{
- g.setClip(0, (int) clip.getBounds().getY(), viewportWidth * charWidth,
- (int) clip.getBounds().getHeight());
+ g.setClip(0, (int) clip.getBounds().getY(),
+ viewportWidth * charWidth, (int) clip.getBounds().getHeight());
}
/*
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.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 res = pos - startColumn;
- if (res < 0 || res > endColumn - startColumn)
+ if (res < 0 || res > endColumn - startColumn + 1)
{
continue;
}
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())
}
}
}
-
- if (av.cursorMode && cursorY == i && cursorX >= startRes
- && cursorX <= endRes)
- {
- seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
- offset + ((i - startSeq) * charHeight));
- }
}
if (av.getSelectionGroup() != null
return selectionImage;
}
+ /**
+ * 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 = av.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(cursorY);
+
+ // don't do work unless we have to
+ if (!av.getAlignment().getHiddenSequences().isHidden(cursorY)
+ && cursor_ypos >= startSeq && cursor_ypos <= endSeq)
+ {
+ int yoffset = 0;
+ int xoffset = 0;
+ int startx = startRes;
+ int endx = endRes;
+
+ // convert the cursorX into a position on the visible alignment
+ int cursor_xpos = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(cursorX);
+
+ if (av.getAlignment().getHiddenColumns().isVisible(cursorX))
+ {
+
+ if (av.getWrapAlignment())
+ {
+ // 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())
+ {
+ hgap += charHeight;
+ }
+
+ int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
+ / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
+
+ endx = startx + cWidth - 1;
+ int ypos = hgap; // vertical offset
+
+ // iterate down the wrapped panels
+ while ((ypos <= canvasHeight) && (endx < cursor_xpos))
+ {
+ // 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());
+ }
+ }
+ }
+ }
+
+
/*
* Set up graphics for selection group
*/
private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
int startRes, int endRes, int startSeq, int endSeq, int offset)
{
- int charWidth = av.getCharWidth();
-
+ int charWidth = av.getCharWidth();
+
if (!av.hasHiddenColumns())
{
drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
int startRes, int endRes, int startSeq, int endSeq,
int verticalOffset)
{
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
-
+ int charHeight = av.getCharHeight();
+ int charWidth = av.getCharWidth();
+
int visWidth = (endRes - startRes + 1) * charWidth;
int oldY = -1;
{
fastPaint = true;
repaint();
+ return;
+ }
+ else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
+ {
+ fastPaint = false;
+ repaint();
+ return;
}
- else if (eventName.equals(ViewportRanges.STARTRES))
+
+ int scrollX = 0;
+ if (eventName.equals(ViewportRanges.STARTRES)
+ || eventName.equals(ViewportRanges.STARTRESANDSEQ))
{
- int scrollX = 0;
+ // Make sure we're not trying to draw a panel
+ // larger than the visible window
if (eventName.equals(ViewportRanges.STARTRES))
{
- // Make sure we're not trying to draw a panel
- // larger than the visible window
- ViewportRanges vpRanges = av.getRanges();
scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
- int range = vpRanges.getEndRes() - vpRanges.getStartRes();
- if (scrollX > range)
- {
- scrollX = range;
- }
- else if (scrollX < -range)
- {
- scrollX = -range;
- }
+ }
+ else
+ {
+ scrollX = ((int[]) evt.getNewValue())[0]
+ - ((int[]) evt.getOldValue())[0];
+ }
+ ViewportRanges vpRanges = av.getRanges();
- // 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.
-
- // scroll - startres and endres both change
- if (av.getWrapAlignment())
+ int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+ if (scrollX > range)
+ {
+ scrollX = range;
+ }
+ else 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))
+ {
+ 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);
}
{
fastPaint(scrollX, 0);
}
- }
- else if (eventName.equals(ViewportRanges.STARTSEQ))
- {
- // scroll
- fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ // bizarrely, we only need to scroll on the x value here as fastpaint
+ // copies the full height of the image anyway. Passing in the y value
+ // causes nasty repaint artefacts, which only disappear on a full
+ // repaint.
}
}
}
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