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///////////////////////////////////////////////////////////////////////////////////////////////////
// File : SeqList.h
// Purpose : Handles the sequence file functions for ParsInsert
//
// Developer : David Knox (david.knox@colorado.edu) Jan 2011
// Copyright : Copyright (C) 2007-2011 David Knox
//
// Web site : http://parsinsert.sourceforge.net/
//
///////////////////////////////////////////////////////////////////////////////////////////////////
// This file is part of ParsInsert.
//
// ParsInsert is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// ParsInsert is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with ParsInsert. If not, see <http://www.gnu.org/licenses/>.
///////////////////////////////////////////////////////////////////////////////////////////////////
#if !defined(__SEQLIST_H__)
#define __SEQLIST_H__
#if _MSC_VER > 1000
#pragma once
#endif // _MSC_VER > 1000
#include "Knox_Stddef.h"
#include <vector>
#include <string>
#include <map>
using namespace std;
#define MAX_SEQ_SIZE (64*1024)
class CPNode;
///////////////////////////////////////////////////////////////////////////////////////////////////
class CBestLocationEntry
{
public:
CPNode *node; // pointer to node with best match
int score; // score of match at this position
string tax; // taxonomy assignd to this position
int levels; // number of ranks in taxonomy
public:
CBestLocationEntry(int s, CPNode *n, LPCSTR t)
{
score = s;
node = n;
tax = t;
levels = 0;
if (!tax.empty())
{
for (int i=0; i < tax.length() ; ++i)
if (tax[i] == ';')
++levels;
}
}
};
typedef vector<CBestLocationEntry> CBestList;
///////////////////////////////////////////////////////////////////////////////////////////////////
class CBestLocation
{
public:
static int default_len;
CBestList list; // list of best matches
int len; // number of matches to keep
public:
CBestLocation(int _len=-1)
{
if (_len > 0)
len = _len;
else
len = default_len;
}
void Add(int score, CPNode *node, LPCSTR t);
int WorstScore();
};
///////////////////////////////////////////////////////////////////////////////////////////////////
class CSequenceItem
{
public:
long offset; // offset in sequence file where sequence entry begins
string name; // id from the fasta file
int len; // length of the sequence data (sequence only)
LPSTR data; // sequence string
LPSTR hdr; // header line from fasta file
public:
CSequenceItem();
CSequenceItem(LPCSTR _name, long _offset, int _len, LPCSTR _data=NULL);
~CSequenceItem();
LPCSTR GetSeqData();
BOOL AllocateSeqData();
BOOL ReleaseSeqData();
BOOL AllocateSeqHeader(int size);
BOOL ReleaseSeqHeader();
LPCSTR ReadSeqHeader(FILE *f);
LPCSTR ReadSeqData(FILE *f);
BOOL WriteSeqData(FILE *f);
};
typedef map<string,CSequenceItem*> CSequenceList;
typedef CSequenceList::iterator CSequenceListIter;
///////////////////////////////////////////////////////////////////////////////////////////////////
class CSequenceFile
{
public:
FILE *f; // file to read data
string fname; // name of file opened
int seqCount; // number of sequences used in array
int seqN; // number of items allocated in array
CSequenceItem* *seqArray; // array of sequence numbers
CSequenceList seqlist; // map of name to sequence
CSequenceListIter seqIter; // iterator to step thru map
int posArray; // iterator position in array
static int progressCount; // number of sequences between progress reports
static int verbose;
public:
CSequenceFile(LPCSTR _fname=NULL, int size=MAX_SEQ_SIZE, int hashsize=10*1024);
~CSequenceFile();
CSequenceItem * GetSequence(LPCSTR name);
CSequenceItem * GetSequenceHeader(LPCSTR name);
BOOL Open(LPCSTR _fname, LPCSTR mode="r");
void Close();
int GetCount()
{
return seqCount;
}
int ReadSequenceIndexFile(LPCSTR filename);
int ReadSequenceFile(int type);
CSequenceItem *GetSeq(LPCSTR name);
BOOL WriteSequence(CSequenceItem *seq);
void ResetSeqIterator();
CSequenceItem *GetNextSeq();
int ReadTaxonomyFile();
};
#endif // __SEQLIST_H__
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