protected void runAlgorithm() {
// Retrieve a list of string values dictating where elements are supposed to occur in a table.
tableStructure = buildingModel.getTableStructure();
headers = new ArrayList<String>();
colsToUse = new ListOrderedSet<Integer>();
int count = tableStructure.size() + 1;
for (int i = 0; i < tableStructure.size(); i++) {
// modify this to only add those factors which appear in temp factors.
if (tableStructure.get(i)[0].toLowerCase().equals("factors")) {
for (TempFactors factor : factorsToAdd) {
String newFactor = "Factor Value[" + factor.getFactorName().trim() + "]";
addFactor(count, newFactor, factor, i);
}
} else if (tableStructure.get(i)[0].toLowerCase().contains("factor value[")) {
// doing nothing with this factor
} else if (tableStructure.get(i)[0].toLowerCase().contains("characteristics[")) {
String newChar = tableStructure.get(i)[0];
headers.add(newChar);
colsToUse.add(i);
} else {
headers.add(tableStructure.get(i)[0]);
colsToUse.add(i);
}
}
performAssayCentricTask();
}
/**
* This is a check employed to ensure that we are not adding factors that are already defined
* inside the configuration.
*
* @param columnName - Name of column to be added.
* @return boolean - true if already present, false otherwise
*/
protected boolean checkForFactorExistence(String columnName) {
for (TempFactors tf : factorsToAdd) {
String fullFactorName = "Factor Value[" + tf.getFactorName() + "]";
if (fullFactorName.equalsIgnoreCase(columnName)) {
return true;
}
}
return false;
}
private int addFactor(int count, String newFactor, TempFactors factor, int nextIndex) {
headers.add(newFactor);
colsToUse.add(nextIndex);
TableFieldObject newFo;
boolean unitAdded = false;
for (TimeUnitPair tup : factor.getFactorLevels()) {
if (!tup.getUnit().trim().equals("")) {
headers.add("Unit");
unitAdded = true;
break;
}
}
if (unitAdded) {
// add factor column field first
newFo =
new TableFieldObject(
count, newFactor, "Factor", DataTypes.STRING, "", false, false, false);
buildingModel.addField(newFo);
count++;
newFo =
new TableFieldObject(
count,
"Unit",
"Unit to give meaning to it's associated value",
DataTypes.ONTOLOGY_TERM,
"",
false,
false,
false);
buildingModel.addField(newFo);
count++;
} else {
newFo =
new TableFieldObject(
count, newFactor, "Factor", DataTypes.ONTOLOGY_TERM, "", false, false, false);
buildingModel.addField(newFo);
count++;
}
return count;
}