X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=537af58e6d5b8fde5317c50400d7b2e9dfd30739;hb=29bb043dfab1b0bdc1efca22f2e5e3d3e8549368;hp=2139b6b78814830eeaed2742911a6142f2f70b6a;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 2139b6b..537af58 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -20,24 +20,13 @@
*/
package jalview.gui;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-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 jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
+import java.awt.Rectangle;
import java.awt.RenderingHints;
import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
@@ -46,16 +35,31 @@ import java.util.List;
import javax.swing.JPanel;
+import jalview.api.SequenceRenderer;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+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 jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
/**
* 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.
*
*/
+@SuppressWarnings("serial")
public class SeqCanvas extends JPanel implements ViewportListenerI
{
- /*
- * pixels gap between sequences and annotations when in wrapped mode
+ /**
+ * vertical gap in pixels between sequences and annotations when in wrapped
+ * mode
*/
static final int SEQS_ANNOTATION_GAP = 3;
@@ -73,7 +77,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
private final SequenceRenderer seqRdr;
- private boolean fastPaint = false;
+ boolean fastPaint = false;
private boolean fastpainting = false;
@@ -93,7 +97,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
private int wrappedVisibleWidths; // number of wrapped widths displayed
// Don't do this! Graphics handles are supposed to be transient
- //private Graphics2D gg;
+ // private Graphics2D gg;
/**
* Creates a new SeqCanvas object.
@@ -104,7 +108,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
{
this.av = ap.av;
fr = new FeatureRenderer(ap);
- seqRdr = new SequenceRenderer(av);
+ seqRdr = new jalview.gui.SequenceRenderer(av);
setLayout(new BorderLayout());
PaintRefresher.Register(this, av.getSequenceSetId());
setBackground(Color.white);
@@ -114,7 +118,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
public SequenceRenderer getSequenceRenderer()
{
- return seqRdr;
+ return seqRdr;
}
public FeatureRenderer getFeatureRenderer()
@@ -200,7 +204,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
int yPos = ypos + charHeight;
int startX = startx;
int endX = endx;
-
+
if (av.hasHiddenColumns())
{
HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
@@ -236,7 +240,6 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
}
}
-
/*
* white fill the space for the scale
*/
@@ -275,6 +278,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
* scrolling by trackpad, middle mouse button, or other device
* by moving the box in the Overview window
* programmatically to make a highlighted position visible
+ * pasting a block of sequences
*
*
* @param horizontal
@@ -284,18 +288,21 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
*/
public void fastPaint(int horizontal, int vertical)
{
- if (fastpainting || img == null)
+
+ // effectively:
+ // if (horizontal != 0 && vertical != 0)
+ // throw new InvalidArgumentException();
+ if (fastpainting || img == null)
{
return;
}
fastpainting = true;
fastPaint = true;
-
try
{
int charHeight = av.getCharHeight();
int charWidth = av.getCharWidth();
-
+
ViewportRanges ranges = av.getRanges();
int startRes = ranges.getStartRes();
int endRes = ranges.getEndRes();
@@ -303,11 +310,6 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
int endSeq = ranges.getEndSeq();
int transX = 0;
int transY = 0;
-
- Graphics gg = img.getGraphics();
- gg.copyArea(horizontal * charWidth, vertical * charHeight,
- img.getWidth(), img.getHeight(), -horizontal * charWidth,
- -vertical * charHeight);
if (horizontal > 0) // scrollbar pulled right, image to the left
{
@@ -342,14 +344,26 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
}
}
+ // jalview.bin.Console.errPrintln(">>> FastPaint to " + transX + " " + transY + " "
+ // + horizontal + " " + vertical + " " + startRes + " " + endRes
+ // + " " + startSeq + " " + endSeq);
+
+ Graphics gg = img.getGraphics();
+ gg.copyArea(horizontal * charWidth, vertical * charHeight,
+ img.getWidth(), img.getHeight(), -horizontal * charWidth,
+ -vertical * charHeight);
+
+ /** @j2sNative xxi = this.img */
+
gg.translate(transX, transY);
- drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
+ drawPanel(seqRdr, gg, startRes, endRes, startSeq, endSeq, 0);
gg.translate(-transX, -transY);
gg.dispose();
-
+
// 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.
+ // jalview.bin.Console.outPrintln("SeqCanvas fastPaint() repaint() request...");
av.getAlignPanel().repaint();
} finally
{
@@ -360,43 +374,74 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
@Override
public void paintComponent(Graphics g)
{
- //super.paintComponent(g); // BH 2019
int charHeight = av.getCharHeight();
int charWidth = av.getCharWidth();
- ViewportRanges ranges = av.getRanges();
-
int width = getWidth();
int height = getHeight();
width -= (width % charWidth);
height -= (height % charHeight);
-
- if ((img != null) && (fastPaint
- || (getVisibleRect().width != g.getClipBounds().width)
- || (getVisibleRect().height != g.getClipBounds().height)))
- {
- g.drawImage(img, 0, 0, this);
+ // BH 2019 can't possibly fastPaint if either width or height is 0
- drawSelectionGroup((Graphics2D) g, ranges.getStartRes(),
- ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq());
+ if (width == 0 || height == 0)
+ {
+ return;
+ }
+ ViewportRanges ranges = av.getRanges();
+ int startRes = ranges.getStartRes();
+ int startSeq = ranges.getStartSeq();
+ int endRes = ranges.getEndRes();
+ int endSeq = ranges.getEndSeq();
+
+ // [JAL-3226] problem that JavaScript (or Java) may consolidate multiple
+ // repaint() requests in unpredictable ways. In this case, the issue was
+ // that in response to a CTRL-C/CTRL-V paste request, in Java a fast
+ // repaint request preceded two full requests, thus resulting
+ // in a full request for paint. In constrast, in JavaScript, the three
+ // requests were bundled together into one, so the fastPaint flag was
+ // still present for the second and third request.
+ //
+ // This resulted in incomplete painting.
+ //
+ // The solution was to set seqCanvas.fastPaint and idCanvas.fastPaint false
+ // in PaintRefresher when the target to be painted is one of those two
+ // components.
+ //
+ // BH 2019.04.22
+ //
+ // An initial idea; can be removed once we determine this issue is closed:
+ // if (av.isFastPaintDisabled())
+ // {
+ // fastPaint = false;
+ // }
+
+ Rectangle vis, clip;
+ if (img != null
+ && (fastPaint
+ || (vis = getVisibleRect()).width != (clip = g
+ .getClipBounds()).width
+ || vis.height != clip.height))
+ {
+ g.drawImage(img, 0, 0, this);
+ drawSelectionGroup((Graphics2D) g, startRes, endRes, startSeq,
+ endSeq);
fastPaint = false;
}
- else if (width > 0 && height > 0)
+ else
{
- /*
- * 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
- */
+ // img is a cached version of the last view we drew.
+ // If we have no img or the size has changed, make a new one.
+ //
if (img == null || width != img.getWidth()
|| height != img.getHeight())
{
img = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
}
-
+
Graphics2D gg = (Graphics2D) img.getGraphics();
gg.setFont(av.getFont());
@@ -411,16 +456,14 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
if (av.getWrapAlignment())
{
- drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+ drawWrappedPanel(seqRdr, gg, getWidth(), getHeight(), ranges.getStartRes());
}
else
{
- drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
- ranges.getStartSeq(), ranges.getEndSeq(), 0);
+ drawPanel(seqRdr,gg, startRes, endRes, startSeq, endSeq, 0);
}
- drawSelectionGroup(gg, ranges.getStartRes(),
- ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq());
+ drawSelectionGroup(gg, startRes, endRes, startSeq, endSeq);
g.drawImage(img, 0, 0, this);
gg.dispose();
@@ -428,11 +471,10 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
if (av.cursorMode)
{
- drawCursor(g, ranges.getStartRes(), ranges.getEndRes(),
- ranges.getStartSeq(), ranges.getEndSeq());
+ drawCursor(g, startRes, endRes, startSeq, endSeq);
}
}
-
+
/**
* Draw an alignment panel for printing
*
@@ -450,10 +492,10 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
public void drawPanelForPrinting(Graphics g1, int startRes, int endRes,
int startSeq, int endSeq)
{
- drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
+ SequenceRenderer localSeqR = new jalview.gui.SequenceRenderer(av);
+ drawPanel(localSeqR,g1, startRes, endRes, startSeq, endSeq, 0);
- drawSelectionGroup((Graphics2D) g1, startRes, endRes,
- startSeq, endSeq);
+ drawSelectionGroup((Graphics2D) g1, startRes, endRes, startSeq, endSeq);
}
/**
@@ -471,13 +513,14 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth,
int canvasHeight, int startRes)
{
- drawWrappedPanel(g, canvasWidth, canvasHeight, startRes);
+ SequenceRenderer localSeqR = new jalview.gui.SequenceRenderer(av);
+ drawWrappedPanel(localSeqR, g, canvasWidth, canvasHeight, startRes);
SequenceGroup group = av.getSelectionGroup();
if (group != null)
{
drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight,
- startRes);
+ startRes);
}
}
@@ -497,7 +540,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
FontMetrics fm = getFontMetrics(av.getFont());
int labelWidth = 0;
-
+
if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
{
labelWidth = getLabelWidth(fm);
@@ -510,6 +553,20 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
}
+ public int getMinimumWrappedCanvasWidth()
+ {
+ int charWidth = av.getCharWidth();
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int labelWidth = 0;
+ if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
+ {
+ labelWidth = getLabelWidth(fm);
+ }
+ labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
+ labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
+ return labelWidthEast + labelWidthWest + charWidth;
+ }
+
/**
* Returns a pixel width sufficient to show the largest sequence coordinate
* (end position) in the alignment, calculated as the FontMetrics width of
@@ -554,7 +611,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
* @param startColumn
* the first column (0...) of the alignment to draw
*/
- public void drawWrappedPanel(Graphics g, int canvasWidth,
+ public void drawWrappedPanel(SequenceRenderer seqRdr, Graphics g, int canvasWidth,
int canvasHeight, final int startColumn)
{
int wrappedWidthInResidues = calculateWrappedGeometry(canvasWidth,
@@ -581,9 +638,9 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
int currentWidth = 0;
while ((currentWidth < wrappedVisibleWidths) && (start < maxWidth))
{
- int endColumn = Math
- .min(maxWidth, start + wrappedWidthInResidues - 1);
- drawWrappedWidth(g, ypos, start, endColumn, canvasHeight);
+ int endColumn = Math.min(maxWidth,
+ start + wrappedWidthInResidues - 1);
+ drawWrappedWidth(seqRdr, g, ypos, start, endColumn, canvasHeight);
ypos += wrappedRepeatHeightPx;
start += wrappedWidthInResidues;
currentWidth++;
@@ -622,8 +679,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
* - start with space above plus sequences
*/
wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
- wrappedRepeatHeightPx += av.getAlignment().getHeight()
- * charHeight;
+ wrappedRepeatHeightPx += av.getAlignment().getHeight() * charHeight;
/*
* add annotations panel height if shown
@@ -651,7 +707,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
* compute width in residues; this also sets East and West label widths
*/
int wrappedWidthInResidues = getWrappedCanvasWidth(canvasWidth);
-
+ av.setWrappedWidth(wrappedWidthInResidues); // update model accordingly
/*
* limit visibleWidths to not exceed width of alignment
*/
@@ -677,7 +733,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
* @param endColumn
* @param canvasHeight
*/
- protected void drawWrappedWidth(Graphics g, final int ypos,
+ protected void drawWrappedWidth(SequenceRenderer seqRdr, Graphics g, final int ypos,
final int startColumn, final int endColumn,
final int canvasHeight)
{
@@ -694,7 +750,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
int charWidth = av.getCharWidth();
int xOffset = labelWidthWest
+ ((startColumn - ranges.getStartRes()) % viewportWidth)
- * charWidth;
+ * charWidth;
g.translate(xOffset, 0);
@@ -706,7 +762,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
g.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
wrappedRepeatHeightPx);
- drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1,
+ drawPanel(seqRdr, g, startColumn, endx, 0, av.getAlignment().getHeight() - 1,
ypos);
int cHeight = av.getAlignment().getHeight() * av.getCharHeight();
@@ -761,7 +817,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
if (av.getScaleRightWrapped())
{
int x = labelWidthWest + viewportWidth * charWidth;
-
+
g.translate(x, 0);
drawVerticalScale(g, startCol, endColumn, ypos, false);
g.translate(-x, 0);
@@ -773,8 +829,9 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
*/
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);
@@ -845,38 +902,26 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
* Draw a selection group over a wrapped alignment
*/
private void drawWrappedSelection(Graphics2D g, SequenceGroup group,
- int canvasWidth,
- int canvasHeight, int startRes)
+ 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().getVisibleWidth();
-
// 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);
+
+ int charWidth = av.getCharWidth();
+ int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
+ / charWidth;
+ int startx = startRes;
+ int maxwidth = av.getAlignment().getVisibleWidth();
+ int ypos = wrappedSpaceAboveAlignment;
+
while ((ypos <= canvasHeight) && (startx < maxwidth))
{
// set end value to be start + width, or maxwidth, whichever is smaller
- endx = startx + cWidth - 1;
+ int endx = startx + cWidth - 1;
if (endx > maxwidth)
{
@@ -884,22 +929,23 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
}
g.translate(labelWidthWest, 0);
-
drawUnwrappedSelection(g, group, startx, endx, 0,
- av.getAlignment().getHeight() - 1,
- ypos);
-
+ av.getAlignment().getHeight() - 1, ypos);
g.translate(-labelWidthWest, 0);
- // update vertical offset
- ypos += cHeight + getAnnotationHeight() + hgap;
+ ypos += wrappedRepeatHeightPx;
- // update horizontal offset
startx += cWidth;
}
g.setStroke(new BasicStroke());
}
+ /**
+ * Answers zero if annotations are not shown, otherwise recalculates and
+ * answers the total height of all annotation rows in pixels
+ *
+ * @return
+ */
int getAnnotationHeight()
{
if (!av.isShowAnnotation())
@@ -920,6 +966,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
* are hidden column markers in the visible region, then each sub-region
* between the markers is drawn separately, followed by the hidden column
* marker.
+ * @param localSeqR - sequence renderer implementation - when null, uses the one used for rendering interactive GUI
*
* @param g1
* the graphics context, positioned at the first residue to be drawn
@@ -934,15 +981,19 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
* @param yOffset
* vertical offset at which to draw (for wrapped alignments)
*/
- public void drawPanel(Graphics g1, final int startRes, final int endRes,
+ public void drawPanel(SequenceRenderer localSeqR, Graphics g1, final int startRes, final int endRes,
final int startSeq, final int endSeq, final int yOffset)
{
int charHeight = av.getCharHeight();
int charWidth = av.getCharWidth();
+ if (localSeqR==null)
+ {
+ localSeqR = seqRdr;
+ }
if (!av.hasHiddenColumns())
{
- draw(g1, startRes, endRes, startSeq, endSeq, yOffset);
+ draw(localSeqR, g1, startRes, endRes, startSeq, endSeq, yOffset);
}
else
{
@@ -966,7 +1017,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
*/
g1.translate(screenY * charWidth, 0);
- draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
+ draw(localSeqR, g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
/*
* draw the downline of the hidden column marker (ScalePanel draws the
@@ -991,6 +1042,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
/**
* Draws a region of the visible alignment
+ * @param seqRdr
*
* @param g1
* @param startRes
@@ -1004,7 +1056,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
* @param yOffset
* vertical offset at which to draw (for wrapped alignments)
*/
- private void draw(Graphics g, int startRes, int endRes, int startSeq,
+ private void draw(SequenceRenderer seqRdr, Graphics g, int startRes, int endRes, int startSeq,
int endSeq, int offset)
{
int charHeight = av.getCharHeight();
@@ -1157,8 +1209,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
* the cursor drawn on it, if any
*/
private void drawCursor(Graphics g, int startRes, int endRes,
- int startSeq,
- int endSeq)
+ int startSeq, int endSeq)
{
// convert the cursorY into a position on the visible alignment
int cursor_ypos = cursorY;
@@ -1229,7 +1280,6 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
}
}
-
/**
* Draw a selection group over an unwrapped alignment
*
@@ -1252,7 +1302,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
int startRes, int endRes, int startSeq, int endSeq, int offset)
{
int charWidth = av.getCharWidth();
-
+
if (!av.hasHiddenColumns())
{
drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
@@ -1275,8 +1325,8 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
blockStart = region[0];
g.translate(screenY * charWidth, 0);
- drawPartialGroupOutline(g, group,
- blockStart, blockEnd, startSeq, endSeq, offset);
+ drawPartialGroupOutline(g, group, blockStart, blockEnd, startSeq,
+ endSeq, offset);
g.translate(-screenY * charWidth, 0);
screenY += blockEnd - blockStart + 1;
@@ -1348,8 +1398,8 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
}
else if (inGroup)
{
- drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
- drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
+ drawVerticals(g, sx, xwidth, visWidth, oldY, bottom);
+ drawHorizontals(g, sx, xwidth, visWidth, top, bottom+1);
// reset top and bottom
top = -1;
@@ -1360,8 +1410,8 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
if (inGroup)
{
sy = verticalOffset + ((i - startSeq) * charHeight);
- drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
- drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
+ drawVerticals(g, sx, xwidth, visWidth, oldY, bottom);
+ drawHorizontals(g, sx, xwidth, visWidth, top, bottom+1);
}
}
}
@@ -1445,7 +1495,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
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
@@ -1461,7 +1511,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
return highlightSearchResults(results, false);
}
-
+
/**
* Highlights search results in the visible region by rendering as white text
* on a black background. Any previous highlighting is removed. Answers true
@@ -1619,13 +1669,14 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
{
firstCol = alignment.getHiddenColumns()
.absoluteToVisibleColumn(firstCol);
- lastCol = alignment.getHiddenColumns().absoluteToVisibleColumn(lastCol);
+ lastCol = alignment.getHiddenColumns()
+ .absoluteToVisibleColumn(lastCol);
}
int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
Graphics gg = img.getGraphics();
gg.translate(transX, transY);
- drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0);
+ drawPanel(seqRdr, gg, firstCol, lastCol, firstSeq, lastSeq, 0);
gg.translate(-transX, -transY);
gg.dispose();
}
@@ -1637,7 +1688,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
public void propertyChange(PropertyChangeEvent evt)
{
String eventName = evt.getPropertyName();
-
+ // jalview.bin.Console.errPrintln(">>SeqCanvas propertyChange " + eventName);
if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
{
fastPaint = true;
@@ -1647,6 +1698,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
{
fastPaint = false;
+ // jalview.bin.Console.errPrintln("!!!! fastPaint false from MOVE_VIEWPORT");
repaint();
return;
}
@@ -1678,37 +1730,37 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
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))
+ // 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())
{
- if (av.getWrapAlignment())
- {
- fastPaintWrapped(scrollX);
- }
- else
- {
- fastPaint(scrollX, 0);
- }
+ fastPaintWrapped(scrollX);
}
- else if (eventName.equals(ViewportRanges.STARTSEQ))
+ else
{
- // scroll
- fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ fastPaint(scrollX, 0);
}
- else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+ }
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
+ {
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ if (av.getWrapAlignment())
{
- if (av.getWrapAlignment())
- {
- fastPaintWrapped(scrollX);
- }
- else
- {
- fastPaint(scrollX, 0);
- }
+ fastPaintWrapped(scrollX);
+ }
+ else
+ {
+ fastPaint(scrollX, 0);
+ }
}
else if (eventName.equals(ViewportRanges.STARTSEQ))
{
@@ -1758,9 +1810,9 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
try
{
-
+
Graphics gg = img.getGraphics();
-
+
calculateWrappedGeometry(getWidth(), getHeight());
/*
@@ -1776,8 +1828,8 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
if (scrollX < 0)
{
int startRes = ranges.getStartRes();
- drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes, startRes
- - scrollX - 1, getHeight());
+ drawWrappedWidth(seqRdr,gg, wrappedSpaceAboveAlignment, startRes,
+ startRes - scrollX - 1, getHeight());
}
else
{
@@ -1790,7 +1842,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
drawWrappedDecorators(gg, ranges.getStartRes());
gg.dispose();
-
+
repaint();
} finally
{
@@ -1815,7 +1867,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
}
Graphics gg = img.getGraphics();
-
+
ViewportRanges ranges = av.getRanges();
int viewportWidth = ranges.getViewportWidth();
int charWidth = av.getCharWidth();
@@ -1826,7 +1878,8 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
*/
int visibleWidths = wrappedVisibleWidths;
int canvasHeight = getHeight();
- boolean lastWidthPartHeight = (wrappedVisibleWidths * wrappedRepeatHeightPx) > canvasHeight;
+ boolean lastWidthPartHeight = (wrappedVisibleWidths
+ * wrappedRepeatHeightPx) > canvasHeight;
if (lastWidthPartHeight)
{
@@ -1842,16 +1895,15 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
/*
* white fill first to erase annotations
*/
-
-
+
gg.translate(xOffset, 0);
gg.setColor(Color.white);
- gg.fillRect(labelWidthWest, ypos,
- (endRes - startRes + 1) * charWidth, wrappedRepeatHeightPx);
+ gg.fillRect(labelWidthWest, ypos, (endRes - startRes + 1) * charWidth,
+ wrappedRepeatHeightPx);
gg.translate(-xOffset, 0);
- drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
-
+ drawWrappedWidth(seqRdr, gg, ypos, startRes, endRes, canvasHeight);
+
}
/*
@@ -1883,7 +1935,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
if (startRes < ranges.getVisibleAlignmentWidth())
{
- drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
+ drawWrappedWidth(seqRdr, gg, ypos, startRes, endRes, canvasHeight);
}
/*
@@ -1896,7 +1948,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow);
}
gg.dispose();
- }
+ }
/**
* Shifts the visible alignment by the specified number of columns - left if
@@ -1984,8 +2036,8 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
if (y + wrappedRepeatHeightPx < canvasHeight - wrappedRepeatHeightPx
&& (xpos + viewportWidth <= xMax))
{
- gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx, -positions
- * charWidth, heightToCopy, widthToCopy,
+ gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx,
+ -positions * charWidth, heightToCopy, widthToCopy,
-wrappedRepeatHeightPx);
}
y += wrappedRepeatHeightPx;
@@ -1995,7 +2047,6 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
gg.dispose();
}
-
/**
* Redraws any positions in the search results in the visible region of a
* wrapped alignment. Any highlights are drawn depending on the search results
@@ -2029,8 +2080,8 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
}
int firstVisibleColumn = ranges.getStartRes();
- int lastVisibleColumn = ranges.getStartRes() + repeats
- * ranges.getViewportWidth() - 1;
+ int lastVisibleColumn = ranges.getStartRes()
+ + repeats * ranges.getViewportWidth() - 1;
AlignmentI alignment = av.getAlignment();
if (av.hasHiddenColumns())
@@ -2043,7 +2094,6 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
-
Graphics gg = img.getGraphics();
for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
@@ -2087,8 +2137,8 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
* transX: offset from left edge of canvas to residue position
*/
int transX = labelWidthWest
- + ((displayColumn - ranges.getStartRes()) % wrappedWidth)
- * av.getCharWidth();
+ + ((displayColumn - ranges.getStartRes())
+ % wrappedWidth) * av.getCharWidth();
/*
* transY: offset from top edge of canvas to residue position
@@ -2106,7 +2156,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
{
matchFound = true;
gg.translate(transX, transY);
- drawPanel(gg, displayColumn, displayColumn, seqNo, seqNo,
+ drawPanel(seqRdr,gg, displayColumn, displayColumn, seqNo, seqNo,
yOffset);
gg.translate(-transX, -transY);
}
@@ -2115,7 +2165,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
}
}
}
-
+
gg.dispose();
return matchFound;
@@ -2130,4 +2180,5 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
{
return labelWidthWest;
}
+
}