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/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
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, version 3 of the License.
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 have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#ifndef _ColorSet_h
#define _ColorSet_h
#include "VirtualKmerColor.h"
#include <stdint.h>
#include <vector>
#include <map>
#include <iostream>
using namespace std;
#define NULL_VIRTUAL_COLOR 0
// maximum value for a uint64_t:
// 18446744073709551615
// xxxxyyyyyyyyyyyyyyyy
// 10000000000000000
#define COLOR_NAMESPACE_MULTIPLIER 10000000000000000ULL
// colors in the phylogeny namespace: 1024 * 10000000000000000 + identifier
// available slots: 0 to 1844
// each -search uses one slot, starting at 0
#define COLOR_NAMESPACE_EMBL_CDS 789
#define COLOR_NAMESPACE_PHYLOGENY 1024
#define COLOR_NAMESPACE_SAMPLE 1200
typedef uint32_t VirtualKmerColorHandle;
/** This class is a translation table for
* allocated virtual colors.
*
* This is the Flyweight design pattern.
*
* \author: Sébastien Boisvert
*
* Frédéric Raymond proposed the idea of using color namespaces.
*/
class ColorSet{
int OPERATION_IN_PLACE_ONE_REFERENCE;
int OPERATION_NO_VIRTUAL_COLOR_HAS_PHYSICAL_COLOR_CREATION;
int OPERATION_NO_VIRTUAL_COLOR_HAS_COUNT_CREATION;
int OPERATION_NO_VIRTUAL_COLOR_HAS_HASH_CREATION;
int OPERATION_VIRTUAL_COLOR_HAS_COLORS_FETCH;
int OPERATION_NO_VIRTUAL_COLOR_HAS_COLORS_CREATION;
int OPERATION_NEW_FROM_EMPTY;
int OPERATION_NEW_FROM_SCRATCH;
int OPERATION_applyHashOperation;
int OPERATION_getHash;
int OPERATION_getVirtualColorFrom;
int OPERATION_createVirtualColorFrom ;
int OPERATION_incrementReferences ;
int OPERATION_decrementReferences ;
int OPERATION_purgeVirtualColor ;
int OPERATION_allocateVirtualColorHandle ;
int OPERATION_DUMMY ;
LargeCount m_operations[32];
/** a list of available handles **/
set<VirtualKmerColorHandle> m_availableHandles;
/** the table of virtual colors **/
vector<VirtualKmerColor> m_virtualColors;
/** a list of physical colors **/
set<PhysicalKmerColor> m_physicalColors;
map<LargeIndex,set<VirtualKmerColorHandle> > m_index;
LargeCount m_collisions;
/** get the hash value for a set of colors **/
uint64_t getHash(set<PhysicalKmerColor>*colors);
/** allocates a virtual color handle **/
VirtualKmerColorHandle allocateVirtualColorHandle();
VirtualKmerColor*getVirtualColor(VirtualKmerColorHandle handle);
void purgeVirtualColor(VirtualKmerColorHandle handle);
uint64_t applyHashOperation(uint64_t hashValue,PhysicalKmerColor color);
VirtualKmerColorHandle createVirtualColorFrom(VirtualKmerColorHandle handle,PhysicalKmerColor color);
bool virtualColorHasAllPhysicalColorsOf(VirtualKmerColorHandle toInvestigate,VirtualKmerColorHandle list);
void addVirtualColorToIndex(VirtualKmerColorHandle handle);
void removeVirtualColorFromIndex(VirtualKmerColorHandle handle);
VirtualKmerColorHandle createVirtualColorHandleFromScratch();
void assertNoVirtualColorDuplicates(VirtualKmerColorHandle handle,PhysicalKmerColor color,int id);
void printPhysicalColors(set<PhysicalKmerColor>*colors);
VirtualKmerColorHandle lookupVirtualColor(set<PhysicalKmerColor>*colors);
VirtualKmerColorHandle createVirtualColorFromPhysicalColors(set<PhysicalKmerColor>*colors);
public:
ColorSet();
/** increment the references for a virtual color **/
void incrementReferences(VirtualKmerColorHandle handle);
/** decrement the references for a virtual color **/
void decrementReferences(VirtualKmerColorHandle handle);
LargeCount getNumberOfReferences(VirtualKmerColorHandle handle);
int getNumberOfPhysicalColors(VirtualKmerColorHandle handle);
VirtualKmerColorHandle getVirtualColorFrom(VirtualKmerColorHandle handle,PhysicalKmerColor color);
int getTotalNumberOfPhysicalColors();
LargeCount getTotalNumberOfVirtualColors();
void printSummary(ostream*out,bool xml);
void printColors(ostream*out);
set<PhysicalKmerColor>*getPhysicalColors(VirtualKmerColorHandle handle);
bool virtualColorHasPhysicalColor(VirtualKmerColorHandle handle,PhysicalKmerColor color);
/*
* Returns a virtual color with exactly the physical colors provided.
*/
VirtualKmerColorHandle findVirtualColor(set<PhysicalKmerColor>*colors);
};
#endif
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