org.jcamp.spectrum.NMR2DSpectrum Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of jcamp-dx Show documentation
The JCAMP-DX project is the reference implemention of the IUPAC JCAMP-DX spectroscopy data standard.
The newest version!
package org.jcamp.spectrum;

import org.jcamp.math.AxisMap;
import org.jcamp.math.LinearAxisMap;
import org.jcamp.math.Range1D;
import org.jcamp.math.ReversedLinearAxisMap;

/**
 * 2D nmr spectrum.
 * 
 * @author Thomas Weber 
 */
public class NMR2DSpectrum
  extends Spectrum2D {
  
  /** for serialization. */
  private static final long serialVersionUID = 3003976458790246674L;
  
  String[] nucleus = new String[] { "^13C", "^13C" };
  double[] frequency = new double[] { 300.0, 300.0 };
  double[] reference = new double[] { 0.0, 0.0 };
  boolean fullSpectrum = true;

  /**
   * NMR2DSpectrum 
   */
  public NMR2DSpectrum(
      IOrderedDataArray1D x,
      IOrderedDataArray1D y,
      IDataArray1D z,
      String[] nucleus,
      double[] freq,
      double[] ref) {
    super(x, y, z);
    this.nucleus = nucleus;
    this.frequency = freq;
    this.reference = ref;
    adjustFullViewRange();
  }

  /**
   * adjust data ranges for pretty full spectrum view
   */
  private void adjustFullViewRange() {
    if (isFullSpectrum()) {
      Range1D.Double xrange = getXData().getRange1D();
      double w = xrange.getXWidth();
      xrange.set(xrange.getXMin() - .05 * w, xrange.getXMax() + .05 * w);
      setXFullViewRange(xrange);
      Range1D.Double yrange = getYData().getRange1D();
      w = yrange.getXWidth();
      yrange.set(yrange.getXMin() - .05 * w, yrange.getXMax() + .05 * w);
      setYFullViewRange(yrange);
      Range1D.Double zrange = getZData().getRange1D();
      w = zrange.getXWidth();
      zrange.set(zrange.getXMin() - .05 * w, zrange.getXMax() + .05 * w);
      setZFullViewRange(zrange);
    } else {
      /* include 0.0 in y-range and add 5% on to all borders */
      /*
            Range1D xrange = getXData().getRange();
            double w = xrange.getWidth();
            xrange.left -= 0.05 * w;
            xrange.right += 0.05 * w;
            setFullViewRangeX(xrange);
            Range1D yrange = getYData().getRange();
            yrange.left = Math.min(yrange.left, 0.0);
            yrange.right = Math.max(yrange.right, 0.0);
            w = yrange.getWidth();
            if (yrange.left == 0.0) {
            yrange.right += 0.05 * w;
            } else {
            yrange.left -= 0.05 * w;
            }
            setFullViewRangeY(yrange);
       */
    }
  }

  /**
   * cloning.
   * 
   * @return java.lang.Object
   */
  @Override
  public Object clone() {
    NMR2DSpectrum o = (NMR2DSpectrum) super.clone();
    o.nucleus = new String[] { this.nucleus[0], this.nucleus[1] };
    o.frequency = new double[] { this.frequency[0], this.frequency[1] };
    o.reference = new double[] { this.reference[0], this.reference[1] };
    return o;
  }

  /**
   * gets spectrum ID
   * @return int
   */
  @Override
  public int getIdentifier() {
    return ISpectrumIdentifier.NMR2D;
  }

  /**
   * Insert the method's description here.
   * Creation date: (01/18/00 17:22:51)
   * @return java.lang.String
   */
  public java.lang.String getXNucleus() {
    return nucleus[0];
  }

  /**
   * Insert the method's description here.
   * Creation date: (1/27/00 1:13:28 PM)
   * @return double
   */
  public double getXReference() {
    return reference[0];
  }

  /**
   * getYAxisMap method comment.
   */
  @Override
  public AxisMap getYAxisMap() {
    return yAxisMap;
  }

  /**
   * Insert the method's description here.
   * Creation date: (01/19/00 20:12:58)
   * @return double
   */
  public double getYFrequency() {
    return frequency[1];
  }

  /**
   * Insert the method's description here.
   * Creation date: (01/18/00 17:22:51)
   * @return java.lang.String
   */
  public java.lang.String getYNucleus() {
    return nucleus[1];
  }

  /**
   * Insert the method's description here.
   * Creation date: (1/27/00 1:13:28 PM)
   * @return double
   */
  public double getYReference() {
    return reference[1];
  }

  /**
   * @return boolean
   */
  @Override
  public boolean isFullSpectrum() {
    return fullSpectrum;
  }

  /**
   * isSameType method comment.
   */
  @Override
  public boolean isSameType(Spectrum otherSpectrum) {
    if (otherSpectrum instanceof NMR2DSpectrum)
      return true;
    return false;
  }

  /**
   * sets full view range on x axis.
   */
  @Override
  public void setXFullViewRange(Range1D.Double dataRange) {
    xAxisMap = new ReversedLinearAxisMap(getXData(), dataRange);
  }

  /**
   * sets full view range on y axis.
   */
  @Override
  public void setYFullViewRange(Range1D.Double dataRange) {
    yAxisMap = new ReversedLinearAxisMap(getYData(), dataRange);
  }

  /**
   * sets full view range on z axis.
   */
  @Override
  public void setZFullViewRange(Range1D.Double dataRange) {
    zAxisMap = new LinearAxisMap(zData, dataRange);
  }
}