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#ifndef _INTERVAL_H_
#define _INTERVAL_H_
/**
* WHAM - high-throughput sequence aligner
* Copyright (C) 2011 WHAM Group, University of Wisconsin
*
* This program 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.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
*/
/* $Id: interval.h 157 2012-07-25 05:58:09Z yinan $ */
#include "lib.h"
/* interval tree leaf level entry */
typedef struct IntervalLEntry {
uint32 key; /* the offset in compact sequence */
uint32 len;
uint32 sid; /* the sequence id */
uint32 offset; /* the offset in the originial sequence */
} IntervalLEntry;
/* interval tree internal level entry */
typedef struct IntervalIEntry {
uint32 key; /* the offset in compact sequence */
uint32 offset; /* the position of the node in its child level */
} IntervalIEntry;
/* interval tree level */
typedef struct IntervalLevel {
uint32 curNode; /* the current node in the level */
uint32 curEntry;/* the current entry in the current node */
} IntervalLevel;
class IntervalTree {
private:
uint32 lenNSeg;
uint32 numIEntry; /* the number of internal entries */
uint32 numLEntry; /* the number of leaf entries */
uint32 numLevel; /* the number of levels */
uint32 fl; /* the fanout of leaf node */
uint32 fi; /* the fanout of internal node */
uint32 curLNode; /* the current allocation position in leaf node pool */
uint32 curINode; /* the current allocation position in internal node pool */
IntervalLEntry * lpool; /* the leaf node pool */
IntervalIEntry * ipool; /* the internal node pool */
IntervalLevel * level; /* the levels */
public:
IntervalTree();
IntervalTree(uint32 num, uint32 len);
int append(uint32 key, uint32 len, uint32 sid, uint32 offset);
int flush(uint32 key, uint32 len, uint32 sid, uint32 offset);
int lookup(uint32 key, uint32 & sid, uint32 & offset);
int save(char * path);
int load(char * path);
private:
int append(uint32 key, uint32 offset, uint32 l);
int flush(uint32 key, uint32 offset, uint32 l);
};
#endif
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