it = parameters.find("phylip");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["phylip"] = inputDir + it->second; }
}
it = parameters.find("column");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["column"] = inputDir + it->second; }
}
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
else {
if (calc == "default") { calc = "jclass-thetayc"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
string temp;
temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
//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"){
outputDir = "";
- outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
}
//**********************************************************************************************************************
TreeGroupCommand::~TreeGroupCommand(){
+ globaldata->Groups.clear();
if (abort == false) {
if (format == "sharedfile") { delete read; delete input; globaldata->ginput = NULL; }
//used in tree constructor
globaldata->runParse = false;
+ //clear globaldatas old tree names if any
+ globaldata->Treenames.clear();
+
+ //fills globaldatas tree names
+ globaldata->Treenames = globaldata->Groups;
+
+ //create treemap class from groupmap for tree class to use
+ tmap = new TreeMap();
+ tmap->makeSim(globaldata->gGroupmap);
+ globaldata->gTreemap = tmap;
+
+ if (m->control_pressed) { return 0; }
+
//create tree file
makeSimsShared();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
}else{
//read in dist file
filename = globaldata->inputFileName;
//make treemap
tmap = new TreeMap();
+
+ if (m->control_pressed) { return 0; }
+
tmap->makeSim(list);
globaldata->gTreemap = tmap;
//used in tree constructor
globaldata->runParse = false;
+ if (m->control_pressed) { return 0; }
+
makeSimsDist();
+
+ if (m->control_pressed) { return 0; }
//create a new filename
- outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "tre";
+ outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "tre";
outputNames.push_back(outputFile);
createTree();
+
+ if (m->control_pressed) { return 0; }
+
m->mothurOut("Tree complete. "); m->mothurOutEndLine();
+
}
//reset groups parameter
}
//**********************************************************************************************************************
-void TreeGroupCommand::createTree(){
+int TreeGroupCommand::createTree(){
try {
//create tree
t = new Tree();
//there are numGroups - 1 merges to do
for (int i = 0; i < (numGroups - 1); i++) {
float largest = -1000.0;
-
+
+ if (m->control_pressed) { delete t; return 1; }
+
int row, column;
//find largest value in sims matrix by searching lower triangle
for (int j = 1; j < simMatrix.size(); j++) {
//assemble tree
t->assembleTree();
+ if (m->control_pressed) { delete t; return 1; }
+
//print newick file
t->createNewickFile(outputFile);
//delete tree
delete t;
+
+ if (m->control_pressed) { remove(outputFile.c_str()); outputNames.pop_back(); return 1; }
+
+ return 0;
}
catch(exception& e) {
}
}
/***********************************************************/
-void TreeGroupCommand::makeSimsDist() {
+int TreeGroupCommand::makeSimsDist() {
try {
numGroups = list->size();
//initialize simMatrix
simMatrix.clear();
simMatrix.resize(numGroups);
- for (int m = 0; m < simMatrix.size(); m++) {
+ for (int k = 0; k < simMatrix.size(); k++) {
for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[m].push_back(0.0);
+ simMatrix[k].push_back(0.0);
}
}
for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
//similairity = -(distance-1)
simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
- simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
+ simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
+
+ if (m->control_pressed) { return 1; }
+
}
-
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "TreeGroupCommand", "makeSimsDist");
}
/***********************************************************/
-void TreeGroupCommand::makeSimsShared() {
+int TreeGroupCommand::makeSimsShared() {
try {
-
- //clear globaldatas old tree names if any
- globaldata->Treenames.clear();
-
- //fills globaldatas tree names
- globaldata->Treenames = globaldata->Groups;
-
- //create treemap class from groupmap for tree class to use
- tmap = new TreeMap();
- tmap->makeSim(globaldata->gGroupmap);
- globaldata->gTreemap = tmap;
-
set<string> processedLabels;
set<string> userLabels = labels;
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } return 1; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
userLabels.erase(lookup[0]->getLabel());
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup[0]->getLabel();
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
}
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } return 1; }
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
}
for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; }
+
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
}
/***********************************************************/
-void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
+int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
try{
EstOutput data;
vector<SharedRAbundVector*> subset;
//initialize simMatrix
simMatrix.clear();
simMatrix.resize(numGroups);
- for (int m = 0; m < simMatrix.size(); m++) {
+ for (int k = 0; k < simMatrix.size(); k++) {
for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[m].push_back(0.0);
+ simMatrix[k].push_back(0.0);
}
}
for (int g = 0; g < numGroups; g++) { index[g] = g; }
//create a new filename
- outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
+ outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
outputNames.push_back(outputFile);
for (int k = 0; k < thisLookup.size(); k++) {
subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
+
+ if (m->control_pressed) { return 1; }
+
//save values in similarity matrix
simMatrix[k][l] = data[0];
simMatrix[l][k] = data[0];
}
}
}
-
+
+ if (m->control_pressed) { return 1; }
//creates tree from similarity matrix and write out file
createTree();
+
+ if (m->control_pressed) { return 1; }
}
+
+ return 0;
}
catch(exception& e) {
projects / mothur.git / blobdiff