Re: [Denovoassembler-devel] git diff kmersmatrix branch

[Sébastien B. <se...@bo...>]

Hey Maxime,

You did not provide KmersMatrixOwner.h, KmersMatrixOwner.cpp, and changes
to the Surveyor Makefile.


OTher comments are below.

----------------------------------------
> Date: Sat, 22 Feb 2014 10:03:30 +0000
> From: ma...@de...
> To: se...@bo...
> Subject: git diff kmersmatrix branch
>
> diff --git a/code/Surveyor/MatrixOwner.cpp b/code/Surveyor/MatrixOwner.cpp
> index ffaae00..47cf84a 100644
> --- a/code/Surveyor/MatrixOwner.cpp
> +++ b/code/Surveyor/MatrixOwner.cpp
> @@ -65,9 +65,12 @@ void MatrixOwner::receive(Message & message) {
> assert(m_parameters != NULL);
> assert(m_sampleNames != NULL);
> #endif
> -
> m_mother = source;
>
> + //open the buffer of the file
> + // createKmersMatrixOutputFile();
> +
> +
> } else if(tag == PUSH_PAYLOAD) {
>
> SampleIdentifier sample1 = -1;
> @@ -89,10 +92,10 @@ void MatrixOwner::receive(Message & message) {
> assert(count>= 0);
> #endif
>
> - /*
> +
> printName();
> - cout << "DEBUG add " << sample1 << " " << sample2 << " "
> << count << endl;
> -*/
> + // cout << "DEBUG add " << sample1 << " " << sample2 <<

Commented lines should be removed.

> " " << count << endl;
> +
> m_receivedPayloads ++;
>
> m_localGramMatrix[sample1][sample2] += count;
> @@ -100,14 +103,14 @@ void MatrixOwner::receive(Message & message) {
> Message response;
> response.setTag(PUSH_PAYLOAD_OK);
> send(source, response);
> + }
> + else if(tag == PUSH_PAYLOAD_END) {

Use '} else if (' and not '}
else if'


This is the coding style of the project.
see https://github.com/sebhtml/ray/blob/master/Documentation/CodingStyle.txt

* Kernighan and Ritchie style, variant "The One True Brace Style" (1TBS)
http://en.wikipedia.org/wiki/Indent_style#Variant:_1TBS


(you used K&R Variant: Stroustrup).

>
> - } else if(tag == PUSH_PAYLOAD_END) {
> -
> + cout << "PUSH_PAYLOAD_END" <<endl;

Remove this debug message.

> m_completedStoreActors++;
>
> if(m_completedStoreActors == getSize()) {
>
> -
> printName();
> cout << "MatrixOwner received " <<
> m_receivedPayloads << " payloads" << endl;
>
> @@ -151,10 +154,9 @@ void MatrixOwner::receive(Message & message) {
>
>
> // tell Mother that the matrix is ready now.
> -
> - Message coolMessage;
> - coolMessage.setTag(MATRIX_IS_READY);
> - send(m_mother, coolMessage);
> + Message coolMessage;
> + coolMessage.setTag(GRAM_MATRIX_IS_READY);
> + send(m_mother, coolMessage);
>
>
> // clear matrices
> @@ -275,3 +277,4 @@ void
> MatrixOwner::printLocalGramMatrixWithHash(ostream & stream, map<SampleIdent
> stream << endl;
> }
> }
> +
> diff --git a/code/Surveyor/MatrixOwner.h b/code/Surveyor/MatrixOwner.h
> index ceb17e2..afa9278 100644
> --- a/code/Surveyor/MatrixOwner.h
> +++ b/code/Surveyor/MatrixOwner.h
> @@ -28,6 +28,7 @@
>
> #include <map>
> #include <iostream>
> +#include <sstream>
> using namespace std;
>
> class MatrixOwner : public Actor {
> @@ -62,7 +63,7 @@ public:
> PUSH_PAYLOAD,
> PUSH_PAYLOAD_OK,
> PUSH_PAYLOAD_END,
> - MATRIX_IS_READY,
> + GRAM_MATRIX_IS_READY,
> LAST_TAG
> };
>
> diff --git a/code/Surveyor/Mother.cpp b/code/Surveyor/Mother.cpp
> index 4d2ef9c..103a583 100644
> --- a/code/Surveyor/Mother.cpp
> +++ b/code/Surveyor/Mother.cpp
> @@ -27,6 +27,7 @@
> #include "GenomeGraphReader.h"
> #include "GenomeAssemblyReader.h"
> #include "MatrixOwner.h"
> +#include "KmersMatrixOwner.h"
>
> #include <RayPlatform/cryptography/crypto.h>
>
> @@ -39,11 +40,13 @@ using namespace std;
> #define INPUT_TYPE_GRAPH 0
> #define INPUT_TYPE_ASSEMBLY 1
>
> -
> Mother::Mother() {
>
> m_coalescenceManager = -1;
> m_matrixOwner = -1;
> + m_kmersMatrixOwner = -1;
> +
> + // m_matricesAreReady = true;

Remove this commented line.

>
> m_parameters = NULL;
> m_bigMother = -1;
> @@ -91,7 +94,7 @@ void Mother::receive(Message & message) {
> notifyController();
> }
>
> - } else if(tag == MERGE) {
> + } else if(tag == MERGE_GRAM_MATRIX) {
>
> int matrixOwner = -1;
> memcpy(&matrixOwner, buffer, sizeof(matrixOwner));
> @@ -102,7 +105,7 @@ void Mother::receive(Message & message) {
> #endif
>
> Message theMessage;
> - theMessage.setTag(StoreKeeper::MERGE);
> + theMessage.setTag(StoreKeeper::MERGE_GRAM_MATRIX);
> theMessage.setBuffer(&matrixOwner);
> theMessage.setNumberOfBytes(sizeof(matrixOwner));
>
> @@ -111,10 +114,33 @@ void Mother::receive(Message & message) {
> send(destination, theMessage);
>
> Message response;
> - response.setTag(MERGE_OK);
> + response.setTag(MERGE_GRAM_MATRIX_OK);
> + send(source, response);
> +
> + } else if (tag == MERGE_KMERS_MATRIX) {
> +
> + int kmersMatrixOwner = -1;
> + memcpy(&kmersMatrixOwner, buffer, sizeof(kmersMatrixOwner));
> +
> +#ifdef CONFIG_ASSERT
> + assert(kmersMatrixOwner>= 0);
> + assert(m_storeKeepers.size() == 1);
> +#endif
> +
> + Message theMessage;
> + theMessage.setTag(StoreKeeper::MERGE_KMERS_MATRIX);

The name should be MERGE_KMER_MATRIX and not MERGE_KMERS_MATRIX.

> + theMessage.setBuffer(&kmersMatrixOwner);
> + theMessage.setNumberOfBytes(sizeof(kmersMatrixOwner));
> +
> + int destination = m_storeKeepers[0];
> +
> + send(destination, theMessage);
> +
> + Message response;
> + response.setTag(MERGE_KMERS_MATRIX_OK);
> send(source, response);
>
> - } else if(tag == SHUTDOWN) {
> + } else if(tag == SHUTDOWN) {
>
> Message response;
> response.setTag(SHUTDOWN_OK);
> @@ -122,18 +148,16 @@ void Mother::receive(Message & message) {
>
> stop();
>
> - } else if(tag == StoreKeeper::MERGE_OK) {
> + } else if(tag == StoreKeeper::MERGE_GRAM_MATRIX_OK) {
>
> // TODO: the bug https://github.com/sebhtml/ray/issues/216
> // is caused by the fact that this message is not
> // received .
>
> - /*
> - Message newMessage;
> - newMessage.setTag(MERGE_OK);
> + // Message newMessage;
> + // newMessage.setTag(MERGE_OK);
>
> - send(m_bigMother, newMessage);
> - */
> + // send(m_bigMother, newMessage);

Remove these commented lines.

>
> } else if(tag == FINISH_JOB) {
>
> @@ -153,6 +177,7 @@ void Mother::receive(Message & message) {
>
> sendToFirstMother(FLUSH_AGGREGATOR,
> FLUSH_AGGREGATOR_RETURN);
> }
> +
> } else if(tag == FLUSH_AGGREGATOR) {
>
> /*
> @@ -188,64 +213,52 @@ void Mother::receive(Message & message) {
> cout << "DEBUG sending FLUSH_AGGREGATOR_OK to
> m_bigMother" << endl;
> */
>
> - } else if(tag == MatrixOwner::MATRIX_IS_READY) {
> + } else if(tag == MatrixOwner::GRAM_MATRIX_IS_READY) {
> +
> + //TODO : check if all matrices are ready
> + if(m_matricesAreReady){
> + sendToFirstMother(SHUTDOWN, SHUTDOWN_OK);
> + }else {
> + cout << "GRAM_MATRIX_IS_READY" << endl;

When an actor speak, you must print its name too in stdout.
(with printName()).

> + m_matricesAreReady = true;
> + }
>
> - sendToFirstMother(SHUTDOWN, SHUTDOWN_OK);
> + }
> + else if(tag == KmersMatrixOwner::KMERS_MATRIX_IS_READY) {
> +
> + cout << "KMERS_MATRIX_IS_READY" << endl;
> + if(m_matricesAreReady){
> + sendToFirstMother(SHUTDOWN, SHUTDOWN_OK);
> + }else {
> + cout << "KMERS_MATRIX_IS_READY" << endl;
> + m_matricesAreReady = true;


In one comment above, I saw that m_matricesAreReady = false 
was commented. Check that out.

> + }
>
> } else if(tag == FLUSH_AGGREGATOR_OK) {
>
> - /*
> printName();
> cout << "DEBUG received FLUSH_AGGREGATOR_OK" << endl;
> - */
>
> m_flushedMothers++;
>
> if(m_flushedMothers < getSize())
> return;
>
> - // spawn the MatrixOwner here !
> -
> - MatrixOwner * matrixOwner = new MatrixOwner();
> - spawn(matrixOwner);
> -
> - m_matrixOwner = matrixOwner->getName();
> -
> - printName();
> - cout << "Spawned MatrixOwner actor !" << endl;
> -
> - // tell the StoreKeeper actors to send their stuff to the
> - // MatrixOwner actor
> - // The Mother of Mother will wait for a signal from
> MatrixOwner
> -
> - Message greetingMessage;
> -
> - vector<string> * names = & m_sampleNames;
> -
> - char buffer[32];
> - int offset = 0;
> - memcpy(buffer + offset, &m_parameters,
> sizeof(m_parameters));
> - offset += sizeof(m_parameters);
> - memcpy(buffer + offset, &names, sizeof(names));
> - offset += sizeof(names);
> -
> - greetingMessage.setBuffer(&buffer);
> - greetingMessage.setNumberOfBytes(offset);
> -
> - greetingMessage.setTag(MatrixOwner::GREETINGS);
> - send(m_matrixOwner, greetingMessage);
> -
> - sendToFirstMother(MERGE, MERGE_OK);
> -
> + spawnMatrixOwner();

I like that. A method to spawn an actor. Good !

>
> } else if(tag == m_responseTag) {
>
> -
> if(m_responseTag == SHUTDOWN_OK) {
>
> - } else if(m_responseTag == MERGE_OK) {
> -
> - } else if(m_responseTag == FLUSH_AGGREGATOR_RETURN) {
> + } else if(m_responseTag == MERGE_GRAM_MATRIX_OK) {
> + // All mothers merged their GRAM MATRIX
> + // Spawn KmersMatrixOwner to print
> + if(m_motherToKill < getSize() &&
> m_printKmersMatrix){
> + spawnKmersMatrixOwner();
> + }
> + } else if(m_responseTag == MERGE_KMERS_MATRIX_OK) {
> + }
> + else if(m_responseTag == FLUSH_AGGREGATOR_RETURN) {

Again, put closing brace on same line (} else if ( ...) {

>
> /*
> printName();
> @@ -254,9 +267,8 @@ void Mother::receive(Message & message) {
> */
> }
>
> - // every mother was informed.
> + // every mother was not informed.

Good catch !

> if(m_motherToKill>= getSize()) {
> -
> sendMessageWithReply(m_motherToKill, m_forwardTag);
> m_motherToKill--;
> }
> @@ -284,11 +296,15 @@ void Mother::sendMessageWithReply(int & actor, int
> tag) {
> Message message;
> message.setTag(tag);
>
> - if(tag == MERGE) {
> + if(tag == MERGE_GRAM_MATRIX) {
> message.setBuffer(&m_matrixOwner);
> message.setNumberOfBytes(sizeof(m_matrixOwner));
> -
> - } else if(tag == FLUSH_AGGREGATOR) {
> + }
> + else if(tag == MERGE_KMERS_MATRIX) {
> + message.setBuffer(&m_kmersMatrixOwner);
> + message.setNumberOfBytes(sizeof(m_kmersMatrixOwner));
> + }
> + else if(tag == FLUSH_AGGREGATOR) {
>
> /*
> printName();
> @@ -328,6 +344,10 @@ void Mother::stop() {
> m_matrixOwner = -1;
> }
>
> + if(m_kmersMatrixOwner>= 0) {
> + send(m_kmersMatrixOwner, kill);
> + m_kmersMatrixOwner = -1;
> + }
>
> die();
>
> @@ -410,39 +430,44 @@ void Mother::startSurveyor() {
>
> bool isRoot = (getName() % getSize()) == 0;
>
> - //cout << "DEBUG startSurveyor isRoot" << isRoot << endl;
> -
> - // get a list of files.
> + // Set matricesAreReady to true in case user doesn't want
> + // to print out kmers matrix.
> + m_matricesAreReady = true;
>
> vector<string> * commands = m_parameters->getCommands();
>
> -
> for(int i = 0 ; i < (int) commands->size() ; ++i) {
>
> string & element = commands->at(i);
>
> - // DONE: Check bounds for file names
> + if (element != "-print-kmers-matrix") {

The name should be kmer-matrix, not kmers-matrix.

It is like groceries store vs grocery store.

> + // DONE: Check bounds for file names
>
> - map<string,int> fastTable;
> + map<string,int> fastTable;
>
> - fastTable["-read-sample-graph"] = INPUT_TYPE_GRAPH;
> - fastTable["-read-sample-assembly"] = INPUT_TYPE_ASSEMBLY;
> + fastTable["-read-sample-graph"] = INPUT_TYPE_GRAPH;
> + fastTable["-read-sample-assembly"] =
> INPUT_TYPE_ASSEMBLY;
>
> - // Unsupported option
> - if(fastTable.count(element) == 0 || i+2> (int)
> commands->size())
> - continue;
> + // Unsupported option
> + if(fastTable.count(element) == 0 || i+2> (int)
> commands->size())
> + continue;
>
> - string sampleName = commands->at(++i);
> - string fileName = commands->at(++i);
> + string sampleName = commands->at(++i);
> + string fileName = commands->at(++i);
>
> - m_sampleNames.push_back(sampleName);
> + m_sampleNames.push_back(sampleName);
>
> - // DONE implement this m_assemblyFileNames + type
> - m_inputFileNames.push_back(fileName);
> + // DONE implement this m_assemblyFileNames + type
> + m_inputFileNames.push_back(fileName);
>
> - int type = fastTable[element];
> + int type = fastTable[element];
>
> - m_sampleInputTypes.push_back(type);
> + m_sampleInputTypes.push_back(type);
> +
> + } else {
> + m_matricesAreReady = false;
> + m_printKmersMatrix = true;


Question: if m_printKmersMatrix is false, I suppose the code
follows the usual path of printing just one matrix, right ?

> + }
>
> }
>
> @@ -468,6 +493,9 @@ void Mother::startSurveyor() {
>
> m_storeKeepers.push_back(actor->getName());
>
> + actor->setOutputKmersMatrixPath(m_parameters->getPrefix());

The path should be prefix/Surveyor/<whatever the kmer matrix's name is>

> + actor->setSamplesSize(m_sampleNames.size());

sample size, not samples size.

> +
> // tell the CoalescenceManager about the local StoreKeeper
> Message dummyMessage;
> int localStore = actor->getName();
> @@ -568,6 +596,80 @@ void Mother::spawnReader() {
> }
> }
>
> +
> +void Mother::spawnMatrixOwner() {
> +
> + // spawn the MatrixOwner here !
> + MatrixOwner * matrixOwner = new MatrixOwner();
> + spawn(matrixOwner);
> +
> + m_matrixOwner = matrixOwner->getName();
> +
> + printName();
> + cout << "Spawned MatrixOwner actor !" << m_matrixOwner << endl;
> +
> + // tell the StoreKeeper actors to send their stuff to the
> + // MatrixOwner actor
> + // The Mother of Mother will wait for a signal from MatrixOwner
> +
> + Message greetingMessage;
> +
> + vector<string> * names = & m_sampleNames;
> +
> + char buffer[32];
> + int offset = 0;
> + memcpy(buffer + offset, &m_parameters, sizeof(m_parameters));
> + offset += sizeof(m_parameters);
> + memcpy(buffer + offset, &names, sizeof(names));
> + offset += sizeof(names);
> +
> + greetingMessage.setBuffer(&buffer);
> + greetingMessage.setNumberOfBytes(offset);
> +
> + greetingMessage.setTag(MatrixOwner::GREETINGS);
> + send(m_matrixOwner, greetingMessage);
> +
> + sendToFirstMother(MERGE_GRAM_MATRIX, MERGE_GRAM_MATRIX_OK);
> +}
> +
> +void Mother::spawnKmersMatrixOwner() {
> +
> + // spawn the MatrixOwner here !
> + KmersMatrixOwner * kmersMatrixOwner = new KmersMatrixOwner();
> + spawn(kmersMatrixOwner);
> +
> + m_kmersMatrixOwner = kmersMatrixOwner->getName();
> +
> + printName();
> + cout << "Spawned KmersMatrixOwner actor !" <<
> m_kmersMatrixOwner << endl;
> +
> + // tell the StoreKeeper actors to send their stuff to the
> + // KmersMatrixOwner actor
> + // The Mother of Mother will wait for a signal from MatrixOwner
> +
> + Message greetingMessage;
> +
> + vector<string> * names = & m_sampleNames;
> +
> + char buffer[32];
> + int offset = 0;
> + memcpy(buffer + offset, &m_parameters, sizeof(m_parameters));
> + offset += sizeof(m_parameters);
> + memcpy(buffer + offset, &names, sizeof(names));
> + offset += sizeof(names);
> +
> + greetingMessage.setBuffer(&buffer);
> + greetingMessage.setNumberOfBytes(offset);
> +
> + greetingMessage.setTag(KmersMatrixOwner::GREETINGS);
> + send(m_kmersMatrixOwner, greetingMessage);
> +
> + sendToFirstMother(MERGE_KMERS_MATRIX, MERGE_KMERS_MATRIX_OK);
> +
> +}
> +
> +
> void Mother::setParameters(Parameters * parameters) {
> m_parameters = parameters;
> }
> +
> diff --git a/code/Surveyor/Mother.h b/code/Surveyor/Mother.h
> index 092920f..9774c4b 100644
> --- a/code/Surveyor/Mother.h
> +++ b/code/Surveyor/Mother.h
> @@ -28,6 +28,7 @@
>
> #include <vector>
> #include <string>
> +#include <iostream>
> using namespace std;
>
> /**
> @@ -55,9 +56,12 @@ class Mother: public Actor {
> private:
>
> int m_matrixOwner;
> + int m_kmersMatrixOwner;
>
> int m_flushedMothers;
> int m_finishedMothers;
> + bool m_matricesAreReady;
> + bool m_printKmersMatrix;
>
> Parameters * m_parameters;
>
> @@ -93,6 +97,13 @@ private:
> */
> void sendToFirstMother(int forwardTag, int responseTag);
>
> + /* int m_kmersMatrixBlocNumber; */
> + void printLocalKmersMatrix(string & kmer, string &
> samples_kmers, bool force);
> + void createKmersMatrixOutputFile();
> +
> + void spawnMatrixOwner();
> + void spawnKmersMatrixOwner();
> +

That's a good design -- private methods for private uses.

> public:
>
> Mother();
> @@ -109,8 +120,10 @@ public:
> FLUSH_AGGREGATOR,
> FLUSH_AGGREGATOR_OK,
> FLUSH_AGGREGATOR_RETURN,
> - MERGE,
> - MERGE_OK,
> + MERGE_GRAM_MATRIX,
> + MERGE_GRAM_MATRIX_OK,
> + MERGE_KMERS_MATRIX,
> + MERGE_KMERS_MATRIX_OK,

kmer matrix, not kmers matrix.

> LAST_TAG,
> };
>
> diff --git a/code/Surveyor/StoreKeeper.cpp b/code/Surveyor/StoreKeeper.cpp
> index 84eef34..492208c 100644
> --- a/code/Surveyor/StoreKeeper.cpp
> +++ b/code/Surveyor/StoreKeeper.cpp
> @@ -22,10 +22,16 @@
> #include "StoreKeeper.h"
> #include "CoalescenceManager.h"
> #include "MatrixOwner.h"
> +#include "KmersMatrixOwner.h"
>
> #include <code/VerticesExtractor/Vertex.h>
> +#include <RayPlatform/structures/MyHashTableIterator.h>
> +#include <RayPlatform/core/OperatingSystem.h>
>
> #include <iostream>
> +#include <sstream>
> +#include <iomanip>
> +#include <fstream>
> using namespace std;
>
> #include <string.h>
> @@ -83,15 +89,21 @@ void StoreKeeper::receive(Message & message) {
>
> die();
>
> - } else if(tag == MERGE) {
> + } else if(tag == MERGE_GRAM_MATRIX) {
>
>
> - printName();
> - cout << "DEBUG at MERGE message reception ";
> - cout << "(StoreKeeper) received " << m_receivedObjects
> << " objects in total";
> - cout << " with " << m_receivedPushes << " push
> operations" << endl;
> + // printName();
> + // cout << "DEBUG at MERGE_GRAM_MATRIX message reception ";
> + // cout << "(StoreKeeper) received " <<
> m_receivedObjects << " objects in total";
> + // cout << " with " << m_receivedPushes << " push

You can remove commented lines.

> operations" << endl;
> computeLocalGramMatrix();
>
> +
> + // TODEL Print matrix bloc
> + // m_kmersMatrixBlocNumber = 0;
> + // printLocalKmersMatrix();
> +

You can remove commented lines.

> +
> m_mother = source;
>
> memcpy(&m_matrixOwner, buffer, sizeof(m_matrixOwner));
> @@ -108,19 +120,32 @@ void StoreKeeper::receive(Message & message) {
> m_iterator2 = m_iterator1->second.begin();
> }
>
> - /*
> - printName();
> - cout << "DEBUG printLocalGramMatrix before first
> sendMatrixCell" << endl;
> - printLocalGramMatrix();
> - */
> -
> + // printName();
> + // cout << "DEBUG printLocalGramMatrix before first
> sendMatrixCell" << endl;
> + // printLocalGramMatrix();

You can remove commented lines.

> sendMatrixCell();
>
> } else if(tag == MatrixOwner::PUSH_PAYLOAD_OK) {
> -
> sendMatrixCell();
> + } else if(tag == MERGE_KMERS_MATRIX) {
> + // cout << "DEBUG at MERGE_GRAM_MATRIX message reception ";
> + // cout << "(StoreKeeper) received " <<
> m_receivedObjects << " objects in total";
> + // cout << " with " << m_receivedPushes << " push
> operations" << endl;

You can remove commented lines.

Otherwise, add a "#ifdef DEBUG_SOMETHING_SOMETHING / #endif around that lines".


> +
> + m_mother = source;
>
> - } else if(tag == CoalescenceManager::SET_KMER_LENGTH) {
> + memcpy(&m_kmersMatrixOwner, buffer,
> sizeof(m_kmersMatrixOwner));
> +
> + m_hashTableIterator.constructor(&m_hashTable);
> +
> + sendKmersSamples();
> + }
> + else if (tag == KmersMatrixOwner::PUSH_KMER_SAMPLES_END) {
> + }
> + else if(tag == KmersMatrixOwner::PUSH_KMER_SAMPLES_OK) {
> + sendKmersSamples();
> + }
> + else if(tag == CoalescenceManager::SET_KMER_LENGTH) {
>
> int kmerLength = 0;
> int position = 0;
> @@ -181,8 +206,6 @@ void StoreKeeper::sendMatrixCell() {
> message.setNumberOfBytes(offset);
> message.setTag(MatrixOwner::PUSH_PAYLOAD);
>
> - //cout << " DEBUG send PUSH_PAYLOAD to " <<
> m_matrixOwner << endl;
> -
> send(m_matrixOwner, message);
>
> m_iterator2++;
> @@ -207,10 +230,7 @@ void StoreKeeper::sendMatrixCell() {
> // free memory.
> m_localGramMatrix.clear();
>
> - /*
> printName();
> - cout << "DEBUG send PUSH_PAYLOAD_END to " << m_matrixOwner << endl;
> - */
>
> Message response;
> response.setTag(MatrixOwner::PUSH_PAYLOAD_END);
> @@ -236,6 +256,7 @@ void StoreKeeper::configureHashTable() {
> );
>
> m_configured = true;
> +
> }
>
> void StoreKeeper::printColorReport() {
> @@ -375,6 +396,7 @@ void StoreKeeper::computeLocalGramMatrix() {
> //printLocalGramMatrix();
> }
>
> +
> void StoreKeeper::printLocalGramMatrix() {
>
> printName();
> @@ -623,3 +645,73 @@ void StoreKeeper::storeData(Vertex & vertex, int &
> sample) {
>
> */
> }
> +
> +
> +void StoreKeeper::setSamplesSize(int sampleSize) {
> + m_sampleSize = sampleSize;
> +}
> +
> +void StoreKeeper::setOutputKmersMatrixPath(string pathPrefix) {
> + // m_outputKmersMatrixPath = pathPrefix;
> + // m_outputKmersMatrixPath += "/KmersMatrixDump/";
> + // createDirectory(m_outputKmersMatrixPath.c_str());

You can remove commented lines.


This file could be in prefix/Surveyor/<...>

> +}
> +
> +
> +void StoreKeeper::sendKmersSamples() {
> +
> + char buffer[4000];

For portability, use MAXIMUM_MESSAGE_SIZE_IN_BYTES instead of 4000.

> + int bytes = 0;
> +
> + ExperimentVertex * currentVertex = NULL;
> + VirtualKmerColorHandle currentVirtualColor = NULL_VIRTUAL_COLOR;
> +
> + vector<bool> samplesVector (m_sampleSize, false);
> +
> + if(m_hashTableIterator.hasNext()){
> +
> + // fill(samplesVector.begin(),samplesVector.end(),false);
> +

You can remove commented lines.

> + currentVertex = m_hashTableIterator.next();
> + Kmer kmer = currentVertex->getKey();
> +
> + bytes += kmer.dump(buffer);
> +
> + currentVirtualColor = currentVertex->getVirtualColor();
> + set<PhysicalKmerColor> * samples =
> m_colorSet.getPhysicalColors(currentVirtualColor);
> +
> + for(set<PhysicalKmerColor>:: iterator sampleIterator =
> samples->begin();
> + sampleIterator != samples->end(); ++sampleIterator) {
> + PhysicalKmerColor value = *sampleIterator;
> + samplesVector[value] = true;
> + // cout << " " << value;
> + }
> +
> + for (std::vector<bool>::iterator it =
> samplesVector.begin();
> + it != samplesVector.end(); ++it) {
> + buffer[bytes] = *it;
> + bytes++;
> + }
> + // buffer[bytes] = '\0';

You can remove commented lines.

> + }
> +
> +
> + Message message;
> + message.setNumberOfBytes(bytes);
> + message.setBuffer(buffer);
> +
> + // message.setTag(MatrixOwner::PUSH_KMERS_SAMPLES);
> + if(m_hashTableIterator.hasNext()){
> + message.setTag(KmersMatrixOwner::PUSH_KMER_SAMPLES);
> + }else{
> + message.setTag(KmersMatrixOwner::PUSH_KMER_SAMPLES_END);
> + }
> +
> + // Message response;
> + // response.setTag(MatrixOwner::PUSH_PAYLOAD_END);
> + // send(m_matrixOwner, response);
> +
> + send(m_kmersMatrixOwner, message);
> +
> +}
> +
> diff --git a/code/Surveyor/StoreKeeper.h b/code/Surveyor/StoreKeeper.h
> index e44cf98..36adf77 100644
> --- a/code/Surveyor/StoreKeeper.h
> +++ b/code/Surveyor/StoreKeeper.h
> @@ -34,6 +34,10 @@
>
> #include <RayPlatform/actors/Actor.h>
> #include <RayPlatform/structures/MyHashTable.h>
> +#include <RayPlatform/structures/MyHashTableIterator.h>
> +
> +#include <iostream>
> +#include <sstream>
>
> /**
> * Provides genomic storage.
> @@ -55,6 +59,7 @@ private:
>
> int m_mother;
> int m_matrixOwner;
> + int m_kmersMatrixOwner;
>
> bool m_configured;
>
> @@ -64,6 +69,8 @@ private:
> */
> MyHashTable<Kmer,ExperimentVertex> m_hashTable;
>
> + MyHashTableIterator<Kmer,ExperimentVertex> m_hashTableIterator;
> +
> int m_kmerLength;
> bool m_colorSpaceMode;
>
> @@ -79,6 +86,13 @@ private:
> void printLocalGramMatrix();
> void printColorReport();
>
> + /* ostringstream m_currentKmer; */
> + /* ostringstream m_currentSamplesKmers; */
> + int m_sampleSize;
> + string m_outputKmersMatrixPath;
> + void printLocalKmersMatrix(string & m_kmer, string &
> m_samplesKmers);
> + void sendKmersSamples();
> +
> void sendMatrixCell();
>
> public:
> @@ -86,14 +100,19 @@ public:
> StoreKeeper();
> ~StoreKeeper();
>
> + void setOutputKmersMatrixPath(string pathPrefix);
> + void setSamplesSize(int sampleSize);
> +
> void receive(Message & message);
>
> enum {
> FIRST_TAG = 10250,
> PUSH_SAMPLE_VERTEX,
> PUSH_SAMPLE_VERTEX_OK,
> - MERGE,
> - MERGE_OK,
> + MERGE_GRAM_MATRIX,
> + MERGE_GRAM_MATRIX_OK,
> + MERGE_KMERS_MATRIX,
> + MERGE_KMERS_MATRIX_OK,
> LAST_TAG
> };
> };