Suppressing some warnings and adding some explanatory comments

1. readFirstLineOfPhylipSequenceFile() hived off from
   Sequences::loadSequencesFromPhylip() (to avoid a warning
   from Lizard)
2. Deleted FakeMatrix's copy constructor (It's a local class, that is
   used only in  SequenceLoader::writeDistanceMatrixToFile)
3. Added some missing initializations to UPGMA_Matrix's ctor.

Author: James Barbetti

bionj.cpp

@@ -860,8 +860,13 @@ public StartTree::BuilderInterface {
                       //enclosing parentheses and a trailing semi-colon
                       //is not supported.
     }
+
     /**
-     * @brief 
+     * @brief  Given the path of a (possibly compressed) file that contains a
+     *         distance matrix in phylip format (square, upper or lower triangle),
+     *         and the path of an output file to write it to, infer a phylogenetic 
+     *         tree, and write a representation of the tree (in Newick format) to 
+     *         the output file.  
      * 
      * @param  distanceMatrixFilePath - the path of the input phylip format file
      * @param  newickTreeFilePath - the path to which the output newick format

distancematrix.h

@@ -177,7 +177,7 @@ template <class T=double> class Matrix
      *        divisible by MATRIX_ALIGNMENT.
      */
     void setDimensions(size_t r, size_t c) {
-        clear();
+        actual_clear();
         if (0==c || 0==r) {
             return;
         }

nj.h

@@ -542,6 +542,7 @@ template <class T=NJFloat> class BIONJMatrix : public NJMatrix<T> {
  *         using it with SUPER=UPGMAMatrix<T>!), because 
  *         that has a rather different getRowMinima().
  *         There's a separate class for vectorizing that.
+ *         Nor can it vectorize FancyNJMatrix.
  */
 template <class T=NJFloat, class SUPER=BIONJMatrix<T>, 
           class V=FloatVector, class VB=FloatBoolVector>

sequence.cpp

@@ -405,6 +405,52 @@ bool Sequences::loadSequencesFromFasta(const std::string& fastaFilePath,
     return true;
 }
 
+/**
+ * @brief  Read the first line of a Phylip Alignment file (which is the number of sequences,
+ *         white space, and the length of all the sequences)
+ * 
+ * @tparam S                the stream type
+ * @param  in               the stream itself
+ * @param  num_sequences    reference - will have the number of sequences
+ *                          in the alignment assigned to it (on success)
+ * @param  sequence_length  reference - will have the length of the sequences
+ *                          (every sequence must have the same length)
+ *                          assigned to it (on success)
+ * @return true             on success
+ * @return false            on failure (an error message will have been written
+ *                          to standard output).
+ * 
+ * @note   it is assumed that failbit is not already set on the stream when this 
+ *         function is called.
+ */
+template <class S> bool readFirstLineOfPhylipAlignmentFile(S& in, size_t& num_sequences, size_t& sequence_length) {
+    if (in.eof()) {
+        std::cerr << "Sequence file was empty.";
+        return false;
+    }
+    std::string line;
+    safeGetLine(in, line);
+    //Read the header line
+    std::stringstream linestream(line);
+    linestream >> num_sequences;
+    if (in.fail()) {
+        std::cerr << "Could not read number of sequences.";
+        return false;
+    }
+    linestream >> sequence_length;
+    if (in.fail()) {
+        std::cerr << "Could not read sequence length.";
+        return false;
+    }
+    if (num_sequences < 1 || sequence_length < 1 ) {
+        std::cerr << "Number of sequences " << num_sequences
+                    << " or Sequence length " << sequence_length
+                    << " was invalid.";
+        return false;
+    }
+    return true;
+}
+
 /**
  * @brief  Load a sequence alignment from a phylip format file
  * @param  phylipFilePath   - the path to the file
@@ -443,27 +489,19 @@ bool Sequences::loadSequencesFromPhylip(const std::string& phylipFilePath,
     }
     size_t num_sequences       = 0;
     size_t sequence_length     = 0;
+    if (!readFirstLineOfPhylipAlignmentFile(in, num_sequences, sequence_length))
+    {
+        in.close();
+        return false;
+    }
+
     bool   have_read_names     = 0;
     size_t name_length         = 0; //Number of characters to use for sequence name
     size_t sequence_num        = 0; //Ordinal sequence # to read next
 
     for (; !in.eof(); ++line_num) {
         std::string line;
         safeGetLine(in, line);
-        if (line_num == 1) {
-            //Read the header line
-            std::stringstream linestream(line);
-            linestream >> num_sequences;
-            linestream >> sequence_length;
-            if (num_sequences < 1 || sequence_length < 1 ) {
-                in.close();
-                std::cerr << "Number of sequences " << num_sequences
-                          << " or Sequence length " << sequence_length
-                          << " was invalid.";
-                return false;
-            }
-            continue;
-        }
         if (line == "") {
             if (sequence_num!=0 && sequence_num!=num_sequences) {
                 in.close();
@@ -817,7 +855,7 @@ SequenceLoader::SequenceLoader(char unknown, bool isDNA,
     , is_site_variant(site_variant)
     , report_progress(report_progress_while_loading), unkLen(0)
     , buffer(nullptr), sequence_data(nullptr)
-    , unk_buffer(nullptr), unknown_data(nullptr) {
+    , unk_buffer(nullptr), unknown_data(nullptr), num_states(4) {
     rank      = sequences.size();
     rawSeqLen = sequences.front().sequenceLength();
     seqLen    = 0;
@@ -982,6 +1020,7 @@ bool SequenceLoader::writeDistanceMatrixToFile(bool numbered_names,
         progress_display& show_progress;
     public:
         typedef FlatMatrix super;
+        FakeMatrix(const FakeMatrix& rhs) = delete;
         FakeMatrix(SequenceLoader& my_owner, progress_display& progress_bar)
             : super(), owner(my_owner), show_progress(progress_bar) {}
         virtual void setSize(intptr_t rows) { rowCount=rows;}

upgma.h

@@ -180,7 +180,9 @@ template <class T=NJFloat> class UPGMA_Matrix: public SquareMatrix<T> {
     bool                 subtreeOnly;
 public:
     UPGMA_Matrix(): super(), silent(false)
-                  , isOutputToBeZipped(false), isRooted(false)
+                  , isOutputToBeZipped(false)
+                  , isOutputToBeAppended(false)
+                  , isRooted(false)
                   , subtreeOnly(false) {
     }
     /**