if (key == "scale") { scale = value; }
if (key == "ends" ) { ends = value; }
if (key == "processors" ) { processors = value; }
+ if (key == "size" ) { size = value; }
+
+
+
+
if (key == "template") { templatefile = value; }
if (key == "search") { search = value; }
if (key == "ksize") { ksize = value; }
if (key == "scale") { scale = value; }
if (key == "ends" ) { ends = value; }
if (key == "processors" ) { processors = value; }
+ if (key == "size" ) { size = value; }
+
if (key == "template") { templatefile = value; }
if (key == "search") { search = value; }
if (key == "ksize") { ksize = value; }
//input defaults for calculators
if (commandName == "collect.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+ if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
splitAtDash(calc, Estimators);
}
if (commandName == "summary.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
+ if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson-efron-boneh-solow"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
string GlobalData::getScale() { return scale; }
string GlobalData::getEnds() { return ends; }
string GlobalData::getProcessors() { return processors; }
+string GlobalData::getSize() { return size; }
+
+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;}
string GlobalData::getTemplateFile() { return templatefile;}
string GlobalData::getSearch() { return search; }
string GlobalData::getKSize() { return ksize; }
string GlobalData::getGapopen() { return gapopen; }
string GlobalData::getGapextend() { return gapextend; }
-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;}
void GlobalData::setNameFile(string file) { namefile = file; }
void GlobalData::setFormat(string Format) { format = Format; }
scale = "log10";
ends = "T"; //yes
processors = "1";
+ size = "1000";
search = "suffix";
ksize = "7";
align = "blast";
mismatch = "-1.0";
gapopen = "-5.0";
gapextend = "-2.0";
-
-
}
//*******************************************************/
form = "integral";
ends = "T";
processors = "1";
+ size = "1000";
search = "suffix";
ksize = "7";
align = "blast";