added trim.seqs command

[mothur.git] / fastamap.cpp

diff --git a/fastamap.cpp b/fastamap.cpp
index 1cc9abf08da58bad5497079d46185413e0c23ff4..a0652d996fa648a7130928e93c7f3c6b0fae583a 100644 (file)
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -8,27 +8,33 @@
  */
 
 #include "fastamap.h"
+#include "sequence.hpp"
 
 /*******************************************************************************/
+
 void FastaMap::readFastaFile(ifstream& in) {
        try {
                string name, sequence, line;
                sequence = "";
-               int c;
+//             int c;
                string temp;
                
                
                //read through file
-               while ((c = in.get()) != EOF) {
-                       name = ""; sequence = ""; 
-                       //is this a name
-                       if (c == '>') { 
-                               name = readName(in); 
-                               sequence = readSequence(in); 
-                       }else {  cout << "Error fasta in your file. Please correct." << endl; }
+//             while ((c = in.get()) != EOF) {
+//                     name = ""; sequence = ""; 
+//                     //is this a name
+//                     if (c == '>') { 
+//                             name = readName(in); 
+//                             sequence = readSequence(in); 
+//                     }else {  cout << "Error fasta in your file. Please correct." << endl; }
 
                        //store info in map
                        //input sequence info into map
+               while(!in.eof()){
+                       Sequence currSeq(in);
+                       name = currSeq.getName();
+                       sequence = currSeq.getUnaligned();
                        seqmap[name] = sequence;  
                        it = data.find(sequence);
                        if (it == data.end()) {         //it's unique.
@@ -53,77 +59,27 @@ void FastaMap::readFastaFile(ifstream& in) {
                exit(1);
        }
 }
-/*******************************************************************************/
-string FastaMap::readName(ifstream& in) {
-       try{
-               string name = "";
-               int c;
-               string temp;
-               
-               while ((c = in.get()) != EOF) {
-                       //if c is not a line return
-                       if (c != 10) {
-                               name += c;
-                       }else { break;  }
-               }
-                       
-               return name;
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the FastaMap class function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-}
 
 /*******************************************************************************/
-string FastaMap::readSequence(ifstream& in) {
-       try{
-               string sequence = "";
-               string line;
-               int pos, c;
-               
-               while (!in.eof()) {
-                       //save position in file in case next line is a new name.
-                       pos = in.tellg();
-                       line = "";
-                       in >> line;                     
-                       //if you are at a new name
-                       if (line[0] == '>') {
-                               //put file pointer back since you are now at a new name
-                               in.seekg(pos, ios::beg);
-                               c = in.get();  //because you put it back to a newline char
-                               break;
-                       }else {  sequence += line;      }
-               }
-                       
-               return sequence;
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the FastaMap class function readSequence. 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;
 }
+
 /*******************************************************************************/
+
 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;
 }
+
 /*******************************************************************************/
+
 string FastaMap::getSequence(string name) {
        it2 = seqmap.find(name);
        if (it2 == seqmap.end()) {      //it's not found
@@ -132,7 +88,9 @@ string FastaMap::getSequence(string name) {
                return it2->second;
        }
 }      
+
 /*******************************************************************************/
+
 void FastaMap::push_back(string name, string seq) {
        it = data.find(seq);
        if (it == data.end()) {         //it's unique.
@@ -146,11 +104,15 @@ void FastaMap::push_back(string name, string seq) {
        
        seqmap[name] = seq;
 }
+
 /*******************************************************************************/
+
 int FastaMap::sizeUnique(){ //returns datas size which is the number of unique sequences
        return data.size();
 }
+
 /*******************************************************************************/
+
 void FastaMap::printNamesFile(ostream& out){ //prints data
        try {
                // two column file created with groupname and them list of identical sequence names
@@ -167,7 +129,9 @@ void FastaMap::printNamesFile(ostream& out){ //prints data
                exit(1);
        }
 }
+
 /*******************************************************************************/
+
 void FastaMap::printCondensedFasta(ostream& out){ //prints data
        try {
                //creates a fasta file
@@ -185,5 +149,6 @@ void FastaMap::printCondensedFasta(ostream& out){ //prints data
                exit(1);
        }
 }
+
 /*******************************************************************************/