//check for required parameters
groupfile = validParameter.validFile(parameters, "group", true);
//check for required parameters
groupfile = validParameter.validFile(parameters, "group", true);
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
}
string temp;
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "10000"; }
}
string temp;
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "10000"; }
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "1.0"; }
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "1.0"; }
temp = validParameter.validFile(parameters, "step", false); if (temp == "not found") { temp = "0.01"; }
temp = validParameter.validFile(parameters, "step", false); if (temp == "not found") { temp = "0.01"; }
m->openOutputFile(newGroupFile, outGroups);
for (int i = 0; i < matrix->getNumSeqs(); i++) {
m->openOutputFile(newGroupFile, outGroups);
for (int i = 0; i < matrix->getNumSeqs(); i++) {
/********************************************************************************************/
//this is needed because when we read the matrix we sort it into groups in alphabetical order
//the rest of the command and the classes used in this command assume specific order
/********************************************************************************************/
/********************************************************************************************/
//this is needed because when we read the matrix we sort it into groups in alphabetical order
//the rest of the command and the classes used in this command assume specific order
/********************************************************************************************/
pValueCounts.resize(numGroups);
for(int i=0;i<numGroups;i++){
pValueCounts[i].assign(numGroups, 0);
}
pValueCounts.resize(numGroups);
for(int i=0;i<numGroups;i++){
pValueCounts[i].assign(numGroups, 0);
}
Progress* reading = new Progress();
for(int i=0;i<numGroups-1;i++) {
for(int j=i+1;j<numGroups;j++) {
Progress* reading = new Progress();
for(int i=0;i<numGroups-1;i++) {
for(int j=i+1;j<numGroups;j++) {
reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
reading->newLine(groupNames[i]+'-'+groupNames[j], iters);
int spoti = groupMap->groupIndex[groupNames[i]]; //neccessary in case user selects groups so you know where they are in the matrix
form->randomizeGroups(spoti,spotj);
if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj]) { pValueCounts[i][j]++; }
if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti]) { pValueCounts[j][i]++; }
form->randomizeGroups(spoti,spotj);
if(form->evaluatePair(spoti,spotj) >= savedDXYValues[spoti][spotj]) { pValueCounts[i][j]++; }
if(form->evaluatePair(spotj,spoti) >= savedDXYValues[spotj][spoti]) { pValueCounts[j][i]++; }
- for (int i = 0; i < m->Groups.size(); i++) {
- if (groupMap->isValidGroup(m->Groups[i]) != true) {
- m->mothurOut(m->Groups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
+ for (int i = 0; i < myGroups.size(); i++) {
+ if (groupMap->isValidGroup(myGroups[i]) != true) {
+ m->mothurOut(myGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();