*/
#include "otuhierarchycommand.h"
+#include "inputdata.h"
//**********************************************************************************************************************
vector<string> OtuHierarchyCommand::setParameters(){
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 {
- m->splitAtDash(label, labels);
- if (labels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
+ m->splitAtDash(label, mylabels);
+ if (mylabels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
}
output = validParameter.validFile(parameters, "output", false); if (output == "not found") { output = "name"; }
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();
+ vector< vector<string> > 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 (lists.size() == 4) {
//if big is first swap them
- if (lists[0].getNumBins() < lists[1].getNumBins()) {
- reverse(lists.begin(), lists.end());
+ if (lists[0].size() < lists[2].size()) {
+ vector< vector<string> > tempLists;
+ tempLists.push_back(lists[2]);
+ tempLists.push_back(lists[3]);
+ tempLists.push_back(lists[0]);
+ tempLists.push_back(lists[1]);
+ lists = tempLists;
+ string tempLabel = list2Label;
+ list2Label = list1Label;
+ list1Label = tempLabel;
}
}else{
m->mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); m->mothurOutEndLine(); return 0;
}
//map sequences to bin number in the "little" otu
- map<string, int> littleBins;
- for (int i = 0; i < lists[0].getNumBins(); i++) {
+ map<string, int> littleBins;
+ vector<string> binLabels0 = lists[0];
+ for (int i = 0; i < lists[0].size(); i++) {
if (m->control_pressed) { return 0; }
-
- string bin = lists[0].get(i);
+ string bin = lists[1][i];
vector<string> names; m->splitAtComma(bin, names);
for (int j = 0; j < names.size(); j++) { littleBins[names[j]] = i; }
}
ofstream out;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
- variables["[distance1]"] = lists[0].getLabel();
+ variables["[distance1]"] = list1Label;
variables["[tag]"] = "-";
- variables["[distance2]"] = lists[1].getLabel();
+ variables["[distance2]"] = list2Label;
string outputFileName = getOutputFileName("otuheirarchy",variables);
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++) {
+ vector<string> binLabels1 = lists[2];
+ for (int i = 0; i < lists[2].size(); i++) {
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
- string binnames = lists[1].get(i);
+ string binnames = lists[3][i];
vector<string> names; m->splitAtComma(binnames, names);
-
//output column 1
if (output == "name") { out << binnames << '\t'; }
- else { out << (i+1) << '\t'; }
+ else { out << binLabels1[i] << '\t'; }
map<int, int> bins; //bin numbers in little that are in this bin in big
map<int, int>::iterator it;
string col2 = "";
for (it = bins.begin(); it != bins.end(); it++) {
- if (output == "name") { col2 += lists[0].get(it->first) + "\t"; }
- else { col2 += toString(it->first) + "\t"; }
+ if (output == "name") { col2 += lists[1][it->first] + "\t"; }
+ else { col2 += binLabels0[it->first] + "\t"; }
}
//output column 2
//**********************************************************************************************************************
//returns a vector of listVectors where "little" vector is first
-vector<ListVector> OtuHierarchyCommand::getListVectors() {
+vector< vector<string> > OtuHierarchyCommand::getListVectors() { //return value [0] -> otulabelsFirstLabel [1] -> binsFirstLabel [2] -> otulabelsSecondLabel [3] -> binsSecondLabel
try {
-
- int pos; //to use in smart distancing, position of last read in file
- int lastPos;
- vector<ListVector> lists;
+ vector< vector<string> > lists;
+
+ int count = 0;
+ for (set<string>::iterator it = mylabels.begin(); it != mylabels.end(); it++) {
+ string realLabel;
+ vector< vector<string> > thisList = getListVector(*it, realLabel);
+
+ if (m->control_pressed) { return lists; }
+
+ for (int i = 0; i < thisList.size(); i++) { lists.push_back(thisList[i]); }
+
+ if (count == 0) { list1Label = realLabel; count++; }
+ else { list2Label = realLabel; }
+ }
+
+ return lists;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "getListVectors");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector< vector<string> > OtuHierarchyCommand::getListVector(string label, string& realLabel){ //return value [0] -> otulabels [1] -> bins
+ try {
+ vector< vector<string> > myList;
+
+ InputData input(listFile, "list");
+ ListVector* list = input.getListVector();
+ string lastLabel = list->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> labels; labels.insert(label);
set<string> processedLabels;
set<string> userLabels = labels;
-
- //open file
- ifstream in;
- m->openInputFile(listFile, in);
- //get first list vector in file
- ListVector* list = NULL;
- string lastLabel = "";
- if (!in.eof()) {
- pos = in.tellg();
- lastPos = pos;
- list = new ListVector(in);
- m->gobble(in);
- lastLabel = list->getLabel();
- }
-
- while ((list != NULL) && (userLabels.size() != 0)) {
-
- if (m->control_pressed) { in.close(); delete list; return lists; }
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((list != NULL) && (userLabels.size() != 0)) {
+ if (m->control_pressed) { return myList; }
- //is this a listvector that we want?
if(labels.count(list->getLabel()) == 1){
-
- //make copy of listvector
- ListVector temp(*list);
- lists.push_back(temp);
-
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
+ break;
}
-
- //you have a label the user want that is smaller than this label and the last label has not already been processed
+
if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
- int savePos = in.tellg();
- //get smart distance line
delete list;
- in.seekg(lastPos);
- if (!in.eof()) {
- list = new ListVector(in);
- }else { list = NULL; }
+ list = input.getListVector(lastLabel);
- //make copy of listvector
- ListVector temp(*list);
- lists.push_back(temp);
-
processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
-
+ userLabels.erase(list->getLabel());
+
//restore real lastlabel to save below
- list->setLabel(saveLabel);
- in.seekg(savePos);
+ //list->setLabel(saveLabel);
+ break;
}
lastLabel = list->getLabel();
- lastPos = pos;
- //get next line
+ //get next line to process
+ //prevent memory leak
delete list;
- if (!in.eof()) {
- pos = in.tellg();
- list = new ListVector(in);
- m->gobble(in);
- }else { list = NULL; }
+ list = input.getListVector();
}
- if (m->control_pressed) { in.close(); return lists; }
+
+ if (m->control_pressed) { return myList; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}
}
- if (m->control_pressed) { in.close(); return lists; }
-
//run last label if you need to
if (needToRun == true) {
- if (list != NULL) { delete list; }
-
- in.seekg(lastPos);
- if (!in.eof()) {
- list = new ListVector(in);
-
- //make copy of listvector
- ListVector temp(*list);
- lists.push_back(temp);
-
- delete list;
- }
+ delete list;
+ list = input.getListVector(lastLabel);
}
- in.close();
- return lists;
+ //at this point the list vector has the right distance
+ myList.push_back(list->getLabels());
+ vector<string> bins;
+ for (int i = 0; i < list->getNumBins(); i++) {
+ if (m->control_pressed) { return myList; }
+ bins.push_back(list->get(i));
+ }
+ myList.push_back(bins);
+ realLabel = list->getLabel();
+
+ delete list;
+
+ return myList;
}
catch(exception& e) {
- m->errorOut(e, "OtuHierarchyCommand", "getListVectors");
+ m->errorOut(e, "OtuHierarchyCommand", "getListVector");
exit(1);
}
}
projects / mothur.git / blobdiff