globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
Groups.clear();
Estimators.clear();
else {
//valid paramters for this command
- string Array[] = {"line","label","calc","groups", "phylip", "column", "name", "precision","cutoff"};
+ string Array[] = {"label","calc","groups", "phylip", "column", "name", "precision","cutoff"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
else if (namefile == "not found") { namefile = ""; }
else { globaldata->setNameFile(namefile); }
-// format = globaldata->getFormat();
+ format = globaldata->getFormat();
//error checking on files
- if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { cout << "You must run the read.otu command or provide a distance file before running the tree.shared command." << endl; abort = true; }
- else if ((phylipfile != "") && (columnfile != "")) { cout << "When running the tree.shared command with a distance file you may not use both the column and the phylip parameters." << endl; abort = true; }
+ 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 (columnfile != "") {
- if (namefile == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
+ if (namefile == "") { mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
- line = validParameter.validFile(parameters, "line", false);
- if (line == "not found") { line = ""; }
- else {
- if(line != "all") { splitAtDash(line, lines); allLines = 0; }
- else { allLines = 1; }
- }
-
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
- //if the user has not specified any line or labels use the ones from read.otu
- else if((line == "") && (label == "")) {
+ //if the user has not specified any labels use the ones from read.otu
+ if(label == "") {
allLines = globaldata->allLines;
labels = globaldata->labels;
- lines = globaldata->lines;
}
groups = validParameter.validFile(parameters, "groups", false);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
void TreeGroupCommand::help(){
try {
- cout << "The tree.shared command creates a .tre to represent the similiarity between groups or sequences." << "\n";
- cout << "The tree.shared command can only be executed after a successful read.otu command or by providing a distance file." << "\n";
- cout << "The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision, line and label. You may not use line and label at the same time." << "\n";
- cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
- cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n";
- cout << "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";
- cout << "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";
- cout << "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
- cout << "Example tree.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund)." << "\n";
- cout << "The default value for groups is all the groups in your groupfile." << "\n";
- cout << "The default value for calc is jclass-thetayc." << "\n";
- cout << "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose." << "\n";
+ 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");
validCalculator->printCalc("treegroup", cout);
- cout << "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile)." << "\n";
- cout << "Example tree.shared(phylip=abrecovery.dist)." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ 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");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
TreeGroupCommand::~TreeGroupCommand(){
- delete input;
- if (format == "sharedfile") {delete read;}
- else { delete readMatrix; delete matrix; delete list; }
- delete tmap;
- delete validCalculator;
+ if (abort == false) {
+
+ if (format == "sharedfile") { delete read; delete input; globaldata->ginput = NULL; }
+ else { delete readMatrix; delete matrix; delete list; }
+ delete tmap; globaldata->gTreemap = NULL;
+ delete validCalculator;
+ }
}
if (format == "sharedfile") {
//if the users entered no valid calculators don't execute command
- if (treeCalculators.size() == 0) { cout << "You have given no valid calculators." << endl; return 0; }
+ if (treeCalculators.size() == 0) { mothurOut("You have given no valid calculators."); mothurOutEndLine(); return 0; }
//you have groups
read = new ReadOTUFile(globaldata->inputFileName);
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- lastLookup = lookup;
+ lastLabel = lookup[0]->getLabel();
+
+ if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups. I cannot run the command."); mothurOutEndLine(); return 0; }
+
+ //used in tree constructor
+ globaldata->runParse = false;
- if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0; }
-
//create tree file
makeSimsShared();
}else{
if(namefile != ""){
nameMap = new NameAssignment(namefile);
- nameMap->readMap(1,2);
+ nameMap->readMap();
}
else{
nameMap = NULL;
//fills globaldatas tree names
globaldata->Treenames = globaldata->Groups;
-
+
+ //used in tree constructor
+ globaldata->runParse = false;
+
makeSimsDist();
//create a new filename
outputFile = getRootName(globaldata->inputFileName) + "tre";
createTree();
- cout << "Tree complete. " << endl;
+ mothurOut("Tree complete. "); mothurOutEndLine();
}
//reset groups parameter
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "createTree");
exit(1);
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "printSims");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
void TreeGroupCommand::makeSimsDist() {
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "makeSimsDist");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
void TreeGroupCommand::makeSimsShared() {
try {
- int count = 1;
//clear globaldatas old tree names if any
globaldata->Treenames.clear();
set<string> processedLabels;
set<string> userLabels = labels;
- set<int> userLines = lines;
-
+
//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) || (userLines.size() != 0))) {
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
- cout << lookup[0]->getLabel() << '\t' << count << endl;
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
process(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- process(lastLookup);
+ if ((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(lastLabel);
+
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ process(lookup);
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
- //prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
+ lastLabel = lookup[0]->getLabel();
//get next line to process
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
- count++;
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- process(lastLookup);
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ process(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "makeSimsShared");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
}
}
}
-
+
//creates tree from similarity matrix and write out file
createTree();
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "process");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
projects / mothur.git / blobdiff