--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package org.jalview;
+
+import org.jalview.HiddenColumnsBenchmark.HiddenColsAndStartState;
+import org.openjdk.jmh.annotations.Benchmark;
+import org.openjdk.jmh.annotations.BenchmarkMode;
+import org.openjdk.jmh.annotations.Fork;
+import org.openjdk.jmh.annotations.Measurement;
+import org.openjdk.jmh.annotations.Mode;
+import org.openjdk.jmh.annotations.Setup;
+import org.openjdk.jmh.annotations.State;
+import org.openjdk.jmh.annotations.Warmup;
+import org.openjdk.jmh.annotations.Scope;
+import org.openjdk.jmh.annotations.Param;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Random;
+import java.util.concurrent.TimeUnit;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+/*
+ * A class to benchmark hidden columns performance
+ */
+@Warmup(iterations = 10, time = 500, timeUnit = TimeUnit.MILLISECONDS)
+@Measurement(iterations = 10, time = 500, timeUnit = TimeUnit.MILLISECONDS)
+@Fork(1)
+public class SeqWidthBenchmark {
+
+ /*
+ * State with multiple hidden columns and a start position set
+ */
+ @State(Scope.Thread)
+ public static class AlignmentState
+ {
+ @Param({"100", "1000", "10000", "100000"})
+ public int numSeqs;
+
+ Random rand = new Random();
+
+ AlignmentI al;
+
+ @Setup
+ public void setup()
+ {
+ rand.setSeed(1234);
+
+ SequenceI[] seqs = new Sequence[numSeqs];
+ for (int i = 0; i < numSeqs; i++)
+ {
+ int count = rand.nextInt(10000);
+ StringBuilder aas = new StringBuilder();
+ for (int j=0; j<count; j++)
+ {
+ aas.append("a");
+ }
+
+ seqs[i] = new Sequence("Sequence" + i, aas.toString());
+ }
+ al = new Alignment(seqs);
+ }
+ }
+
+
+ @Benchmark
+ @BenchmarkMode({Mode.Throughput})
+ public int benchSeqGetWidth(AlignmentState tstate)
+ {
+ return tstate.al.getWidth();
+ }
+
+}
if (!od.isPositionInBox(evt.getX(), evt.getY()))
{
draggingBox = false;
+
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+
od.updateViewportFromMouse(evt.getX(), evt.getY(),
av.getAlignment().getHiddenSequences(),
av.getAlignment().getHiddenColumns());
@Override
public void mouseReleased(MouseEvent evt)
{
+ draggingBox = false;
}
@Override
{
private Alignment dataset;
- protected List<SequenceI> sequences;
+ private List<SequenceI> sequences;
protected List<SequenceGroup> groups;
return sequences.get(i);
}
}
+
return null;
}
public int getWidth()
{
int maxLength = -1;
-
+
for (int i = 0; i < sequences.size(); i++)
{
if (getSequenceAt(i).getLength() > maxLength)
maxLength = getSequenceAt(i).getLength();
}
}
-
+
return maxLength;
}
+ /*
+ @Override
+ public int getWidth()
+ {
+ final Wrapper temp = new Wrapper();
+
+ forEachSequence(new Consumer<SequenceI>()
+ {
+ @Override
+ public void accept(SequenceI s)
+ {
+ if (s.getLength() > temp.inner)
+ {
+ temp.inner = s.getLength();
+ }
+ }
+ }, 0, sequences.size() - 1);
+
+ return temp.inner;
+ }
+
+ public static class Wrapper
+ {
+ public int inner;
+ }*/
/**
* DOCUMENT ME!
@Override
public void paintComponent(Graphics g)
{
- invalidate();
+ invalidate(); // needed so that the id width adjuster works correctly
Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
idPanelHolder.setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
- validate();
+
+ validate(); // needed so that the id width adjuster works correctly
/*
- * set scroll bar positions
+ * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
+ * though I still think this call should be elsewhere.
*/
ViewportRanges ranges = av.getRanges();
setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
@Override
public void paintComponent(Graphics g)
{
+ super.paintComponent(g);
+
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
gg.fillRect(0, 0, imgWidth, image.getHeight());
imageFresh = true;
}
-
+
drawComponent(gg, av.getRanges().getStartRes(),
av.getRanges().getEndRes() + 1);
imageFresh = false;
int er = av.getRanges().getEndRes() + 1;
int transX = 0;
- long stime = System.currentTimeMillis();
gg.copyArea(0, 0, imgWidth, getHeight(),
-horizontal * av.getCharWidth(), 0);
- long mtime = System.currentTimeMillis();
if (horizontal > 0) // scrollbar pulled right, image to the left
{
drawComponent(gg, sr, er);
gg.translate(-transX, 0);
- long dtime = System.currentTimeMillis();
+
fastPaint = true;
- repaint();
- long rtime = System.currentTimeMillis();
- if (debugRedraw)
- {
- System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t"
- + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime)
- + "\tRepaint call:\t" + (rtime - dtime));
- }
+ // 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();
}
private volatile boolean lastImageGood = false;
frame.setResizable(resizable);
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
+ frame.setOpaque(false);
if (frame.getX() < 1 && frame.getY() < 1)
{
this.av = av;
PaintRefresher.Register(this, av.getSequenceSetId());
av.getRanges().addPropertyChangeListener(this);
- }
+ }
/**
* DOCUMENT ME!
gg.translate(0, -transY);
fastPaint = true;
- 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();
}
/**
@Override
public void paintComponent(Graphics g)
{
+ super.paintComponent(g);
+
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
-
+
if (fastPaint)
{
fastPaint = false;
g.drawImage(image, 0, 0, this);
-
+
return;
}
-
+
int oldHeight = imgHeight;
-
+
imgHeight = getHeight();
imgHeight -= (imgHeight % av.getCharHeight());
-
+
if (imgHeight < 1)
{
return;
}
-
+
if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
{
- image = new BufferedImage(getWidth(), imgHeight,
- BufferedImage.TYPE_INT_RGB);
+ image = new BufferedImage(getWidth(), imgHeight,
+ BufferedImage.TYPE_INT_RGB);
}
-
+
gg = (Graphics2D) image.getGraphics();
-
+
// Fill in the background
gg.setColor(Color.white);
gg.fillRect(0, 0, getWidth(), imgHeight);
-
+
drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
-
+
g.drawImage(image, 0, 0, this);
}
@Override
public void paintComponent(Graphics g)
{
- // super.paintComponent(g);
+ super.paintComponent(g);
if (restart)
{
@Override
public void mouseMoved(MouseEvent evt)
{
- if (od.isPositionInBox(evt.getX(), evt.getY()))
+ if (!draggingBox)
+ // don't bother changing the cursor if we're dragging the box
+ // as we can't have moved inside or out of the box in that case
{
- // display drag cursor at mouse position
- setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
- }
- else
- {
- // reset cursor
- setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+ if (od.isPositionInBox(evt.getX(), evt.getY()))
+ {
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+ }
+ else
+ {
+ // reset cursor
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+ }
}
}
});
if (!od.isPositionInBox(evt.getX(), evt.getY()))
{
draggingBox = false;
+
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+
od.updateViewportFromMouse(evt.getX(), evt.getY(),
av.getAlignment().getHiddenSequences(),
av.getAlignment().getHiddenColumns());
showPopupMenu(evt);
}
}
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ draggingBox = false;
+ }
+
});
}
@Override
public void paintComponent(Graphics g)
{
+ super.paintComponent(g);
+
/*
* shouldn't get called in wrapped mode as the scale above is
* drawn instead by SeqCanvas.drawNorthScale
|| evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
{
// scroll event, repaint panel
- 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();
}
}
int endSeq = ranges.getEndSeq();
int transX = 0;
int transY = 0;
-
+
gg.copyArea(horizontal * charWidth, vertical * charHeight,
img.getWidth(), img.getHeight(), -horizontal * charWidth,
-vertical * charHeight);
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;
int charHeight = av.getCharHeight();
int charWidth = av.getCharWidth();
-
+
ViewportRanges ranges = av.getRanges();
-
+
int width = getWidth();
int height = getHeight();
-
+
width -= (width % charWidth);
height -= (height % charHeight);
-
+
// selectImage is the selection group outline image
BufferedImage selectImage = drawSelectionGroup(
ranges.getStartRes(), ranges.getEndRes(),
ranges.getStartSeq(), ranges.getEndSeq());
-
+
if ((img != null) && (fastPaint
|| (getVisibleRect().width != g.getClipBounds().width)
|| (getVisibleRect().height != g.getClipBounds().height)))
gg = (Graphics2D) img.getGraphics();
gg.setFont(av.getFont());
}
-
+
if (av.antiAlias)
{
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());
drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
ranges.getStartSeq(), ranges.getEndSeq(), 0);
}
-
+
// 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);
private BufferedImage buildLocalImage(BufferedImage selectImage)
{
// clone the cached image
- BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
- img.getType());
+ BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+ img.getType());
+
+ // BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+ // img.getType());
Graphics2D g2d = lcimg.createGraphics();
g2d.drawImage(img, 0, 0, null);
try
{
- lcimg = new BufferedImage(width, height,
- BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
+ lcimg = new BufferedImage(width, height,
+ BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
} catch (OutOfMemoryError er)
{
System.gc();
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)
{
seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
- visibleResults[r + 1], (visibleResults[r] - startRes)
- * charWidth, offset
- + ((i - startSeq) * charHeight));
+ visibleResults[r + 1],
+ (visibleResults[r] - startRes) * charWidth,
+ offset + ((i - startSeq) * charHeight));
}
}
}
{
ViewportRanges ranges = av.getRanges();
- // if (Math.abs(scrollX) > ranges.getViewportWidth())
- // JAL-2836, 2836 temporarily removed wrapped fastpaint for release 2.10.3
- if (true)
+ if (Math.abs(scrollX) > ranges.getViewportWidth())
{
/*
* shift of more than one view width is
protected int alheight;
+ protected float widthRatio;
+
+ protected float heightRatio;
+
/**
* Create an OverviewDimensions object
*
public float getPixelsPerCol()
{
resetAlignmentDims();
- return (float) width / alwidth;
+ return 1 / widthRatio;
}
public float getPixelsPerSeq()
{
resetAlignmentDims();
- return (float) sequencesHeight / alheight;
+ return 1 / heightRatio;
}
public void setWidth(int w)
{
width = w;
+ widthRatio = (float) alwidth / width;
}
public void setHeight(int h)
{
sequencesHeight = h - graphHeight;
+ heightRatio = (float) alheight / sequencesHeight;
}
/**
// boxX, boxY is the x,y location equivalent to startRes, startSeq
int xPos = Math.min(startRes, alwidth - vpwidth + 1);
- boxX = Math.round((float) xPos * width / alwidth);
- boxY = Math.round((float) startSeq * sequencesHeight / alheight);
+ boxX = Math.round(xPos / widthRatio);
+ boxY = Math.round(startSeq / heightRatio);
// boxWidth is the width in residues translated to pixels
- boxWidth = Math.round((float) vpwidth * width / alwidth);
+ boxWidth = Math.round(vpwidth / widthRatio);
// boxHeight is the height in sequences translated to pixels
- boxHeight = Math.round((float) vpheight * sequencesHeight / alheight);
+ boxHeight = Math.round(vpheight / heightRatio);
}
/**
public void updateViewportFromMouse(int mousex, int mousey,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
+ resetAlignmentDims();
+
int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
public void adjustViewportFromMouse(int mousex, int mousey,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
+ resetAlignmentDims();
+
// calculate translation in pixel terms:
// get mouse location in viewport coords, add translation in viewport
// coords, and update viewport as usual
- int vpx = Math.round((float) mousex * alwidth / width);
- int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+ int vpx = Math.round(mousex * widthRatio);
+ int vpy = Math.round(mousey * heightRatio);
updateViewportFromTopLeft(vpx + xdiff, vpy + ydiff, hiddenSeqs,
hiddenCols);
}
+ /**
+ * {@inheritDoc} Callers should have already called resetAlignmentDims to
+ * refresh alwidth, alheight and width/height ratios
+ */
@Override
protected void updateViewportFromTopLeft(int leftx, int topy,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
int xAsRes = leftx;
int yAsSeq = topy;
- resetAlignmentDims();
if (xAsRes < 0)
{
{
alwidth = ranges.getVisibleAlignmentWidth();
alheight = ranges.getVisibleAlignmentHeight();
+
+ widthRatio = (float) alwidth / width;
+ heightRatio = (float) alheight / sequencesHeight;
}
+ /**
+ * {@inheritDoc} Callers should have already called resetAlignmentDims to
+ * refresh widthRatio
+ */
@Override
protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
{
- int vpx = Math.round((float) mousex * alwidth / width);
+ int vpx = Math.round(mousex * widthRatio);
return vpx - ranges.getViewportWidth() / 2;
}
+ /**
+ * {@inheritDoc} Callers should have already called resetAlignmentDims to
+ * refresh heightRatio
+ */
@Override
protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
{
- int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+ int vpy = Math.round(mousey * heightRatio);
return vpy - ranges.getViewportHeight() / 2;
}
public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
HiddenColumns hiddenCols)
{
+ resetAlignmentDims();
+
// get alignment position of x and box (can get directly from vpranges) and
// calculate difference between the positions
- int vpx = Math.round((float) x * alwidth / width);
- int vpy = Math.round((float) y * alheight / sequencesHeight);
+ int vpx = Math.round(x * widthRatio);
+ int vpy = Math.round(y * heightRatio);
xdiff = ranges.getStartRes() - vpx;
ydiff = ranges.getStartSeq() - vpy;
public void updateViewportFromMouse(int mousex, int mousey,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
+ resetAlignmentDims();
+
// convert mousex and mousey to alignment units as well as
// translating to top left corner of viewport - this is an absolute position
int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
public void adjustViewportFromMouse(int mousex, int mousey,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
+ resetAlignmentDims();
+
// calculate translation in pixel terms:
// get mouse location in viewport coords, add translation in viewport
// coords,
// convert back to pixel coords
- int vpx = Math.round((float) mousex * alwidth / width);
+ int vpx = Math.round(mousex * widthRatio);
int visXAsRes = hiddenCols.findColumnPosition(vpx) + xdiff;
- int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+ int vpy = Math.round(mousey * heightRatio);
int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + ydiff;
// update viewport accordingly
updateViewportFromTopLeft(visXAsRes, visYAsRes, hiddenSeqs, hiddenCols);
}
+ /**
+ * {@inheritDoc} Callers should have already called resetAlignmentDims to
+ * refresh alwidth, alheight and width/height ratios
+ */
@Override
protected void updateViewportFromTopLeft(int leftx, int topy,
HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
{
int visXAsRes = leftx;
int visYAsSeq = topy;
- resetAlignmentDims();
if (visXAsRes < 0)
{
{
alwidth = ranges.getAbsoluteAlignmentWidth();
alheight = ranges.getAbsoluteAlignmentHeight();
+
+ widthRatio = (float) alwidth / width;
+ heightRatio = (float) alheight / sequencesHeight;
}
+
+ /**
+ * {@inheritDoc} Callers should have already called resetAlignmentDims to
+ * refresh widthRatio
+ */
@Override
protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
{
- int vpx = Math.round((float) mousex * alwidth / width);
+ int vpx = Math.round(mousex * widthRatio);
return hidden.subtractVisibleColumns(ranges.getViewportWidth() / 2,
vpx);
}
+ /**
+ * {@inheritDoc} Callers should have already called resetAlignmentDims to
+ * refresh heightRatio
+ */
@Override
protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
{
- int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+ int vpy = Math.round(mousey * heightRatio);
return hidden.subtractVisibleRows(ranges.getViewportHeight() / 2, vpy);
}
public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
HiddenColumns hiddenCols)
{
+ resetAlignmentDims();
+
// get alignment position of x and box (can get directly from vpranges) and
// calculate difference between the positions
- int vpx = Math.round((float) x * alwidth / width);
- int vpy = Math.round((float) y * alheight / sequencesHeight);
+ int vpx = Math.round(x * widthRatio);
+ int vpy = Math.round(y * heightRatio);
xdiff = ranges.getStartRes() - hiddenCols.findColumnPosition(vpx);
ydiff = ranges.getStartSeq()
git://source.jalview.org / jalview.git / commitdiff