#include "readcolumn.h"
#include "readmatrix.hpp"
-ReadDistCommand::ReadDistCommand(string option){
+ReadDistCommand::ReadDistCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
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; }
}
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, 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("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);
//if files don't match...
if (matrix->getNumSeqs() < groupMap->getNumSeqs()) {
- mothurOut("Your distance file contains " + toString(matrix->getNumSeqs()) + " sequences, and your group file contains " + toString(groupMap->getNumSeqs()) + " sequences."); mothurOutEndLine();
+ 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 += hasPath(groupfile); }
string newGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "editted.groups";
+ outputNames.push_back(newGroupFile);
ofstream outGroups;
openOutputFile(newGroupFile, outGroups);
}
outGroups.close();
- mothurOut(newGroupFile + " is a new group file containing only the sequence that are in your distance file. I will read this file instead."); mothurOutEndLine();
+ 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;
//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();
+ //m->mothurOut(dist_string); m->mothurOutEndLine(); m->mothurOut(count_string); m->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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