#include "unifracweightedcommand.h"
+//**********************************************************************************************************************
+vector<string> UnifracWeightedCommand::getValidParameters(){
+ try {
+ string Array[] = {"groups","iters","distance","random","processors","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+UnifracWeightedCommand::UnifracWeightedCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["weighted"] = tempOutNames;
+ outputTypes["wsummary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> UnifracWeightedCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> UnifracWeightedCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"tree","group"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracWeightedCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
/***********************************************************/
UnifracWeightedCommand::UnifracWeightedCommand(string option) {
try {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["weighted"] = tempOutNames;
+ outputTypes["wsummary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+
if (globaldata->gTree.size() == 0) {//no trees were read
m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); m->mothurOutEndLine(); abort = true; }
tmap = globaldata->gTreemap;
sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".wsummary";
m->openOutputFile(sumFile, outSum);
- outputNames.push_back(sumFile);
+ outputNames.push_back(sumFile); outputTypes["wsummary"].push_back(sumFile);
util = new SharedUtil();
string s; //to make work with setgroups
void UnifracWeightedCommand::help(){
try {
m->mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n");
- m->mothurOut("The unifrac.weighted command parameters are groups, iters, distance and random. No parameters are required.\n");
+ m->mothurOut("The unifrac.weighted command parameters are groups, iters, distance, processors and random. No parameters are required.\n");
m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n");
m->mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n");
m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is false, meaning don't compare your trees with randomly generated trees.\n");
+ m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
m->mothurOut("The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n");
m->mothurOut("Example unifrac.weighted(groups=A-B-C, iters=500).\n");
m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
if (random) {
output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted", itersString);
outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted");
+ outputTypes["weighted"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted");
}
userData = weighted->getValues(T[i], processors, outputDir); //userData[0] = weightedscore
}
if (random) {
- vector<double> sums = weighted->getBranchLengthSums(T[i]);
//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
vector< vector<string> > namesOfGroupCombos;
for (int a=0; a<numGroups; a++) {
- for (int l = a+1; l < numGroups; l++) {
+ for (int l = 0; l < a; l++) {
vector<string> groups; groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
namesOfGroupCombos.push_back(groups);
}
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
- driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
+ driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
}else{
- createProcesses(T[i], namesOfGroupCombos, sums, rScores);
+ createProcesses(T[i], namesOfGroupCombos, rScores);
}
#else
- driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
+ driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), rScores);
#endif
if (m->control_pressed) { delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
}
/**************************************************************************************************/
-int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector<double>& sums, vector< vector<double> >& scores) {
+int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector< vector<double> >& scores) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 1;
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, sums, scores);
+ driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, scores);
//pass numSeqs to parent
ofstream out;
}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
- driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, sums, scores);
+ driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, scores);
//force parent to wait until all the processes are done
for (int i=0;i<(processors-1);i++) {
}
/**************************************************************************************************/
-int UnifracWeightedCommand::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums, vector< vector<double> >& scores) {
+int UnifracWeightedCommand::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector< vector<double> >& scores) {
try {
Tree* randT = new Tree();
if (m->control_pressed) { delete randT; return 0; }
//get wscore of random tree
- EstOutput randomData = weighted->getValues(randT, groupA, groupB, sums);
+ EstOutput randomData = weighted->getValues(randT, groupA, groupB);
if (m->control_pressed) { delete randT; return 0; }
string phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.dist";
outputNames.push_back(phylipFileName);
+ outputTypes["phylip"].push_back(phylipFileName);
ofstream out;
m->openOutputFile(phylipFileName, out);
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