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///////////////////////////////////////////////////////////////////////////////////////////////////
// File : ParsInsert.h
// Purpose : Parsimonious Insertion of unclassified seqeunces into Phylogenetic Tree
//
// 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/>.
///////////////////////////////////////////////////////////////////////////////////////////////////
#ifndef PARS_INSERT_H
#include "SeqList.h"
#include "ParsimonySet.h"
#define RC_ERROR_OPTIONS -1000 // Error in the command line options
#define RC_ERROR_CMDLINE -1001 // Error not enough parameters supplied
#define RC_ERROR_MASKFILE -1002 // Error accessing mask file
#define RC_ERROR_TAXFILE -1003 // Error accessing taxonomy file
#define RC_ERROR_TREEFILE -1004 // Error accessing newick tree file
#define RC_ERROR_TREESEQ -1005 // Error accessing tree seq for tree
#define RC_ERROR_TREESEQ_MISSING -1006 // Error could not find tree leaf in sequences
#define RC_ERROR_NO_INSERT_SEQ -1007 // Error no insertion sequences to process
#define RC_ERROR_
#define RC_ERROR_
#define RC_ERROR_
///////////////////////////////////////////////////////////////////////////////////////////////////
class CInsertPos // class stores a possible seqeunce insertion location into a tree
{
public:
CSequenceItem *seq; // sequence being inserted
int nSites; // number of active sites being scored
CParsimonySet pars; // parsimony sequence for insertion
CBestLocation best; // location with best match
public:
CInsertPos()
{
seq = NULL;
nSites = 0;
}
~CInsertPos()
{
seq = NULL;
best.list.clear();
}
};
typedef vector<CInsertPos*> CInsertPosArray;
///////////////////////////////////////////////////////////////////////////////////////////////////
#endif //PARS_INSERT_H
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