Re: [Denovoassembler-devel] [PATCH] Added an example plugin.
Ray -- Parallel genome assemblies for parallel DNA sequencing
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Re: [Denovoassembler-devel] [PATCH] Added an example plugin.
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From: Sébastien B. <se...@bo...> - 2013-02-03 16:19:18
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(Please CC denovoassembler-devel)
I merged the patch.
However, the methods registerPlugin and resolveSymbols should be the two
last in the .cpp file of any plugin. I fixed that.
Sébastien
On 02/02/2013 10:03 PM, Charles Joly Beauparlant wrote:
> This plugin comes from RayPlatform-example.
>
> The example is activated with the -example option. Will work without input sequences.
>
> Signed-off-by: Charles Joly Beauparlant <Cha...@cr...>
> ---
> code/application_core/Machine.cpp | 4 +-
> code/application_core/Machine.h | 5 +-
> code/plugin_Example/Example.cpp | 273 +++++++++++++++++++++++++++
> code/plugin_Example/Example.h | 117 ++++++++++++
> code/plugin_Example/Makefile | 3 +
> code/plugin_MachineHelper/MachineHelper.cpp | 64 ++++---
> code/plugin_MachineHelper/MachineHelper.h | 9 +-
> 7 files changed, 443 insertions(+), 32 deletions(-)
> create mode 100644 code/plugin_Example/Example.cpp
> create mode 100644 code/plugin_Example/Example.h
> create mode 100644 code/plugin_Example/Makefile
>
> diff --git a/code/application_core/Machine.cpp b/code/application_core/Machine.cpp
> index 704c477..dc5c184 100644
> --- a/code/application_core/Machine.cpp
> +++ b/code/application_core/Machine.cpp
> @@ -1,6 +1,7 @@
> /*
> - Ray
> + Ray -- Parallel genome assemblies for parallel DNA sequencing
> Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
> + Copyright (C) 2013 Charles Joly Beauparlant
>
> http://DeNovoAssembler.SourceForge.Net/
>
> @@ -813,6 +814,7 @@ void Machine::registerPlugins(){
> m_computeCore.registerPlugin(&m_genomeNeighbourhood);
> m_computeCore.registerPlugin(&m_ontologyPlugin);
> m_computeCore.registerPlugin(&m_mock);
> + m_computeCore.registerPlugin(&m_example);
>
> // resolve the symbols
> // this is done here because we want to write a summary for
> diff --git a/code/application_core/Machine.h b/code/application_core/Machine.h
> index a65a0a5..65ea98c 100644
> --- a/code/application_core/Machine.h
> +++ b/code/application_core/Machine.h
> @@ -1,6 +1,7 @@
> /*
> - Ray
> + Ray -- Parallel genome assemblies for parallel DNA sequencing
> Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
> + Copyright (C) 2013 Charles Joly Beauparlant
>
> http://DeNovoAssembler.SourceForge.Net/
>
> @@ -63,6 +64,7 @@
> #include <code/plugin_GenomeNeighbourhood/GenomeNeighbourhood.h>
> #include <code/plugin_GeneOntology/GeneOntology.h>
> #include <code/plugin_Mock/Mock.h>
> +#include <code/plugin_Example/Example.h>
>
>
>
> @@ -159,6 +161,7 @@ class Machine : public MiniRank{
> EdgePurger m_edgePurger;
> PhylogenyViewer m_phylogeny;
> GeneOntology m_ontologyPlugin;
> + Example m_example;
>
> KmerAcademyBuilder m_kmerAcademyBuilder;
> bool m_initialisedAcademy;
> diff --git a/code/plugin_Example/Example.cpp b/code/plugin_Example/Example.cpp
> new file mode 100644
> index 0000000..d3ee9a4
> --- /dev/null
> +++ b/code/plugin_Example/Example.cpp
> @@ -0,0 +1,273 @@
> +/*
> + Ray -- Parallel genome assemblies for parallel DNA sequencing
> + Copyright (C) 2013 Charles Joly Beauparlant
> +
> + 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/>
> +
> + This is derived from RayPlatform-example.
> +
> +*/
> +
> +#include "Example.h"
> +
> +__CreatePlugin(Example);
> +
> +__CreateMasterModeAdapter(Example,RAY_MASTER_MODE_STEP_A);
> +__CreateMasterModeAdapter(Example,RAY_MASTER_MODE_STEP_B);
> +__CreateMasterModeAdapter(Example,RAY_MASTER_MODE_STEP_C);
> +
> +__CreateSlaveModeAdapter(Example,RAY_SLAVE_MODE_STEP_A);
> +__CreateSlaveModeAdapter(Example,RAY_SLAVE_MODE_STEP_B);
> +__CreateSlaveModeAdapter(Example,RAY_SLAVE_MODE_STEP_C);
> +
> +__CreateMessageTagAdapter(Example,RAY_MPI_TAG_STOP_AND_DIE);
> +__CreateMessageTagAdapter(Example,RAY_MPI_TAG_TIME_BOMB);
> +
> +Example::Example(){
> + m_doneA=false;
> + m_doneB=false;
> + m_doneC=false;
> +}
> +
> +void Example::call_RAY_MASTER_MODE_STEP_A(){
> + if(m_doneA==false){
> + m_doneA=true;
> + cout<<"Rank "<<m_core->getRank()<<" call_RAY_MASTER_MODE_STEP_A"<<endl;
> +
> + m_core->getSwitchMan()->openMasterMode(m_core->getOutbox(),m_core->getRank());
> + }else if(m_core->getSwitchMan()->allRanksAreReady()){
> + m_core->getSwitchMan()->closeMasterMode();
> + }
> +}
> +
> +void Example::call_RAY_MASTER_MODE_STEP_B(){
> + if(m_doneB==false){
> + m_doneB=true;
> + cout<<"Rank "<<MASTER_RANK<<" call_RAY_MASTER_MODE_STEP_B"<<endl;
> + m_core->getSwitchMan()->openMasterMode(m_core->getOutbox(),m_core->getRank());
> + }else if(m_core->getSwitchMan()->allRanksAreReady()){
> + m_core->getSwitchMan()->closeMasterMode();
> + }
> +}
> +
> +void Example::call_RAY_MASTER_MODE_STEP_C(){
> + if(m_doneC==false){
> + m_doneC=true;
> + cout<<"Rank "<<MASTER_RANK<<" call_RAY_MASTER_MODE_STEP_C"<<endl;
> + m_core->getSwitchMan()->openMasterMode(m_core->getOutbox(),m_core->getRank());
> + }else if(m_core->getSwitchMan()->allRanksAreReady()){
> + m_core->getSwitchMan()->closeMasterMode();
> + }
> +}
> +
> +void Example::call_RAY_SLAVE_MODE_STEP_A(){
> + cout<<"I am "<<m_core->getRank()<<" doing call_RAY_SLAVE_MODE_STEP_A"<<endl;
> +
> + m_core->getSwitchMan()->closeSlaveModeLocally(m_core->getOutbox(),m_core->getRank());
> +}
> +
> +void Example::call_RAY_SLAVE_MODE_STEP_B(){
> + cout<<"I am "<<m_core->getRank()<<" doing call_RAY_SLAVE_MODE_STEP_B"<<endl;
> +
> + m_core->getSwitchMan()->closeSlaveModeLocally(m_core->getOutbox(),m_core->getRank());
> +}
> +
> +void Example::call_RAY_SLAVE_MODE_STEP_C(){
> +
> + cout<<"I am "<<m_core->getRank()<<" doing call_RAY_SLAVE_MODE_STEP_C, now I die"<<endl;
> + cout<<"This is over "<<endl;
> +
> + if(m_core->getRank()==0){
> + uint64_t*buffer=(uint64_t*)m_core->getOutboxAllocator()->allocate(1*sizeof(uint64_t));
> + buffer[0]=100;
> +
> + // compute the next destination
> + Rank destination=m_core->getRank()+1;
> + if(destination==m_core->getSize())
> + destination=0;
> +
> + Message aMessage(buffer,1,destination,RAY_MPI_TAG_TIME_BOMB,m_core->getRank());
> +
> + // send the bomb to another rank
> + m_core->getOutbox()->push_back(&aMessage);
> + }
> +
> + // do nothing now
> + m_core->getSwitchMan()->setSlaveMode(RAY_SLAVE_MODE_DO_NOTHING);
> +}
> +
> +void Example::call_RAY_MPI_TAG_TIME_BOMB(Message*message){
> + uint64_t*buffer=message->getBuffer();
> +
> + if(buffer[0]==0){
> + cout<<"The bomb exploded on rank "<<m_core->getRank()<<" !"<<endl;
> +
> + // kill everyone
> +
> + m_core->sendEmptyMessageToAll(RAY_MPI_TAG_STOP_AND_DIE);
> + }else{
> + uint64_t*bufferOut=(uint64_t*)m_core->getOutboxAllocator()->allocate(1*sizeof(uint64_t));
> + bufferOut[0]=buffer[0]-1;
> +
> + cout<<"Remaining time before the explosion is "<<bufferOut[0]<<" according to rank "<<m_core->getRank()<<endl;
> +
> + // compute the next destination
> + Rank destination=m_core->getRank()+1;
> + if(destination==m_core->getSize())
> + destination=0;
> +
> + Message aMessage(bufferOut,1,destination,RAY_MPI_TAG_TIME_BOMB,m_core->getRank());
> +
> + // send the bomb to another rank
> + m_core->getOutbox()->push_back(&aMessage);
> + }
> +}
> +
> +void Example::call_RAY_MPI_TAG_STOP_AND_DIE(Message*message){
> +
> + cout<<"rank "<<m_core->getRank()<<" received message RAY_MPI_TAG_STOP_AND_DIE, this kills the batman"<<endl;
> +
> + m_core->stop();
> +}
> +
> +void Example::registerPlugin(ComputeCore*core){
> +
> + /** register the m_plugin with the core **/
> +
> + m_plugin=core->allocatePluginHandle();
> +
> + core->setPluginName(m_plugin,"Example");
> + core->setPluginDescription(m_plugin,"Minimal plugin example");
> + core->setPluginAuthors(m_plugin,"Charles Joly Beauparlant");
> + core->setPluginLicense(m_plugin,"GNU General Public License version 3");
> +
> + // for each master mode, we allocate a handle after that, we register a handler for it
> + //
> + // allocateMasterModeHandle takes 1 arguments
> + // - the plugin handle
> +
> + RAY_MASTER_MODE_STEP_A=core->allocateMasterModeHandle(m_plugin);
> + core->setMasterModeObjectHandler(m_plugin,RAY_MASTER_MODE_STEP_A,
> + __GetAdapter(Example,RAY_MASTER_MODE_STEP_A));
> +
> + core->setMasterModeSymbol(m_plugin,RAY_MASTER_MODE_STEP_A,"RAY_MASTER_MODE_STEP_A");
> +
> + core->setMasterModePublicAccess(m_plugin, RAY_MASTER_MODE_STEP_A);
> +
> + RAY_MASTER_MODE_STEP_B=core->allocateMasterModeHandle(m_plugin);
> + core->setMasterModeObjectHandler(m_plugin,RAY_MASTER_MODE_STEP_B,
> + __GetAdapter(Example,RAY_MASTER_MODE_STEP_B));
> +
> + core->setMasterModeSymbol(m_plugin,RAY_MASTER_MODE_STEP_B,"RAY_MASTER_MODE_STEP_B");
> +
> + RAY_MASTER_MODE_STEP_C=core->allocateMasterModeHandle(m_plugin);
> + core->setMasterModeObjectHandler(m_plugin,RAY_MASTER_MODE_STEP_C,
> + __GetAdapter(Example,RAY_MASTER_MODE_STEP_C));
> +
> + core->setMasterModeSymbol(m_plugin,RAY_MASTER_MODE_STEP_C,"RAY_MASTER_MODE_STEP_C");
> +
> + // for each slave mode, we allocate a handle after that, we register a handler for it
> +
> + RAY_SLAVE_MODE_STEP_A=core->allocateSlaveModeHandle(m_plugin);
> + core->setSlaveModeObjectHandler(m_plugin,RAY_SLAVE_MODE_STEP_A,
> + __GetAdapter(Example,RAY_SLAVE_MODE_STEP_A));
> +
> + core->setSlaveModeSymbol(m_plugin,RAY_SLAVE_MODE_STEP_A,"RAY_SLAVE_MODE_STEP_A");
> +
> + RAY_SLAVE_MODE_STEP_B=core->allocateSlaveModeHandle(m_plugin);
> + core->setSlaveModeObjectHandler(m_plugin,RAY_SLAVE_MODE_STEP_B,
> + __GetAdapter(Example,RAY_SLAVE_MODE_STEP_B));
> +
> + core->setSlaveModeSymbol(m_plugin,RAY_SLAVE_MODE_STEP_B,"RAY_SLAVE_MODE_STEP_B");
> +
> + RAY_SLAVE_MODE_STEP_C=core->allocateSlaveModeHandle(m_plugin);
> + core->setSlaveModeObjectHandler(m_plugin,RAY_SLAVE_MODE_STEP_C,
> + __GetAdapter(Example,RAY_SLAVE_MODE_STEP_C));
> +
> + core->setSlaveModeSymbol(m_plugin,RAY_SLAVE_MODE_STEP_C,"RAY_SLAVE_MODE_STEP_C");
> +
> + RAY_MPI_TAG_START_STEP_A=core->allocateMessageTagHandle(m_plugin);
> + core->setMessageTagSymbol(m_plugin, RAY_MPI_TAG_START_STEP_A, "RAY_MPI_TAG_START_STEP_A");
> + RAY_MPI_TAG_START_STEP_B=core->allocateMessageTagHandle(m_plugin);
> + core->setMessageTagSymbol(m_plugin, RAY_MPI_TAG_START_STEP_B, "RAY_MPI_TAG_START_STEP_B");
> + RAY_MPI_TAG_START_STEP_C=core->allocateMessageTagHandle(m_plugin);
> + core->setMessageTagSymbol(m_plugin, RAY_MPI_TAG_START_STEP_C, "RAY_MPI_TAG_START_STEP_C");
> +
> + // now, we register the order of the master modes
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_STEP_A,RAY_MASTER_MODE_STEP_B);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_STEP_B,RAY_MASTER_MODE_STEP_C);
> +
> + // configure which control message to send given a master mode
> + core->setMasterModeToMessageTagSwitch(m_plugin,RAY_MASTER_MODE_STEP_A,RAY_MPI_TAG_START_STEP_A);
> + core->setMasterModeToMessageTagSwitch(m_plugin,RAY_MASTER_MODE_STEP_B,RAY_MPI_TAG_START_STEP_B);
> + core->setMasterModeToMessageTagSwitch(m_plugin,RAY_MASTER_MODE_STEP_C,RAY_MPI_TAG_START_STEP_C);
> +
> + // configure which slave mode to set given a message tag
> + core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_START_STEP_A,RAY_SLAVE_MODE_STEP_A);
> + core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_START_STEP_B,RAY_SLAVE_MODE_STEP_B);
> + core->setMessageTagToSlaveModeSwitch(m_plugin,RAY_MPI_TAG_START_STEP_C,RAY_SLAVE_MODE_STEP_C);
> +
> + m_core=core;
> +
> + // configure the two message tags
> + RAY_MPI_TAG_TIME_BOMB=core->allocateMessageTagHandle(m_plugin);
> + core->setMessageTagObjectHandler(m_plugin,RAY_MPI_TAG_TIME_BOMB,
> + __GetAdapter(Example,RAY_MPI_TAG_TIME_BOMB));
> +
> + core->setMessageTagSymbol(m_plugin, RAY_MPI_TAG_TIME_BOMB, "RAY_MPI_TAG_TIME_BOMB");
> +
> + RAY_MPI_TAG_STOP_AND_DIE=core->allocateMessageTagHandle(m_plugin);
> + core->setMessageTagObjectHandler(m_plugin,RAY_MPI_TAG_STOP_AND_DIE,
> + __GetAdapter(Example,RAY_MPI_TAG_STOP_AND_DIE));
> +
> + core->setMessageTagSymbol(m_plugin, RAY_MPI_TAG_STOP_AND_DIE, "RAY_MPI_TAG_STOP_AND_DIE");
> +
> + /* a plugin can share any of its object with other plugins **/
> + /** other plugins have to resolve the symbol. **/
> + void*object=&m_doneA;
> + core->setObjectSymbol(m_plugin,object,"BooleanState");
> +}
> +
> +void Example::resolveSymbols(ComputeCore*core){
> +
> + // here, we resolve symbols owned by other m_plugins
> + // but needed by the current m_plugin
> + // obviously, this is not needed here because
> + // we only have one m_plugin
> +
> + RAY_SLAVE_MODE_STEP_A=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_STEP_A");
> +
> + // this slave mode is registered somewhere in RayPlatform
> + RAY_SLAVE_MODE_DO_NOTHING=core->getSlaveModeFromSymbol(m_plugin,"RAY_SLAVE_MODE_DO_NOTHING");
> +
> + bool*example=(bool*) core->getObjectFromSymbol(m_plugin,"BooleanState");
> +
> + if(*example)
> + *example=false;
> +
> + __BindPlugin(Example);
> +
> + __BindAdapter(Example,RAY_MASTER_MODE_STEP_A);
> + __BindAdapter(Example,RAY_MASTER_MODE_STEP_B);
> + __BindAdapter(Example,RAY_MASTER_MODE_STEP_C);
> +
> + __BindAdapter(Example,RAY_SLAVE_MODE_STEP_A);
> + __BindAdapter(Example,RAY_SLAVE_MODE_STEP_B);
> + __BindAdapter(Example,RAY_SLAVE_MODE_STEP_C);
> +
> + __BindAdapter(Example,RAY_MPI_TAG_STOP_AND_DIE);
> + __BindAdapter(Example,RAY_MPI_TAG_TIME_BOMB);
> +}
> diff --git a/code/plugin_Example/Example.h b/code/plugin_Example/Example.h
> new file mode 100644
> index 0000000..01fb444
> --- /dev/null
> +++ b/code/plugin_Example/Example.h
> @@ -0,0 +1,117 @@
> +/*
> + Ray -- Parallel genome assemblies for parallel DNA sequencing
> + Copyright (C) 2013 Charles Joly Beauparlant
> +
> + 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/>
> +
> + This is derived from RayPlatform-example.
> +
> +*/
> +
> +#ifndef _Example_h
> +#define _Example_h
> +
> +#include <RayPlatform/core/ComputeCore.h>
> +
> +__DeclarePlugin(Example);
> +
> +__DeclareMasterModeAdapter(Example,RAY_MASTER_MODE_STEP_A);
> +__DeclareMasterModeAdapter(Example,RAY_MASTER_MODE_STEP_B);
> +__DeclareMasterModeAdapter(Example,RAY_MASTER_MODE_STEP_C);
> +
> +__DeclareSlaveModeAdapter(Example,RAY_SLAVE_MODE_STEP_A);
> +__DeclareSlaveModeAdapter(Example,RAY_SLAVE_MODE_STEP_B);
> +__DeclareSlaveModeAdapter(Example,RAY_SLAVE_MODE_STEP_C);
> +
> +__DeclareMessageTagAdapter(Example,RAY_MPI_TAG_STOP_AND_DIE);
> +__DeclareMessageTagAdapter(Example,RAY_MPI_TAG_TIME_BOMB);
> +
> +/**
> + * The plugin Example
> + *
> + * \author Charles Joly Beauparlant
> + **/
> +class Example: public CorePlugin{
> +
> + __AddAdapter(Example,RAY_MASTER_MODE_STEP_A);
> + __AddAdapter(Example,RAY_MASTER_MODE_STEP_B);
> + __AddAdapter(Example,RAY_MASTER_MODE_STEP_C);
> +
> + __AddAdapter(Example,RAY_SLAVE_MODE_STEP_A);
> + __AddAdapter(Example,RAY_SLAVE_MODE_STEP_B);
> + __AddAdapter(Example,RAY_SLAVE_MODE_STEP_C);
> +
> + __AddAdapter(Example,RAY_MPI_TAG_STOP_AND_DIE);
> + __AddAdapter(Example,RAY_MPI_TAG_TIME_BOMB);
> +
> +/**
> + * A list of master modes
> + */
> + MasterMode RAY_MASTER_MODE_STEP_A;
> + MasterMode RAY_MASTER_MODE_STEP_B;
> + MasterMode RAY_MASTER_MODE_STEP_C;
> +
> +/** slave modes **/
> + SlaveMode RAY_SLAVE_MODE_STEP_A;
> + SlaveMode RAY_SLAVE_MODE_STEP_B;
> + SlaveMode RAY_SLAVE_MODE_STEP_C;
> + SlaveMode RAY_SLAVE_MODE_DO_NOTHING;
> +
> +
> + MessageTag RAY_MPI_TAG_START_STEP_A;
> + MessageTag RAY_MPI_TAG_START_STEP_B;
> + MessageTag RAY_MPI_TAG_START_STEP_C;
> +
> + MessageTag RAY_MPI_TAG_TIME_BOMB;
> + MessageTag RAY_MPI_TAG_STOP_AND_DIE;
> +
> + ComputeCore*m_core;
> +
> +/** states for progression **/
> + bool m_doneA;
> + bool m_doneB;
> + bool m_doneC;
> + bool m_doneExample;
> +
> +/** Example state **/
> + bool m_example;
> +public:
> +
> + Example();
> +
> +/** callbacks for master modes **/
> + void call_RAY_MASTER_MODE_STEP_A();
> + void call_RAY_MASTER_MODE_STEP_B();
> + void call_RAY_MASTER_MODE_STEP_C();
> +
> +/** callbacks for slave modes **/
> + void call_RAY_SLAVE_MODE_STEP_A();
> + void call_RAY_SLAVE_MODE_STEP_B();
> + void call_RAY_SLAVE_MODE_STEP_C();
> +
> + void call_RAY_MPI_TAG_TIME_BOMB(Message*message);
> + void call_RAY_MPI_TAG_STOP_AND_DIE(Message*message);
> +
> +/** the following two methods are required by the interface CorePlugin **/
> +
> +/** register the plugin with the core **/
> + void registerPlugin(ComputeCore*core);
> +
> +/** resolve symbols not owned by the current plugin **/
> + void resolveSymbols(ComputeCore*core);
> +};
> +
> +#endif
> diff --git a/code/plugin_Example/Makefile b/code/plugin_Example/Makefile
> new file mode 100644
> index 0000000..50b1ba4
> --- /dev/null
> +++ b/code/plugin_Example/Makefile
> @@ -0,0 +1,3 @@
> +Example-y += code/plugin_Example/Example.o
> +
> +obj-y += $(Example-y)
> diff --git a/code/plugin_MachineHelper/MachineHelper.cpp b/code/plugin_MachineHelper/MachineHelper.cpp
> index fbe52a5..04ec687 100644
> --- a/code/plugin_MachineHelper/MachineHelper.cpp
> +++ b/code/plugin_MachineHelper/MachineHelper.cpp
> @@ -1,6 +1,7 @@
> /*
> - Ray
> - Copyright (C) 2012 Sébastien Boisvert
> + Ray -- Parallel genome assemblies for parallel DNA sequencing
> + Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
> + Copyright (C) 2013 Charles Joly Beauparlant
>
> http://DeNovoAssembler.SourceForge.Net/
>
> @@ -1225,6 +1226,7 @@ void MachineHelper::resolveSymbols(ComputeCore*core){
> RAY_MASTER_MODE_UPDATE_DISTANCES=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_UPDATE_DISTANCES");
> RAY_MASTER_MODE_WRITE_KMERS=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_WRITE_KMERS");
> RAY_MASTER_MODE_WRITE_SCAFFOLDS=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_WRITE_SCAFFOLDS");
> + RAY_MASTER_MODE_STEP_A=core->getMasterModeFromSymbol(m_plugin,"RAY_MASTER_MODE_STEP_A");
>
> RAY_MPI_TAG_FINISH_FUSIONS=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_FINISH_FUSIONS");
> RAY_MPI_TAG_GET_CONTIG_CHUNK=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GET_CONTIG_CHUNK");
> @@ -1312,31 +1314,13 @@ void MachineHelper::resolveSymbols(ComputeCore*core){
> RAY_MPI_TAG_SET_FILE_ENTRIES=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_SET_FILE_ENTRIES");
> RAY_MPI_TAG_SET_FILE_ENTRIES_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_SET_FILE_ENTRIES_REPLY");
>
> - core->setFirstMasterMode(m_plugin,RAY_MASTER_MODE_LOAD_CONFIG);
> -
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_LOAD_CONFIG, RAY_MASTER_MODE_TEST_NETWORK);
> -
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_PREPARE_SEEDING,RAY_MASTER_MODE_TRIGGER_SEEDING);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_TRIGGER_SEEDING,RAY_MASTER_MODE_START_UPDATING_DISTANCES);
> -
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_LOAD_SEQUENCES,RAY_MASTER_MODE_TRIGGER_VERTICE_DISTRIBUTION);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_TRIGGER_VERTICE_DISTRIBUTION,RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS,RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS_WITH_ANSWERS);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS_WITH_ANSWERS,RAY_MASTER_MODE_SEND_COVERAGE_VALUES);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_SEND_COVERAGE_VALUES,RAY_MASTER_MODE_TRIGGER_GRAPH_BUILDING);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_TRIGGER_GRAPH_BUILDING,RAY_MASTER_MODE_PURGE_NULL_EDGES);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_PURGE_NULL_EDGES,RAY_MASTER_MODE_WRITE_KMERS);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_WRITE_KMERS,RAY_MASTER_MODE_TRIGGER_INDEXING);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_TRIGGER_INDEXING,RAY_MASTER_MODE_PREPARE_SEEDING);
> -
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_START_UPDATING_DISTANCES,RAY_MASTER_MODE_UPDATE_DISTANCES);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_TRIGGER_FUSIONS,RAY_MASTER_MODE_TRIGGER_FIRST_FUSIONS);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_TRIGGER_FIRST_FUSIONS,RAY_MASTER_MODE_START_FUSION_CYCLE);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_START_FUSION_CYCLE,RAY_MASTER_MODE_ASK_EXTENSIONS);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_ASK_EXTENSIONS,RAY_MASTER_MODE_SCAFFOLDER);
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_SCAFFOLDER,RAY_MASTER_MODE_WRITE_SCAFFOLDS);
> -
> - core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_KILL_RANKS,RAY_MASTER_MODE_KILL_ALL_MPI_RANKS);
> + if (m_parameters->hasOption("-example")) {
> + cout << "************** Example Mode **************" << endl;
> + core->setFirstMasterMode(m_plugin, RAY_MASTER_MODE_STEP_A);
> + }
> + else {
> + performAssemblyWorkflow(core);
> + }
>
> RAY_MPI_TAG_GOOD_JOB_SEE_YOU_SOON=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GOOD_JOB_SEE_YOU_SOON");
> RAY_MPI_TAG_GOOD_JOB_SEE_YOU_SOON_REPLY=core->getMessageTagFromSymbol(m_plugin,"RAY_MPI_TAG_GOOD_JOB_SEE_YOU_SOON_REPLY");
> @@ -1382,4 +1366,30 @@ void MachineHelper::resolveSymbols(ComputeCore*core){
> m_startedToSendCounts=false;
> }
>
> +void MachineHelper::performAssemblyWorkflow(ComputeCore*core) {
> + core->setFirstMasterMode(m_plugin,RAY_MASTER_MODE_LOAD_CONFIG);
> +
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_LOAD_CONFIG, RAY_MASTER_MODE_TEST_NETWORK);
> +
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_PREPARE_SEEDING,RAY_MASTER_MODE_TRIGGER_SEEDING);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_TRIGGER_SEEDING,RAY_MASTER_MODE_START_UPDATING_DISTANCES);
> +
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_LOAD_SEQUENCES,RAY_MASTER_MODE_TRIGGER_VERTICE_DISTRIBUTION);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_TRIGGER_VERTICE_DISTRIBUTION,RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS,RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS_WITH_ANSWERS);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_PREPARE_DISTRIBUTIONS_WITH_ANSWERS,RAY_MASTER_MODE_SEND_COVERAGE_VALUES);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_SEND_COVERAGE_VALUES,RAY_MASTER_MODE_TRIGGER_GRAPH_BUILDING);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_TRIGGER_GRAPH_BUILDING,RAY_MASTER_MODE_PURGE_NULL_EDGES);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_PURGE_NULL_EDGES,RAY_MASTER_MODE_WRITE_KMERS);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_WRITE_KMERS,RAY_MASTER_MODE_TRIGGER_INDEXING);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_TRIGGER_INDEXING,RAY_MASTER_MODE_PREPARE_SEEDING);
> +
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_START_UPDATING_DISTANCES,RAY_MASTER_MODE_UPDATE_DISTANCES);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_TRIGGER_FUSIONS,RAY_MASTER_MODE_TRIGGER_FIRST_FUSIONS);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_TRIGGER_FIRST_FUSIONS,RAY_MASTER_MODE_START_FUSION_CYCLE);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_START_FUSION_CYCLE,RAY_MASTER_MODE_ASK_EXTENSIONS);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_ASK_EXTENSIONS,RAY_MASTER_MODE_SCAFFOLDER);
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_SCAFFOLDER,RAY_MASTER_MODE_WRITE_SCAFFOLDS);
>
> + core->setMasterModeNextMasterMode(m_plugin,RAY_MASTER_MODE_KILL_RANKS,RAY_MASTER_MODE_KILL_ALL_MPI_RANKS);
> +}
> diff --git a/code/plugin_MachineHelper/MachineHelper.h b/code/plugin_MachineHelper/MachineHelper.h
> index c58e680..c2b94d6 100644
> --- a/code/plugin_MachineHelper/MachineHelper.h
> +++ b/code/plugin_MachineHelper/MachineHelper.h
> @@ -1,6 +1,7 @@
> /*
> - Ray
> - Copyright (C) 2012 Sébastien Boisvert
> + Ray -- Parallel genome assemblies for parallel DNA sequencing
> + Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
> + Copyright (C) 2013 Charles Joly Beauparlant
>
> http://DeNovoAssembler.SourceForge.Net/
>
> @@ -24,6 +25,7 @@
> #include <code/plugin_Mock/Parameters.h>
> #include <code/plugin_FusionData/FusionData.h>
> #include <code/plugin_NetworkTest/NetworkTest.h>
> +#include <code/plugin_Example/Example.h>
> #include <code/plugin_Partitioner/Partitioner.h>
> #include <code/plugin_SequencesLoader/SequencesLoader.h>
> #include <code/plugin_SeedingData/SeedingData.h>
> @@ -251,6 +253,7 @@ class MachineHelper: public CorePlugin{
> MasterMode RAY_MASTER_MODE_UPDATE_DISTANCES;
> MasterMode RAY_MASTER_MODE_WRITE_KMERS;
> MasterMode RAY_MASTER_MODE_WRITE_SCAFFOLDS;
> + MasterMode RAY_MASTER_MODE_STEP_A;
>
> SlaveMode RAY_SLAVE_MODE_EXTENSION;
> SlaveMode RAY_SLAVE_MODE_ADD_COLORS;
> @@ -359,7 +362,7 @@ class MachineHelper: public CorePlugin{
>
> int getRank();
> int getSize();
> -
> + void performAssemblyWorkflow(ComputeCore*core);
>
> public:
> void constructor(int argc,char**argv,Parameters*parameters,
>
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