+++ /dev/null
-/*
- * heatmapsimcommand.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 6/8/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "heatmapsimcommand.h"
-#include "sharedjabund.h"
-#include "sharedsorabund.h"
-#include "sharedjclass.h"
-#include "sharedsorclass.h"
-#include "sharedjest.h"
-#include "sharedsorest.h"
-#include "sharedthetayc.h"
-#include "sharedthetan.h"
-#include "sharedmorisitahorn.h"
-#include "sharedbraycurtis.h"
-
-
-//**********************************************************************************************************************
-vector<string> HeatMapSimCommand::setParameters(){
- try {
- CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
- CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-
- vector<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapSimCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string HeatMapSimCommand::getHelpString(){
- try {
- string helpString = "";
- ValidCalculators validCalculator;
- helpString += "The heatmap.sim command parameters are shared, phylip, column, name, groups, calc, fontsize and label. shared or phylip or column and name are required unless valid current files exist.\n";
- helpString += "There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n";
- helpString += "With the read.otu command you may use the groups, label and calc parameters. \n";
- helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n";
- helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and is also separated by dashes.\n";
- helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
- helpString += "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n";
- helpString += "Example heatmap.sim(groups=A-B-C, calc=jabund).\n";
- helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
- helpString += validCalculator.printCalc("heat");
- helpString += "The default value for calc is jclass-thetayc.\n";
- helpString += "The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n";
- helpString += "The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n";
- helpString += "Using the command this way, the phylip or column parameter are required, and only one may be used. If you use a column file the name filename is required. \n";
- helpString += "The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n";
- helpString += "Example heatmap.sim(phylip=amazonGroups.dist).\n";
- helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapSimCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-HeatMapSimCommand::HeatMapSimCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["svg"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-HeatMapSimCommand::HeatMapSimCommand(string option) {
- try {
- abort = false; calledHelp = false;
- allLines = 1;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- 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; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["svg"] = tempOutNames;
-
- format = "";
-
- //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 = ""; }
- else {
- string path;
- it = parameters.find("phylip");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["phylip"] = inputDir + it->second; }
- }
-
- it = parameters.find("column");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["column"] = inputDir + it->second; }
- }
-
- it = parameters.find("name");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["name"] = inputDir + it->second; }
- }
-
- it = parameters.find("shared");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["shared"] = inputDir + it->second; }
- }
- }
-
- //required parameters
- phylipfile = validParameter.validFile(parameters, "phylip", true);
- if (phylipfile == "not open") { abort = true; }
- else if (phylipfile == "not found") { phylipfile = ""; }
- else { format = "phylip"; inputfile = phylipfile; m-> setPhylipFile(phylipfile); if (outputDir == "") { outputDir += m->hasPath(phylipfile); } }
-
- columnfile = validParameter.validFile(parameters, "column", true);
- if (columnfile == "not open") { abort = true; }
- else if (columnfile == "not found") { columnfile = ""; }
- else { format = "column"; inputfile = columnfile; m->setColumnFile(columnfile); if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
-
- sharedfile = validParameter.validFile(parameters, "shared", true);
- if (sharedfile == "not open") { abort = true; }
- else if (sharedfile == "not found") { sharedfile = ""; }
- else { format = "shared"; inputfile = sharedfile; m->setSharedFile(sharedfile); if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
-
- namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
- else if (namefile == "not found") { namefile = ""; }
- else { m->setNameFile(namefile); }
-
-
- //error checking on files
- if ((sharedfile == "") && ((phylipfile == "") && (columnfile == ""))) {
- sharedfile = m->getSharedFile();
- if (sharedfile != "") { format = "shared"; inputfile = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
- else {
- //is there are current file available for either of these?
- //give priority to column, then phylip
- columnfile = m->getColumnFile();
- if (columnfile != "") { format = "column"; inputfile = columnfile; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
- else {
- phylipfile = m->getPhylipFile();
- if (phylipfile != "") { format = "phylip"; inputfile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("No valid current files. You must provide a shared or phylip or column file."); m->mothurOutEndLine();
- abort = true;
- }
- }
- }
- }
- else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the heatmap.sim command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; }
-
- if (columnfile != "") {
- if (namefile == "") {
- namefile = m->getNameFile();
- if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
- abort = true;
- }
- }
- }
-
-
- //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 = m->hasPath(inputfile); }
-
- //check for optional parameter and set defaults
- // ...at some point should added some additional type checking...
-
- label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; }
- else {
- if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
- calc = validParameter.validFile(parameters, "calc", false);
- if (calc == "not found") { calc = "jest-thetayc"; }
- else {
- if (calc == "default") { calc = "jest-thetayc"; }
- }
- m->splitAtDash(calc, Estimators);
- if (m->inUsersGroups("citation", Estimators)) {
- ValidCalculators validCalc; validCalc.printCitations(Estimators);
- //remove citation from list of calcs
- for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
- }
-
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
- else {
- m->splitAtDash(groups, Groups);
- m->setGroups(Groups);
- }
-
- string temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
- m->mothurConvert(temp, fontsize);
-
- if (abort == false) {
- ValidCalculators validCalculator;
-
- int i;
- for (i=0; i<Estimators.size(); i++) {
- if (validCalculator.isValidCalculator("heat", Estimators[i]) == true) {
- if (Estimators[i] == "jabund") {
- heatCalculators.push_back(new JAbund());
- }else if (Estimators[i] == "sorabund") {
- heatCalculators.push_back(new SorAbund());
- }else if (Estimators[i] == "jclass") {
- heatCalculators.push_back(new Jclass());
- }else if (Estimators[i] == "sorclass") {
- heatCalculators.push_back(new SorClass());
- }else if (Estimators[i] == "jest") {
- heatCalculators.push_back(new Jest());
- }else if (Estimators[i] == "sorest") {
- heatCalculators.push_back(new SorEst());
- }else if (Estimators[i] == "thetayc") {
- heatCalculators.push_back(new ThetaYC());
- }else if (Estimators[i] == "thetan") {
- heatCalculators.push_back(new ThetaN());
- }else if (Estimators[i] == "morisitahorn") {
- heatCalculators.push_back(new MorHorn());
- }else if (Estimators[i] == "braycurtis") {
- heatCalculators.push_back(new BrayCurtis());
- }
- }
- }
-
- }
- }
-
-
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int HeatMapSimCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- heatmap = new HeatMapSim(outputDir, inputfile, fontsize);
-
- if (format == "shared") {
- runCommandShared();
- }else{ runCommandDist(); }
-
- delete heatmap;
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); 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, "HeatMapSimCommand", "execute");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-int HeatMapSimCommand::runCommandShared() {
- try {
- //if the users entered no valid calculators don't execute command
- if (heatCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
-
- input = new InputData(sharedfile, "sharedfile");
- lookup = input->getSharedRAbundVectors();
- string lastLabel = lookup[0]->getLabel();
-
- if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); 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> processedLabels;
- set<string> userLabels = labels;
-
- if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
-
- //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) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
-
- if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); }
-
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
- }
-
- 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);
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); }
-
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
-
- //restore real lastlabel to save below
- lookup[0]->setLabel(saveLabel);
- }
-
- //prevent memory leak
-
- lastLabel = lookup[0]->getLabel();
-
- //get next line to process
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- lookup = input->getSharedRAbundVectors();
-
- }
-
-
- if (m->control_pressed) { delete input; m->clearGroups(); 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();
- }
- }
-
- if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
-
- //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);
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- vector<string> outfilenames = heatmap->getPic(lookup, heatCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); }
-
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- }
-
- if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
-
- //reset groups parameter
- m->clearGroups();
-
- delete input;
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapSimCommand", "runCommandShared");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int HeatMapSimCommand::runCommandDist() {
- try {
-
- vector< vector<double> > matrix;
- vector<string> names;
- ifstream in;
-
- //read distance file and create distance vector and names vector
- if (format == "phylip") {
- //read phylip file
- m->openInputFile(phylipfile, in);
-
- string name;
- int numSeqs;
- in >> numSeqs >> name;
-
- //save name
- names.push_back(name);
-
- //resize the matrix and fill with zeros
- matrix.resize(numSeqs);
- for(int i = 0; i < numSeqs; i++) {
- matrix[i].resize(numSeqs, 0.0);
- }
-
- //determine if matrix is square or lower triangle
- //if it is square read the distances for the first sequence
- char d;
- bool square;
- while((d=in.get()) != EOF){
-
- //is d a number meaning its square
- if(isalnum(d)){
- square = true;
- in.putback(d);
-
- for(int i=0;i<numSeqs;i++){
- in >> matrix[0][i];
- }
- break;
- }
-
- //is d a line return meaning its lower triangle
- if(d == '\n'){
- square = false;
- break;
- }
- }
-
- //read rest of matrix
- if (square == true) {
- for(int i=1;i<numSeqs;i++){
- in >> name;
- names.push_back(name);
-
- if (m->control_pressed) { return 0; }
-
- for(int j=0;j<numSeqs;j++) { in >> matrix[i][j]; }
- m->gobble(in);
- }
- }else {
- double dist;
- for(int i=1;i<numSeqs;i++){
- in >> name;
- names.push_back(name);
-
- if (m->control_pressed) { return 0; }
-
- for(int j=0;j<i;j++){
- in >> dist;
- matrix[i][j] = dist; matrix[j][i] = dist;
- }
- m->gobble(in);
- }
- }
- in.close();
- }else {
- //read names file
- NameAssignment* nameMap = new NameAssignment(namefile);
- nameMap->readMap();
-
- //put names in order in vector
- for (int i = 0; i < nameMap->size(); i++) {
- names.push_back(nameMap->get(i));
- }
-
- //resize matrix
- matrix.resize(nameMap->size());
- for (int i = 0; i < nameMap->size(); i++) {
- matrix[i].resize(nameMap->size(), 0.0);
- }
-
- //read column file
- string first, second;
- double dist;
- m->openInputFile(columnfile, in);
-
- while (!in.eof()) {
- in >> first >> second >> dist; m->gobble(in);
-
- if (m->control_pressed) { return 0; }
-
- map<string, int>::iterator itA = nameMap->find(first);
- map<string, int>::iterator itB = nameMap->find(second);
-
- if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1); }
- if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1); }
-
- //save distance
- matrix[itA->second][itB->second] = dist;
- matrix[itB->second][itA->second] = dist;
- }
- in.close();
-
- delete nameMap;
- }
-
-
- string outputFileName = heatmap->getPic(matrix, names);
- outputNames.push_back(outputFileName); //vector<vector<double>>, vector<string>
- outputTypes["svg"].push_back(outputFileName);
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapSimCommand", "runCommandDist");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
-
-
-
-
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