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 /*******************************************************************************/
  36 ReadPhylip::~ReadPhylip(){
  37 //      for(int i = 0; i < sequencedb.getNumSeqs(); i++)
  38 //              delete sequencedb.get(i);
  39 }
  40 /*******************************************************************************/
  41 void ReadPhylip::read() {
  42         string temp;
  43         string name;
  44         string sequence;
  45
  46         int count = 0;
  47         int letterCount = 0;
  48         int numCols = 0;
  49         filehandle >> temp;
  50         int numSeqs = atoi(temp.c_str());
  51         filehandle >> temp;
  52         int numLetters = atoi(temp.c_str());
  53
  54         bool firstDone = false;
  55         bool last = false;
  56         filehandle >> name;
  57
  58         while(!filehandle.eof()) {
  59                 if(!firstDone) {
  60                         sequence = "";
  61                         if(count == 0) {
  62                                 filehandle >> temp;
  63                                 while(isSeq(temp)) {
  64                                         sequence += temp;
  65                                         numCols++;
  66                                         filehandle >> temp;
  67                                 }
  68                                 letterCount += sequence.length();
  69                         }
  70                         else {
  71                                 for(int i = 0; i < numCols; i++) {
  72                                         filehandle >> temp;
  73                                         sequence += temp;
  74                                 }
  75                                 if(count < numSeqs-1)
  76                                         filehandle >> temp;
  77                         }
  78                         Sequence newSeq(name, sequence);
  79                         sequencedb.add(newSeq);
  80                         if(count < numSeqs-1)
  81                                 name = temp;
  82                 }
  83                 else {
  84                         sequence = "";
  85                         for(int i = 0; i < numCols; i++) {
  86                                 filehandle >> temp;
  87                                 sequence += temp;
  88                                 if(count == 0)
  89                                         letterCount += temp.length();
  90                                 if(letterCount == numLetters && count == 0) {
  91                                         numCols = i + 1;
  92                                         i = numCols;
  93                                 }
  94                         }
  95                         if(!(last && count == 0))
  96                                 sequencedb.set(count, sequencedb.get(count).getUnaligned() + sequence);
  97                         if(letterCount == numLetters && count == 0)
  98                                 last = true;
  99                 }
 100
 101                 count++;
 102
 103                 if(count == numSeqs) {
 104                         firstDone = true;
 105                         count = 0;
 106                 }
 107         }
 108         filehandle.close();
 109 }
 110
 111 /*********************************************************************************/
 112 SequenceDB* ReadPhylip::getDB() {
 113         return &sequencedb;
 114 }