gGroupmap = NULL;
gTree.clear();
Treenames.clear();
- labels.clear(); lines.clear(); groups.clear();
+ labels.clear(); lines.clear(); Groups.clear();
allLines = 1;
}
}
//set default value for cutoff
- if (commandName == "dist.seq") { cutoff = "1.0"; }
+ if (commandName == "dist.seqs") { cutoff = "1.0"; }
string key, value;
//reads in parameters and values
if (key == "sorted") { sorted = value; }
if (key == "vertical") { vertical = value; }
if (key == "trump") { trump = value; }
- if (key == "filter") { filter = value; }
+ if (key == "hard") { hard = value; }
if (key == "soft") { soft = value; }
if (key == "scale") { scale = value; }
- if (key == "ends" ) { ends = value; }
+ if (key == "countends" ) { countends = value; }
if (key == "processors" ) { processors = value; }
-
-
-
-
+ if (key == "size" ) { size = value; }
+ if (key == "candidate") { candidatefile = value; }
+ if (key == "search") { search = value; }
+ if (key == "ksize") { ksize = value; }
+ if (key == "align") { align = value; }
+ if (key == "match") { match = value; }
+ if (key == "mismatch") { mismatch = value; }
+ if (key == "gapopen") { gapopen = value; }
+ if (key == "gapextend" ) { gapextend = value; }
if (key == "line") {//stores lines to be used in a set
lines.clear();
if (key == "sorted") { sorted = value; }
if (key == "vertical") { vertical = value; }
if (key == "trump") { trump = value; }
- if (key == "filter") { filter = value; }
+ if (key == "hard") { hard = value; }
if (key == "soft") { soft = value; }
if (key == "scale") { scale = value; }
- if (key == "ends" ) { ends = value; }
+ if (key == "countends" ) { countends = value; }
if (key == "processors" ) { processors = value; }
-
+ if (key == "size" ) { size = value; }
+ if (key == "candidate") { candidatefile = value; }
+ if (key == "search") { search = value; }
+ if (key == "ksize") { ksize = value; }
+ if (key == "align") { align = value; }
+ if (key == "match") { match = value; }
+ if (key == "mismatch") { mismatch = value; }
+ if (key == "gapopen") { gapopen = value; }
+ if (key == "gapextend" ) { gapextend = value; }
if (key == "line") {//stores lines to be used in a vector
lines.clear();
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if (commandName == "dist.seq") {
- if ((calc == "default") || (calc == "")) { calc = "onegap"; }
+ if (commandName == "dist.seqs") {
+ if ((calc == "default") || (calc == "")) { calc = "onegap"; }
+ if (countends == "") { countends = "T"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if ((commandName == "tree.shared") || (commandName == "bootstrap.shared")) {
- if (calc != "") {
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }else { cout << "You have not specified any calculators." << endl; }
+ if ((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) {
+ if ((calc == "default") || (calc == "")) {
+ calc = "jclass-thetayc";
+ }
+ Estimators.clear();
+ splitAtDash(calc, Estimators);
}
+
+ if(commandName == "filter.seqs"){
+ if(trump == "" && vertical == "" && hard == "" && soft == ""){
+ trump = '.';
+ }
+ }
//if you have done a read.otu with a groupfile but don't want to use it anymore because you want to do single commands
if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
string GlobalData::getStep() { return step; }
string GlobalData::getForm() { return form; }
string GlobalData::getSorted() { return sorted; }
+string GlobalData::getVertical() { return vertical; }
string GlobalData::getTrump() { return trump; }
string GlobalData::getSoft() { return soft; }
-string GlobalData::getFilter() { return filter; }
+string GlobalData::getHard() { return hard; }
string GlobalData::getScale() { return scale; }
-string GlobalData::getEnds() { return ends; }
+string GlobalData::getCountEnds() { return countends; }
string GlobalData::getProcessors() { return processors; }
-
-void GlobalData::setListFile(string file) { listfile = file; inputFileName = file;}
-void GlobalData::setGroupFile(string file) { groupfile = file; }
-void GlobalData::setRabundFile(string file) { rabundfile = file; inputFileName = file;}
-void GlobalData::setSabundFile(string file) { sabundfile = file; inputFileName = file;}
-void GlobalData::setPhylipFile(string file) { phylipfile = file; inputFileName = file;}
-void GlobalData::setColumnFile(string file) { columnfile = file; inputFileName = file;}
-void GlobalData::setSharedFile(string file) { sharedfile = file; inputFileName = file; fileroot = file;}
+string GlobalData::getSize() { return size; }
+string GlobalData::getCandidateFile() { return candidatefile;}
+string GlobalData::getSearch() { return search; }
+string GlobalData::getKSize() { return ksize; }
+string GlobalData::getAlign() { return align; }
+string GlobalData::getMatch() { return match; }
+string GlobalData::getMismatch() { return mismatch; }
+string GlobalData::getGapopen() { return gapopen; }
+string GlobalData::getGapextend() { return gapextend; }
+
+
+void GlobalData::setListFile(string file) { listfile = file; inputFileName = file; }
+void GlobalData::setRabundFile(string file) { rabundfile = file; inputFileName = file; }
+void GlobalData::setSabundFile(string file) { sabundfile = file; inputFileName = file; }
+void GlobalData::setPhylipFile(string file) { phylipfile = file; inputFileName = file; }
+void GlobalData::setColumnFile(string file) { columnfile = file; inputFileName = file; }
+void GlobalData::setGroupFile(string file) { groupfile = file; }
+void GlobalData::setSharedFile(string file) { sharedfile = file; inputFileName = file; fileroot = file; }
void GlobalData::setNameFile(string file) { namefile = file; }
void GlobalData::setFormat(string Format) { format = Format; }
void GlobalData::setRandomTree(string Random) { randomtree = Random; }
void GlobalData::setGroups(string g) { groups = g; }
void GlobalData::setCalc(string Calc) { calc = Calc; }
-void GlobalData::setEnds(string e) { ends = e; }
+void GlobalData::setCountEnds(string e) { countends = e; }
void GlobalData::setProcessors(string p) { processors = p; }
clustalfile = "";
treefile = "";
sharedfile = "";
+ candidatefile = "";
cutoff = "10.00";
format = "";
precision = "100";
form = "integral";
sorted = "T"; //F means don't sort, T means sort.
vertical = "";
- trump = "";
- filter = "";
+ trump = "";
+ hard = "";
soft = "";
scale = "log10";
- ends = "T"; //yes
+ countends = "T"; //yes
processors = "1";
-
+ size = "0";
+ search = "kmer";
+ ksize = "7";
+ align = "needleman";
+ match = "1.0";
+ mismatch = "-1.0";
+ gapopen = "-1.0";
+ gapextend = "-2.0";
}
//*******************************************************/
abund = "10";
step = "0.01";
form = "integral";
- ends = "T";
+ countends = "T";
processors = "1";
+ size = "0";
+ search = "kmer";
+ ksize = "7";
+ align = "needleman";
+ match = "1.0";
+ mismatch = "-1.0";
+ gapopen = "-1.0";
+ gapextend = "-2.0";
+ vertical = "";
+ trump = "";
+ hard = "";
+ soft = "";
+
}
/*******************************************************/
projects / mothur.git / blobdiff