deconvolute command

[mothur.git] / fastamap.cpp

diff --git a/fastamap.cpp b/fastamap.cpp
index 4f4bf33206d77e437dd32bd2ff14b7f5f1290042..0e6c22e21f48aec62b4a365db1e2454cd65ce7c9 100644 (file)
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -10,65 +10,78 @@
 #include "fastamap.h"
 
 /*******************************************************************************/
- FastaMap::FastaMap(ifstream& in) {
-       //int numberOfSequences = 0;
+void FastaMap::readFastaFile(ifstream& in) {
+       try {
+               string name, sequence, line;
+               sequence = "";
        
-       string name, sequence, line;
-       sequence = "";
+               getline(in, line);
+               name = line.substr(1, line.length());  //rips off '>'
        
-       getline(in, line);
-       name = line.substr(1, line.length());  //rips off '>'
-       
-       //read through file
-       while (getline(in, line)) {
-               if (isalnum(line.at(0))){  //if it's a sequence line
-                       sequence += line;
-               }
-               else{
-                       //input sequence info into map
-                       it = data.find(sequence);
-                       if (it == data.end()) {         //it's unique.
-                               data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
-                               data[sequence].groupnumber = 1;
-                               data[sequence].names = name;
-                       }else { // its a duplicate.
-                               data[sequence].names += "," + name;
-                               data[sequence].groupnumber++;   
+               //read through file
+               while (getline(in, line)) {
+                       if (isalnum(line.at(0))){  //if it's a sequence line
+                               sequence += line;
+                       }
+                       else{
+                               //input sequence info into map
+                               it = data.find(sequence);
+                               if (it == data.end()) {         //it's unique.
+                                       data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
+                                       data[sequence].groupnumber = 1;
+                                       data[sequence].names = name;
+                               }else { // its a duplicate.
+                                       data[sequence].names += "," + name;
+                                       data[sequence].groupnumber++;
+                               }
+                               name = (line.substr(1, (line.npos))); //The line you just read is a new name so rip off '>'
+                               sequence = "";
                        }
-                       name = (line.substr(1, (line.npos))); //The line you just read is a new name so rip off '>'
                }
-       }
        
-       //store last sequence and name info.
-       it = data.find(sequence);
-       if (it == data.end()) {         //it's unique.
-               data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
-               data[sequence].groupnumber = 1;
-               data[sequence].names = name;
-       }else { // its a duplicate.
-               data[sequence].names += "," + name;
-               data[sequence].groupnumber++;   
-       }       
+               //store last sequence and name info.
+               it = data.find(sequence);
+               if (it == data.end()) {         //it's unique.
+                       data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
+                       data[sequence].groupnumber = 1;
+                       data[sequence].names = name;
+               }else { // its a duplicate.
+                       data[sequence].names += "," + name;
+                       data[sequence].groupnumber++;
+               }       
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function readFastaFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the FastaMap class function readFastaFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
 }
 /*******************************************************************************/
 string FastaMap::getGroupName(string seq) {  //pass a sequence name get its group
        return data[seq].groupname;
 }
 /*******************************************************************************/
-int FastaMap::getGroupNumber(string seq) {  //pass a sequence name get number of sequence in its group
-       return data[seq].groupnumber;
-}
-/*******************************************************************************/
 string FastaMap::getNames(string seq) {        //pass a sequence get the string of names in the group separated by ','s.
        return data[seq].names;
 }
 /*******************************************************************************/
+int FastaMap::getGroupNumber(string seq) {     //pass a sequence get the number of identical sequences.
+       return data[seq].groupnumber;
+}
+/*******************************************************************************/
 void FastaMap::push_back(string seq, string Name) {//sequencename, name
        data[seq].groupname = Name;
-       data[seq].groupnumber = 1;
        data[seq].names = Name;
 }
 /*******************************************************************************/
+void FastaMap::set(string seq, string groupName, string Names) {
+       data[seq].groupname = groupName;
+       data[seq].names = Names;
+}
+/*******************************************************************************/
 void FastaMap::clear() { //clears out data
        data.clear();
 }
@@ -77,7 +90,20 @@ int FastaMap::size(){ //returns datas size which is the number of unique sequenc
        return data.size();
 }
 /*******************************************************************************/
-void FastaMap::print(ostream&){ //prints data
-
+void FastaMap::print(ostream& out){ //prints data
+       try {
+               // two column file created with groupname and them list of identical sequence names
+               for (it = data.begin(); it != data.end(); it++) {
+                       out << it->second.groupname << '\t' << it->second.names << endl;
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the FastaMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
 }
 /*******************************************************************************/