//**********************************************************************************************************************
-TreeGroupCommand::TreeGroupCommand(string option){
+TreeGroupCommand::TreeGroupCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
else { globaldata->setNameFile(namefile); }
//error checking on files
- if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { mothurOut("You must run the read.otu command or provide a distance file before running the tree.shared command."); mothurOutEndLine(); abort = true; }
- else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); mothurOutEndLine(); abort = true; }
+ if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { m->mothurOut("You must run the read.otu command or provide a distance file before running the tree.shared command."); m->mothurOutEndLine(); abort = true; }
+ else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; }
if (columnfile != "") {
- if (namefile == "") { mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
+ if (namefile == "") { m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); abort = true; }
}
//check for optional parameter and set defaults
}
catch(exception& e) {
- errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
+ m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
exit(1);
}
}
void TreeGroupCommand::help(){
try {
- mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n");
- mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n");
- mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision and label.\n");
- mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
- mothurOut("The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n");
- mothurOut("The phylip or column parameter are required if you do not run the read.otu command first, and only one may be used. If you use a column file the name filename is required. \n");
- mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
- mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
- mothurOut("Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n");
- mothurOut("The default value for groups is all the groups in your groupfile.\n");
- mothurOut("The default value for calc is jclass-thetayc.\n");
- mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n");
+ m->mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n");
+ m->mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n");
+ m->mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision and label.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
+ m->mothurOut("The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n");
+ m->mothurOut("The phylip or column parameter are required if you do not run the read.otu command first, and only one may be used. If you use a column file the name filename is required. \n");
+ m->mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
+ m->mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
+ m->mothurOut("Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
+ m->mothurOut("The default value for calc is jclass-thetayc.\n");
+ m->mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n");
validCalculator->printCalc("treegroup", cout);
- mothurOut("Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n");
- mothurOut("Example tree.shared(phylip=abrecovery.dist).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ m->mothurOut("Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n");
+ m->mothurOut("Example tree.shared(phylip=abrecovery.dist).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
}
catch(exception& e) {
- errorOut(e, "TreeGroupCommand", "help");
+ m->errorOut(e, "TreeGroupCommand", "help");
exit(1);
}
}
//**********************************************************************************************************************
TreeGroupCommand::~TreeGroupCommand(){
+ globaldata->Groups.clear();
if (abort == false) {
if (format == "sharedfile") { delete read; delete input; globaldata->ginput = NULL; }
if (format == "sharedfile") {
//if the users entered no valid calculators don't execute command
- if (treeCalculators.size() == 0) { mothurOut("You have given no valid calculators."); mothurOutEndLine(); return 0; }
+ if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
//you have groups
read = new ReadOTUFile(globaldata->inputFileName);
lookup = input->getSharedRAbundVectors();
lastLabel = lookup[0]->getLabel();
- if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups. I cannot run the command."); mothurOutEndLine(); return 0; }
+ if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0; }
//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";
+ outputNames.push_back(outputFile);
createTree();
- mothurOut("Tree complete. "); mothurOutEndLine();
+
+ if (m->control_pressed) { return 0; }
+
+ m->mothurOut("Tree complete. "); m->mothurOutEndLine();
+
}
//reset groups parameter
globaldata->Groups.clear();
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
- errorOut(e, "TreeGroupCommand", "execute");
+ m->errorOut(e, "TreeGroupCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
-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) {
- errorOut(e, "TreeGroupCommand", "createTree");
+ m->errorOut(e, "TreeGroupCommand", "createTree");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "TreeGroupCommand", "printSims");
+ m->errorOut(e, "TreeGroupCommand", "printSims");
exit(1);
}
}
/***********************************************************/
-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) {
- errorOut(e, "TreeGroupCommand", "makeSimsDist");
+ m->errorOut(e, "TreeGroupCommand", "makeSimsDist");
exit(1);
}
}
/***********************************************************/
-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){
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
processedLabels.insert(lookup[0]->getLabel());
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
processedLabels.insert(lookup[0]->getLabel());
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 (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; }
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "TreeGroupCommand", "makeSimsShared");
+ m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
exit(1);
}
}
/***********************************************************/
-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);
}
}
//create a new filename
outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
+ outputNames.push_back(outputFile);
for (int k = 0; k < thisLookup.size(); k++) {
for (int l = k; l < thisLookup.size(); l++) {
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) {
- errorOut(e, "TreeGroupCommand", "process");
+ m->errorOut(e, "TreeGroupCommand", "process");
exit(1);
}
}