#include "globaldata.hpp"
-#include "sparsematrix.hpp"
#include "tree.h"
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-#include "listvector.hpp"
+#include "sparsematrix.hpp"
/*******************************************************/
clear();
gGroupmap = NULL;
gTree.clear();
+ Treenames.clear();
labels.clear(); lines.clear(); groups.clear();
allLines = 1;
}
cutoff = "1.0";
}
+ //set default value for cutoff
+ if (commandName == "distance") { cutoff = "1.0"; }
+
string key, value;
//reads in parameters and values
if((optionText != "") && (commandName != "help")){
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 == "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 == "calc") { calc = value; }
if (key == "step") { step = value; }
if (key == "form") { form = value; }
+ if (key == "sorted") { sorted = value; }
+ if (key == "vertical") { vertical = value; }
+ if (key == "trump") { trump = value; }
+ if (key == "filter") { filter = value; }
+ if (key == "soft") { soft = value; }
+ if (key == "scale") { scale = value; }
+ if (key == "ends" ) { ends = value; }
+ if (key == "processors" ) { processors = value; }
+
+
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 == "fileroot" ) { fileroot = value; }
if (key == "abund" ) { abund = value; }
if (key == "random" ) { randomtree = value; }
- if (key == "calc") { calc = value; }
+ if (key == "calc") { calc = value; }
if (key == "step") { step = value; }
if (key == "form") { form = value; }
+ if (key == "sorted") { sorted = value; }
+ if (key == "vertical") { vertical = value; }
+ if (key == "trump") { trump = value; }
+ if (key == "filter") { filter = value; }
+ if (key == "soft") { soft = value; }
+ if (key == "scale") { scale = value; }
+ if (key == "ends" ) { ends = value; }
+ if (key == "processors" ) { processors = value; }
+
if (key == "line") {//stores lines to be used in a vector
lines.clear();
if (line != "all") { splitAtDash(value, lines); allLines = 0; }
else { allLines = 1; }
}
+
if (key == "label") {//stores lines to be used in a vector
labels.clear();
lines.clear();
//input defaults for calculators
if (commandName == "collect.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; }
+
+ if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
splitAtDash(calc, Estimators);
}
if (commandName == "collect.shared") {
- if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
+
+ if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
if (commandName == "summary.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; }
+ if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
if (commandName == "summary.shared") {
- if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
+ if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
Estimators.clear();
splitAtDash(calc, Estimators);
}
+ if (commandName == "distance") {
+ if ((calc == "default") || (calc == "")) { calc = "onegap"; }
+ Estimators.clear();
+ splitAtDash(calc, Estimators);
+ }
+ if (commandName == "venn") {
+ if ((calc == "default") || (calc == "")) {
+ if (format == "list") { calc = "sobs"; }
+ else { calc = "sharedsobs"; }
+ }
+ 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 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::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::getGroups() { return groups; }
string GlobalData::getStep() { return step; }
string GlobalData::getForm() { return form; }
+string GlobalData::getSorted() { return sorted; }
+string GlobalData::getTrump() { return trump; }
+string GlobalData::getSoft() { return soft; }
+string GlobalData::getFilter() { return filter; }
+string GlobalData::getScale() { return scale; }
+string GlobalData::getEnds() { return ends; }
+string GlobalData::getProcessors() { return processors; }
+
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::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::setProcessors(string p) { processors = p; }
+
/*******************************************************/
//option definitions should go here...
helpRequest = "";
clear();
+ gListVector == NULL;
+ gSparseMatrix == NULL;
}
/*******************************************************/
groupfile = "";
orderfile = "";
fastafile = "";
+ nexusfile = "";
+ clustalfile = "";
treefile = "";
sharedfile = "";
cutoff = "10.00";
abund = "10";
step = "0.01";
form = "integral";
+ sorted = "T"; //F means don't sort, T means sort.
+ vertical = "";
+ trump = "";
+ filter = "";
+ soft = "";
+ scale = "log10";
+ ends = "T"; //yes
+ processors = "1";
+
}
//*******************************************************/
iters = "1000";
groups = "";
jumble = "1"; //0 means don't jumble, 1 means jumble.
+ sorted = "T"; //F means don't sort, T means sort.
randomtree = ""; //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
freq = "100";
method = "furthest";
abund = "10";
step = "0.01";
form = "integral";
+ ends = "T";
+ processors = "1";
}
/*******************************************************/
if(gorder != NULL) { delete gorder; }
}
/*******************************************************/
+
+/*******************************************************/
+void GlobalData::parseTreeFile() {
+ //only takes names from the first tree and assumes that all trees use the same names.
+ try {
+ string filename = treefile;
+ ifstream filehandle;
+ openInputFile(filename, filehandle);
+ int c, comment;
+ comment = 0;
+
+ //if you are not a nexus file
+ if ((c = filehandle.peek()) != '#') {
+ while((c = filehandle.peek()) != ';') {
+ while ((c = filehandle.peek()) != ';') {
+ // get past comments
+ if(c == '[') {
+ comment = 1;
+ }
+ if(c == ']'){
+ comment = 0;
+ }
+ if((c == '(') && (comment != 1)){ break; }
+ filehandle.get();
+ }
+
+ readTreeString(filehandle);
+ }
+ //if you are a nexus file
+ }else if ((c = filehandle.peek()) == '#') {
+ string holder = "";
+
+ // get past comments
+ while(holder != "translate" && holder != "Translate"){
+ if(holder == "[" || holder == "[!"){
+ comment = 1;
+ }
+ if(holder == "]"){
+ comment = 0;
+ }
+ filehandle >> holder;
+
+ //if there is no translate then you must read tree string otherwise use translate to get names
+ if(holder == "tree" && comment != 1){
+ //pass over the "tree rep.6878900 = "
+ while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
+
+ if (c == EOF ) { break; }
+ filehandle.putback(c); //put back first ( of tree.
+ readTreeString(filehandle);
+ break;
+ }
+ }
+
+ //use nexus translation rather than parsing tree to save time
+ if ((holder == "translate") || (holder == "Translate")) {
+
+ string number, name, h;
+ h = ""; // so it enters the loop the first time
+ while((h != ";") && (number != ";")) {
+ filehandle >> number;
+ filehandle >> name;
+
+ //c = , until done with translation then c = ;
+ h = name.substr(name.length()-1, name.length());
+ name.erase(name.end()-1); //erase the comma
+ Treenames.push_back(number);
+ }
+ if (number == ";") { Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name
+ }
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/*******************************************************/
+
+/*******************************************************/
+void GlobalData::readTreeString(ifstream& filehandle) {
+ try {
+ int c;
+ string name; //k
+
+ while((c = filehandle.peek()) != ';') {
+ //if you are a name
+ if ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
+ name = "";
+ c = filehandle.get();
+ // k = c;
+//cout << k << endl;
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
+ name += c;
+ c = filehandle.get();
+ // k = c;
+//cout << " in name while " << k << endl;
+ }
+
+//cout << "name = " << name << endl;
+ Treenames.push_back(name);
+ filehandle.putback(c);
+//k = c;
+//cout << " after putback" << k << endl;
+ }
+
+ if (c == ':') { //read until you reach the end of the branch length
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
+ c = filehandle.get();
+ // k = c;
+ //cout << " in branch while " << k << endl;
+ }
+ filehandle.putback(c);
+ }
+ c = filehandle.get();
+ if (c == ';') { break; }
+ // k = c;
+//cout << k << endl;
+
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/*******************************************************/
+
+/*******************************************************/
+
+
projects / mothur.git / blobdiff