5 * Created by Sarah Westcott on 1/20/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "readdistcommand.h"
11 #include "readphylip.h"
12 #include "readcolumn.h"
13 #include "readmatrix.hpp"
15 ReadDistCommand::ReadDistCommand(string option){
17 globaldata = GlobalData::getInstance();
20 //allow user to run help
21 if(option == "help") { help(); abort = true; }
24 //valid paramters for this command
25 string Array[] = {"phylip", "column", "name", "cutoff", "precision", "group"};
26 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
28 OptionParser parser(option);
29 map<string, string> parameters = parser.getParameters();
31 ValidParameters validParameter;
33 //check to make sure all parameters are valid for command
34 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
35 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
38 globaldata->newRead();
40 //check for required parameters
41 phylipfile = validParameter.validFile(parameters, "phylip", true);
42 if (phylipfile == "not open") { abort = true; }
43 else if (phylipfile == "not found") { phylipfile = ""; }
44 else { globaldata->setPhylipFile(phylipfile); globaldata->setFormat("phylip"); }
46 columnfile = validParameter.validFile(parameters, "column", true);
47 if (columnfile == "not open") { abort = true; }
48 else if (columnfile == "not found") { columnfile = ""; }
49 else { globaldata->setColumnFile(columnfile); globaldata->setFormat("column"); }
51 groupfile = validParameter.validFile(parameters, "group", true);
52 if (groupfile == "not open") { abort = true; }
53 else if (groupfile == "not found") { groupfile = ""; }
55 globaldata->setGroupFile(groupfile);
56 groupMap = new GroupMap(groupfile);
60 namefile = validParameter.validFile(parameters, "name", true);
61 if (namefile == "not open") { abort = true; }
62 else if (namefile == "not found") { namefile = ""; }
63 else { globaldata->setNameFile(namefile); }
66 //you are doing a list and group shared
67 if ((phylipfile != "") && (groupfile != "")) {
68 globaldata->setFormat("matrix"); }
70 if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist command you must enter a phylip or a column." << endl; abort = true; }
71 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; }
73 if (columnfile != "") {
74 if (namefile == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
77 //check for optional parameter and set defaults
78 // ...at some point should added some additional type checking...
79 //get user cutoff and precision or use defaults
81 temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
82 convert(temp, precision);
84 temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; }
85 convert(temp, cutoff);
86 cutoff += (5 / (precision * 10.0));
89 distFileName = globaldata->inputFileName;
90 format = globaldata->getFormat();
92 if (format == "column") { read = new ReadColumnMatrix(distFileName); }
93 else if (format == "phylip") { read = new ReadPhylipMatrix(distFileName); }
94 else if (format == "matrix") {
95 groupMap = new GroupMap(groupfile);
97 if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
98 globaldata->gGroupmap = groupMap;
101 if (format != "matrix" ) {
102 read->setCutoff(cutoff);
105 nameMap = new NameAssignment(namefile);
106 nameMap->readMap(1,2);
116 catch(exception& e) {
117 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
121 cout << "An unknown error has occurred in the ReadDistCommand class function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
125 //**********************************************************************************************************************
127 void ReadDistCommand::help(){
129 cout << "The read.dist command parameter options are phylip or column, group, name, cutoff and precision" << "\n";
130 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";
131 cout << "For this use the read.dist command should be in the following format: " << "\n";
132 cout << "read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
133 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";
134 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";
135 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";
136 cout << "For this use the read.dist command should be in the following format: " << "\n";
137 cout << "read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use. " << "\n";
138 cout << "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile)." << "\n" << "\n";
140 catch(exception& e) {
141 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
145 cout << "An unknown error has occurred in the ReadDistCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
150 //**********************************************************************************************************************
152 ReadDistCommand::~ReadDistCommand(){
157 //**********************************************************************************************************************
158 int ReadDistCommand::execute(){
161 if (abort == true) { return 0; }
163 if (format == "matrix") {
165 openInputFile(distFileName, in);
166 matrix = new FullMatrix(in); //reads the matrix file
167 //memory leak prevention
168 //if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix; }
169 globaldata->gMatrix = matrix; //save matrix for coverage commands
172 //to prevent memory leak
173 if (globaldata->gListVector != NULL) { delete globaldata->gListVector; }
174 globaldata->gListVector = read->getListVector();
175 if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix; }
176 globaldata->gSparseMatrix = read->getMatrix();
180 catch(exception& e) {
181 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
185 cout << "An unknown error has occurred in the ReadDistCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";