if (key == "mismatch") { mismatch = value; }
if (key == "gapopen") { gapopen = value; }
if (key == "gapextend" ) { gapextend = value; }
+ if (key == "start" ) { startPos = value; }
+ if (key == "end" ) { endPos = value; }
+ if (key == "maxambig" ) { maxAmbig = value; }
+ if (key == "maxhomop" ) { maxHomoPolymer = value; }
+ if (key == "minlength" ) { minLength = value; }
+ if (key == "maxlength" ) { maxLength = value; }
if (key == "line") {//stores lines to be used in a vector
lines.clear();
if (key == "mismatch") { mismatch = value; }
if (key == "gapopen") { gapopen = value; }
if (key == "gapextend" ) { gapextend = value; }
+ if (key == "start" ) { startPos = value; }
+ if (key == "end" ) { endPos = value; }
+ if (key == "maxambig" ) { maxAmbig = value; }
+ if (key == "maxhomop" ) { maxHomoPolymer = value; }
+ if (key == "minlength" ) { minLength = value; }
+ if (key == "maxlength" ) { maxLength = value; }
+
if (key == "line") {//stores lines to be used in a vector
lines.clear();
splitAtDash(calc, Estimators);
}
if (commandName == "collect.shared") {
-
if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
Estimators.clear();
splitAtDash(calc, Estimators);
string GlobalData::getMismatch() { return mismatch; }
string GlobalData::getGapopen() { return gapopen; }
string GlobalData::getGapextend() { return gapextend; }
+string GlobalData::getStartPos() { return startPos; }
+string GlobalData::getEndPos() { return endPos; }
+string GlobalData::getMaxAmbig() { return maxAmbig; }
+string GlobalData::getMaxHomoPolymer() { return maxHomoPolymer; }
+string GlobalData::getMinLength() { return minLength; }
+string GlobalData::getMaxLength() { return maxLength; }
void GlobalData::setListFile(string file) { listfile = file; inputFileName = file; }
mismatch = "-1.0";
gapopen = "-1.0";
gapextend = "-2.0";
+ startPos = "-1";
+ endPos = "-1";
+ maxAmbig = "-1";
+ maxHomoPolymer = "-1";
+ minLength = "-1";
+ maxLength = "-1";
+
}
//*******************************************************/
trump = "";
hard = "";
soft = "";
-
+ startPos = "-1";
+ endPos = "-1";
+ maxAmbig = "-1";
+ maxHomoPolymer = "-1";
+ minLength = "-1";
+ maxLength = "-1";
+
}
/*******************************************************/
/*******************************************************/
void GlobalData::parseTreeFile() {
+ //Why is THIS in GlobalData??? - PDS
+
//only takes names from the first tree and assumes that all trees use the same names.
try {
string filename = treefile;