private void writeListErrors(
FileWriter fileOut,
Vector deviationMessages,
Vector databaseValues,
String ind,
char delimeter,
String variable,
String value,
String date,
String ref,
String comm) {
try {
if (errorList.size() > 0 || deviationMessages.size() > 0 || warningList.size() > 0) {
fileOut.write("#--------------------------------------------------\n");
}
if (errorList.size() > 0) {
for (int i = 0; i < errorList.size(); i++) {
fileOut.write("#" + (String) errorList.get(i) + "\n");
}
}
if (warningList.size() > 0) {
for (int i = 0; i < warningList.size(); i++) {
fileOut.write("#" + (String) warningList.get(i) + "\n");
}
}
if (deviationMessages.size() > 0) {
for (int i = 0; i < deviationMessages.size(); i++) {
fileOut.write("#" + (String) deviationMessages.elementAt(i) + "\n");
}
// write old values
fileOut.write("#" + databaseValues.elementAt(0) + "\n");
}
// if there are errors, the string is "Outcommented"
if (errorList.size() > 0) {
fileOut.write("#");
}
// write original string
fileOut.write(
ind + delimeter + variable + delimeter + value + delimeter + date + delimeter + ref
+ delimeter + comm + "\n");
if (errorList.size() > 0 || deviationMessages.size() > 0 || warningList.size() > 0) {
fileOut.write("#--------------------------------------------------\n");
}
} // try
catch (Exception e) {
e.printStackTrace(System.err);
}
}
/** Check if object support this format. If a match is found return true else return false */
public boolean supportFormat(FileHeader hdr) {
boolean out = false;
try {
for (int i = 0; i < headers.size(); i++) {
if ((headers.get(i).formatTypeName().equals(hdr.formatTypeName()))
&& (headers.get(i).objectTypeName().equals(hdr.objectTypeName()))
&& (headers.get(i).version() == hdr.version())) {
return true;
}
}
} catch (Exception e) {
e.printStackTrace();
}
return false;
}
/**
* @param fileOut
* @param errorMessages
* @param warningMessages
* @param deviationMessages
* @param databaseValues
* @param newAlleles
* @param ind
* @param delim
* @param marker
* @param allele1
* @param allele2
*/
private void writeMatrixErrors(
FileWriter fileOut,
Vector deviationMessages,
Vector databaseValues,
Vector values,
String ind,
char delim,
String variable,
String value) {
try {
// if row contains comments
if (errorList.size() > 0 || deviationMessages.size() > 0 || warningList.size() > 0) {
fileOut.write("#--------------------------------------------------------\n");
}
if (errorList.size() > 0) {
for (int i = 0; i < errorList.size(); i++) {
fileOut.write("#" + (String) errorList.get(i) + "\n");
}
}
if (warningList.size() > 0) {
for (int i = 0; i < warningList.size(); i++) {
fileOut.write("#" + (String) warningList.get(i) + "\n");
}
}
if (deviationMessages.size() > 0) {
for (int i = 0; i < deviationMessages.size(); i++) {
fileOut.write("#" + (String) deviationMessages.elementAt(i) + "\n");
}
// write database values
fileOut.write("#" + ind);
for (int i = 0; i < databaseValues.size(); i++) {
fileOut.write(delim + (String) databaseValues.elementAt(i));
}
fileOut.write("\n");
}
// write row from file:
if (errorList.size() > 0) {
fileOut.write("#");
}
fileOut.write(ind);
for (int i = 0; i < values.size(); i++) {
fileOut.write(delim + (String) values.elementAt(i));
}
fileOut.write("\n");
/*
for (int i=0;i<newAlleles.size();i++)
{
fileOut.write(delim+(String)newAlleles.elementAt(i));
}
fileOut.write("\n");
*/
// fileOut.write(delim+allele1);
// fileOut.write(delim+allele2);
// fileOut.write("\n");
if (errorList.size() > 0 || deviationMessages.size() > 0 || warningList.size() > 0) {
fileOut.write("#--------------------------------------------------------\n");
}
} // try
catch (Exception e) {
e.printStackTrace(System.err);
}
}