#include "otuhierarchycommand.h"
+//**********************************************************************************************************************
+vector<string> OtuHierarchyCommand::getValidParameters(){
+ try {
+ string Array[] = {"list","label","output","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+OtuHierarchyCommand::OtuHierarchyCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["otuheirarchy"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> OtuHierarchyCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"list","label"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> OtuHierarchyCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
OtuHierarchyCommand::OtuHierarchyCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["otuheirarchy"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
it = parameters.find("list");
//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["list"] = inputDir + it->second; }
}
//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(listFile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
else {
- splitAtDash(label, labels);
+ m->splitAtDash(label, labels);
if (labels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
}
int OtuHierarchyCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get listvectors that correspond to labels requested, (or use smart distancing to get closest listvector)
vector<ListVector> lists = getListVectors();
+ if (m->control_pressed) { outputTypes.clear(); return 0; }
+
//determine which is little and which is big, putting little first
if (lists.size() == 2) {
//if big is first swap them
//map sequences to bin number in the "little" otu
map<string, int> littleBins;
for (int i = 0; i < lists[0].getNumBins(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
string names = lists[0].get(i);
//parse bin
}
ofstream out;
- string outputFileName = outputDir + getRootName(getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
- openOutputFile(outputFileName, out);
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+ m->openOutputFile(outputFileName, out);
//go through each bin in "big" otu and output the bins in "little" otu which created it
for (int i = 0; i < lists[1].getNumBins(); i++) {
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+
string names = lists[1].get(i);
//output column 1
out.close();
+ if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
+
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName);
m->mothurOutEndLine();
return 0;
//open file
ifstream in;
- openInputFile(listFile, in);
+ m->openInputFile(listFile, in);
//get first list vector in file
ListVector* list = NULL;
pos = in.tellg();
lastPos = pos;
list = new ListVector(in);
- gobble(in);
+ m->gobble(in);
lastLabel = list->getLabel();
}
while ((list != NULL) && (userLabels.size() != 0)) {
+
+ if (m->control_pressed) { in.close(); delete list; return lists; }
//is this a listvector that we want?
if(labels.count(list->getLabel()) == 1){
}
//you have a label the user want that is smaller than this label and the last label has not already been processed
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
int savePos = in.tellg();
if (!in.eof()) {
pos = in.tellg();
list = new ListVector(in);
- gobble(in);
+ m->gobble(in);
}else { list = NULL; }
}
-
+ if (m->control_pressed) { in.close(); return lists; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
}
+ if (m->control_pressed) { in.close(); return lists; }
+
//run last label if you need to
if (needToRun == true) {
if (list != NULL) { delete list; }
}
}
-
+ in.close();
return lists;
}
catch(exception& e) {
projects / mothur.git / blobdiff