Major API change

* Problem: We needed a way to read in the matrix into a Matrix
  datastructure in addition to building the graph. This has multiple
  reasons:
  1. We may need to compute the compressed matrix using the input
     matrix.
  2. We need to obtain the number of rows of the input matrix to
     generate the seed matrix.
* This required major API changes, mainly the split of IReader's Read
  into ReadGraph and ReadMatrix
* I was able to avoid major code duplication in MMReader, nonetheless:
  The file is currently a mess that uses many shortcuts and is generally
  unclean

src/SparseTransform.CLI/Program.cs

@@ -25,11 +25,11 @@ public class Program
                 {
                     Output = Partition2ColoredDot(MMMatrix, o.TextColor);
                 }
-                else if (o.Format == Formats.ColoredDot)
+                else if (o.Format == Formats.SeedMatrix)
                 {
                     Output = Partition2SeedMatrix(MMMatrix);
                 }
-                else if (o.Format == Formats.ColoredDot)
+                else if (o.Format == Formats.CompressedMatrix)
                 {
                     Output = Partition2CompressedMatrix(MMMatrix);
                 }

src/SparseTransform/ConversionManager.cs

@@ -14,7 +14,7 @@ namespace SparseTransform
         public static String Convert2Dot(String MMMatrix)
         {
             MatrixMarketReader reader = new MatrixMarketReader();
-            IGraph graph = reader.Read(MMMatrix);
+            IGraph graph = reader.ReadGraph(MMMatrix);
             DotWriter writer = new DotWriter();
             return writer.Write(graph);
         }
@@ -29,7 +29,7 @@ namespace SparseTransform
         public static String Partition2ColoredDot(String MMMatrix, bool textColor= false)
         {
             MatrixMarketReader reader = new MatrixMarketReader();
-            IGraph graph = reader.Read(MMMatrix);
+            IGraph graph = reader.ReadGraph(MMMatrix);
             Colorer color = new Colorer();
             if (graph is AdjacencyGraph)
             {
@@ -52,7 +52,7 @@ namespace SparseTransform
         public static String Partition2SeedMatrix(String MMMatrix)
         {
             MatrixMarketReader reader = new MatrixMarketReader();
-            IGraph graph = reader.Read(MMMatrix);
+            IGraph graph = reader.ReadGraph(MMMatrix);
             Colorer color = new Colorer();
             if (graph is AdjacencyGraph)
             {
@@ -63,7 +63,8 @@ namespace SparseTransform
             }
             else
                 color.PartialD2Color((BipartiteGraph)graph);
-            MatrixMarketWriter writer = new MatrixMarketWriter(true);
+            DoubleMatrix inputMatrix = reader.ReadMatrix(MMMatrix);
+            MatrixMarketWriter writer = new MatrixMarketWriter(true, inputMatrix);
             return writer.Write(graph);
         }
         /// <summary>
@@ -74,7 +75,7 @@ namespace SparseTransform
         public static String Partition2CompressedMatrix(String MMMatrix)
         {
             MatrixMarketReader reader = new MatrixMarketReader();
-            IGraph graph = reader.Read(MMMatrix);
+            IGraph graph = reader.ReadGraph(MMMatrix);
             Colorer color = new Colorer();
             if (graph is AdjacencyGraph)
             {
@@ -85,7 +86,8 @@ namespace SparseTransform
             }
             else
                 color.PartialD2Color((BipartiteGraph)graph);
-            MatrixMarketWriter writer = new MatrixMarketWriter(false);
+            DoubleMatrix inputMatrix = reader.ReadMatrix(MMMatrix);
+            MatrixMarketWriter writer = new MatrixMarketWriter(false, inputMatrix);
             return writer.Write(graph);
         }
     }

src/SparseTransform/Convert/IReader.cs

@@ -15,7 +15,9 @@ namespace SparseTransform.Convert
         /// </summary>
         /// <param name="matrix"></param>
         /// <returns>transformed graph <c>IGraph</c></returns>
-        public IGraph Read(String matrix);
+        public IGraph ReadGraph(String matrix);
+
+        public DoubleMatrix ReadMatrix(String matrix);
 
 
         /// <summary>

src/SparseTransform/Convert/MatrixMarketReader.cs

@@ -10,6 +10,7 @@ using Antlr4.Runtime;
 using DataStructures;
 using Transform;
 using Transform.Convert;
+using System.Text.RegularExpressions;
 
 
 namespace SparseTransform.Convert
@@ -17,7 +18,7 @@ namespace SparseTransform.Convert
     internal class MatrixMarketReader : IReader
     {
 
-        public IGraph Read(string matrix)
+        public IGraph ReadGraph(string matrix)
         {
             string[] lines = matrix.Split(
             new string[] { "\r\n", "\r", "\n" },
@@ -29,15 +30,40 @@ namespace SparseTransform.Convert
             if (checkHeader(lines[0]))
             {
                 BipartiteGraph graph = new BipartiteGraph();
-                return ReadGraph(lines, graph);
+                ReadContent(lines, (i, j, value) => {
+                    graph.AddEdge(i, j);
+                });
+                return graph;
             }
             else
             {
                 AdjacencyGraph graph = new AdjacencyGraph();
-                return ReadGraph(lines, graph);
+                ReadContent(lines, (i, j, value) => {
+                    graph.AddEdge(i, j);
+                });
+                return graph;
             }
         }
 
+        public DoubleMatrix ReadMatrix(string matrix)
+        {
+            string[] lines = matrix.Split(
+            new string[] { "\r\n", "\r", "\n" },
+            StringSplitOptions.None
+            );
+
+            checkComments(lines);
+
+            String dimLine = lines[getFirstDataLine(lines)];
+            String[] dimensions = dimLine.Split(" ");
+            DoubleMatrix mat = new DoubleMatrix(Int32.Parse(dimensions[0]), Int32.Parse(dimensions[1]));
+            ReadContent(lines, (i, j, value) =>
+            {
+                mat[i - 1, j - 1] = value;
+            });
+            return mat;
+        }
+
         /// <summary>
         /// checks with ANTLR4.0 whether the header is a valid instance. The header grammar can be found in the file MMFHeader.g4 
         /// </summary>
@@ -95,13 +121,13 @@ namespace SparseTransform.Convert
         /// <param name="graph"></param>
         /// <returns></returns>
         /// <exception cref="Exception"></exception>
-        public IGraph ReadGraph(string[] matrix, IGraph graph)
+        public void ReadContent(string[] matrix, Action<int, int, double> processor)
         {
             string[] values;
             int lineCount = getFirstDataLine(matrix);
             matrix[lineCount] = "% " + matrix[lineCount];
-            try
-            {
+            // try
+            // {
                 foreach (String line in matrix)
                 {
                     if (line != "")
@@ -116,20 +142,19 @@ namespace SparseTransform.Convert
                             }
                             int xCoordinate = Int32.Parse(values[0]);
                             int yCoordinate = Int32.Parse(values[1]);
-                            String value = values[2];
-                            if (xCoordinate != yCoordinate)
-                            {
-                                graph.AddEdge(xCoordinate, yCoordinate);
-                            }
+                            // if (xCoordinate != yCoordinate)
+                            // {
+                                processor(xCoordinate, yCoordinate, Double.Parse(values[2]));
+                                // graph.AddEdge(xCoordinate, yCoordinate);
+                            // }
                         }
                     }
                 }
-                return graph;
-            }
-            catch (Exception e)
-            {
-                throw new Exception("data section mismatch on input");
-            }
+            // }
+            // catch (Exception e)
+            // {
+            //     throw e;
+            // }
         }