A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */; };
A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87F12D37EC400DA6239 /* whittaker.cpp */; };
A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC480D12D788F20055BC5C /* linearalgebra.cpp */; };
+ A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC486612D795D60055BC5C /* pcacommand.cpp */; };
/* End PBXBuildFile section */
/* Begin PBXCopyFilesBuildPhase section */
A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
A7FC480C12D788F20055BC5C /* linearalgebra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = linearalgebra.h; sourceTree = "<group>"; };
A7FC480D12D788F20055BC5C /* linearalgebra.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = linearalgebra.cpp; sourceTree = "<group>"; };
+ A7FC486512D795D60055BC5C /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = "<group>"; };
+ A7FC486612D795D60055BC5C /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = "<group>"; };
C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = "<group>"; };
/* End PBXFileReference section */
A7E9B78212D37EC400DA6239 /* parselistscommand.h */,
A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */,
A7E9B78612D37EC400DA6239 /* parsimonycommand.h */,
+ A7FC486512D795D60055BC5C /* pcacommand.h */,
+ A7FC486612D795D60055BC5C /* pcacommand.cpp */,
A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */,
A7E9B78812D37EC400DA6239 /* pcoacommand.h */,
A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */,
A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */,
A70332B712D3A13400761E33 /* makefile in Sources */,
A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */,
+ A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
#include "trimflowscommand.h"
#include "corraxescommand.h"
#include "shhhercommand.h"
+#include "pcacommand.h"
/*******************************************************/
commands["indicator"] = "indicator";
commands["consensus.seqs"] = "consensus.seqs";
commands["corr.axes"] = "corr.axes";
+ commands["pca"] = "pca";
commands["pairwise.seqs"] = "MPIEnabled";
commands["pipeline.pds"] = "MPIEnabled";
commands["classify.seqs"] = "MPIEnabled";
else if(commandName == "phylotype") { command = new PhylotypeCommand(optionString); }
else if(commandName == "mgcluster") { command = new MGClusterCommand(optionString); }
else if(commandName == "pre.cluster") { command = new PreClusterCommand(optionString); }
- else if(commandName == "pcoa") { command = new PCOACommand(optionString); }
+ else if(commandName == "pcoa") { command = new PCOACommand(optionString); }
+ else if(commandName == "pca") { command = new PCACommand(optionString); }
else if(commandName == "otu.hierarchy") { command = new OtuHierarchyCommand(optionString); }
else if(commandName == "set.dir") { command = new SetDirectoryCommand(optionString); }
else if(commandName == "set.logfile") { command = new SetLogFileCommand(optionString); }
else if(commandName == "phylotype") { pipecommand = new PhylotypeCommand(optionString); }
else if(commandName == "mgcluster") { pipecommand = new MGClusterCommand(optionString); }
else if(commandName == "pre.cluster") { pipecommand = new PreClusterCommand(optionString); }
- else if(commandName == "pcoa") { pipecommand = new PCOACommand(optionString); }
+ else if(commandName == "pcoa") { pipecommand = new PCOACommand(optionString); }
+ else if(commandName == "pca") { pipecommand = new PCACommand(optionString); }
else if(commandName == "otu.hierarchy") { pipecommand = new OtuHierarchyCommand(optionString); }
else if(commandName == "set.dir") { pipecommand = new SetDirectoryCommand(optionString); }
else if(commandName == "set.logfile") { pipecommand = new SetLogFileCommand(optionString); }
else if(commandName == "mgcluster") { shellcommand = new MGClusterCommand(); }
else if(commandName == "pre.cluster") { shellcommand = new PreClusterCommand(); }
else if(commandName == "pcoa") { shellcommand = new PCOACommand(); }
+ else if(commandName == "pca") { shellcommand = new PCACommand(); }
else if(commandName == "otu.hierarchy") { shellcommand = new OtuHierarchyCommand(); }
else if(commandName == "set.dir") { shellcommand = new SetDirectoryCommand(); }
else if(commandName == "set.logfile") { shellcommand = new SetLogFileCommand(); }
// use smart distancing to get right sharedRabund and convert to relabund if needed //
/************************************************************************************/
if (sharedfile != "") {
- getShared();
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
- if (lookup[0] == NULL) { m->mothurOut("[ERROR] reading shared file."); m->mothurOutEndLine(); return 0; }
+ InputData* input = new InputData(sharedfile, "sharedfile");
+ getSharedFloat(input);
+ delete input;
- //fills lookupFloat with relative abundance values from lookup
- convertToRelabund();
-
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
+ if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
}else if (relabundfile != "") {
- getSharedFloat();
+ InputData* input = new InputData(relabundfile, "relabund");
+ getSharedFloat(input);
+ delete input;
+
if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
- if (pickedGroups) { eliminateZeroOTUS(lookupFloat); }
-
}else if (metadatafile != "") {
getMetadata(); //reads metadata file and store in lookupFloat, saves column headings in metadataLabels for later
if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
}
}
//**********************************************************************************************************************
-int CorrAxesCommand::getShared(){
+int CorrAxesCommand::getSharedFloat(InputData* input){
try {
- InputData* input = new InputData(sharedfile, "sharedfile");
- lookup = input->getSharedRAbundVectors();
- string lastLabel = lookup[0]->getLabel();
-
- if (label == "") { label = lastLabel; delete input; return 0; }
-
- //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;
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((lookup[0] != NULL) && (userLabels.size() != 0)) {
- if (m->control_pressed) { delete input; return 0; }
-
- if(labels.count(lookup[0]->getLabel()) == 1){
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
- break;
- }
-
- 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(lastLabel);
-
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
-
- //restore real lastlabel to save below
- lookup[0]->setLabel(saveLabel);
- break;
- }
-
- lastLabel = lookup[0]->getLabel();
-
- //get next line to process
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- lookup = input->getSharedRAbundVectors();
- }
-
-
- if (m->control_pressed) { delete input; return 0; }
-
- //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);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
- lookup = input->getSharedRAbundVectors(lastLabel);
- }
-
- delete input;
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "CorrAxesCommand", "getShared");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int CorrAxesCommand::getSharedFloat(){
- try {
- InputData* input = new InputData(relabundfile, "relabund");
lookupFloat = input->getSharedRAbundFloatVectors();
string lastLabel = lookupFloat[0]->getLabel();
- if (label == "") { label = lastLabel; delete input; return 0; }
+ if (label == "") { label = lastLabel; return 0; }
//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);
//as long as you are not at the end of the file or done wih the lines you want
while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
- if (m->control_pressed) { delete input; return 0; }
+ if (m->control_pressed) { return 0; }
if(labels.count(lookupFloat[0]->getLabel()) == 1){
processedLabels.insert(lookupFloat[0]->getLabel());
}
- if (m->control_pressed) { delete input; return 0; }
+ if (m->control_pressed) { return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
}
- delete input;
return 0;
}
catch(exception& e) {
exit(1);
}
}
-/*****************************************************************/
-int CorrAxesCommand::convertToRelabund(){
- try {
-
- vector<SharedRAbundFloatVector*> newLookup;
- for (int i = 0; i < lookup.size(); i++) {
- SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
- temp->setLabel(lookup[i]->getLabel());
- temp->setGroup(lookup[i]->getGroup());
- newLookup.push_back(temp);
- }
-
- for (int i = 0; i < lookup.size(); i++) {
-
- for (int j = 0; j < lookup[i]->getNumBins(); j++) {
-
- if (m->control_pressed) { return 0; }
-
- int abund = lookup[i]->getAbundance(j);
-
- float relabund = abund / (float) lookup[i]->getNumSeqs();
-
- newLookup[i]->push_back(relabund, lookup[i]->getGroup());
- }
- }
-
- if (pickedGroups) { eliminateZeroOTUS(newLookup); }
-
- lookupFloat = newLookup;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "CorrAxesCommand", "convertToRelabund");
- exit(1);
- }
-}
//**********************************************************************************************************************
int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thislookup) {
try {
*/
#include "command.hpp"
-#include "sharedrabundvector.h"
#include "sharedrabundfloatvector.h"
#include "inputdata.h"
vector<string> outputNames, Groups;
map<string, vector<string> > outputTypes;
- vector<SharedRAbundVector*> lookup;
vector<SharedRAbundFloatVector*> lookupFloat;
vector<string> metadataLabels;
- int getShared();
- int getSharedFloat();
+ int getSharedFloat(InputData*);
int getMetadata();
- int convertToRelabund();
int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
map<string, vector<float> > readAxes();
int calcPearson(map<string, vector<float> >&, ofstream&);
class SharedOrderVector;
class SharedSAbundVector;
class SharedRAbundVector;
+class SharedRAbundFloatVector;
class DataVector {
int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
try {
- if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
-
for (int i = 0; i < thisLookUp.size(); i++) {
out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t';
}
}
//**********************************************************************************************************************
-int GetRelAbundCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
- try {
-
- vector<SharedRAbundVector*> newLookup;
- for (int i = 0; i < thislookup.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector();
- temp->setLabel(thislookup[i]->getLabel());
- temp->setGroup(thislookup[i]->getGroup());
- newLookup.push_back(temp);
- }
-
- //for each bin
- for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
- if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
-
- //look at each sharedRabund and make sure they are not all zero
- bool allZero = true;
- for (int j = 0; j < thislookup.size(); j++) {
- if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
- }
-
- //if they are not all zero add this bin
- if (!allZero) {
- for (int j = 0; j < thislookup.size(); j++) {
- newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
- }
- }
- }
-
- for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
-
- thislookup = newLookup;
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "eliminateZeroOTUS");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
map<string, vector<string> > outputTypes;
int getRelAbundance(vector<SharedRAbundVector*>&, ofstream&);
- int eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup);
};
if (SharedRelAbund != NULL) {
return SharedRelAbund->getSharedRAbundFloatVectors();
}
+ }else if (format == "sharedfile") {
+ SharedRAbundVector* SharedRAbund = new SharedRAbundVector(fileHandle);
+ if (SharedRAbund != NULL) {
+ vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors();
+ vector<SharedRAbundFloatVector*> lookupFloat = SharedRAbund->getSharedRAbundFloatVectors(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup.clear();
+ return lookupFloat;
+ }
+
}
m->gobble(fileHandle);
}
}else{ break; }
m->gobble(in);
}
- }
+ }else if (format == "sharedfile") {
+ while (in.eof() != true) {
+
+ SharedRAbundVector* SharedRAbund = new SharedRAbundVector(in);
+ if (SharedRAbund != NULL) {
+ thisLabel = SharedRAbund->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) {
+ in.close();
+ vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors();
+ vector<SharedRAbundFloatVector*> lookupFloat = SharedRAbund->getSharedRAbundFloatVectors(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup.clear();
+ return lookupFloat;
+ }else {
+ //so you don't loose this memory
+ vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors();
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup.clear();
+ delete SharedRAbund;
+ }
+ }else{ break; }
+ m->gobble(in);
+ }
+ }
}
+
//this is created to signal to calling function that the input file is at eof
vector<SharedRAbundFloatVector*> null; null.push_back(NULL);
product.resize(first_rows);
for(int i=0;i<first_rows;i++){
- product[i].resize(second_cols);
+ product[i].resize(first_cols);
}
for(int i=0;i<first_rows;i++){
}
}
/*********************************************************************************************************************************/
+vector< vector<double> > LinearAlgebra::calculateEuclidianDistance(vector< vector<double> >& axes, int dimensions){
+ try {
+ //make square matrix
+ vector< vector<double> > dists; dists.resize(axes.size());
+ for (int i = 0; i < dists.size(); i++) { dists[i].resize(axes.size(), 0.0); }
+
+ if (dimensions == 1) { //one dimension calc = abs(x-y)
+
+ for (int i = 0; i < dists.size(); i++) {
+
+ if (m->control_pressed) { return dists; }
+
+ for (int j = 0; j < i; j++) {
+ dists[i][j] = abs(axes[i][0] - axes[j][0]);
+ dists[j][i] = dists[i][j];
+ }
+ }
+
+ }else if (dimensions == 2) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2)
+
+ for (int i = 0; i < dists.size(); i++) {
+
+ if (m->control_pressed) { return dists; }
+
+ for (int j = 0; j < i; j++) {
+ double firstDim = ((axes[i][0] - axes[j][0]) * (axes[i][0] - axes[j][0]));
+ double secondDim = ((axes[i][1] - axes[j][1]) * (axes[i][1] - axes[j][1]));
+
+ dists[i][j] = sqrt((firstDim + secondDim));
+ dists[j][i] = dists[i][j];
+ }
+ }
+
+ }else if (dimensions == 3) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2 + (x3 - y3)^2)
+
+ for (int i = 0; i < dists.size(); i++) {
+
+ if (m->control_pressed) { return dists; }
+
+ for (int j = 0; j < i; j++) {
+ double firstDim = ((axes[i][0] - axes[j][0]) * (axes[i][0] - axes[j][0]));
+ double secondDim = ((axes[i][1] - axes[j][1]) * (axes[i][1] - axes[j][1]));
+ double thirdDim = ((axes[i][2] - axes[j][2]) * (axes[i][2] - axes[j][2]));
+
+ dists[i][j] = sqrt((firstDim + secondDim + thirdDim));
+ dists[j][i] = dists[i][j];
+ }
+ }
+
+ }else { m->mothurOut("[ERROR]: too many dimensions, aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ return dists;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "calculateEuclidianDistance");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+double LinearAlgebra::calcPearson(vector< vector<double> >& euclidDists, vector< vector<double> >& userDists){
+ try {
+
+ //find average for - X
+ vector<float> averageEuclid; averageEuclid.resize(euclidDists.size(), 0.0);
+ for (int i = 0; i < euclidDists.size(); i++) {
+ for (int j = 0; j < euclidDists[i].size(); j++) {
+ averageEuclid[i] += euclidDists[i][j];
+ }
+ }
+ for (int i = 0; i < averageEuclid.size(); i++) { averageEuclid[i] = averageEuclid[i] / (float) euclidDists.size(); }
+
+ //find average for - Y
+ vector<float> averageUser; averageUser.resize(userDists.size(), 0.0);
+ for (int i = 0; i < userDists.size(); i++) {
+ for (int j = 0; j < userDists[i].size(); j++) {
+ averageUser[i] += userDists[i][j];
+ }
+ }
+ for (int i = 0; i < averageUser.size(); i++) { averageUser[i] = averageUser[i] / (float) userDists.size(); }
+
+ double numerator = 0.0;
+ double denomTerm1 = 0.0;
+ double denomTerm2 = 0.0;
+
+ for (int i = 0; i < euclidDists.size(); i++) {
+
+ for (int k = 0; k < i; k++) {
+
+ float Yi = userDists[i][k];
+ float Xi = euclidDists[i][k];
+
+ numerator += ((Xi - averageEuclid[k]) * (Yi - averageUser[k]));
+ denomTerm1 += ((Xi - averageEuclid[k]) * (Xi - averageEuclid[k]));
+ denomTerm2 += ((Yi - averageUser[k]) * (Yi - averageUser[k]));
+ }
+ }
+
+ double denom = (sqrt(denomTerm1) * sqrt(denomTerm2));
+ double r = numerator / denom;
+
+ return r;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LinearAlgebra", "calculateEuclidianDistance");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
vector<vector<double> > matrix_mult(vector<vector<double> >, vector<vector<double> >);
int tred2(vector<vector<double> >&, vector<double>&, vector<double>&);
int qtli(vector<double>&, vector<double>&, vector<vector<double> >&);
-
+ vector< vector<double> > calculateEuclidianDistance(vector<vector<double> >&, int);
+ double calcPearson(vector<vector<double> >&, vector<vector<double> >&);
private:
MothurOut* m;
int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
try {
- if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
}
}
//**********************************************************************************************************************
-int MetaStatsCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
- try {
-
- vector<SharedRAbundVector*> newLookup;
- for (int i = 0; i < thislookup.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector();
- temp->setLabel(thislookup[i]->getLabel());
- temp->setGroup(thislookup[i]->getGroup());
- newLookup.push_back(temp);
- }
-
- //for each bin
- for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
- if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
-
- //look at each sharedRabund and make sure they are not all zero
- bool allZero = true;
- for (int j = 0; j < thislookup.size(); j++) {
- if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
- }
-
- //if they are not all zero add this bin
- if (!allZero) {
- for (int j = 0; j < thislookup.size(); j++) {
- newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
- }
- }
- }
-
- for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
-
- thislookup = newLookup;
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "MetaStatsCommand", "eliminateZeroOTUS");
- exit(1);
- }
-}
-//**********************************************************************************************************************
float threshold;
int process(vector<SharedRAbundVector*>&);
- int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
int driver(int, int, vector<SharedRAbundVector*>&);
};
--- /dev/null
+/*
+ * pcacommand.cpp
+ * mothur
+ *
+ * Created by westcott on 1/7/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "pcacommand.h"
+#include "inputdata.h"
+
+//**********************************************************************************************************************
+vector<string> PCACommand::getValidParameters(){
+ try {
+ string Array[] = {"label", "groups","metric","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PCACommand::PCACommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["pca"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "PCACommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PCACommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PCACommand::getRequiredFiles(){
+ try {
+ string Array[] = {"shared","relabund","or"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+PCACommand::PCACommand(string option) {
+ try {
+ abort = false;
+
+ globaldata = GlobalData::getInstance();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"label","groups","metric","outputdir", "inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser. getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+ //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 = ""; }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["pca"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
+
+ //make sure the user has already run the read.otu command
+ if ((globaldata->getSharedFile() == "") && (globaldata->getRelAbundFile() == "")) {
+ m->mothurOut("You must read a list and a group, shared or relabund file before you can use the pca command."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if (globaldata->getSharedFile() != "") { mode = "shared"; inputFile = globaldata->getSharedFile(); }
+ if (globaldata->getRelAbundFile() != "") { mode = "relabund"; inputFile = globaldata->getRelAbundFile(); }
+
+ //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 += m->hasPath(inputFile); //if user entered a file with a path then preserve it
+ }
+
+ string temp = validParameter.validFile(parameters, "metric", false); if (temp == "not found"){ temp = "T"; }
+ metric = m->isTrue(temp);
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); }
+ else { m->splitAtDash(label, labels); }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else { m->splitAtDash(groups, Groups); }
+ globaldata->Groups = Groups;
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "PCACommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void PCACommand::help(){
+ try {
+ m->mothurOut("The pca command can only be run after a successful read.otu command."); m->mothurOutEndLine();
+ m->mothurOut("The pca command parameters are label, groups and metric. No parameters are required."); m->mothurOutEndLine();
+ m->mothurOut("The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multpile labels may be separated by dashes.\n");
+ m->mothurOut("The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n");
+ m->mothurOut("The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"); m->mothurOutEndLine();
+ m->mothurOut("Example pca(groups=yourGroups).\n");
+ m->mothurOut("Example pca(groups=A-B-C).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "help");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PCACommand::~PCACommand(){}
+//**********************************************************************************************************************
+int PCACommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ cout.setf(ios::fixed, ios::floatfield);
+ cout.setf(ios::showpoint);
+ cerr.setf(ios::fixed, ios::floatfield);
+ cerr.setf(ios::showpoint);
+
+ //get first line of shared file
+ vector< vector<double> > matrix;
+ InputData* input;
+ if (mode == "shared") {
+ input = new InputData(inputFile, "sharedfile");
+ }else if (mode == "relabund") {
+ input = new InputData(inputFile, "relabund");
+ }else { m->mothurOut("[ERROR]: filetype not recognized."); m->mothurOutEndLine(); return 0; }
+
+ vector<SharedRAbundFloatVector*> lookupFloat = input->getSharedRAbundFloatVectors();
+ string lastLabel = lookupFloat[0]->getLabel();
+
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //if the user gave no labels, then use the first one read
+ if (labels.size() == 0) {
+ label = lastLabel;
+
+ process(lookupFloat);
+ }
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } lookupFloat.clear(); return 0; }
+
+ if(labels.count(lookupFloat[0]->getLabel()) == 1){
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+
+ process(lookupFloat);
+ }
+
+ if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookupFloat[0]->getLabel();
+
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } lookupFloat.clear();
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+
+ process(lookupFloat);
+
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookupFloat[0]->setLabel(saveLabel);
+ }
+
+ lastLabel = lookupFloat[0]->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } lookupFloat.clear();
+ lookupFloat = input->getSharedRAbundFloatVectors();
+ }
+
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } lookupFloat.clear(); return 0; }
+
+ //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);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } } lookupFloat.clear();
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+
+ process(lookupFloat);
+
+ for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } } lookupFloat.clear();
+ }
+
+ for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } } lookupFloat.clear();
+ delete input;
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ 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) {
+ m->errorOut(e, "PCACommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector< vector<double> > PCACommand::createMatrix(vector<SharedRAbundFloatVector*> lookupFloat){
+ try {
+ vector< vector<double> > matrix; matrix.resize(lookupFloat.size());
+
+ //fill matrix with shared files relative abundances
+ for (int i = 0; i < lookupFloat.size(); i++) {
+ for (int j = 0; j < lookupFloat[i]->getNumBins(); j++) {
+ matrix[i].push_back(lookupFloat[i]->getAbundance(j));
+ }
+ }
+
+ vector< vector<double> > transposeMatrix; transposeMatrix.resize(matrix[0].size());
+ for (int i = 0; i < transposeMatrix.size(); i++) {
+ for (int j = 0; j < matrix.size(); j++) {
+ transposeMatrix[i].push_back(matrix[j][i]);
+ }
+ }
+
+ matrix = linearCalc.matrix_mult(matrix, transposeMatrix);
+
+ return matrix;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "createMatrix");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
+ try {
+ m->mothurOut("\nProcessing " + lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+
+ vector< vector<double> > matrix; matrix.resize(lookupFloat.size());
+
+ //fill matrix with shared files relative abundances
+ for (int i = 0; i < lookupFloat.size(); i++) {
+ for (int j = 0; j < lookupFloat[i]->getNumBins(); j++) {
+ matrix[i].push_back(lookupFloat[i]->getAbundance(j));
+ }
+ }
+
+ vector< vector<double> > transposeMatrix; transposeMatrix.resize(matrix[0].size());
+ for (int i = 0; i < transposeMatrix.size(); i++) {
+ for (int j = 0; j < matrix.size(); j++) {
+ transposeMatrix[i].push_back(matrix[j][i]);
+ }
+ }
+
+ matrix = linearCalc.matrix_mult(matrix, transposeMatrix);
+
+ double offset = 0.0000;
+ vector<double> d;
+ vector<double> e;
+ vector<vector<double> > G = matrix;
+ vector<vector<double> > copy_G;
+
+ for(int count=0;count<2;count++){
+ linearCalc.tred2(G, d, e); if (m->control_pressed) { return 0; }
+ linearCalc.qtli(d, e, G); if (m->control_pressed) { return 0; }
+ offset = d[d.size()-1];
+ if(offset > 0.0) break;
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
+ string outputFileName = fbase + lookupFloat[0]->getLabel();
+ output(outputFileName, globaldata->Groups, G, d);
+
+ if (metric) {
+
+ for (int i = 1; i < 4; i++) {
+
+ vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ double corr = linearCalc.calcPearson(EuclidDists, matrix); //G is the pcoa file, D is the users distance matrix
+
+ m->mothurOut("Pearson's coefficient using " + toString(i) + " axis: " + toString(corr)); m->mothurOutEndLine();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "process");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+
+void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
+ try {
+ int rank = name_list.size();
+ double dsum = 0.0000;
+ for(int i=0;i<rank;i++){
+ dsum += d[i];
+ for(int j=0;j<rank;j++){
+ if(d[j] >= 0) { G[i][j] *= pow(d[j],0.5); }
+ else { G[i][j] = 0.00000; }
+ }
+ }
+
+ ofstream pcaData((fnameRoot+".pca").c_str(), ios::trunc);
+ pcaData.setf(ios::fixed, ios::floatfield);
+ pcaData.setf(ios::showpoint);
+ outputNames.push_back(fnameRoot+".pca");
+ outputTypes["pca"].push_back(fnameRoot+".pca");
+
+ ofstream pcaLoadings((fnameRoot+".pca.loadings").c_str(), ios::trunc);
+ pcaLoadings.setf(ios::fixed, ios::floatfield);
+ pcaLoadings.setf(ios::showpoint);
+ outputNames.push_back(fnameRoot+".pca.loadings");
+ outputTypes["loadings"].push_back(fnameRoot+".pca.loadings");
+
+ pcaLoadings << "axis\tloading\n";
+ for(int i=0;i<rank;i++){
+ pcaLoadings << i+1 << '\t' << d[i] * 100.0 / dsum << endl;
+ }
+
+ pcaData << "group";
+ for(int i=0;i<rank;i++){
+ pcaData << '\t' << "axis" << i+1;
+ }
+ pcaData << endl;
+
+ for(int i=0;i<rank;i++){
+ pcaData << name_list[i] << '\t';
+ for(int j=0;j<rank;j++){
+ pcaData << G[i][j] << '\t';
+ }
+ pcaData << endl;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "output");
+ exit(1);
+ }
+}
+/*********************************************************************************************************************************/
+
+
--- /dev/null
+#ifndef PCACOMMAND_H
+#define PCACOMMAND_H
+
+/*
+ * pcacommand.h
+ * mothur
+ *
+ * Created by westcott on 1/7/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "linearalgebra.h"
+#include "globaldata.hpp"
+
+
+/*****************************************************************/
+class PCACommand : public Command {
+
+public:
+ PCACommand(string);
+ PCACommand();
+ ~PCACommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ int execute();
+ void help();
+
+private:
+ GlobalData* globaldata;
+
+ bool abort, metric;
+ string outputDir, mode, inputFile, label, groups;
+ vector<string> outputNames, Groups;
+ set<string> labels;
+ map<string, vector<string> > outputTypes;
+ LinearAlgebra linearCalc;
+
+ vector< vector<double> > createMatrix(vector<SharedRAbundFloatVector*>);
+ int process(vector<SharedRAbundFloatVector*>&);
+ void output(string, vector<string>, vector<vector<double> >&, vector<double>);
+
+};
+
+/*****************************************************************/
+
+#endif
+
+
vector<string> tempOutNames;
outputTypes["pcoa"] = tempOutNames;
outputTypes["loadings"] = tempOutNames;
- outputTypes["corr"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "PCOACommand", "PCOACommand");
vector<string> tempOutNames;
outputTypes["pcoa"] = tempOutNames;
outputTypes["loadings"] = tempOutNames;
- outputTypes["corr"] = tempOutNames;
//required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
for (int i = 1; i < 4; i++) {
- vector< vector<double> > EuclidDists = calculateEuclidianDistance(G, i); //G is the pcoa file
+ vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
- double corr = calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
+ double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
m->mothurOut("Pearson's coefficient using " + toString(i) + " axis: " + toString(corr)); m->mothurOutEndLine();
}
}
/*********************************************************************************************************************************/
-vector< vector<double> > PCOACommand::calculateEuclidianDistance(vector< vector<double> >& axes, int dimensions){
- try {
- //make square matrix
- vector< vector<double> > dists; dists.resize(axes.size());
- for (int i = 0; i < dists.size(); i++) { dists[i].resize(axes.size(), 0.0); }
-
- if (dimensions == 1) { //one dimension calc = abs(x-y)
-
- for (int i = 0; i < dists.size(); i++) {
-
- if (m->control_pressed) { return dists; }
-
- for (int j = 0; j < i; j++) {
- dists[i][j] = abs(axes[i][0] - axes[j][0]);
- dists[j][i] = dists[i][j];
- }
- }
-
- }else if (dimensions == 2) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2)
-
- for (int i = 0; i < dists.size(); i++) {
-
- if (m->control_pressed) { return dists; }
-
- for (int j = 0; j < i; j++) {
- double firstDim = ((axes[i][0] - axes[j][0]) * (axes[i][0] - axes[j][0]));
- double secondDim = ((axes[i][1] - axes[j][1]) * (axes[i][1] - axes[j][1]));
-
- dists[i][j] = sqrt((firstDim + secondDim));
- dists[j][i] = dists[i][j];
- }
- }
-
- }else if (dimensions == 3) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2 + (x3 - y3)^2)
-
- for (int i = 0; i < dists.size(); i++) {
-
- if (m->control_pressed) { return dists; }
-
- for (int j = 0; j < i; j++) {
- double firstDim = ((axes[i][0] - axes[j][0]) * (axes[i][0] - axes[j][0]));
- double secondDim = ((axes[i][1] - axes[j][1]) * (axes[i][1] - axes[j][1]));
- double thirdDim = ((axes[i][2] - axes[j][2]) * (axes[i][2] - axes[j][2]));
-
- dists[i][j] = sqrt((firstDim + secondDim + thirdDim));
- dists[j][i] = dists[i][j];
- }
- }
-
- }else { m->mothurOut("[ERROR]: too many dimensions, aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
-
- return dists;
- }
- catch(exception& e) {
- m->errorOut(e, "PCOACommand", "calculateEuclidianDistance");
- exit(1);
- }
-}
-/*********************************************************************************************************************************/
-double PCOACommand::calcPearson(vector< vector<double> >& euclidDists, vector< vector<double> >& userDists){
- try {
-
- //find average for - X
- vector<float> averageEuclid; averageEuclid.resize(euclidDists.size(), 0.0);
- for (int i = 0; i < euclidDists.size(); i++) {
- for (int j = 0; j < euclidDists[i].size(); j++) {
- averageEuclid[i] += euclidDists[i][j];
- }
- }
- for (int i = 0; i < averageEuclid.size(); i++) { averageEuclid[i] = averageEuclid[i] / (float) euclidDists.size(); }
-
- //find average for - Y
- vector<float> averageUser; averageUser.resize(userDists.size(), 0.0);
- for (int i = 0; i < userDists.size(); i++) {
- for (int j = 0; j < userDists[i].size(); j++) {
- averageUser[i] += userDists[i][j];
- }
- }
- for (int i = 0; i < averageUser.size(); i++) { averageUser[i] = averageUser[i] / (float) userDists.size(); }
-
- double numerator = 0.0;
- double denomTerm1 = 0.0;
- double denomTerm2 = 0.0;
-
- for (int i = 0; i < euclidDists.size(); i++) {
-
- for (int k = 0; k < i; k++) {
-
- float Yi = userDists[i][k];
- float Xi = euclidDists[i][k];
-
- numerator += ((Xi - averageEuclid[k]) * (Yi - averageUser[k]));
- denomTerm1 += ((Xi - averageEuclid[k]) * (Xi - averageEuclid[k]));
- denomTerm2 += ((Yi - averageUser[k]) * (Yi - averageUser[k]));
- }
- }
-
- double denom = (sqrt(denomTerm1) * sqrt(denomTerm2));
- double r = numerator / denom;
-
- return r;
- }
- catch(exception& e) {
- m->errorOut(e, "PCOACommand", "calculateEuclidianDistance");
- exit(1);
- }
-}
-/*********************************************************************************************************************************/
void PCOACommand::get_comment(istream& f, char begin, char end){
try {
void read(string, vector<string>&, vector<vector<double> >&);
void recenter(double, vector<vector<double> >, vector<vector<double> >&);
void output(string, vector<string>, vector<vector<double> >&, vector<double>);
- vector< vector<double> > calculateEuclidianDistance(vector<vector<double> >&, int);
- double calcPearson(vector<vector<double> >&, vector<vector<double> >&);
};
util = new SharedUtil();
util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
-
+
+ bool remove = false;
for (int i = 0; i < lookup.size(); i++) {
//if this sharedrabund is not from a group the user wants then delete it.
if (util->isValidGroup(lookup[i]->getGroup(), globaldata->Groups) == false) {
delete lookup[i]; lookup[i] = NULL;
lookup.erase(lookup.begin()+i);
i--;
+ remove = true;
}
}
delete util;
+
+ if (remove) { eliminateZeroOTUS(lookup); }
return lookup;
}
exit(1);
}
}
-
+//**********************************************************************************************************************
+int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thislookup) {
+ try {
+
+ vector<SharedRAbundFloatVector*> newLookup;
+ for (int i = 0; i < thislookup.size(); i++) {
+ SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+
+ //look at each sharedRabund and make sure they are not all zero
+ bool allZero = true;
+ for (int j = 0; j < thislookup.size(); j++) {
+ if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
+ }
+
+ //if they are not all zero add this bin
+ if (!allZero) {
+ for (int j = 0; j < thislookup.size(); j++) {
+ newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+ }
+ }
+ }
+
+ for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
+
+ thislookup = newLookup;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundFloatVector", "eliminateZeroOTUS");
+ exit(1);
+ }
+}
/***********************************************************************/
float numSeqs;
string group;
int index;
+
+ int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
};
string holdLabel, nextLabel, groupN;
individual newguy;
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
- lookup.clear();
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; } lookup.clear();
if (globaldata->saveNextLabel == "") { f >> label; }
else { label = globaldata->saveNextLabel; }
util = new SharedUtil();
util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
-
+
+ bool remove = false;
for (int i = 0; i < lookup.size(); i++) {
//if this sharedrabund is not from a group the user wants then delete it.
if (util->isValidGroup(lookup[i]->getGroup(), globaldata->Groups) == false) {
+ remove = true;
delete lookup[i]; lookup[i] = NULL;
lookup.erase(lookup.begin()+i);
i--;
}
delete util;
+
+ if (remove) { eliminateZeroOTUS(lookup); }
return lookup;
}
exit(1);
}
}
+//**********************************************************************************************************************
+int SharedRAbundVector::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+ try {
+
+ vector<SharedRAbundVector*> newLookup;
+ for (int i = 0; i < thislookup.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+
+ //look at each sharedRabund and make sure they are not all zero
+ bool allZero = true;
+ for (int j = 0; j < thislookup.size(); j++) {
+ if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
+ }
+
+ //if they are not all zero add this bin
+ if (!allZero) {
+ for (int j = 0; j < thislookup.size(); j++) {
+ newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+ }
+ }
+ }
+
+ for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
+
+ thislookup = newLookup;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "eliminateZeroOTUS");
+ exit(1);
+ }
+ }
+
+/***********************************************************************/
+vector<SharedRAbundFloatVector*> SharedRAbundVector::getSharedRAbundFloatVectors(vector<SharedRAbundVector*> thislookup){
+ try {
+ vector<SharedRAbundFloatVector*> newLookupFloat;
+ for (int i = 0; i < lookup.size(); i++) {
+ SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookupFloat.push_back(temp);
+ }
+
+ for (int i = 0; i < thislookup.size(); i++) {
+
+ for (int j = 0; j < thislookup[i]->getNumBins(); j++) {
+
+ if (m->control_pressed) { return newLookupFloat; }
+
+ int abund = thislookup[i]->getAbundance(j);
+
+ float relabund = abund / (float) thislookup[i]->getNumSeqs();
+
+ newLookupFloat[i]->push_back(relabund, thislookup[i]->getGroup());
+ }
+ }
+
+ return newLookupFloat;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors");
+ exit(1);
+ }
+}
/***********************************************************************/
RAbundVector SharedRAbundVector::getRAbundVector() {
#include "datavector.hpp"
#include "sharedordervector.h"
#include "sharedsabundvector.h"
+#include "sharedrabundfloatvector.h"
#include "rabundvector.hpp"
#include "groupmap.h"
SharedSAbundVector getSharedSAbundVector();
SharedRAbundVector getSharedRAbundVector();
vector<SharedRAbundVector*> getSharedRAbundVectors();
+ vector<SharedRAbundFloatVector*> getSharedRAbundFloatVectors(vector<SharedRAbundVector*>);
private:
vector<individual> data;
int numSeqs;
string group;
int index;
+
+ int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
};
projects / mothur.git / commitdiff