if (key == "rabund" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
if (key == "sabund" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
if (key == "fasta" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; }
- if (key == "nexus" ) { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus"; }
- if (key == "clustal" ) { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
if (key == "tree" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
if (key == "shared" ) { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile"; }
if (key == "name" ) { namefile = value; }
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 set
+ if (key == "line") {//stores lines to be used in a vector
lines.clear();
labels.clear();
line = value;
label = "";
- splitAtDash(value, lines);
- allLines = 0;
+ if (line != "all") { splitAtDash(value, lines); allLines = 0; }
+ else { allLines = 1; }
}
- if (key == "label") {//stores labels to be used in a set
+
+ if (key == "label") {//stores lines to be used in a vector
labels.clear();
lines.clear();
label = value;
line = "";
- splitAtDash(value, labels);
- allLines = 0;
+ if (label != "all") { splitAtDash(value, labels); allLines = 0; }
+ else { allLines = 1; }
}
if (key == "groups") {//stores groups to be used in a vector
if (key == "rabund" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
if (key == "sabund" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
if (key == "fasta" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; }
- if (key == "nexus" ) { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus"; }
- if (key == "clustal" ) { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; }
if (key == "tree" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
- if (key == "shared" ) { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile"; }
+ if (key == "shared" ) { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile"; }
if (key == "name" ) { namefile = value; }
if (key == "order" ) { orderfile = value; }
if (key == "group" ) { groupfile = value; }
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::getTreeFile() { return treefile; }
string GlobalData::getSharedFile() { return sharedfile; }
string GlobalData::getFastaFile() { return fastafile; }
-string GlobalData::getNexusFile() { return nexusfile; }
-string GlobalData::getClustalFile() { return clustalfile; }
string GlobalData::getCutOff() { return cutoff; }
string GlobalData::getFormat() { return format; }
string GlobalData::getPrecision() { return precision; }
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; }
//option definitions should go here...
helpRequest = "";
clear();
- gListVector == NULL;
- gSparseMatrix == NULL;
+ gListVector = NULL;
+ gSparseMatrix = NULL;
}
/*******************************************************/
groupfile = "";
orderfile = "";
fastafile = "";
- nexusfile = "";
- clustalfile = "";
treefile = "";
sharedfile = "";
candidatefile = "";
step = "0.01";
form = "integral";
sorted = "T"; //F means don't sort, T means sort.
- vertical = "";
+ vertical = "F";
trump = "";
hard = "";
soft = "";
processors = "1";
size = "0";
search = "kmer";
- ksize = "7";
+ ksize = "8";
align = "needleman";
match = "1.0";
mismatch = "-1.0";
gapopen = "-1.0";
gapextend = "-2.0";
+ startPos = "-1";
+ endPos = "-1";
+ maxAmbig = "-1";
+ maxHomoPolymer = "-1";
+ minLength = "-1";
+ maxLength = "-1";
+
}
//*******************************************************/
/******************************************************/
void GlobalData::reset() {
+ label = "";
+ line = "";
cutoff = "10.00";
precision = "100";
iters = "1000";
processors = "1";
size = "0";
search = "kmer";
- ksize = "7";
+ ksize = "8";
align = "needleman";
match = "1.0";
mismatch = "-1.0";
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;