/*
* 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.
*/
/*
* TrackPanel.java
*
* Created on Sep 5, 2007, 4:09:39 PM
*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.ui.panel;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.feature.Chromosome;
import org.broad.igv.feature.genome.ChromosomeCoordinate;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.sam.InsertionManager;
import org.broad.igv.sam.InsertionMarker;
import org.broad.igv.ui.FontManager;
import org.broad.igv.ui.UIConstants;
import org.broad.igv.ui.WaitCursorManager;
import org.broad.igv.util.LongRunningTask;
import org.broad.igv.util.NamedRunnable;
import javax.swing.*;
import javax.swing.event.MouseInputAdapter;
import java.awt.*;
import java.awt.event.MouseEvent;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.List;
import static org.broad.igv.prefs.Constants.DEFAULT_GENOME;
import static org.broad.igv.prefs.Constants.ENABLE_ANTIALISING;
/**
* @author jrobinso
*/
public class RulerPanel extends JPanel {
private static Logger log = Logger.getLogger(RulerPanel.class);
private static final DecimalFormat DECIMAL_FORMAT = new DecimalFormat();
private static Color grey1 = new Color(120, 120, 120);
private static Color grey2 = new Color(200, 200, 200);
private static Color gene1 = new Color(0, 0, 150, 150);
private static Color gene2 = new Color(0, 150, 0, 150);
// TODO -- get from preferences
boolean drawSpan = true;
private Font tickFont = FontManager.getFont(Font.BOLD, 9);
private Font spanFont = FontManager.getFont(Font.BOLD, 12);
private List<ClickLink> chromosomeRects = new ArrayList();
private List<MouseRect> mouseRects = new ArrayList<MouseRect>();
private static Color dragColor = new Color(.5f, .5f, 1f, .3f);
private static Color zoomBoundColor = new Color(0.5f, 0.5f, 0.5f);
boolean dragging = false;
int dragStart;
int dragEnd;
public static final String WHOLE_GENOME_TOOLTIP = "<html>Click on a chromosome number to jump to that chromosome," +
"<br>or click and drag to zoom in.";
public static final String CHROM_TOOLTIP = "Click and drag to zoom in.";
ReferenceFrame frame;
public RulerPanel(ReferenceFrame frame) {
this.frame = frame;
init();
}
private boolean isWholeGenomeView() {
return frame.getChrName().equals(Globals.CHR_ALL);
}
@Override
protected void paintComponent(Graphics g) {
super.paintComponent(g);
if (PreferencesManager.getPreferences().getAsBoolean(ENABLE_ANTIALISING)) {
((Graphics2D) g).setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
}
render(g);
if (dragging) {
g.setColor(dragColor);
int start = Math.min(dragStart, dragEnd);
int w = Math.abs(dragEnd - dragStart);
final int height = getHeight();
g.fillRect(start, 0, w, height);
g.setColor(zoomBoundColor);
g.drawLine(dragStart, 0, dragStart, height);
g.drawLine(dragEnd, 0, dragEnd, height);
}
((Graphics2D) g).setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_DEFAULT);
}
private void render(Graphics g) {
g.setColor(Color.black);
if (isWholeGenomeView()) {
drawChromosomeTicks(g);
} else {
InsertionMarker i = InsertionManager.getInstance().getSelectedInsertion(frame.getChrName());
drawTicks(g, i);
if (drawSpan) {
drawSpan(g, i);
}
}
}
private void drawSpan(Graphics g, InsertionMarker i) {
//TODO -- hack
int w = getWidth();
g.setFont(spanFont);
int range = (int) (frame.getScale() * w) + 1;
// TODO -- hack, assumes location unit for whole genome is kilo-base
boolean scaleInKB = frame.getChrName().equals(Globals.CHR_ALL);
TickSpacing ts = findSpacing(range, scaleInKB);
String rangeString = formatNumber((double) range / ts.getUnitMultiplier()) + " " + ts.getMajorUnit();
int strWidth = g.getFontMetrics().stringWidth(rangeString);
int strHeight = g.getFontMetrics().getAscent();
int strPosition = (w - strWidth) / 2;
int lineY = getHeight() - 35 - strHeight / 2;
g.drawLine(0, lineY, (w - strWidth) / 2 - 10, lineY);
int[] arrowX = {0, 10, 10};
int[] arrowY = {lineY, lineY + 3, lineY - 3};
g.fillPolygon(arrowX, arrowY, arrowX.length);
g.drawLine((w + strWidth) / 2 + 10, lineY, w, lineY);
arrowX = new int[]{w, w - 10, w - 10};
g.fillPolygon(arrowX, arrowY, arrowX.length);
g.drawString(rangeString, strPosition, getHeight() - 35);
}
private void drawTicks(Graphics g, InsertionMarker i) {
int w = getWidth();
if (w < 200) {
return;
}
g.setFont(tickFont);
// location unit for whole genome is kilobase
boolean scaleInKB = frame.getChrName().equals(Globals.CHR_ALL);
int range = (int) (w * frame.getScale());
TickSpacing ts = findSpacing(range, scaleInKB);
double spacing = ts.getMajorTick();
// Find starting point closest to the current origin
int nTick = (int) (frame.getOrigin() / spacing) - 1;
int l = (int) (nTick * spacing);
int x = frame.getScreenPosition(l - 1 + 0.5); // 0 vs 1 based coordinates, then center over base
//int strEnd = Integer.MIN_VALUE;
while (x < getWidth()) {
l = (int) (nTick * spacing);
x = frame.getScreenPosition(l - 1 + 0.5);
String chrPosition = formatNumber((double) l / ts.getUnitMultiplier()) +
" " + ts.getMajorUnit();
int strWidth = g.getFontMetrics().stringWidth(chrPosition);
int strPosition = x - strWidth / 2;
//if (strPosition > strEnd) {
final int height = getHeight();
if (nTick % 2 == 0) {
g.drawString(chrPosition, strPosition, height - 15);
}
g.drawLine(x, height - 10, x, height - 2);
nTick++;
}
}
private void drawChromosomeTicks(Graphics g) {
Font chrFont = FontManager.getFont(10);
//this.removeAll();
this.setLayout(null);
// TODO -- remove hardcoded value
int locationUnit = 1000;
g.setFont(chrFont);
Genome genome = GenomeManager.getInstance().getCurrentGenome();
if (genome == null) {
log.warn("No genome found");
PreferencesManager.getPreferences().remove(DEFAULT_GENOME);
return;
}
boolean even = true;
long offset = 0;
chromosomeRects.clear();
List<String> chrNames = genome.getLongChromosomeNames();
if (chrNames == null) {
log.info("No chromosomes found for genome: " + PreferencesManager.getPreferences().getDefaultGenome());
PreferencesManager.getPreferences().remove(DEFAULT_GENOME);
}
if (chrNames.size() > 500) {
return;
}
final FontMetrics fontMetrics = g.getFontMetrics();
for (String chrName : chrNames) {
Chromosome c = genome.getChromosome(chrName);
if (c == null) {
log.info("Chromosome '" + chrName + "' not found");
continue;
}
int chrLength = c.getLength();
double scale = frame.getScale();
int gStart = genome.getGenomeCoordinate(chrName, 0);
int x = (int) (gStart / scale);
int dw = (int) (chrLength / (locationUnit * scale));
g.drawLine(x, getHeight() - 10, x, getHeight() - 2);
// Don't label chromosome if its width is < 5 pixels
if (dw > 5) {
int center = x + dw / 2;
String displayName = null;
if (chrName.startsWith("gi|")) {
displayName = Genome.getNCBIName(chrName);
} else {
displayName = chrName.replace("chr", "");
}
int strWidth = fontMetrics.stringWidth(displayName);
int strPosition = center - strWidth / 2;
int y = (even ? getHeight() - 35 : getHeight() - 25);
g.drawString(displayName, strPosition, y);
int sw = (int) fontMetrics.getStringBounds(displayName, g).getWidth();
Rectangle clickRect = new Rectangle(strPosition, y - 15, sw, 15);
String tooltipText = "Jump to chromosome: " + chrName;
chromosomeRects.add(new ClickLink(clickRect, chrName, tooltipText));
even = !even;
}
offset += chrLength;
}
}
public static String formatNumber(double position) {
//NumberFormatter f = new NumberFormatter();
return DECIMAL_FORMAT.format((int) position);
//return f.valueToString(position);
}
public static TickSpacing findSpacing(long maxValue, boolean scaleInKB) {
if (maxValue < 10) {
return new TickSpacing(1, "bp", 1);
}
// Now man zeroes?
int nZeroes = (int) Math.log10(maxValue);
String majorUnit = scaleInKB ? "kb" : "bp";
int unitMultiplier = 1;
if (nZeroes > 9) {
majorUnit = scaleInKB ? "tb" : "gb";
unitMultiplier = 1000000000;
}
if (nZeroes > 6) {
majorUnit = scaleInKB ? "gb" : "mb";
unitMultiplier = 1000000;
} else if (nZeroes > 3) {
majorUnit = scaleInKB ? "mb" : "kb";
unitMultiplier = 1000;
}
double nMajorTicks = maxValue / Math.pow(10, nZeroes - 1);
if (nMajorTicks < 25) {
return new TickSpacing(Math.pow(10, nZeroes - 1), majorUnit, unitMultiplier);
} else {
return new TickSpacing(Math.pow(10, nZeroes) / 2, majorUnit, unitMultiplier);
}
}
private void init() {
setBorder(BorderFactory.createLineBorder(UIConstants.TRACK_BORDER_GRAY));
setCursor(Cursor.getDefaultCursor());
if (isWholeGenomeView()) {
this.setToolTipText(WHOLE_GENOME_TOOLTIP);
} else {
this.setToolTipText("Click and drag to zoom");
}
MouseInputAdapter mouseAdapter = new MouseInputAdapter() {
int lastMousePressX;
@Override
public void mouseClicked(MouseEvent evt) {
final MouseEvent e = evt;
setCursor(Cursor.getDefaultCursor());
WaitCursorManager.CursorToken token = WaitCursorManager.showWaitCursor();
try {
if (!isWholeGenomeView()) {
double newLocation = frame.getChromosomePosition(e.getX());
frame.centerOnLocation(newLocation);
} else {
for (final ClickLink link : chromosomeRects) {
if (link.region.contains(e.getPoint())) {
final String chrName = link.value;
frame.changeChromosome(chrName, true);
}
}
}
} finally {
WaitCursorManager.removeWaitCursor(token);
}
}
@Override
public void mouseMoved(MouseEvent e) {
if (isWholeGenomeView()) {
for (ClickLink link : chromosomeRects) {
if (link.region.contains(e.getPoint())) {
setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
setToolTipText(link.tooltipText);
return;
}
}
setCursor(Cursor.getDefaultCursor());
setToolTipText(WHOLE_GENOME_TOOLTIP);
} else {
for (MouseRect mr : mouseRects) {
if (mr.containsPoint(e.getPoint())) {
RulerPanel.this.setToolTipText(mr.getText());
return;
}
}
RulerPanel.this.setToolTipText(CHROM_TOOLTIP);
}
}
@Override
public void mouseEntered(MouseEvent e) {
setCursor(Cursor.getDefaultCursor());
if (isWholeGenomeView()) {
setToolTipText(WHOLE_GENOME_TOOLTIP);
} else {
setToolTipText(CHROM_TOOLTIP);
}
}
@Override
public void mouseDragged(MouseEvent e) {
if (Math.abs(e.getPoint().getX() - dragStart) > 1) {
dragEnd = e.getX();
dragging = true;
repaint();
}
}
@Override
public void mousePressed(MouseEvent e) {
dragStart = e.getX();
}
@Override
public void mouseReleased(MouseEvent e) {
if (dragging) {
dragEnd = e.getX();
dragging = false;
zoom();
}
}
//@Override
//public void mouseExited(MouseEvent e) {
//dragging = false;
//}
};
addMouseMotionListener(mouseAdapter);
addMouseListener(mouseAdapter);
}
private void zoom() {
NamedRunnable runnable = new NamedRunnable() {
public void run() {
double s = frame.getChromosomePosition(dragStart);
double e = frame.getChromosomePosition(dragEnd);
if (e < s) {
double tmp = s;
s = e;
e = tmp;
}
if (e - s < 40) {
double c = (s + e) / 2;
s = c - 20;
e = c + 20;
}
s = Math.max(0.0, s);
String chr = null;
if (isWholeGenomeView()) {
Genome genome = GenomeManager.getInstance().getCurrentGenome();
ChromosomeCoordinate start = genome.getChromosomeCoordinate((int) s);
ChromosomeCoordinate end = genome.getChromosomeCoordinate((int) e);
chr = start.getChr();
s = start.getCoordinate();
e = end.getCoordinate();
if (end.getChr() != start.getChr()) {
e = genome.getChromosome(start.getChr()).getLength();
}
} else {
chr = frame.getChrName();
}
frame.jumpTo(chr, (int) Math.min(s, e), (int) Math.max(s, e));
frame.recordHistory();
}
public String getName() {
return "Rule panel zoom";
}
};
LongRunningTask.submit(runnable);
}
public static class TickSpacing {
private double majorTick;
private double minorTick;
private String majorUnit = "";
private int unitMultiplier = 1;
TickSpacing(double majorTick, String majorUnit, int unitMultiplier) {
this.majorTick = majorTick;
this.minorTick = majorTick / 10.0;
this.majorUnit = majorUnit;
this.unitMultiplier = unitMultiplier;
}
public double getMajorTick() {
return majorTick;
}
public double getMinorTick() {
return minorTick;
}
public String getMajorUnit() {
return majorUnit;
}
public void setMajorUnit(String majorUnit) {
this.majorUnit = majorUnit;
}
public int getUnitMultiplier() {
return unitMultiplier;
}
public void setUnitMultiplier(int unitMultiplier) {
this.unitMultiplier = unitMultiplier;
}
}
// TODO -- possibly generalize?
class ClickLink {
Rectangle region;
String value;
String tooltipText;
ClickLink(Rectangle region, String value, String tooltipText) {
this.region = region;
this.value = value;
this.tooltipText = tooltipText;
}
}
static class MouseRect {
Rectangle bounds;
String text;
MouseRect(Rectangle bounds, String text) {
this.bounds = bounds;
this.text = text;
}
boolean containsPoint(Point p) {
return bounds.contains(p);
}
String getText() {
return text;
}
public int width() {
return bounds.width;
}
}
}