Fasta: add() method to add other sequences to a Fasta object

The constructor now uses the add() method which, itself, relies on the >> operator which has been overloaded.
Unit tests added for the add() method.

algo/core/fasta.cpp

@@ -38,23 +38,27 @@ Fasta::Fasta(const string &input,
   // oout = out;
   this -> extract_field = extract_field ;
   this -> extract_separator = extract_separator ;
+  total_size = 0;
 
-  ifstream is(input.c_str());
+  add(input);  
 
+  out << "  <== " << input
+      << "\t" << setw(6) << total_size << " bp in " << setw(3) << size() << " sequences" << endl ;
+}
+
+void Fasta::add(istream &in) {
+  in >> *this;
+}
+
+void Fasta::add(const string &filename) {
+  ifstream is(filename.c_str());
   if (is.fail())
     {
-      out << "  !! Error in opening file: " << input << endl ;
+      cerr << "  !! Error in opening file: " << filename << endl ;
       exit(1);
     }
-
-  out << "  <== " << input ;
-
-  while (is.good()) {
-    is >> *this;
-  }
+  add(is);
   is.close();
-
-  out << "\t" << setw(6) << total_size << " bp in " << setw(3) << size() << " sequences" << endl ;
 }
 
 int Fasta::size() const{ return (int)reads.size(); }
@@ -234,7 +238,6 @@ istream& operator>>(istream& in, Fasta& fasta){
 	string line;
 	Sequence read;
         OnlineFasta of(in, fasta.extract_field, fasta.extract_separator);
-	fasta.total_size = 0 ;
 
         while (of.hasNext()) {
           of.next();

algo/core/fasta.h

@@ -56,6 +56,9 @@ public:
 	const string& label_full(int index) const;
         const Sequence &read(int index) const;
 	const string& sequence(int index) const;
+
+        void add(istream &in);
+        void add(const string &filename);
 	
 	friend istream& operator>>(istream&, Fasta&);
 };

algo/tests/testTools.cpp

@@ -14,6 +14,24 @@ void testFasta1() {
   }
 }
 
+void testFastaAdd() {
+  Fasta fa1("../../data/test1.fa");
+  Fasta fa2("../../data/test1.fa");
+  fa2.add("../../data/test1.fa");
+
+  TAP_TEST(fa1.size() * 2 == fa2.size(), TEST_FASTA_ADD, "");
+  for (int i=0; i < fa1.size(); i++) {
+    TAP_TEST(fa1.label(i) == fa2.label(i)
+             && fa1.label(i) == fa2.label(i+fa1.size()), TEST_FASTA_ADD, "");
+    TAP_TEST(fa1.label_full(i) == fa2.label_full(i)
+             && fa1.label_full(i) == fa2.label_full(i+fa1.size()), 
+             TEST_FASTA_ADD, "");
+    TAP_TEST(fa1.sequence(i) == fa2.sequence(i)
+             && fa1.sequence(i) == fa2.sequence(i+fa1.size()), 
+             TEST_FASTA_ADD, "");
+  }
+}
+
 void testRevcomp() {
   TAP_TEST(complement("AATCAGactgactagATCGAn") == "TTAGTCTGACTGATCTAGCTN", TEST_REVCOMP, "");
   TAP_TEST(revcomp("AATCAGactgactagATCGAn") == "NTCGATCTAGTCAGTCTGATT", TEST_REVCOMP, "");

algo/tests/tests.h

@@ -8,6 +8,7 @@ enum {
   TEST_FASTA_LABEL,
   TEST_FASTA_LABEL_FULL,
   TEST_FASTA_SEQUENCE,
+  TEST_FASTA_ADD,
   TEST_CREATE_SEQUENCE_LABEL_FULL,
   TEST_CREATE_SEQUENCE_LABEL,
   TEST_CREATE_SEQUENCE_SEQUENCE,
@@ -104,6 +105,7 @@ inline void declare_tests() {
   RECORD_TAP_TEST(TEST_FASTA_LABEL, "Fasta/Fastq label");
   RECORD_TAP_TEST(TEST_FASTA_LABEL_FULL, "Fasta/Fastq full label");
   RECORD_TAP_TEST(TEST_FASTA_SEQUENCE, "Fasta/Fastq sequence");
+  RECORD_TAP_TEST(TEST_FASTA_ADD, "Fasta add() method");
   RECORD_TAP_TEST(TEST_CREATE_SEQUENCE_LABEL_FULL, "create_sequence: label_full field");
   RECORD_TAP_TEST(TEST_CREATE_SEQUENCE_LABEL, "create_sequence: label field");
   RECORD_TAP_TEST(TEST_CREATE_SEQUENCE_SEQUENCE, "create_sequence: sequence field");