Example #1
0
 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];
 }
Example #2
0
  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;
        }
      }
    }
Example #4
0
 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));
  }
Example #7
0
 /**
  * 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
 }
Example #8
0
  /**
   * 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());
      }
    }
  }
Example #9
0
  // 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();
    }
  }