/**
* Gets the label <code>infoType</code>. It's equivalent to <code>getParameter</code> (<code>
* infoType</code>). If the LDR is not available an empty <code>String</code> is returned.
*
* @param infoType Description of the Parameter
* @return the data for the requested label.
*/
public String getAdditionalInformation(String infoType) {
LabelData set = new LabelData();
set = getParameter(infoType);
if (set == null) {
return "";
}
return set.getData();
}
public final LabelData getParameter(String wanted) {
LabelData back = new LabelData();
back.setLabel(wanted);
back.setData((String) parameterTable.get(wanted));
if (back.getData() == null) {
// logger.warn("JCAMP label \"" + wanted + "\" does not exist");
return null;
}
return back;
}
/**
* Gets the label for the Y axis. It's equivalent to <code>getParameter</code> ("YUNITS"). If the
* LDR is not available an empty <code>String</code> is returned.
*
* @return the label for the Y axis.
*/
public final String getYLabel() {
LabelData set = new LabelData();
if (dataDecoded) {
set = getParameter("YUNITS");
if (set == null) {
return "";
}
return set.getData();
} else {
logger.warn("Can't get JCAMP YUNITS label. Data not decoded.");
return null;
}
}
/**
* Returns a string of all LDR's (label data records.
*
* @return a string of all LDR's (label data records
*/
public String toString() {
// HashTable in String umwandeln;
String s = "";
Enumeration en;
// int i=0;
String dummy;
LabelData dummy2 = null;
dummy2 = getParameter("TITLE");
if (dummy2 == null) {
dummy2 = new LabelData();
dummy2.label = "TITLE";
dummy2.data = "";
}
s = s.concat("##" + dummy2.label + "=" + dummy2.data + "\r\n");
for (en = parameterTable.keys(); en.hasMoreElements(); ) {
dummy = (String) en.nextElement();
if (!dummy.equals("TITLE") && !dummy.equals("END")) {
s = s.concat("##" + dummy + "=" + (String) parameterTable.get(dummy) + "\r\n");
}
// i=i+2;
}
dummy2 = getParameter("END");
if (dummy2 == null) {
dummy2 = new LabelData();
dummy2.label = "END";
dummy2.data = "";
}
s = s.concat("##" + dummy2.label + "=" + dummy2.data + "\r\n");
return s;
}
/**
* Gets the <code>double</code> from <code>ld.data</code>.
*
* @param ld Description of the Parameter
* @return The double value
* @exception NumberFormatException Description of the Exception
*/
protected final double getDouble(LabelData ld) throws NumberFormatException {
if (ld == null) {
return 0.0;
}
double dummy = 0;
try {
// alle ',' gleich durch '.' ersetzen, sonst gibts eine NumberFormatException
dummy = (new Double(ld.getData().replace(',', '.'))).doubleValue();
} catch (NumberFormatException e) {
if (e.toString().indexOf("empty") >= 0) {
return 0.0;
} else {
throw new NumberFormatException(
"The Label " + ld.getLabel() + " contains not a valid double value: " + ld.getData());
}
}
return dummy;
}
/**
* Decide which data type this JCAMP data set contains and decodes this data. After decoding the
* data is available with <code>getXData()</code> and <code>getYData()</code>, if the data
* contains a spectra.<br>
* Chemical structures are not supported, until now !
*
* @param decodeDataNow if <code>true</code> the data type is estimated and the data is decoded.
* if <code>false</code> only the data type is estimated.
* @exception JCAMPException Description of the Exception
* @exception NumberFormatException Description of the Exception
*/
private void decodeData() throws JCAMPException, NumberFormatException {
if (dataDecoded) {
return;
}
LabelData set;
int end = 0;
String s1 = "";
// which data type ?
boolean xypairsState = true;
boolean xydataState = true;
set = getParameter("XYPAIRS");
if (set == null) {
xypairsState = false;
}
if (xypairsState) {
end = set.getData().indexOf("\n", 0);
if (end == -1) {
throw new JCAMPException("Carriage return after \"=\" is not allowed");
}
s1 = set.getData().substring(0, end).trim();
if (!s1.equals("(XY..XY)")) {
xypairsState = false;
} else {
dataType = XYPAIRS;
decodeXYPAIRSandPEAKTABLE();
dataDecoded = true;
return;
}
}
if (!xypairsState) {
set = getParameter("XYDATA");
if (set == null) {
xydataState = false;
}
if (xydataState) {
end = set.getData().indexOf("\n", 0);
if (end == -1) {
throw new JCAMPException("Carriage return after \"=\" is not allowed");
}
s1 = set.getData().substring(0, end).trim();
if (!s1.equals("(X++(Y..Y))")) {
xydataState = false;
} else {
dataType = XYDATA_X_YY;
decodeXYDATA();
dataDecoded = true;
return;
}
}
}
/*
* if(dataType==XYPAIRS || dataType==XYDATA_X_YY){
* if(decodeDataNow){
* decodeXYDATAorXYPAIRS();
* }
* dataDecoded=true;
* return;
* }
*/
boolean chemicalStructureState = true;
set = getParameter("MOLFORM");
if (set == null) {
chemicalStructureState = false;
}
set = getParameter("ATOMLIST");
if (set == null) {
chemicalStructureState = false;
}
set = getParameter("BONDLIST");
if (set == null) {
chemicalStructureState = false;
}
if (chemicalStructureState) {
dataType = CHEMICAL_STRUCTURE;
// if(state)decodeChemicalStructure();
// dataDecoded=true;
return;
}
set = getParameter("XYPOINTS");
if (set != null) {
throw new JCAMPException("Data XYPOINTS is not supported ");
// dataType=XYPOINTS;
// dataDecoded=true;
// return;
}
set = getParameter("PEAK TABLE");
if (set != null) {
end = set.getData().indexOf("\n", 0);
if (end == -1) {
throw new JCAMPException("Carriage return after \"=\" is not allowed");
}
s1 = set.getData().substring(0, end).trim();
if (s1.equals("(XY..XY)")) {
dataType = PEAK_TABLE;
decodeXYPAIRSandPEAKTABLE();
dataDecoded = true;
return;
}
}
set = getParameter("PEAK ASSIGNMENTS");
if (set != null) {
throw new JCAMPException("Data PEAK ASSIGNMENTS is not supported ");
// dataType=PEAK_ASSIGNMENTS;
// dataDecoded=true;
// return;
}
set = getParameter("RADATA");
if (set != null) {
throw new JCAMPException("Data RADATA is not supported ");
// dataType=RADATA;
// dataDecoded=true;
// return;
}
set = getParameter("DATA TYPE");
if (set != null) {
if (set.getData().trim().equals("LINK")) {
dataType = LINK;
// dataDecoded=true;
return;
}
}
// irgend ein anderer Datentyp
throw new JCAMPException("Data type not supported ");
}
/**
* Set one LDR (data label record).
*
* @param newLDR the new label and the new data
*/
public final void setParameter(LabelData newLDR) {
if (newLDR != null) {
parameterTable.put(newLDR.getLabel(), newLDR.getData());
}
}
/**
* Decodes XYPAIRS.
*
* @exception JCAMPException Description of the Exception
* @exception NumberFormatException Description of the Exception
*/
private void decodeXYPAIRSandPEAKTABLE() throws JCAMPException, NumberFormatException {
LabelData set = new LabelData();
int begin;
int end = 0;
String s1 = "";
if (dataType == PEAK_TABLE) {
xFactor = 1.0;
yFactor = 1.0;
set = getParameter("PEAK TABLE");
// if (set == null)
// {
// }
} else {
set = getParameter("DELTAX");
if (set == null) {
calculatedDeltaXneeded = true;
}
deltaX = getDouble(set);
set = getParameter("LASTX");
if (set == null) {
String add = "";
if (!calculatedDeltaXneeded) {
add = ". The label DELTAX is missing and " + "can not be calculated";
}
throw new JCAMPException("The label LASTX is missing" + add);
}
lastX = getDouble(set);
set = getParameter("FIRSTX");
if (set == null) {
String add = "";
if (!calculatedDeltaXneeded) {
add = ". The label DELTAX is missing and " + "can not be calculated";
}
throw new JCAMPException("The label FIRSTX is missing" + add);
}
firstX = getDouble(set);
set = getParameter("NPOINTS");
if (set == null) {
String add = "";
if (!calculatedDeltaXneeded) {
add = ". The label NPOINTS is missing and DELTAX" + "can not be calculated";
throw new JCAMPException("The label FIRSTX is missing" + add);
}
logger.warn("The label NPOINTS is missing. Now its estimated");
estimatedNPointsNeeded = true;
}
nPoints = getDouble(set);
// Berechnung von deltaX;
if (calculatedDeltaXneeded) {
deltaX = (lastX - firstX) / (nPoints - 1);
} else {
double dummy = 0;
if (!estimatedNPointsNeeded && (nPoints != 0)) {
// einfach nochmals zur Kontrolle von deltaX. Eigentlich unnoetig !
dummy = (lastX - firstX) / (nPoints - 1);
if (Math.abs(dummy - deltaX) > DELTAX_DIFFERENCE_WARNING_VALUE) {
logger.warn(
"The calculated DELTAX="
+ dummy
+ " (original DELTAX="
+ deltaX
+ ") shows a difference above "
+ DELTAX_DIFFERENCE_WARNING_VALUE);
}
}
}
set = getParameter("XFACTOR");
if (set == null) {
throw new JCAMPException("The label XFACTOR is missing");
}
xFactor = getDouble(set);
set = getParameter("YFACTOR");
if (set == null) {
throw new JCAMPException("The label YFACTOR is missing");
}
yFactor = getDouble(set);
set = getParameter("XYPAIRS");
// if (set == null)
// {
// }
}
end = set.getData().indexOf("\n", 0);
if (end == -1) {
throw new JCAMPException("Carriage return" + " after \"=\" is not allowed");
}
s1 = set.getData().substring(0, end).trim();
s1 = set.getData().substring(end + 1, set.getData().indexOf("\n", end + 1));
// StringTokenizer dataValue = new StringTokenizer(s1, " \t");
xData = new LinkedList();
yData = new LinkedList();
begin = 0;
begin = set.getData().indexOf("\n", begin);
begin++;
do {
end = set.getData().indexOf("\n", begin);
if (set.getData().indexOf(";", begin) != -1) {
end = Math.min(end, set.getData().indexOf(";", begin));
}
if (end == -1) {
break;
}
s1 = set.getData().substring(begin, end).trim();
// dataLine
// println("s1:"+parameterSaetze[1].substring(begin,end));
addXYPAIRSandPEAKTABLEdataLine(s1);
begin = end + 1;
} while (true);
sendDataToDoubleArray();
}
/**
* Decodes XYDATA. Only the uncompressed ASDF format is supported. The compressed AFFN format is
* not supported.
*
* @exception JCAMPException Description of the Exception
* @exception NumberFormatException Description of the Exception
*/
private void decodeXYDATA() throws JCAMPException, NumberFormatException {
LabelData set = new LabelData();
int begin;
int end = 0;
String s1 = "";
String s2 = "";
set = getParameter("DELTAX");
if (set == null) {
logger.warn("The label DELTAX is missing. Now its calculated !;-)");
calculatedDeltaXneeded = true;
}
deltaX = getDouble(set);
set = getParameter("LASTX");
if (set == null) {
String add = "";
if (!calculatedDeltaXneeded) {
add = ". The label DELTAX is missing and " + "can not be calculated";
}
throw new JCAMPException("The label LASTX is missing" + add);
}
lastX = getDouble(set);
set = getParameter("FIRSTX");
if (set == null) {
String add = "";
if (!calculatedDeltaXneeded) {
add = ". The label DELTAX is missing and " + "can not be calculated";
}
throw new JCAMPException("The label FIRSTX is missing" + add);
}
firstX = getDouble(set);
set = getParameter("NPOINTS");
if (set == null) {
String add = "";
if (!calculatedDeltaXneeded) {
add = ". The label NPOINTS is missing and DELTAX" + "can not be calculated";
throw new JCAMPException("The label FIRSTX is missing" + add);
}
logger.warn("The label NPOINTS is missing. Now its estimated");
estimatedNPointsNeeded = true;
}
nPoints = getDouble(set);
// Berechnung von deltaX;
if (calculatedDeltaXneeded) {
deltaX = (lastX - firstX) / (nPoints - 1);
} else {
double dummy = 0;
if (!estimatedNPointsNeeded && (nPoints != 0)) {
// einfach nochmals zur Kontrolle von deltaX. Eigentlich unnoetig !
dummy = (lastX - firstX) / (nPoints - 1);
if (Math.abs(dummy - deltaX) > DELTAX_DIFFERENCE_WARNING_VALUE) {
logger.warn(
"The calculated DELTAX="
+ dummy
+ " (original DELTAX="
+ deltaX
+ ") shows a difference above "
+ DELTAX_DIFFERENCE_WARNING_VALUE);
}
}
}
set = getParameter("XFACTOR");
if (set == null) {
throw new JCAMPException("The label XFACTOR is missing");
}
xFactor = getDouble(set);
set = getParameter("YFACTOR");
if (set == null) {
throw new JCAMPException("The label YFACTOR is missing");
}
yFactor = getDouble(set);
// beginne Dekodierung
set = getParameter("XYPAIRS");
// if (set == null)
// {
// }
// if(dataType==XYPAIRS){
// end=set.getData().indexOf("\n",0);
// if (end==-1)throw new JCAMPException("Carriage return after \"=\" is not allowed");
// s1=set.getData().substring(0, end).trim();
// }
// else
if (dataType == XYDATA_X_YY) {
set = getParameter("XYDATA");
// if (set == null)
// {
// }
end = set.getData().indexOf("\n", 0);
if (end == -1) {
throw new JCAMPException("Carriage return" + " after \"=\" is not allowed");
}
s1 = set.getData().substring(0, end).trim();
}
s1 = set.getData().substring(end + 1, set.getData().indexOf("\n", end + 1));
// s1=s1.trim();
// hier findet keine Unterscheidung zwischen AFFN (ungepackt) oder ASDF (gepackt) statt
// Pseudo-digits or ASDF forms
// ASCII digits 0 1 2 3 4 5 6 7 8 9
// Positive SQZ digits @ A B C D E F G H I
// Negative SQZ digits a b c d e f g h i
// Positive DIF digits % J K L M N O P Q R
// Negative DIF digits j k l m n o p q r
// Positive DUP digits S T U V W X Y Z s
StringTokenizer isAFFN =
new StringTokenizer(s1, "@ABCDEFGHIabcdefghi%JKLMNOPQRjklmnopqrSTUVWXYZs");
try {
s2 = isAFFN.nextToken();
if (s1.equals(s2)) {
// ist ein Token enthalten, so ist s1 ungleich s2
// OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
// nur AFFN !!!
// OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
// wieviele Datenpunkte sind es denn etwa ?
// StringTokenizer dataValue = new StringTokenizer(s1, " \t");
// ruhig groS waehlen, da sie nachher eh geloescht werden.
// int dataPerLine=100;
// Anzahl der Datenwerte ist NPOINTS/countTokens
// dataPerLine=Math.max(dataValue.countTokens(), 100);
// yData= new Vector((int)nPoints, dataPerLine);
// xData= new Vector((int)nPoints, dataPerLine);
xData = new LinkedList();
yData = new LinkedList();
begin = 0;
begin = set.getData().indexOf("\n", begin);
begin++;
do {
end = set.getData().indexOf("\n", begin);
if (set.getData().indexOf(";", begin) != -1) {
end = Math.min(end, set.getData().indexOf(";", begin));
}
if (end == -1) {
break;
}
s1 = set.getData().substring(begin, end).trim();
// dataLine
// println("s1:"+parameterSaetze[1].substring(begin,end));
addXYDATADataLine(s1);
begin = end + 1;
} while (true);
sendDataToDoubleArray();
return;
} else {
throw new JCAMPException("Compressed data in ASDF format is not supported ");
}
} catch (NoSuchElementException e) {
logger.error(e.getMessage());
}
}
