#include "readcolumn.h"
#include "readmatrix.hpp"
-ReadDistCommand::ReadDistCommand(string option){
+ReadDistCommand::ReadDistCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
else {
//valid paramters for this command
- string Array[] = {"phylip", "column", "name", "cutoff", "precision", "group"};
+ string Array[] = {"phylip", "column", "name", "cutoff", "precision", "group","outputdir","inputdir","sim"};
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 (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; }
}
globaldata->newRead();
+ //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("group");
+ //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["group"] = inputDir + it->second; }
+ }
+ }
+
+ //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 = ""; }
+
//check for required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
if ((phylipfile != "") && (groupfile != "")) {
globaldata->setFormat("matrix"); }
- if ((phylipfile == "") && (columnfile == "")) { mothurOut("When executing a read.dist command you must enter a phylip or a column."); mothurOutEndLine(); abort = true; }
- else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When executing a read.dist command you must enter ONLY ONE of the following: phylip or column."); mothurOutEndLine(); abort = true; }
+ if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a read.dist command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; }
+ else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a read.dist command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
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"; }
+ temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
convert(temp, precision);
+ temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
+ sim = m->isTrue(temp);
+ globaldata->sim = sim;
+
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; }
convert(temp, cutoff);
- cutoff += (5 / (precision * 10.0));
+ cutoff += (5 / (precision * 10.0));
if (abort == false) {
distFileName = globaldata->inputFileName;
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;
+ int error = groupMap->readMap();
+ if (error == 1) { delete groupMap; abort = true; }
+ else {
+ if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
+ globaldata->gGroupmap = groupMap;
+ }
}
if (format != "matrix" ) {
}
catch(exception& e) {
- errorOut(e, "ReadDistCommand", "ReadDistCommand");
+ m->errorOut(e, "ReadDistCommand", "ReadDistCommand");
exit(1);
}
}
void ReadDistCommand::help(){
try {
- mothurOut("The read.dist command parameter options are phylip or column, group, name, cutoff and precision\n");
- mothurOut("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");
- mothurOut("For this use the read.dist command should be in the following format: \n");
- mothurOut("read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) \n");
- mothurOut("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");
- mothurOut("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");
- mothurOut("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");
- mothurOut("For this use the read.dist command should be in the following format: \n");
- mothurOut("read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use. \n");
- mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile).\n\n");
+ m->mothurOut("The read.dist command parameter options are phylip or column, group, name, sim, cutoff and precision\n");
+ m->mothurOut("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");
+ m->mothurOut("For this use the read.dist command should be in the following format: \n");
+ m->mothurOut("read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) \n");
+ m->mothurOut("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");
+ m->mothurOut("The sim parameter is used to indicate that your distance file contains similarity values instead of distance values. The default is false, if sim=true then mothur will convert the similarity values to distances. \n");
+ m->mothurOut("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");
+ m->mothurOut("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");
+ m->mothurOut("For this use the read.dist command should be in the following format: \n");
+ m->mothurOut("read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use. \n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile).\n\n");
}
catch(exception& e) {
- errorOut(e, "ReadDistCommand", "help");
+ m->errorOut(e, "ReadDistCommand", "help");
exit(1);
}
}
time_t start = time(NULL);
size_t numDists = 0;
+ vector<string> outputNames;
+
if (format == "matrix") {
ifstream in;
- openInputFile(distFileName, in);
+ m->openInputFile(distFileName, in);
matrix = new FullMatrix(in); //reads the matrix file
in.close();
+
+ if (m->control_pressed) { delete groupMap; delete matrix; return 0; }
+
+ //if files don't match...
+ if (matrix->getNumSeqs() < groupMap->getNumSeqs()) {
+ m->mothurOut("Your distance file contains " + toString(matrix->getNumSeqs()) + " sequences, and your group file contains " + toString(groupMap->getNumSeqs()) + " sequences."); m->mothurOutEndLine();
+ //create new group file
+ if(outputDir == "") { outputDir += m->hasPath(groupfile); }
+
+ string newGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "editted.groups";
+ outputNames.push_back(newGroupFile);
+ ofstream outGroups;
+ m->openOutputFile(newGroupFile, outGroups);
+
+ for (int i = 0; i < matrix->getNumSeqs(); i++) {
+ if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); remove(newGroupFile.c_str()); return 0; }
+
+ Names temp = matrix->getRowInfo(i);
+ outGroups << temp.seqName << '\t' << temp.groupName << endl;
+ }
+ outGroups.close();
+
+ m->mothurOut(newGroupFile + " is a new group file containing only the sequence that are in your distance file. I will read this file instead."); m->mothurOutEndLine();
+
+ //read new groupfile
+ delete groupMap; groupMap = NULL;
+ groupfile = newGroupFile;
+ globaldata->setGroupFile(groupfile);
+
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+
+ if (m->control_pressed) { delete groupMap; delete matrix; remove(newGroupFile.c_str()); return 0; }
+
+ globaldata->gGroupmap = groupMap;
+ }
+
//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 (m->control_pressed) { return 0; }
+
if (globaldata->gListVector != NULL) { delete globaldata->gListVector; }
globaldata->gListVector = read->getListVector();
if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix; }
globaldata->gSparseMatrix = read->getMatrix();
numDists = globaldata->gSparseMatrix->getNNodes();
-
- int lines = cutoff / (1.0/precision);
- vector<float> dist_cutoff(lines+1,0);
- for (int i = 0; i <= lines;i++) {
- dist_cutoff[i] = (i + 0.5) / precision;
- }
- vector<int> dist_count(lines+1,0);
- list<PCell>::iterator currentCell;
- SparseMatrix* smatrix = globaldata->gSparseMatrix;
- for (currentCell = smatrix->begin(); currentCell != smatrix->end(); currentCell++) {
- for (int i = 0; i <= lines;i++) {
- if (currentCell->dist < dist_cutoff[i]) {
- dist_count[i]++;
- break;
- }
- }
- }
+ }
+
+ if (m->control_pressed) { return 0; }
- // string dist_string = "Dist:";
- // string count_string = "Count: ";
- //for (int i = 0; i <= lines;i++) {
- //dist_string = dist_string.append("\t").append(toString(dist_cutoff[i]));
- // count_string = count_string.append("\t").append(toString(dist_count[i]));
- // }
- //mothurOut(dist_string); mothurOutEndLine(); mothurOut(count_string); mothurOutEndLine();
+ if (outputNames.size() != 0) {
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
}
- mothurOut("It took " + toString(time(NULL) - start) + " secs to read "); mothurOutEndLine();
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to read "); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
- errorOut(e, "ReadDistCommand", "execute");
+ m->errorOut(e, "ReadDistCommand", "execute");
exit(1);
}
}
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