org.jcamp.parser.CommonSpectrumJCAMPReader 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.parser;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.StringTokenizer;
import java.util.TreeSet;

import org.jcamp.math.IArray2D;
import org.jcamp.spectrum.Assignment;
import org.jcamp.spectrum.IAssignmentTarget;
import org.jcamp.spectrum.Multiplicity;
import org.jcamp.spectrum.Pattern;
import org.jcamp.spectrum.Peak1D;
import org.jcamp.spectrum.Spectrum;
import org.jcamp.spectrum.assignments.AtomReference;
import org.jcamp.spectrum.notes.NoteDescriptor;
import org.jcamp.units.CommonUnit;
import org.jcamp.units.Unit;

/**
 * common implementation of JCAMPReader, implements shorthands for common LDRs.
 * 
 * @author Thomas Weber
 */
abstract class CommonSpectrumJCAMPReader
  implements ISpectrumJCAMPReader {
  
  /**
   * CommonJCAMPAdapter constructor comment.
   */
  protected CommonSpectrumJCAMPReader() {
    super();
  }
  /**
   * createSpectrum method comment.
   */
  public Spectrum createSpectrum(JCAMPBlock block) throws JCAMPException {
    throw new JCAMPException("unimplemented adapter method");
  }
  /**
   * gets ##LASTX= content
   * 
   * @return double
   * @param block JCAMPBlock
   * @exception JCAMPException The exception description.
   */
  protected double getFirstX(JCAMPBlock block) throws JCAMPException {
    JCAMPVariable x = block.getVariable("X");
    if (x == null || x.getFirst() == null) {
      block.getErrorHandler().error("missing first x");
    }
    return x.getFirst().doubleValue();	
  }
  /**
   * gets ##FIRSTY= content
   * 
   * @return double
   * @param block JCAMPBlock
   * @exception JCAMPException The exception description.
   */
  protected double getFirstY(JCAMPBlock block) throws JCAMPException {
    JCAMPVariable y = block.getVariable("Y");
    if (y == null || y.getFirst() == null) {
      block.getErrorHandler().error("missing first y");
    }
    return y.getFirst().doubleValue();	
  }
  /**
   * gets ##LASTX= content
   * 
   * @return double
   * @param block JCAMPBlock
   * @exception JCAMPException The exception description.
   */
  protected double getLastX(JCAMPBlock block) throws JCAMPException {
    JCAMPVariable x = block.getVariable("X");
    if (x == null || x.getLast() == null) {
      block.getErrorHandler().error("missing last x");
    }
    return x.getLast().doubleValue();
  }
  /**
   * gets ##NPOINTS= content
   * 
   * @return double
   * @param block JCAMPBlock
   * @exception JCAMPException The exception description.
   */
  protected int getNPoints(JCAMPBlock block) throws JCAMPException {
    JCAMPDataRecord ldrNPoints = block.getDataRecord("NPOINTS");
    if (ldrNPoints == null) {
      block.getErrorHandler().error("missing required label ##NPOINTS=");
    }
    String nPoints = ldrNPoints.getContent();
    return Integer.parseInt(nPoints);
  }
  /**
   * gets NTuple Page data.
   * 
   * @param block com.creon.chem.jcamp.JCAMPBlock
   * @param page com.creon.chem.jcamp.JCAMPNTuplePage
   * @return IArray2D
   */
  protected IArray2D getNTuplePageData(JCAMPNTuplePage page)
      throws JCAMPException {
    return page.getXYData();    
  }
  /**
   * gets ##DATATABLE= content
   * 
   * @return double[]
   * @param block JCAMPBlock
   * @param page JCAMPNTuplePage
   * @param firstX double starting x value (from ##FIRSTX=)
   * @param lastX double ending x value (from ##LASTX=)
   * @param nPoints int number of data points (from ##NPOINTS=)
   * @param xFactor double factor to be applied to x values (from ##XFACTOR=)
   * @param yFactor double factor to be applied to y values (from ##YFACTOR=)
   * @exception JCAMPException The exception description.
   * @deprecated
   */
  @Deprecated
  protected double[] getNTupleXYData(
      JCAMPBlock block,
      JCAMPNTuplePage page,
      double firstX,
      double lastX,
      int nPoints,
      double xFactor,
      double yFactor)
	  throws JCAMPException {

    JCAMPDataRecord ldrXYData = page.getDataRecord("DATATABLE");
    if (ldrXYData == null) {
      block.getErrorHandler().fatal("missing required label ##DATATABLE=");
      return null;
    }
    DataVariableInfo varInfo = new DataVariableInfo(ldrXYData);
    if (!varInfo.isIncremental())
      block.getErrorHandler().fatal("data form missmatch");

    double[] y =
	block.getASDFDecoder().decode(ldrXYData, firstX, lastX, xFactor, nPoints);
    int n = y.length;
    double[] yValues = new double[n];
    for (int i = 0; i < n; i++)
      yValues[i] = yFactor * y[i];
    return yValues;
  }
  /**
   * gets ##DATATABLE= content
   * 
   * @return double[]
   * @param block JCAMPBlock
   * @param nPoints int number of data points (from ##NPOINTS=)
   * @exception JCAMPException The exception description.
   * @deprecated
   */
  @Deprecated
  protected double[][] getNTupleXYPoints(JCAMPBlock block, JCAMPNTuplePage page)
      throws JCAMPException {
    JCAMPDataRecord ldrPeaktable = page.getDataRecord("DATATABLE");
    if (ldrPeaktable == null) { 
      block.getErrorHandler().fatal("missing required label ##DATATABLE=");
      return null;
    }
    double[][] xy = new double[2][];
    ArrayList x = new ArrayList(20);
    ArrayList y = new ArrayList(20);
    AFFNTokenizer tokenizer = new AFFNTokenizer(ldrPeaktable);
    while (tokenizer.hasMoreGroups()) {
      AFFNGroup group = tokenizer.nextGroup();
      x.add(new Double(group.getValue(0)));
      y.add(new Double(group.getValue(1)));
    }
    xy[0] = new double[x.size()];
    xy[1] = new double[y.size()];
    for (int i=0; i Double.MIN_VALUE) {
	px.add(new Double(x0));
	py.add(new Double(y0));
	x0 = x;
	y0 = y;
      } else {
	y0 += y;
      }
    }
    px.add(new Double(x0));
    py.add(new Double(y0));
    double[][] xy = new double[2][px.size()];
    for (int i = 0; i < px.size(); i++) {
      xy[0][i] = ((Double) px.get(i)).doubleValue();
      xy[1][i] = ((Double) py.get(i)).doubleValue();
    }
    return xy;
  }
  /**
   * set spectrum note
   * 
   * @param block JCAMPBlock
   * @param ldr JCAMPDataRecord
   * @param spectrum com.creon.chem.spectrum.Spectrum
   */
  protected void setNote(
      JCAMPBlock block,
      JCAMPDataRecord ldr,
      Spectrum spectrum)
	  throws JCAMPException {
    String key = ldr.getKey();
    if (key.length()==0) // comment
      return;

    NoteDescriptor descr = NoteDescriptorFactory.getInstance().findByJCAMPKey(key);
    if (descr.equals(NoteDescriptor.IGNORE))
      return;

    Object content;
    try {
      content =
	  descr.getNoteContentParser().parseContent(
	      ldr.getContent(),
	      descr.getNoteContentClass());
      spectrum.setNote(descr, content);
    } catch (org.jcamp.spectrum.notes.BadContentException ex) {
      StringBuilder msg =
	  new StringBuilder("bad ").append(descr.getName()).append(" note:\n").append(
	      ex.getMessage());
      block.getErrorHandler().warn(msg.toString());
    }
  }
  /**
   * after creation of spectrum, add other notes
   * 
   * @param block com.creon.chem.jcamp.JCAMPBlock
   * @param spectrum com.creon.chem.spectrum.Spectrum
   */
  protected void setNotes(JCAMPBlock block, Spectrum spectrum)
      throws JCAMPException {
    String title = getTitle(block);
    spectrum.setTitle(title);
    /*	String owner = getOwner(block);
    	spectrum.setOwner(owner);
    	String origin = getOrigin(block);
    	spectrum.setOrigin(origin); */
    int n = block.numDataRecords();
    for (int i = 0; i < n; i++) {
      JCAMPDataRecord ldr = (JCAMPDataRecord) block.getDataRecord(i);
      setNote(block, ldr, spectrum);
    }
  }
}