[Denovoassembler-devel] [PATCH] Added a example plugin.
Ray -- Parallel genome assemblies for parallel DNA sequencing
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[Denovoassembler-devel] [PATCH] Added a example plugin.
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From: Charles J. B. <Cha...@cr...> - 2013-02-01 21:44:06
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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 | 278 +++++++++++++++++++++++++++
code/plugin_Example/Example.h | 117 +++++++++++
code/plugin_Example/Makefile | 3 +
code/plugin_MachineHelper/MachineHelper.cpp | 63 ++++---
code/plugin_MachineHelper/MachineHelper.h | 7 +-
7 files changed, 446 insertions(+), 31 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..baf949b
--- /dev/null
+++ b/code/plugin_Example/Example.cpp
@@ -0,0 +1,278 @@
+/*
+ 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);
+
+ // finally, we define an entry point
+// core->setFirstMasterMode(m_plugin,RAY_MASTER_MODE_STEP_A);
+
+ 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..600afe8
--- /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..afc6335 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 +1314,38 @@ 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_KILL_ALL_MPI_RANKS);
+ core->setFirstMasterMode(m_plugin, RAY_MASTER_MODE_STEP_A);
+ }
+ else {
+ 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);
+ }
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");
diff --git a/code/plugin_MachineHelper/MachineHelper.h b/code/plugin_MachineHelper/MachineHelper.h
index c58e680..459d21c 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;
--
1.7.7.6
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