public static String readableFileSize(long size) {
if (size <= 0) return "0";
final String[] units = new String[] {"B", "KB", "MB", "GB", "TB"};
int digitGroups = (int) (Math.log10(size) / Math.log10(1024));
return new DecimalFormat("#,##0.#").format(size / Math.pow(1024, digitGroups))
+ " "
+ units[digitGroups];
}
public LinePlotTest() {
super(new BorderLayout());
setPreferredSize(new Dimension(800, 600));
setBackground(Color.WHITE);
// load data from file ----------------------------------------------
// basemean, log2foldchange
DataTable nonSigData = new DataTable(Double.class, Double.class);
DataTable sigData = new DataTable(Double.class, Double.class);
try (CSVReader reader = new CSVReader(new FileReader("rnaSeqExample.csv"))) {
String[] nextLine;
int row = 0;
while ((nextLine = reader.readNext()) != null) {
if (row != 0) {
// needs to have a p-value
if (nextLine[2].equals("NA")) continue;
double baseMean = Double.parseDouble(nextLine[1]);
double log2Change = Double.parseDouble(nextLine[2]);
if (nextLine[6].equals("NA") || Double.parseDouble(nextLine[6]) > 0.05) {
nonSigData.add(Math.log10(baseMean), log2Change);
} else {
sigData.add(Math.log10(baseMean), log2Change);
}
}
row++;
}
} catch (IOException e) {
e.printStackTrace();
}
System.out.println("Non-significant: " + nonSigData.getRowCount());
System.out.println("Significant: " + sigData.getRowCount());
XYPlot plot = new XYPlot(nonSigData, sigData);
// set point renderer for data
PointRenderer points = new DefaultPointRenderer2D();
points.setShape(new Ellipse2D.Double(-2.0, -2.0, 4.0, 4.0));
points.setColor(NONSIG_COLOR);
plot.setPointRenderer(nonSigData, points);
PointRenderer pointsRed = new DefaultPointRenderer2D();
pointsRed.setShape(new Ellipse2D.Double(-2.0, -2.0, 4.0, 4.0));
pointsRed.setColor(SIG_COLOR);
plot.setPointRenderer(sigData, pointsRed);
// Display on screen
add(new InteractivePanel(plot), BorderLayout.CENTER);
}
public void computeMetricScaleExtremes(
int UTMZone, String hemisphere, GridElement ge, double size) {
if (UTMZone != this.zone) return;
if (size < 1 || size > this.maxResolution) return;
UTMExtremes levelExtremes = this.extremes[(int) Math.log10(size) - 1];
if (ge.type.equals(GridElement.TYPE_LINE_EASTING)
|| ge.type.equals(GridElement.TYPE_LINE_EAST)
|| ge.type.equals(GridElement.TYPE_LINE_WEST)) {
levelExtremes.minX = ge.value < levelExtremes.minX ? ge.value : levelExtremes.minX;
levelExtremes.maxX = ge.value > levelExtremes.maxX ? ge.value : levelExtremes.maxX;
} else if (ge.type.equals(GridElement.TYPE_LINE_NORTHING)
|| ge.type.equals(GridElement.TYPE_LINE_SOUTH)
|| ge.type.equals(GridElement.TYPE_LINE_NORTH)) {
if (hemisphere.equals(levelExtremes.minYHemisphere))
levelExtremes.minY = ge.value < levelExtremes.minY ? ge.value : levelExtremes.minY;
else if (hemisphere.equals(AVKey.SOUTH)) {
levelExtremes.minY = ge.value;
levelExtremes.minYHemisphere = hemisphere;
}
if (hemisphere.equals(levelExtremes.maxYHemisphere))
levelExtremes.maxY = ge.value > levelExtremes.maxY ? ge.value : levelExtremes.maxY;
else if (hemisphere.equals(AVKey.NORTH)) {
levelExtremes.maxY = ge.value;
levelExtremes.maxYHemisphere = hemisphere;
}
}
}
private long normalizeMax(long l) {
int exp = (int) Math.log10((double) l);
long multiple = (long) Math.pow(10.0, exp);
int i = (int) (l / multiple);
l = (i + 1) * multiple;
return l;
}
public void clear() {
int numLevels = (int) Math.log10(this.maxResolution);
this.extremes = new UTMExtremes[numLevels];
for (int i = 0; i < numLevels; i++) {
this.extremes[i] = new UTMExtremes();
this.extremes[i].clear();
}
}
private boolean needToSplit(DrawContext dc, Sector sector) {
Vec4[] corners = sector.computeCornerPoints(dc.getGlobe(), dc.getVerticalExaggeration());
Vec4 centerPoint = sector.computeCenterPoint(dc.getGlobe(), dc.getVerticalExaggeration());
View view = dc.getView();
double d1 = view.getEyePoint().distanceTo3(corners[0]);
double d2 = view.getEyePoint().distanceTo3(corners[1]);
double d3 = view.getEyePoint().distanceTo3(corners[2]);
double d4 = view.getEyePoint().distanceTo3(corners[3]);
double d5 = view.getEyePoint().distanceTo3(centerPoint);
double minDistance = d1;
if (d2 < minDistance) minDistance = d2;
if (d3 < minDistance) minDistance = d3;
if (d4 < minDistance) minDistance = d4;
if (d5 < minDistance) minDistance = d5;
double cellSize =
(Math.PI * sector.getDeltaLatRadians() * dc.getGlobe().getRadius()) / 20; // TODO
return !(Math.log10(cellSize) <= (Math.log10(minDistance) - this.splitScale));
}
/**
* Returns the number of digits in x.
*
* @param x a whole number.
* @return 1 if x is 0, otherwise the number of digits.
*/
public static int numDigits(int x) {
if (x == 0) return 1;
return (int) (Math.log10(x)) + 1; // 250 -> log250 = 2.something -> 2+1 -> 3
}
/**
* Render the track in the given rectangle.
*
* @param track
* @param locusScores
* @param context
* @param arect
*/
public synchronized void renderScores(
Track track, List<LocusScore> locusScores, RenderContext context, Rectangle arect) {
boolean showMissingData =
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SHOW_MISSING_DATA_KEY);
Graphics2D noDataGraphics = context.getGraphic2DForColor(UIConstants.NO_DATA_COLOR);
Graphics2D tickGraphics = context.getGraphic2DForColor(Color.BLACK);
Rectangle adjustedRect = calculateDrawingRect(arect);
double origin = context.getOrigin();
double locScale = context.getScale();
Color posColor = track.getColor();
Color negColor = track.getAltColor();
// Get the Y axis definition, consisting of minimum, maximum, and base value. Often
// the base value is == min value which is == 0.
DataRange dataRange = track.getDataRange();
float maxValue = dataRange.getMaximum();
float baseValue = dataRange.getBaseline();
float minValue = dataRange.getMinimum();
boolean isLog = dataRange.isLog();
if (isLog) {
minValue = (float) (minValue == 0 ? 0 : Math.log10(minValue));
maxValue = (float) Math.log10(maxValue);
}
// Calculate the Y scale factor.
double delta = (maxValue - minValue);
double yScaleFactor = adjustedRect.getHeight() / delta;
// Calculate the Y position in pixels of the base value. Clip to bounds of rectangle
double baseDelta = maxValue - baseValue;
int baseY = (int) (adjustedRect.getY() + baseDelta * yScaleFactor);
if (baseY < adjustedRect.y) {
baseY = adjustedRect.y;
} else if (baseY > adjustedRect.y + adjustedRect.height) {
baseY = adjustedRect.y + adjustedRect.height;
}
int lastPx = 0;
for (LocusScore score : locusScores) {
// Note -- don't cast these to an int until the range is checked.
// could get an overflow.
double pX = ((score.getStart() - origin) / locScale);
double dx = Math.ceil((Math.max(1, score.getEnd() - score.getStart())) / locScale) + 1;
if ((pX + dx < 0)) {
continue;
} else if (pX > adjustedRect.getMaxX()) {
break;
}
float dataY = score.getScore();
if (isLog && dataY <= 0) {
continue;
}
if (!Float.isNaN(dataY)) {
// Compute the pixel y location. Clip to bounds of rectangle.
double dy = isLog ? Math.log10(dataY) - baseValue : (dataY - baseValue);
int pY = baseY - (int) (dy * yScaleFactor);
if (pY < adjustedRect.y) {
pY = adjustedRect.y;
} else if (pY > adjustedRect.y + adjustedRect.height) {
pY = adjustedRect.y + adjustedRect.height;
}
Color color = (dataY >= baseValue) ? posColor : negColor;
drawDataPoint(color, (int) dx, (int) pX, baseY, pY, context);
}
if (showMissingData) {
// Draw from lastPx + 1 to pX - 1;
int w = (int) pX - lastPx - 4;
if (w > 0) {
noDataGraphics.fillRect(lastPx + 2, (int) arect.getY(), w, (int) arect.getHeight());
}
}
if (!Float.isNaN(dataY)) {
lastPx = (int) pX + (int) dx;
}
}
if (showMissingData) {
int w = (int) arect.getMaxX() - lastPx - 4;
if (w > 0) {
noDataGraphics.fillRect(lastPx + 2, (int) arect.getY(), w, (int) arect.getHeight());
}
}
}
// Rendering
public void draw(DrawContext dc) {
GL gl = dc.getGL();
boolean attribsPushed = false;
boolean modelviewPushed = false;
boolean projectionPushed = false;
try {
gl.glPushAttrib(
GL.GL_DEPTH_BUFFER_BIT
| GL.GL_COLOR_BUFFER_BIT
| GL.GL_ENABLE_BIT
| GL.GL_TEXTURE_BIT
| GL.GL_TRANSFORM_BIT
| GL.GL_VIEWPORT_BIT
| GL.GL_CURRENT_BIT);
attribsPushed = true;
gl.glDisable(GL.GL_TEXTURE_2D); // no textures
gl.glEnable(GL.GL_BLEND);
gl.glBlendFunc(GL.GL_SRC_ALPHA, GL.GL_ONE_MINUS_SRC_ALPHA);
gl.glDisable(GL.GL_DEPTH_TEST);
double width = this.size.width;
double height = this.size.height;
// Load a parallel projection with xy dimensions (viewportWidth, viewportHeight)
// into the GL projection matrix.
java.awt.Rectangle viewport = dc.getView().getViewport();
gl.glMatrixMode(javax.media.opengl.GL.GL_PROJECTION);
gl.glPushMatrix();
projectionPushed = true;
gl.glLoadIdentity();
double maxwh = width > height ? width : height;
gl.glOrtho(0d, viewport.width, 0d, viewport.height, -0.6 * maxwh, 0.6 * maxwh);
gl.glMatrixMode(GL.GL_MODELVIEW);
gl.glPushMatrix();
modelviewPushed = true;
gl.glLoadIdentity();
// Scale to a width x height space
// located at the proper position on screen
double scale = this.computeScale(viewport);
Vec4 locationSW = this.computeLocation(viewport, scale);
gl.glTranslated(locationSW.x(), locationSW.y(), locationSW.z());
gl.glScaled(scale, scale, 1);
// Compute scale size in real world
Position referencePosition = dc.getViewportCenterPosition();
if (referencePosition != null) {
Vec4 groundTarget = dc.getGlobe().computePointFromPosition(referencePosition);
Double distance = dc.getView().getEyePoint().distanceTo3(groundTarget);
this.pixelSize = dc.getView().computePixelSizeAtDistance(distance);
Double scaleSize = this.pixelSize * width * scale; // meter
String unitLabel = "m";
if (this.unit.equals(UNIT_METRIC)) {
if (scaleSize > 10000) {
scaleSize /= 1000;
unitLabel = "Km";
}
} else if (this.unit.equals(UNIT_IMPERIAL)) {
scaleSize *= 3.280839895; // feet
unitLabel = "ft";
if (scaleSize > 5280) {
scaleSize /= 5280;
unitLabel = "mile(s)";
}
}
// Rounded division size
int pot = (int) Math.floor(Math.log10(scaleSize));
if (!Double.isNaN(pot)) {
int digit = Integer.parseInt(String.format("%.0f", scaleSize).substring(0, 1));
double divSize = digit * Math.pow(10, pot);
if (digit >= 5) divSize = 5 * Math.pow(10, pot);
else if (digit >= 2) divSize = 2 * Math.pow(10, pot);
double divWidth = width * divSize / scaleSize;
// Draw scale
if (!dc.isPickingMode()) {
// Set color using current layer opacity
Color backColor = this.getBackgroundColor(this.color);
float[] colorRGB = backColor.getRGBColorComponents(null);
gl.glColor4d(
colorRGB[0],
colorRGB[1],
colorRGB[2],
(double) backColor.getAlpha() / 255d * this.getOpacity());
gl.glTranslated((width - divWidth) / 2, 0d, 0d);
this.drawScale(dc, divWidth, height);
colorRGB = this.color.getRGBColorComponents(null);
gl.glColor4d(colorRGB[0], colorRGB[1], colorRGB[2], this.getOpacity());
gl.glTranslated(-1d / scale, 1d / scale, 0d);
this.drawScale(dc, divWidth, height);
// Draw label
String label = String.format("%.0f ", divSize) + unitLabel;
gl.glLoadIdentity();
gl.glDisable(GL.GL_CULL_FACE);
drawLabel(
dc,
label,
locationSW.add3(
new Vec4(divWidth * scale / 2 + (width - divWidth) / 2, height * scale, 0)));
} else {
// Picking
this.pickSupport.clearPickList();
this.pickSupport.beginPicking(dc);
// Draw unique color across the map
Color color = dc.getUniquePickColor();
int colorCode = color.getRGB();
// Add our object(s) to the pickable list
this.pickSupport.addPickableObject(colorCode, this, referencePosition, false);
gl.glColor3ub((byte) color.getRed(), (byte) color.getGreen(), (byte) color.getBlue());
gl.glTranslated((width - divWidth) / 2, 0d, 0d);
this.drawRectangle(dc, divWidth, height);
// Done picking
this.pickSupport.endPicking(dc);
this.pickSupport.resolvePick(dc, dc.getPickPoint(), this);
}
}
}
} finally {
if (projectionPushed) {
gl.glMatrixMode(GL.GL_PROJECTION);
gl.glPopMatrix();
}
if (modelviewPushed) {
gl.glMatrixMode(GL.GL_MODELVIEW);
gl.glPopMatrix();
}
if (attribsPushed) gl.glPopAttrib();
}
}
