org.jcamp.parser.JCAMPNTuple Maven / Gradle / Ivy
package org.jcamp.parser;
import java.util.Vector;
/**
* class for reading a NTUPLE table.
* @author Thomas Weber
*/
public class JCAMPNTuple {
private int pageStart;
private JCAMPDataRecord startLDR; // ##NTUPLES=
private JCAMPDataRecord endLDR; // ##ENDNTUPLES=
private JCAMPBlock containingBlock;
private JCAMPDataRecord[] headers;
private JCAMPNTuplePage[] pages;
private JCAMPVariable[] vars;
private int numHeaders;
private int firstIndex;
private int lastIndex;
/**
* JCAMPNTuple constructor comment.
*/
JCAMPNTuple(JCAMPBlock block, JCAMPDataRecord startLDR, JCAMPDataRecord endLDR) throws JCAMPException {
super();
this.containingBlock = block;
this.startLDR = startLDR;
this.endLDR = endLDR;
initialize();
}
/**
* gets containing block.
* @return JCAMPBlock
*/
public JCAMPBlock getBlock() {
return this.containingBlock;
}
/**
* gets a header LDR.
*
* @return JCAMPDataRecord
* @param key java.lang.String
*/
public JCAMPDataRecord getHeader(String key) {
if (headers != null)
for (int i = 0; i < headers.length; i++) {
if (key.equals(headers[i].getKey()))
return headers[i];
}
return null;
}
/**
* gets array of NTUPLE headers.
*
* @return JCAMPDataRecord[]
*/
public JCAMPDataRecord[] getHeaders() {
return this.headers;
}
/**
* gets containing JCAMP
*
* @return java.lang.String
*/
public String getJCAMP() {
return containingBlock.getJCAMP();
}
/**
* gets NTUPLE page number index.
*
* @return com.labcontrol.jcamp.reader.JCAMPNTuplePage
* @param index int
*/
public JCAMPNTuplePage getPage(int index) {
if (this.pages != null)
return this.pages[index];
return null;
}
/**
* gets array of NTUPLE pages.
*
* @return JCAMPNTuplePage[]
*/
public JCAMPNTuplePage[] getPages() {
return this.pages;
}
/**
* gets the variable by symbol symbol.
* @param String symbol
* @return com.creon.chem.jcamp.JCAMPVariable
*/
public JCAMPVariable getVariable(String symbol) {
symbol = symbol.toUpperCase();
for (int i = 0; i < vars.length; i++) {
if (symbol.equals(vars[i].getSymbol()))
return vars[i];
}
return null;
}
/**
* gets variable by name.
*
* @return com.creon.chem.jcamp.JCAMPVariable
* @param name java.lang.String
*/
public JCAMPVariable getVariableByName(String name) {
name = name.toUpperCase();
for (int i = 0; i < vars.length; i++) {
if (name.equals(vars[i].getName()))
return vars[i];
}
return null;
}
/**
* gets array of variables defined in NTUPLE.
*
* @return com.creon.chem.jcamp.JCAMPVariable[]
*/
public JCAMPVariable[] getVariables() {
return vars;
}
/**
* get variable value array in page dimension.
*
* @return java.lang.String[]
* @param ldrKey java.lang.String
* @param v JCAMPVariable
*/
public String[] getVariableValues(String ldrKey, JCAMPVariable v) {
String[] values = new String[numPages()];
for (int i = 0; i < numPages(); i++) {
JCAMPDataRecord ldr = pages[i].getDataRecord(ldrKey);
if (ldr == null) {
if (v != null) {
values[i] = pages[i].getPageVariableValue(v.getSymbol());
} else
values[i] = null;
} else {
values[i] = ldr.getContent();
}
}
return values;
}
/**
* initialize headers.
*
*/
private void initHeaders() {
JCAMPDataRecord[] blockLDR = containingBlock.getAllDataRecords();
numHeaders = 0;
for (int i = firstIndex; i <= lastIndex; i++) {
if (blockLDR[i].getKey().equals("PAGE")) {
break;
}
numHeaders++;
}
headers = new JCAMPDataRecord[numHeaders];
System.arraycopy(blockLDR, firstIndex, headers, 0, numHeaders);
}
/**
* collect header LDRs
*
*/
private void initialize() throws JCAMPException {
JCAMPDataRecord[] blockLDR = containingBlock.getAllDataRecords();
firstIndex = startLDR.getBlockIndex() + 1;
lastIndex = endLDR.getBlockIndex() - 1;
if (firstIndex > lastIndex)
return;
initHeaders();
initVariables();
initPages();
}
/**
* initialize pages.
*
*/
private void initPages() throws JCAMPException {
JCAMPDataRecord[] blockLDR = containingBlock.getAllDataRecords();
JCAMPDataRecord page1 = blockLDR[firstIndex + numHeaders];
JCAMPDataRecord page2 = null;
Vector tmp = new Vector();
for (int i = firstIndex + numHeaders + 1; i < lastIndex; i++) {
if (blockLDR[i].getKey().equals("PAGE")) {
page2 = blockLDR[i - 1];
JCAMPNTuplePage ntuplePage = new JCAMPNTuplePage(this, page1, page2);
tmp.addElement(ntuplePage);
page1 = blockLDR[i];
}
}
if (page1 != null) {
JCAMPNTuplePage ntuplePage = new JCAMPNTuplePage(this, page1, blockLDR[lastIndex]);
tmp.addElement(ntuplePage);
}
pages = new JCAMPNTuplePage[tmp.size()];
for (int i = 0; i < pages.length; i++)
pages[i] = (JCAMPNTuplePage) tmp.elementAt(i);
}
/**
* init variables for NTUPLE block.
*
* @exception com.creon.chem.jcamp.JCAMPException incorrect variable declarations.
*/
private void initVariables() throws JCAMPException {
JCAMPDataRecord ldr = getHeader("SYMBOL");
if (ldr == null)
throw new JCAMPException("missing variable declaration in NTUPLES");
String[] symbols = Utils.splitStringCSV(ldr.getContent());
vars = new JCAMPVariable[symbols.length];
for (int i = 0; i < vars.length; i++) {
vars[i] = new JCAMPVariable(symbols[i].toUpperCase());
}
ldr = getHeader("VARNAME");
if (ldr != null) {
String[] labels = Utils.splitStringCSV(ldr.getContent());
if (labels.length != vars.length)
throw new JCAMPException("bad ##VARNAME=: number of name entries != number of variables");
for (int i = 0; i < vars.length; i++) {
vars[i].setLabel(labels[i]);
vars[i].setName(Utils.normalizeLabel(labels[i]));
}
}
ldr = getHeader("VARTYPE");
if (ldr != null) {
String[] types = Utils.splitStringCSV(ldr.getContent());
if (types.length != vars.length)
throw new JCAMPException("bad ##VARTYPE=: number of type entries != number of variables");
for (int i = 0; i < vars.length; i++) {
if (types[i].equalsIgnoreCase("INDEPENDENT"))
vars[i].setType(JCAMPVariable.Type.INDEPENDENT);
else if (types[i].equalsIgnoreCase("DEPENDENT"))
vars[i].setType(JCAMPVariable.Type.DEPENDENT);
else if (types[i].equalsIgnoreCase("PAGE"))
vars[i].setType(JCAMPVariable.Type.PAGE);
}
}
ldr = getHeader("VARFORM");
if (ldr != null) {
String[] forms = Utils.splitStringCSV(ldr.getContent());
if (forms.length != vars.length)
throw new JCAMPException("bad ##VARFORM=: number of varform entries != number of variables");
for (int i = 0; i < vars.length; i++) {
if ("AFFN".equalsIgnoreCase(forms[i]))
vars[i].setFormat(JCAMPVariable.Format.AFFN);
else if ("ASDF".equalsIgnoreCase(forms[i]))
vars[i].setFormat(JCAMPVariable.Format.ASDF);
else if ("STRING".equalsIgnoreCase(forms[i]))
vars[i].setFormat(JCAMPVariable.Format.STRING);
else
vars[i].setFormat(JCAMPVariable.Format.TEXT);
}
}
ldr = getHeader("VARDIM");
if (ldr != null) {
String[] dims = Utils.splitStringCSV(ldr.getContent());
if (dims.length != vars.length)
throw new JCAMPException("bad ##VARDIM=: number of dimension entries != number of variables");
for (int i = 0; i < vars.length; i++) {
vars[i].setDimension(Integer.parseInt(dims[i]));
}
}
ldr = getHeader("FIRST");
if (ldr != null) {
String[] firsts = Utils.splitStringCSV(ldr.getContent());
if (firsts.length != vars.length)
throw new JCAMPException("bad ##FIRST=: number of first values != number of variables");
for (int i = 0; i < vars.length; i++) {
vars[i].setFirst(new Double(firsts[i]));
}
}
ldr = getHeader("LAST");
if (ldr != null) {
String[] lasts = Utils.splitStringCSV(ldr.getContent());
if (lasts.length != vars.length)
throw new JCAMPException("bad ##LAST=: number of last values != number of variables");
for (int i = 0; i < vars.length; i++) {
vars[i].setLast(new Double(lasts[i]));
}
}
ldr = getHeader("MIN");
if (ldr != null) {
String[] mins = Utils.splitStringCSV(ldr.getContent());
if (mins.length != vars.length)
throw new JCAMPException("bad ##MIN=: number of min values != number of variables");
for (int i = 0; i < vars.length; i++) {
vars[i].setMin(new Double(mins[i]));
}
}
ldr = getHeader("MAX");
if (ldr != null) {
String[] maxs = Utils.splitStringCSV(ldr.getContent());
if (maxs.length != vars.length)
throw new JCAMPException("bad ##MAX=: number of max values != number of variables");
for (int i = 0; i < vars.length; i++) {
vars[i].setMax(new Double(maxs[i]));
}
}
ldr = getHeader("FACTOR");
if (ldr != null) {
String[] factors = Utils.splitStringCSV(ldr.getContent());
if (factors.length != vars.length)
throw new JCAMPException("bad ##FACTOR=: number of factor values != number of variables");
for (int i = 0; i < vars.length; i++) {
vars[i].setFactor(new Double(factors[i]));
}
}
ldr = getHeader("UNITS");
if (ldr != null) {
String[] units = Utils.splitStringCSV(ldr.getContent());
if (units.length != vars.length)
throw new JCAMPException("bad ##UNITS=: number of unit entries != number of variables");
for (int i = 0; i < units.length; i++) {
vars[i].setUnit(units[i]);
}
}
}
/**
* gets number of header LDRs.
*
* @return int
*/
public int numHeaders() {
return numHeaders;
}
/**
* gets number of pages.
*
* @return int
*/
public int numPages() {
if (pages == null)
return 0;
return pages.length;
}
}
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