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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 _TaxonomyViewer_h
#define _TaxonomyViewer_h
#include "types.h"
#include <code/Searcher/ColorSet.h>
#include <code/Mock/Parameters.h>
#include <code/VerticesExtractor/GridTable.h>
#include <code/Searcher/Searcher.h>
#include <RayPlatform/profiling/TimePrinter.h>
#include <RayPlatform/plugins/CorePlugin.h>
#include <RayPlatform/handlers/MasterModeHandler.h>
#include <RayPlatform/handlers/MessageTagHandler.h>
#include <RayPlatform/handlers/SlaveModeHandler.h>
#include <RayPlatform/core/ComputeCore.h>
#include <set>
#include <stdint.h>
#include <map>
using namespace std;
/*
[sboisver12@colosse1 2012-01-25]$ ls
Genome-to-Taxon.tsv Taxon-Names.tsv Taxon-Types.tsv TreeOfLife-Edges.tsv
1. for each sequence, also add an extra color for its genome identifier using a distinct namespace [DONE]
2. Color things [DONE]
3. Use the vertices to get a list of identifiers. [DONE]
4. With this list, load only the relevant pairs from Genome-to-Taxon.tsv. (use an iterator) [DONE]
5. generate a list of relevant taxon identifiers [DONE]
6. synchronize taxons [DONE]
7. iteratively load the tree of life (using an iterator-like approach) and fetch things to complete paths to root [DONE]
8. load taxon names [DONE]
9. For each vertex, get the best guess in the tree
for instance if a k-mer has 3 things on it, try to find a common ancestor in the tree [DONE]
10. also add a Unknown category, which are the k-mers without colors but assembled de novo [DONE]
11. synchronize the tree with master [DONE]
12. output BiologicalAbundances/_Phylogeny/Hits.txt [DONE]
*/
__DeclarePlugin(TaxonomyViewer);
__DeclareMasterModeAdapter(TaxonomyViewer,RAY_MASTER_MODE_PHYLOGENY_MAIN);
__DeclareSlaveModeAdapter(TaxonomyViewer,RAY_SLAVE_MODE_PHYLOGENY_MAIN);
__DeclareMessageTagAdapter(TaxonomyViewer,RAY_MPI_TAG_TOUCH_TAXON);
__DeclareMessageTagAdapter(TaxonomyViewer,RAY_MPI_TAG_TAXON_OBSERVATIONS);
/**
* a plugin to know what is present in a sample
* \author Sébastien Boisvert
*/
class TaxonomyViewer: public CorePlugin{
__AddAdapter(TaxonomyViewer,RAY_MASTER_MODE_PHYLOGENY_MAIN);
__AddAdapter(TaxonomyViewer,RAY_SLAVE_MODE_PHYLOGENY_MAIN);
__AddAdapter(TaxonomyViewer,RAY_MPI_TAG_TOUCH_TAXON);
__AddAdapter(TaxonomyViewer,RAY_MPI_TAG_TAXON_OBSERVATIONS);
/* slave states */
bool m_extractedColorsForPhylogeny;
bool m_loadedTaxonsForPhylogeny;
bool m_sentTaxonsToMaster;
bool m_sentTaxonControlMessage;
bool m_messageSent;
bool m_messageReceived;
bool m_synced;
bool m_loadedTree;
bool m_gatheredObservations;
bool m_syncedTree;
bool m_unknownSent;
map<TaxonIdentifier,LargeCount>::iterator m_countIterator;
set<TaxonIdentifier>::iterator m_taxonIterator;
/* master states */
int m_ranksThatLoadedTaxons;
bool m_mustSync;
int m_responses;
set<GenomeIdentifier> m_warnings;
set<PhysicalKmerColor> m_colorsForPhylogeny;
set<TaxonIdentifier> m_taxonsForPhylogeny;
set<TaxonIdentifier> m_taxonsForPhylogenyMaster;
map<GenomeIdentifier,TaxonIdentifier> m_genomeToTaxon;
map<TaxonIdentifier,string> m_taxonNames;
map<TaxonIdentifier,string> m_taxonRanks;
map<TaxonIdentifier,LargeCount> m_taxonObservations;
map<TaxonIdentifier,LargeCount> m_taxonObservationsMaster;
map<TaxonIdentifier,LargeCount> m_taxonRecursiveObservations;
TaxonIdentifier UNKNOWN_TAXON;
LargeCount m_unknown;
LargeCount m_unknownMaster;
map<TaxonIdentifier,set<TaxonIdentifier> > m_treeChildren;
map<TaxonIdentifier,TaxonIdentifier> m_treeParents;
GridTable*m_subgraph;
Parameters*m_parameters;
SwitchMan*m_switchMan;
StaticVector*m_outbox;
RingAllocator*m_outboxAllocator;
ColorSet*m_colorSet;
Rank m_rank;
int m_size;
StaticVector*m_inbox;
RingAllocator*m_inboxAllocator;
TimePrinter*m_timePrinter;
ComputeCore*m_core;
bool m_started;
Searcher*m_searcher;
MasterMode RAY_MASTER_MODE_ONTOLOGY_MAIN;
MasterMode RAY_MASTER_MODE_PHYLOGENY_MAIN;
MasterMode RAY_MASTER_MODE_KILL_RANKS;
MasterMode RAY_MASTER_MODE_NEIGHBOURHOOD;
SlaveMode RAY_SLAVE_MODE_PHYLOGENY_MAIN;
MessageTag RAY_MPI_TAG_PHYLOGENY_MAIN;
MessageTag RAY_MPI_TAG_TOUCH_TAXON;
MessageTag RAY_MPI_TAG_TOUCH_TAXON_REPLY;
MessageTag RAY_MPI_TAG_SYNCED_TAXONS;
MessageTag RAY_MPI_TAG_LOADED_TAXONS;
MessageTag RAY_MPI_TAG_TAXON_OBSERVATIONS;
MessageTag RAY_MPI_TAG_TAXON_OBSERVATIONS_REPLY;
bool m_loadAllTree;
LargeCount m_totalNumberOfKmerObservations;
void extractColorsForPhylogeny();
void loadTaxons();
void sendTaxonsToMaster();
void sendTaxonsFromMaster();
void copyTaxonsFromSecondaryTable();
void loadTree();
void testPaths();
void getTaxonPathFromRoot(TaxonIdentifier taxon,vector<TaxonIdentifier>*path);
void loadTaxonNames();
string getTaxonName(TaxonIdentifier taxon);
void gatherKmerObservations();
void classifySignal(vector<TaxonIdentifier>*taxons,int kmerCoverage,Vertex*vertex,Kmer*key);
void printTaxonPath(TaxonIdentifier taxon,vector<TaxonIdentifier>*path,ostream*stream);
TaxonIdentifier getTaxonParent(TaxonIdentifier taxon);
void showObservations(ostream*stream);
void sendTreeCounts();
TaxonIdentifier findCommonAncestor(vector<TaxonIdentifier>*taxons);
string getTaxonRank(TaxonIdentifier taxon);
void showObservations_XML(ostream*stream);
void printTaxonPath_XML(TaxonIdentifier taxon,vector<TaxonIdentifier>*path,ostream*stream);
void printTaxon_XML(TaxonIdentifier taxon,ostream*stream);
LargeCount getRecursiveCount(TaxonIdentifier taxon);
void populateRanks(map<string,LargeCount>*rankSelfObservations,
map<string,LargeCount>*rankRecursiveObservations);
LargeCount getSelfCount(TaxonIdentifier taxon);
public:
void call_RAY_MASTER_MODE_PHYLOGENY_MAIN();
void call_RAY_SLAVE_MODE_PHYLOGENY_MAIN();
void call_RAY_MPI_TAG_TOUCH_TAXON(Message*message);
void call_RAY_MPI_TAG_TAXON_OBSERVATIONS(Message*message);
void registerPlugin(ComputeCore*core);
void resolveSymbols(ComputeCore*core);
};
#endif
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