readseqsphylip.cpp

   1 /*
   2  *  readphylip.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 4/24/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readseqsphylip.h"
  11 #include <iostream>
  12 #include <fstream>
  13
  14 /*******************************************************************************/
  15 bool ReadPhylip::isSeq(string seq) {
  16         string validChars[] = {"A","G","C","T","U","N","-"};
  17
  18         for(int i = 0; i < seq.length(); i++) {
  19                 bool valid = false;
  20                 string c = seq.substr(i,1);
  21                 for(int k = 0; k < 7; k++)
  22                         if(c.compare(validChars[k]) == 0) {
  23                                 valid = true;
  24                                 k = 7;
  25                         }
  26                 if(!valid)
  27                         return false;
  28         }
  29
  30         return true;
  31 }
  32
  33 /*******************************************************************************/
  34 ReadPhylip::ReadPhylip(string file) : ReadSeqs(file) {
  35         try {
  36         }
  37         catch(exception& e) {
  38                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  39                 exit(1);
  40         }
  41         catch(...) {
  42                 cout << "An unknown error has occurred in the ReadTree class function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  43                 exit(1);
  44         }
  45 }
  46 /*******************************************************************************/
  47 ReadPhylip::~ReadPhylip(){
  48 //      for(int i = 0; i < sequencedb.getNumSeqs(); i++)
  49 //              delete sequencedb.get(i);
  50 }
  51 /*******************************************************************************/
  52 void ReadPhylip::read() {
  53         string temp;
  54         string name;
  55         string sequence;
  56
  57         int count = 0;
  58         int letterCount = 0;
  59         int numCols = 0;
  60         filehandle >> temp;
  61         int numSeqs = atoi(temp.c_str());
  62         filehandle >> temp;
  63         int numLetters = atoi(temp.c_str());
  64
  65         bool firstDone = false;
  66         bool last = false;
  67         filehandle >> name;
  68
  69         while(!filehandle.eof()) {
  70                 if(!firstDone) {
  71                         sequence = "";
  72                         if(count == 0) {
  73                                 filehandle >> temp;
  74                                 while(isSeq(temp)) {
  75                                         sequence += temp;
  76                                         numCols++;
  77                                         filehandle >> temp;
  78                                 }
  79                                 letterCount += sequence.length();
  80                         }
  81                         else {
  82                                 for(int i = 0; i < numCols; i++) {
  83                                         filehandle >> temp;
  84                                         sequence += temp;
  85                                 }
  86                                 if(count < numSeqs-1)
  87                                         filehandle >> temp;
  88                         }
  89                         Sequence newSeq(name, sequence);
  90                         sequencedb.add(newSeq);
  91                         if(count < numSeqs-1)
  92                                 name = temp;
  93                 }
  94                 else {
  95                         sequence = "";
  96                         for(int i = 0; i < numCols; i++) {
  97                                 filehandle >> temp;
  98                                 sequence += temp;
  99                                 if(count == 0)
 100                                         letterCount += temp.length();
 101                                 if(letterCount == numLetters && count == 0) {
 102                                         numCols = i + 1;
 103                                         i = numCols;
 104                                 }
 105                         }
 106                         if(!(last && count == 0))
 107                                 sequencedb.set(count, sequencedb.get(count).getUnaligned() + sequence);
 108                         if(letterCount == numLetters && count == 0)
 109                                 last = true;
 110                 }
 111
 112                 count++;
 113
 114                 if(count == numSeqs) {
 115                         firstDone = true;
 116                         count = 0;
 117                 }
 118         }
 119         filehandle.close();
 120 }
 121
 122 /*********************************************************************************/
 123 SequenceDB* ReadPhylip::getDB() {
 124         return &sequencedb;
 125 }