#include "globaldata.hpp"
#include "sparsematrix.hpp"
+#include "tree.h"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
#include "listvector.hpp"
commandName = commandString; //save command name to be used by other classes
//clears out data from previous read
- if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.list")) {
+ if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) {
clear();
}
splitAtComma(value, optionText);
splitAtEquals(key, value);
- if (key == "phylipfile" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";}
- if (key == "columnfile" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column";}
- if (key == "listfile" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
- if (key == "rabundfile" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
- if (key == "sabundfile" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
- if (key == "fastafile" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; }
- if (key == "namefile" ) { namefile = value; }
- if (key == "orderfile" ) { orderfile = value; }
- if (key == "groupfile" ) { groupfile = value; }
- if (key == "cutoff" ) { cutoff = value; }
- if (key == "precision" ) { precision = value; }
- if (key == "iters" ) { iters = value; }
- if (key == "jumble" ) { jumble = value; }
- if (key == "freq" ) { freq = value; }
- if (key == "method" ) { method = value; }
- if (key == "fileroot" ) { fileroot = value; }
+ if (key == "phylip" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; }
+ if (key == "column" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; }
+ if (key == "list" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
+ 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 == "treefile" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
+ if (key == "name" ) { namefile = value; }
+ if (key == "order" ) { orderfile = value; }
+ if (key == "group" ) { groupfile = value; }
+ if (key == "cutoff" ) { cutoff = value; }
+ if (key == "precision" ) { precision = value; }
+ if (key == "iters" ) { iters = value; }
+ if (key == "jumble" ) { jumble = value; }
+ if (key == "freq" ) { freq = value; }
+ if (key == "method" ) { method = value; }
+ if (key == "fileroot" ) { fileroot = value; }
if (key == "single") {//stores estimators in a vector
singleEstimators.clear(); //clears out old values
if (key == "line") {//stores lines to be used in a vector
lines.clear();
line = value;
+ label = "";
splitAtDash(value, lines);
allLines = 0;
}
if (key == "label") {//stores lines to be used in a vector
labels.clear();
label = value;
+ line = "";
splitAtDash(value, labels);
allLines = 0;
}
//saves the last parameter
value = optionText;
splitAtEquals(key, value);
- if (key == "phylipfile" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; }
- if (key == "columnfile" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; }
- if (key == "listfile" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
- if (key == "rabundfile" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
- if (key == "sabundfile" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
- if (key == "fastafile" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; }
- if (key == "namefile" ) { namefile = value; }
- if (key == "orderfile" ) { orderfile = value; }
- if (key == "groupfile" ) { groupfile = value; }
- if (key == "cutoff" ) { cutoff = value; }
- if (key == "precision" ) { precision = value; }
- if (key == "iters" ) { iters = value; }
- if (key == "jumble" ) { jumble = value; }
- if (key == "freq" ) { freq = value; }
- if (key == "method" ) { method = value; }
- if (key == "fileroot" ) { fileroot = value; }
+ if (key == "phylip" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; }
+ if (key == "column" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; }
+ if (key == "list" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
+ 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 == "treefile" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
+ if (key == "name" ) { namefile = value; }
+ if (key == "order" ) { orderfile = value; }
+ if (key == "group" ) { groupfile = value; }
+ if (key == "cutoff" ) { cutoff = value; }
+ if (key == "precision" ) { precision = value; }
+ if (key == "iters" ) { iters = value; }
+ if (key == "jumble" ) { jumble = value; }
+ if (key == "freq" ) { freq = value; }
+ if (key == "method" ) { method = value; }
+ if (key == "fileroot" ) { fileroot = value; }
if (key == "single") {//stores estimators in a vector
singleEstimators.clear(); //clears out old values
if (key == "line") {//stores lines to be used in a vector
lines.clear();
line = value;
+ label = "";
splitAtDash(value, lines);
allLines = 0;
}
if (key == "label") {//stores lines to be used in a vector
labels.clear();
label = value;
+ line = "";
splitAtDash(value, labels);
allLines = 0;
}
}
+ //set format for shared
+ if ((listfile != "") && (groupfile != "")) { format = "shared"; }
//input defaults
- if (commandString == "collect.single") {
- if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
+ if (commandName == "collect.single") {
+ if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
}
- if (commandString == "rarefaction.single") {
+ if (commandName == "rarefaction.single") {
if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators); }
}
- if (commandString == "collect.shared") {
+ if (commandName == "collect.shared") {
if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); }
}
- if (commandString == "summary.single") {
+ if (commandName == "summary.single") {
if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); }
}
- if (commandString == "summary.shared") {
+ if (commandName == "summary.shared") {
if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); }
}
- if (commandString == "rarefaction.shared") {
+ if (commandName == "rarefaction.shared") {
if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); }
}
+
+ //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")) {
+ if (listfile != "") { format = "list"; }
+ else if (sabundfile != "") { format = "sabund"; }
+ else if (rabundfile != "") { format = "rabund"; }
+ }
}
catch(exception& e) {
string GlobalData::getNameFile() { return namefile; }
string GlobalData::getGroupFile() { return groupfile; }
string GlobalData::getOrderFile() { return orderfile; }
+string GlobalData::getTreeFile() { return treefile; }
string GlobalData::getFastaFile() { return fastafile; }
string GlobalData::getCutOff() { return cutoff; }
string GlobalData::getFormat() { return format; }
groupfile = "";
orderfile = "";
fastafile = "";
+ treefile = "";
cutoff = "10.00";
format = "";
precision = "100";
iters = "1000";
line = "";
label = "";
- jumble = "0";
+ jumble = "1";
freq = "100";
method = "furthest";
fileroot = "";
single = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction";
- rarefaction = "rarefaction";
- shared = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
- sharedsummary = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
+ rarefaction = "sobs";
+ shared = "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
+ sharedsummary = "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
summary = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson";
sharedrarefaction = "sharedobserved";
}
projects / mothur.git / blobdiff