/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
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package org.broad.igv.ui.panel;
//~--- non-JDK imports --------------------------------------------------------
import org.apache.log4j.Logger;
import org.broad.igv.sam.AlignmentTrack;
import org.broad.igv.sam.InsertionManager;
import org.broad.igv.sam.InsertionMarker;
import org.broad.igv.track.*;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.UIConstants;
import java.awt.*;
import java.util.*;
import java.util.List;
public class DataPanelPainter {
private static Logger log = Logger.getLogger(DataPanelPainter.class);
public synchronized void paint(Collection<TrackGroup> groups,
RenderContext context,
int width,
Color background,
Rectangle visibleRect) {
//
Graphics2D graphics2D = context.getGraphics2D("BACKGROUND");
graphics2D.setBackground(background);
graphics2D.clearRect(visibleRect.x, visibleRect.y, visibleRect.width, visibleRect.height);
graphics2D.setColor(Color.BLACK);
final ReferenceFrame referenceFrame = context.getReferenceFrame();
context.setInsertionMarkers(InsertionManager.getInstance().getInsertions(referenceFrame.getChrName(), referenceFrame.getOrigin(), referenceFrame.getEnd()));
InsertionMarker i = InsertionManager.getInstance().getSelectedInsertion(referenceFrame.getChrName());
if (i != null) {
final double start = referenceFrame.getOrigin();
try {
double scale = referenceFrame.getScale();
int p0 = 0, w;
w = (int) ((i.position - start) / scale);
paintSection(groups, context, p0, visibleRect.y, w, visibleRect.height, 0);
i.pixelPosition = p0 + w;
p0 += w;
context.multiframe = true;
referenceFrame.origin = i.position;
w = (int) Math.ceil(i.size / context.getScale());
paintExpandedInsertion(i, groups, context, p0, visibleRect.y, w, visibleRect.height);
int g = (int) (i.size / scale);
p0 += g;
context.getReferenceFrame().origin = i.position;
w = width - p0;
if (w > 0) {
paintSection(groups, context, p0, visibleRect.y, width - p0, visibleRect.height, g);
}
} finally {
referenceFrame.origin = start;
}
} else {
paintFrame(groups, context, width, visibleRect);
}
}
private void paintSection(Collection<TrackGroup> groups, RenderContext context, int px, int py, int w, int h, int delta) {
context.clearGraphicsCache();
Graphics2D dG = context.getGraphics();
Rectangle dRect = new Rectangle(0, py, w, h);
dG.translate(delta, 0);
dG.setClip(dRect);
context.translateX = px;
paintFrame(groups, context, w, dRect);
}
private void paintFrame(Collection<TrackGroup> groups, RenderContext dContext, int width, Rectangle dRect) {
int trackX = 0;
int trackY = 0;
for (Iterator<TrackGroup> groupIter = groups.iterator(); groupIter.hasNext(); ) {
TrackGroup group = groupIter.next();
if (dRect != null && (trackY > dRect.y + dRect.height)) {
break;
}
if (group.isVisible()) {
if (groups.size() > 1) {
final Graphics2D greyGraphics = dContext.getGraphic2DForColor(UIConstants.LIGHT_GREY);
greyGraphics.fillRect(0, trackY + 1, width, UIConstants.groupGap - 1);
trackY += UIConstants.groupGap;
}
// Draw a line just above group.
if (group.isDrawBorder()) {
Graphics2D graphics2D = dContext.getGraphic2DForColor(Color.black);
graphics2D.drawLine(0, trackY - 1, width, trackY - 1);
}
List<Track> trackList = group.getVisibleTracks();
synchronized (trackList) {
for (Track track : trackList) {
if (track == null) continue;
int trackHeight = track.getHeight();
if (dRect != null) {
if (trackY > dRect.y + dRect.height) {
break;
} else if (trackY + trackHeight < dRect.y) {
if (track.isVisible()) {
trackY += trackHeight;
}
continue;
}
}
if (track.isVisible()) {
Rectangle rect = new Rectangle(trackX, trackY, width, trackHeight);
draw(track, rect, dContext);
trackY += trackHeight;
}
}
}
// Draw a line just below group.
if (group.isDrawBorder()) {
Graphics2D graphics2D = dContext.getGraphic2DForColor(Color.black);
graphics2D.drawLine(0, trackY, width, trackY);
}
}
}
}
private void paintExpandedInsertion(InsertionMarker insertionMarker, Collection<TrackGroup> groups, RenderContext context, int px, int py, int w, int h) {
context.clearGraphicsCache();
Graphics2D dG = context.getGraphics();
Rectangle dRect = new Rectangle(0, py, w, h);
dG.translate(px, 0);
dG.setClip(dRect);
context.translateX = px;
int trackY = 0;
for (Iterator<TrackGroup> groupIter = groups.iterator(); groupIter.hasNext(); ) {
TrackGroup group = groupIter.next();
if (group.isVisible()) {
List<Track> trackList = group.getVisibleTracks();
synchronized (trackList) {
for (Track track : trackList) {
if (track == null) continue;
int trackHeight = track.getHeight();
if (dRect != null) {
if (trackY > dRect.y + dRect.height) {
break;
} else if (trackY + trackHeight < dRect.y) {
if (track.isVisible()) {
trackY += trackHeight;
}
continue;
}
}
if (track instanceof AlignmentTrack && track.isVisible()) {
Rectangle rect = new Rectangle(dRect.x, trackY, dRect.width, trackHeight);
((AlignmentTrack) track).renderExpandedInsertion(insertionMarker, context, rect);
}
if (track.isVisible()) {
trackY += trackHeight;
}
}
}
}
}
}
final private void draw(Track track, Rectangle rect, RenderContext context) {
track.render(context, rect);
// Get overlays
List<Track> overlayTracks = IGV.getInstance().getOverlayTracks(track);
if (overlayTracks != null) {
for (Track overlayTrack : overlayTracks) {
// Don't overlay on self
if (overlayTrack != track) {
overlayTrack.overlay(context, rect);
}
}
}
}
}