*/
#include "readdistcommand.h"
+#include "readphylip.h"
+#include "readcolumn.h"
+#include "readmatrix.hpp"
-ReadDistCommand::ReadDistCommand(){
+ReadDistCommand::ReadDistCommand(string option){
try {
globaldata = GlobalData::getInstance();
+ abort = false;
- filename = globaldata->inputFileName;
- format = globaldata->getFormat();
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
- if (format == "column") { read = new ReadColumnMatrix(filename); }
- else if (format == "phylip") { read = new ReadPhylipMatrix(filename); }
+ else {
+ //valid paramters for this command
+ string Array[] = {"phylip", "column", "name", "cutoff", "precision", "group"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- if(globaldata->getPrecision() != ""){
- convert(globaldata->getPrecision(), precision);
- }
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ globaldata->newRead();
+
+ //check for required parameters
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { abort = true; }
+ else if (phylipfile == "not found") { phylipfile = ""; }
+ else { globaldata->setPhylipFile(phylipfile); globaldata->setFormat("phylip"); }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not open") { abort = true; }
+ else if (columnfile == "not found") { columnfile = ""; }
+ else { globaldata->setColumnFile(columnfile); globaldata->setFormat("column"); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else {
+ globaldata->setGroupFile(groupfile);
+ //groupMap = new GroupMap(groupfile);
+ //groupMap->readMap();
+ }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { globaldata->setNameFile(namefile); }
+
+ //you are doing a list and group shared
+ if ((phylipfile != "") && (groupfile != "")) {
+ globaldata->setFormat("matrix"); }
+
+ if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist command you must enter a phylip or a column." << endl; abort = true; }
+ else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist command you must enter ONLY ONE of the following: phylip or column." << endl; abort = true; }
- if(globaldata->getCutOff() != ""){
- convert(globaldata->getCutOff(), cutoff);
+ if (columnfile != "") {
+ if (namefile == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ //get user cutoff and precision or use defaults
+ string temp;
+ temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
+ convert(temp, precision);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; }
+ convert(temp, cutoff);
cutoff += (5 / (precision * 10.0));
- }
- read->setCutoff(cutoff);
+
+ if (abort == false) {
+ distFileName = globaldata->inputFileName;
+ format = globaldata->getFormat();
+
+ if (format == "column") { read = new ReadColumnMatrix(distFileName); }
+ else if (format == "phylip") { read = new ReadPhylipMatrix(distFileName); }
+ else if (format == "matrix") {
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+ if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
+ globaldata->gGroupmap = groupMap;
+ }
+
+ if (format != "matrix" ) {
+ read->setCutoff(cutoff);
- if(globaldata->getNameFile() != ""){
- nameMap = new NameAssignment(globaldata->getNameFile());
- nameMap->readMap(1,2);
- }
- else{
- nameMap = NULL;
+ if(namefile != ""){
+ nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
+ }else{
+ nameMap = NULL;
+ }
+ }
+ }
+
}
-
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
+//**********************************************************************************************************************
+
+void ReadDistCommand::help(){
+ try {
+ cout << "The read.dist command parameter options are phylip or column, group, name, cutoff and precision" << "\n";
+ cout << "The read.dist command can be used in two ways. The first is to read a phylip or column and run the cluster command" << "\n";
+ cout << "For this use the read.dist command should be in the following format: " << "\n";
+ cout << "read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
+ cout << "The phylip or column parameter is required, but only one may be used. If you use a column file the name filename is required. " << "\n";
+ cout << "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed." << "\n";
+ cout << "The second way to use the read.dist command is to read a phylip or column and a group, so you can use the libshuff command." << "\n";
+ cout << "For this use the read.dist command should be in the following format: " << "\n";
+ cout << "read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use. " << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile)." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ReadDistCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
//**********************************************************************************************************************
+
ReadDistCommand::~ReadDistCommand(){
- delete read;
- delete nameMap;
+ if (abort == false) {
+ if (format != "matrix") { delete read; delete nameMap; }
+ }
}
//**********************************************************************************************************************
int ReadDistCommand::execute(){
try {
- read->read(nameMap);
- globaldata->setListVector(read->getListVector());
- globaldata->setSparseMatrix(read->getMatrix());
+
+ if (abort == true) { return 0; }
+
+ if (format == "matrix") {
+ ifstream in;
+ openInputFile(distFileName, in);
+ matrix = new FullMatrix(in); //reads the matrix file
+ in.close();
+ //memory leak prevention
+ if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix; }
+ globaldata->gMatrix = matrix; //save matrix for coverage commands
+ }else {
+ read->read(nameMap);
+ //to prevent memory leak
+
+ if (globaldata->gListVector != NULL) { delete globaldata->gListVector; }
+ globaldata->gListVector = read->getListVector();
+
+ if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix; }
+ globaldata->gSparseMatrix = read->getMatrix();
+
+ }
return 0;
}
catch(exception& e) {
cout << "An unknown error has occurred in the ReadDistCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-}
\ No newline at end of file
+}
projects / mothur.git / blobdiff