@@ -1,5 +1,5 @@

 Package: CoGAPS

-Version: 3.1.0

+Version: 3.1.1

 Date: 2018-04-24

 Title: Coordinated Gene Activity in Pattern Sets

 Author: Thomas Sherman, Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey,

@@ -9,7 +9,7 @@

 Rcpp::List cogapsFromFile_cpp(const std::string D)

 {

     CsvParser csv(D);

-

+/*

     while (csv.hasNext())

     {

         MatrixElement m = csv.getNext();

@@ -21,6 +21,8 @@ Rcpp::List cogapsFromFile_cpp(const std::string D)

     for (unsigned i = 0; i < csv.mColNames.size(); ++i)

         Rcpp::Rcout << csv.mColNames[i] << '\n';

+*/

+    Rcpp::Rcout << csv.nRow() << "," << csv.nCol() << '\n';

 }

 // [[Rcpp::export]]

@@ -1,4 +1,5 @@

 #include "Matrix.h"

+#include "../file_parser/CsvParser.h"

 template<class GenericMatrix>

 static Rcpp::NumericMatrix convertToRMatrix(const GenericMatrix &mat)

@@ -51,14 +52,17 @@ RowMatrix::RowMatrix(const Rcpp::NumericMatrix &rmat)

 }

 RowMatrix::RowMatrix(const std::string &path)

-{/*

+{

     CsvParser csv(path);

-    while (csv.hasNext())

+

+    while (csv.hasNextRow())

     {

-        MatrixElement m = csv.getNext();

-        this->operator(m.row, m.col) = m.value;

+        mRows.push_back(Vector(csv.getNextRow()));

     }

-*/}

+

+    mNumRows = mRows.size();

+    mNumCols = mRows[0].size();

+}

 void RowMatrix::operator=(const RowMatrix &mat)

 {

@@ -127,6 +131,8 @@ ColMatrix::ColMatrix(const Rcpp::NumericMatrix &rmat)

     }

 }

+// skip over bytes per row to efficiently get to columns

+// need to be able to read columns in parallel

 ColMatrix::ColMatrix(const std::string &path)

 {

@@ -18,6 +18,7 @@ private:

 public:

     Vector(unsigned size) : mValues(aligned_vector(size, 0.f)) {}

+    Vector(std::vector<float> v) : mValues(aligned_vector(v)) {}

     const float* ptr() const {return &mValues[0];}

     float* ptr() {return &mValues[0];}

@@ -2,9 +2,7 @@

 #include <iostream>

-// TODO need to parse by rows - otherwise it would be neccesary to

-// know dimensions beforehand

-

+// read through whole file once, store row/col names - gives dimensions

 // open file, read column names

 CsvParser::CsvParser(const std::string &path) : mCurrentRow(0), mCurrentCol(0)

 {

@@ -21,15 +19,43 @@ CsvParser::CsvParser(const std::string &path) : mCurrentRow(0), mCurrentCol(0)

         std::getline(mFile, line, ',');

     }

     mColNames.push_back(line.substr(0,pos));

+

     mRowNames.push_back(line.substr(pos+1));

+    while (mFile.peek() != EOF)

+    {

+        while ((pos = line.find('\n')) == std::string::npos)

+        {

+            std::getline(mFile, line, ',');

+        }

+        mRowNames.push_back(line.substr(pos+1));

+    }

+

+    for (unsigned i = 0; i < mRowNames.size(); ++i)

+    {

+        std::cout << mRowNames[i] << '\n';

+    }

+    for (unsigned j = 0; j < mColNames.size(); ++j)

+    {

+        std::cout << mRowNames[j] << '\n';

+    }

+}

+

+bool hasNextRow()

+{

+

 }

-bool CsvParser::hasNext()

+std::vector<float> getNextRow()

 {

-    return mFile.peek() != EOF;

+

+}

+

+void skipNextRow()

+{

+

 }

-MatrixElement CsvParser::getNext()

+/*MatrixElement CsvParser::getNext()

 {

     std::string line;

     std::getline(mFile, line, ',');

@@ -49,4 +75,4 @@ MatrixElement CsvParser::getNext()

     {

         return MatrixElement(mCurrentRow, mCurrentCol++, line);

     }

-}

\ No newline at end of file

+}*/

\ No newline at end of file

@@ -1,16 +1,13 @@

 #ifndef __COGAPS_CSV_PARSER_H__

 #define __COGAPS_CSV_PARSER_H__

-#include "MatrixElement.h"

-

 #include <fstream>

 #include <vector>

 #include <string>

 class CsvParser

 {

-//private:

-public:

+private:

     std::ifstream mFile;

@@ -22,10 +19,19 @@ public:

 public:

+    // read through whole file once, store row/col names - gives dimensions

     CsvParser(const std::string &path);

-    bool hasNext();

-    MatrixElement getNext(); 

+    unsigned nRow() const { return mRowNames.size(); }

+    unsigned nCol() const { return mColNames.size(); }

+

+    bool hasNextRow();

+    std::vector<float> getNextRow(); 

+    void skipNextRow();

+

+    bool hasNextCol();

+    std::vector<float> getNextCol();

+    void skipNextCol();

 };

 #endif

\ No newline at end of file

deleted file mode 100644

@@ -1,25 +0,0 @@

-#ifndef __COGAPS_MATRIX_ELEMENT_H__

-#define __COGAPS_MARRIX_ELEMENT_H__

-

-#include <sstream>

-#include <string>

-

-struct MatrixElement

-{

-    unsigned row;

-    unsigned col;

-    float value;

-

-    MatrixElement(unsigned r, unsigned c, float v)

-        : row(r), col(c), value(v)

-    {}

-

-    MatrixElement(unsigned r, unsigned c, const std::string &v)

-        : row(r), col(c), value(0.f)

-    {

-        std::stringstream ss(v);

-        ss >> value;

-    }

-};

-

-#endif

\ No newline at end of file