/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Image;
import java.awt.Panel;
import java.util.List;
public class SeqCanvas extends Panel
{
FeatureRenderer fr;
SequenceRenderer sr;
Image img;
Graphics gg;
int imgWidth;
int imgHeight;
AlignViewport av;
SearchResults searchResults = null;
boolean fastPaint = false;
int cursorX = 0;
int cursorY = 0;
public SeqCanvas(AlignViewport av)
{
this.av = av;
fr = new FeatureRenderer(av);
sr = new SequenceRenderer(av);
PaintRefresher.Register(this, av.getSequenceSetId());
}
public AlignViewport getViewport()
{
return av;
}
public FeatureRenderer getFeatureRenderer()
{
return fr;
}
public SequenceRenderer getSequenceRenderer()
{
return sr;
}
void drawNorthScale(Graphics g, int startx, int endx, int ypos)
{
int scalestartx = startx - startx % 10 + 10;
g.setColor(Color.black);
// NORTH SCALE
for (int i = scalestartx; i < endx; i += 10)
{
int value = i;
if (av.hasHiddenColumns())
{
value = av.getColumnSelection().adjustForHiddenColumns(value);
}
g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
ypos - (av.charHeight / 2));
g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
(ypos + 2) - (av.charHeight / 2),
((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
ypos - 2);
}
}
void drawWestScale(Graphics g, int startx, int endx, int ypos)
{
FontMetrics fm = getFontMetrics(av.getFont());
ypos += av.charHeight;
if (av.hasHiddenColumns())
{
startx = av.getColumnSelection().adjustForHiddenColumns(startx);
endx = av.getColumnSelection().adjustForHiddenColumns(endx);
}
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
// WEST SCALE
for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
SequenceI seq = av.getAlignment().getSequenceAt(i);
int index = startx;
int value = -1;
while (index < endx)
{
if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
{
index++;
continue;
}
value = av.getAlignment().getSequenceAt(i).findPosition(index);
break;
}
if (value != -1)
{
int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
- av.charWidth / 2;
g.drawString(value + "", x, (ypos + (i * av.charHeight))
- (av.charHeight / 5));
}
}
}
void drawEastScale(Graphics g, int startx, int endx, int ypos)
{
ypos += av.charHeight;
if (av.hasHiddenColumns())
{
endx = av.getColumnSelection().adjustForHiddenColumns(endx);
}
SequenceI seq;
// EAST SCALE
for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
seq = av.getAlignment().getSequenceAt(i);
int index = endx;
int value = -1;
while (index > startx)
{
if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
{
index--;
continue;
}
value = seq.findPosition(index);
break;
}
if (value != -1)
{
g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
- (av.charHeight / 5));
}
}
}
int lastsr = 0;
void fastPaint(int horizontal, int vertical)
{
if (fastPaint || gg == null)
{
return;
}
// Its possible on certain browsers that the call to fastpaint
// is faster than it can paint, so this check here catches
// this possibility
if (lastsr + horizontal != av.startRes)
{
horizontal = av.startRes - lastsr;
}
lastsr = av.startRes;
fastPaint = true;
gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
imgWidth - horizontal * av.charWidth, imgHeight - vertical
* av.charHeight, -horizontal * av.charWidth, -vertical
* av.charHeight);
int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
transX = (er - sr - horizontal) * av.charWidth;
sr = er - horizontal;
}
else if (horizontal < 0)
{
er = sr - horizontal;
}
else if (vertical > 0) // scroll down
{
ss = es - vertical;
if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
{
ss = av.startSeq;
}
else
{
transY = imgHeight - vertical * av.charHeight;
}
}
else if (vertical < 0)
{
es = ss - vertical;
if (es > av.endSeq)
{
es = av.endSeq;
}
}
gg.translate(transX, transY);
drawPanel(gg, sr, er, ss, es, 0);
gg.translate(-transX, -transY);
repaint();
}
/**
* Definitions of startx and endx (hopefully): SMJS This is what I'm working
* towards! startx is the first residue (starting at 0) to display. endx is
* the last residue to display (starting at 0). starty is the first sequence
* to display (starting at 0). endy is the last sequence to display (starting
* at 0). NOTE 1: The av limits are set in setFont in this class and in the
* adjustment listener in SeqPanel when the scrollbars move.
*/
public void update(Graphics g)
{
paint(g);
}
public void paint(Graphics g)
{
if (img != null
&& (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
.getClipBounds().height)))
{
g.drawImage(img, 0, 0, this);
fastPaint = false;
return;
}
if (fastPaint)
{
g.drawImage(img, 0, 0, this);
fastPaint = false;
return;
}
// this draws the whole of the alignment
imgWidth = this.getSize().width;
imgHeight = this.getSize().height;
imgWidth -= imgWidth % av.charWidth;
imgHeight -= imgHeight % av.charHeight;
if (imgWidth < 1 || imgHeight < 1)
{
return;
}
if (img == null || imgWidth != img.getWidth(this)
|| imgHeight != img.getHeight(this))
{
img = createImage(imgWidth, imgHeight);
gg = img.getGraphics();
gg.setFont(av.getFont());
}
gg.setColor(Color.white);
gg.fillRect(0, 0, imgWidth, imgHeight);
if (av.getWrapAlignment())
{
drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
}
else
{
drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
}
g.drawImage(img, 0, 0, this);
}
int LABEL_WEST, LABEL_EAST;
public int getWrappedCanvasWidth(int cwidth)
{
cwidth -= cwidth % av.charWidth;
FontMetrics fm = getFontMetrics(av.getFont());
LABEL_EAST = 0;
LABEL_WEST = 0;
if (av.scaleRightWrapped)
{
LABEL_EAST = fm.stringWidth(getMask());
}
if (av.scaleLeftWrapped)
{
LABEL_WEST = fm.stringWidth(getMask());
}
return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
}
/**
* Generates a string of zeroes.
*
* @return String
*/
String getMask()
{
String mask = "0";
int maxWidth = 0;
int tmp;
AlignmentI alignment = av.getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
tmp = alignment.getSequenceAt(i).getEnd();
if (tmp > maxWidth)
{
maxWidth = tmp;
}
}
for (int i = maxWidth; i > 0; i /= 10)
{
mask += "0";
}
return mask;
}
public void drawWrappedPanel(Graphics g, int canvasWidth,
int canvasHeight, int startRes)
{
AlignmentI al = av.getAlignment();
FontMetrics fm = getFontMetrics(av.getFont());
if (av.scaleRightWrapped)
{
LABEL_EAST = fm.stringWidth(getMask());
}
if (av.scaleLeftWrapped)
{
LABEL_WEST = fm.stringWidth(getMask());
}
int hgap = av.charHeight;
if (av.scaleAboveWrapped)
{
hgap += av.charHeight;
}
int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
int cHeight = av.getAlignment().getHeight() * av.charHeight;
av.setWrappedWidth(cWidth);
av.endRes = av.startRes + cWidth;
int endx;
int ypos = hgap;
int maxwidth = av.getAlignment().getWidth() - 1;
if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
endx = startRes + cWidth - 1;
if (endx > maxwidth)
{
endx = maxwidth;
}
g.setColor(Color.black);
if (av.scaleLeftWrapped)
{
drawWestScale(g, startRes, endx, ypos);
}
if (av.scaleRightWrapped)
{
g.translate(canvasWidth - LABEL_EAST, 0);
drawEastScale(g, startRes, endx, ypos);
g.translate(-(canvasWidth - LABEL_EAST), 0);
}
g.translate(LABEL_WEST, 0);
if (av.scaleAboveWrapped)
{
drawNorthScale(g, startRes, endx, ypos);
}
if (av.hasHiddenColumns() && av.showHiddenMarkers)
{
g.setColor(Color.blue);
int res;
for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
.size(); i++)
{
res = av.getColumnSelection().findHiddenRegionPosition(i)
- startRes;
if (res < 0 || res > endx - startRes)
{
continue;
}
gg.fillPolygon(new int[]
{ res * av.charWidth - av.charHeight / 4,
res * av.charWidth + av.charHeight / 4, res * av.charWidth },
new int[]
{ ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),
ypos - (av.charHeight / 2) + 8 }, 3);
}
}
if (g.getClip() == null)
{
g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
}
drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
g.setClip(null);
if (av.showAnnotation)
{
g.translate(0, cHeight + ypos + 4);
if (annotations == null)
{
annotations = new AnnotationPanel(av);
}
annotations.drawComponent(g, startRes, endx + 1);
g.translate(0, -cHeight - ypos - 4);
}
g.translate(-LABEL_WEST, 0);
ypos += cHeight + getAnnotationHeight() + hgap;
startRes += cWidth;
}
}
AnnotationPanel annotations;
int getAnnotationHeight()
{
if (!av.showAnnotation)
{
return 0;
}
if (annotations == null)
{
annotations = new AnnotationPanel(av);
}
return annotations.adjustPanelHeight();
}
void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
int endSeq, int offset)
{
if (!av.hasHiddenColumns())
{
draw(g1, startRes, endRes, startSeq, endSeq, offset);
}
else
{
List regions = av.getColumnSelection().getHiddenColumns();
int screenY = 0;
int blockStart = startRes;
int blockEnd = endRes;
for (int[] region : regions)
{
int hideStart = region[0];
int hideEnd = region[1];
if (hideStart <= blockStart)
{
blockStart += (hideEnd - hideStart) + 1;
continue;
}
blockEnd = hideStart - 1;
g1.translate(screenY * av.charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
if (av.getShowHiddenMarkers())
{
g1.setColor(Color.blue);
g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
0 + offset, (blockEnd - blockStart + 1) * av.charWidth
- 1, (endSeq - startSeq) * av.charHeight + offset);
}
g1.translate(-screenY * av.charWidth, 0);
screenY += blockEnd - blockStart + 1;
blockStart = hideEnd + 1;
}
if (screenY <= (endRes - startRes))
{
blockEnd = blockStart + (endRes - startRes) - screenY;
g1.translate(screenY * av.charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
g1.translate(-screenY * av.charWidth, 0);
}
}
}
// int startRes, int endRes, int startSeq, int endSeq, int x, int y,
// int x1, int x2, int y1, int y2, int startx, int starty,
void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
int offset)
{
g.setFont(av.getFont());
sr.prepare(g, av.renderGaps);
SequenceI nextSeq;
// / First draw the sequences
// ///////////////////////////
for (int i = startSeq; i < endSeq; i++)
{
nextSeq = av.getAlignment().getSequenceAt(i);
if (nextSeq == null)
{
continue;
}
sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
startRes, endRes, offset + ((i - startSeq) * av.charHeight));
if (av.showSequenceFeatures)
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
+ ((i - startSeq) * av.charHeight));
}
// / Highlight search Results once all sequences have been drawn
// ////////////////////////////////////////////////////////
if (searchResults != null)
{
int[] visibleResults = searchResults.getResults(nextSeq, startRes,
endRes);
if (visibleResults != null)
{
for (int r = 0; r < visibleResults.length; r += 2)
{
sr.drawHighlightedText(nextSeq, visibleResults[r],
visibleResults[r + 1], (visibleResults[r] - startRes)
* av.charWidth, offset
+ ((i - startSeq) * av.charHeight));
}
}
}
if (av.cursorMode && cursorY == i && cursorX >= startRes
&& cursorX <= endRes)
{
sr.drawCursor(nextSeq, cursorX,
(cursorX - startRes) * av.charWidth, offset
+ ((i - startSeq) * av.charHeight));
}
}
if (av.getSelectionGroup() != null
|| av.getAlignment().getGroups().size() > 0)
{
drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
}
}
void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
int startSeq, int endSeq, int offset)
{
//
// ///////////////////////////////////
// Now outline any areas if necessary
// ///////////////////////////////////
SequenceGroup group = av.getSelectionGroup();
int sx = -1;
int sy = -1;
int ex = -1;
int groupIndex = -1;
if ((group == null) && (av.getAlignment().getGroups().size() > 0))
{
group = av.getAlignment().getGroups().get(0);
groupIndex = 0;
}
if (group != null)
{
do
{
int oldY = -1;
int i = 0;
boolean inGroup = false;
int top = -1;
int bottom = -1;
int alHeight = av.getAlignment().getHeight() - 1;
for (i = startSeq; i < endSeq; i++)
{
sx = (group.getStartRes() - startRes) * av.charWidth;
sy = offset + ((i - startSeq) * av.charHeight);
ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;
if (sx + ex < 0 || sx > imgWidth)
{
continue;
}
if ((sx <= (endRes - startRes) * av.charWidth)
&& group.getSequences(null).contains(
av.getAlignment().getSequenceAt(i)))
{
if ((bottom == -1)
&& (i >= alHeight || !group.getSequences(null)
.contains(
av.getAlignment().getSequenceAt(i + 1))))
{
bottom = sy + av.charHeight;
}
if (!inGroup)
{
if (((top == -1) && (i == 0))
|| !group.getSequences(null).contains(
av.getAlignment().getSequenceAt(i - 1)))
{
top = sy;
}
oldY = sy;
inGroup = true;
if (group == av.getSelectionGroup())
{
g.setColor(Color.red);
}
else
{
g.setColor(group.getOutlineColour());
}
}
}
else
{
if (inGroup)
{
if (sx >= 0 && sx < imgWidth)
{
g.drawLine(sx, oldY, sx, sy);
}
if (sx + ex < imgWidth)
{
g.drawLine(sx + ex, oldY, sx + ex, sy);
}
if (sx < 0)
{
ex += sx;
sx = 0;
}
if (sx + ex > imgWidth)
{
ex = imgWidth;
}
else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
{
ex = (endRes - startRes + 1) * av.charWidth;
}
if (top != -1)
{
g.drawLine(sx, top, sx + ex, top);
top = -1;
}
if (bottom != -1)
{
g.drawLine(sx, bottom, sx + ex, bottom);
bottom = -1;
}
inGroup = false;
}
}
}
if (inGroup)
{
sy = offset + ((i - startSeq) * av.charHeight);
if (sx >= 0 && sx < imgWidth)
{
g.drawLine(sx, oldY, sx, sy);
}
if (sx + ex < imgWidth)
{
g.drawLine(sx + ex, oldY, sx + ex, sy);
}
if (sx < 0)
{
ex += sx;
sx = 0;
}
if (sx + ex > imgWidth)
{
ex = imgWidth;
}
else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
{
ex = (endRes - startRes + 1) * av.charWidth;
}
if (top != -1)
{
g.drawLine(sx, top, sx + ex, top);
top = -1;
}
if (bottom != -1)
{
g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
bottom = -1;
}
inGroup = false;
}
groupIndex++;
if (groupIndex >= av.getAlignment().getGroups().size())
{
break;
}
group = av.getAlignment().getGroups()
.get(groupIndex);
} while (groupIndex < av.getAlignment().getGroups().size());
}
}
public void highlightSearchResults(SearchResults results)
{
searchResults = results;
repaint();
}
}