#include "sharedbraycurtis.h"
+//**********************************************************************************************************************
+vector<string> HeatMapSimCommand::setParameters(){
+ try {
+ CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","svg",false,false,true); parameters.push_back(pshared);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","svg",false,false); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pcount);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName","svg",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, count, 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 a shared file, and you may use the groups, label and calc parameter. \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);
+ }
+}
+//**********************************************************************************************************************
+string HeatMapSimCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "svg") { pattern = "[filename],svg"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "HeatMapCommand", "getOutputPattern");
+ 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){
+HeatMapSimCommand::HeatMapSimCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
- lines.clear();
- labels.clear();
- Groups.clear();
- Estimators.clear();
-
+
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string AlignArray[] = {"groups","line","label", "calc"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ 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 (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- //make sure the user has already run the read.otu command
- if (globaldata->getSharedFile() == "") {
- cout << "You must read a list and a group, or a shared before you can use the heatmap.sim command." << endl; 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; }
+ }
+
+ it = parameters.find("count");
+ //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["count"] = inputDir + it->second; }
+ }
}
- //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; }
+ //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); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+
+ //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 {
+ countfile = m->getCountTableFile();
+ if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You need to provide a name or count file 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") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
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 == "")) {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- lines = globaldata->lines;
- }
-
+
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "jest-thetayc"; }
else {
- if (calc == "default") { calc = "jest-thetayc"; }
+ if (calc == "default") { calc = "jest-thetayc"; }
}
- splitAtDash(calc, Estimators);
-
+ 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 {
- splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ 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) {
- validCalculator = new ValidCalculators();
- heatmap = new HeatMapSim();
+ ValidCalculators validCalculator;
int i;
for (i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("heat", Estimators[i]) == true) {
+ if (validCalculator.isValidCalculator("heat", Estimators[i]) == true) {
if (Estimators[i] == "jabund") {
heatCalculators.push_back(new JAbund());
}else if (Estimators[i] == "sorabund") {
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the HeatMapSimCommand class function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
-
//**********************************************************************************************************************
-void HeatMapSimCommand::help(){
+int HeatMapSimCommand::execute(){
try {
- cout << "The heatmap.sim command can only be executed after a successful read.otu command." << "\n";
- cout << "The heatmap.sim command parameters are groups, calc, line and label. No parameters are required, but 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 in your heatmap." << "\n";
- cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes." << "\n";
- cout << "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, line=yourLines, label=yourLabels)." << "\n";
- cout << "Example heatmap.sim(groups=A-B-C, line=1-3-5, calc=jabund)." << "\n";
- cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
- validCalculator->printCalc("heat", cout);
- cout << "The default value for calc is jclass-thetayc." << "\n";
- cout << "The heatmap.sim command outputs a .svg file for each calculator you choose at each line or label you specify." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
-
+
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "HeatMapSimCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the HeatMapSimCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
-
-HeatMapSimCommand::~HeatMapSimCommand(){
- delete input;
- delete read;
- delete heatmap;
- delete validCalculator;
-}
-
-//**********************************************************************************************************************
-
-int HeatMapSimCommand::execute(){
+int HeatMapSimCommand::runCommandShared() {
try {
-
- if (abort == true) { return 0; }
-
- int count = 1;
-
//if the users entered no valid calculators don't execute command
- if (heatCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; }
+ if (heatCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; }
- //you have groups
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
+ input = new InputData(sharedfile, "sharedfile");
lookup = input->getSharedRAbundVectors();
- vector<SharedRAbundVector*> lastLookup = lookup;
-
- if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0;}
+ 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;
- 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))) {
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
- if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ //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){
- cout << lookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lookup, heatCalculators);
+ 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());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastLookup, heatCalculators);
+ 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(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
- lookup = input->getSharedRAbundVectors();
- count++;
+ 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++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ 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 {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
+
+ //run last label if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastLookup, heatCalculators);
+ 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]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//reset groups parameter
- globaldata->Groups.clear();
-
+ m->clearGroups();
+
+ delete input;
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "HeatMapSimCommand", "runCommandShared");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the HeatMapSimCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+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;
+ CountTable ct;
+ if (namefile != "") {
+ 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));
+ }
+ }else if (countfile != "") {
+ nameMap = NULL;
+ ct.readTable(countfile);
+ names = ct.getNamesOfSeqs();
+ }
+
+ //resize matrix
+ matrix.resize(names.size());
+ for (int i = 0; i < names.size(); i++) {
+ matrix[i].resize(names.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; }
+
+ if (namefile != "") {
+ 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;
+ }else if (countfile != "") {
+ int itA = ct.get(first);
+ int itB = ct.get(second);
+ matrix[itA][itB] = dist;
+ matrix[itB][itA] = dist;
+ }
+ }
+ in.close();
+
+ if (namefile != "") { 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);
- }
+ }
}
-
//**********************************************************************************************************************
+
+
+
+
+
+
projects / mothur.git / blobdiff