source: branches/alilink/GDE/MUSCLE/src/fasta.cpp

#include "muscle.h"
#include <stdio.h>
#include <ctype.h>
#include "msa.h"
#include "textfile.h"

const unsigned FASTA_BLOCK = 60;

void MSA::FromFASTAFile(TextFile &File)
        {
        Clear();

        FILE *f = File.GetStdioFile();
        
        unsigned uSeqCount = 0;
        unsigned uColCount = uInsane;
        for (;;)
                {
                char *Label;
                unsigned uSeqLength;
                char *SeqData = GetFastaSeq(f, &uSeqLength, &Label, false);
                if (0 == SeqData)
                        break;
                AppendSeq(SeqData, uSeqLength, Label);
                }
        }

void MSA::ToFASTAFile(TextFile &File) const
        {
        const unsigned uColCount = GetColCount();
        assert(uColCount > 0);
        const unsigned uLinesPerSeq = (GetColCount() - 1)/FASTA_BLOCK + 1;
        const unsigned uSeqCount = GetSeqCount();

        for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
                {
                File.PutString(">");
                File.PutString(GetSeqName(uSeqIndex));
                File.PutString("\n");

                unsigned n = 0;
                for (unsigned uLine = 0; uLine < uLinesPerSeq; ++uLine)
                        {
                        unsigned uLetters = uColCount - uLine*FASTA_BLOCK;
                        if (uLetters > FASTA_BLOCK)
                                uLetters = FASTA_BLOCK;
                        for (unsigned i = 0; i < uLetters; ++i)
                                {
                                char c = GetChar(uSeqIndex, n);
                                File.PutChar(c);
                                ++n;
                                }
                        File.PutChar('\n');
                        }
                }
        }