Changeset 2482

Timestamp:

Apr 25, 2011, 12:17:19 AM (12 years ago)

Author:

Peter

Message:

new class GFF. closes #647

Location:

trunk

Files:

• test/data/small.gff2 (added)
• test/gff.cc (modified) (2 diffs)
• yat/omic/GFF.cc (added)
• yat/omic/GFF.h (added)
• yat/omic/GFF2.cc (added)
• yat/omic/GFF2.h (added)
• yat/omic/GFF3.cc (added)
• yat/omic/GFF3.h (added)
• yat/omic/Makefile.am (modified) (3 diffs)

trunk/test/gff.cc

@@ -22 +22 @@
 #include "Suite.h"
 
+#include "yat/omic/GFF2.h"
+#include "yat/omic/GFF3.h"
+
+#include <fstream>
+
 using namespace theplu::yat;
+using namespace omic;
+
+template<typename T>
+void avoid_pedantic_warning(T t) {}
+
+void gff2(test::Suite&);
+void gff3(test::Suite&);
+
+template<class T>
+void test_gff(test::Suite&, GFF&);
 
 int main(int argc, char* argv[])
@@ -28 +43 @@
   test::Suite suite(argc, argv);
 
+  gff2(suite);
+  gff3(suite);
+
   return suite.return_value();
 }
+
+
+void test_gff(test::Suite& suite, GFF& gff)
+{
+  std::string seqid = gff.seqid();
+  std::string source = gff.source();
+  std::string type = gff.type();
+  avoid_pedantic_warning<const std::string&>(gff.start());
+  avoid_pedantic_warning<const std::string&>(gff.end());
+  avoid_pedantic_warning<const std::string&>(gff.score());
+  avoid_pedantic_warning<const std::string&>(gff.strand());
+  avoid_pedantic_warning<const std::string&>(gff.phase());
+  const std::map<std::string, std::string>& m = gff.attributes();
+  avoid_pedantic_warning(m);
+}
+
+void gff2(test::Suite& suite)
+{
+  suite.out() << "testing GFF2\n";
+  std::ifstream is(test::filename("data/small.gff2").c_str());
+  assert(is);
+  GFF2 gff2;
+  suite.add(getline(is, gff2));
+  test_gff(suite, gff2);
+  const std::string& a = gff2.attribute("genotype");
+  if (!suite.add(a=="T or C"))
+    suite.err() << "incorrect genotype value: `" << a << "'\n"
+                << "expected: `T or C'\n";
+  is.close();
+}
+
+void gff3(test::Suite& suite)
+{
+  suite.out() << "testing GFF3\n";
+  std::ifstream is(test::filename("data/small.gff3").c_str());
+  assert(is);
+  GFF3 gff3;
+  if (!suite.add(getline(is, gff3)))
+    suite.err() << "getline failed\n";
+  test_gff(suite, gff3);
+  const std::string& a = gff3.attribute("genotype");
+  if (!suite.add(a=="T"))
+    suite.err() << "incorrect genotype value: `" << a << "'\n"
+                << "expected: `T'\n";
+  is.close();
+}

trunk/yat/omic/Makefile.am

@@ -3 +3 @@
 ## $Id$
 
-# Copyright (C) 2010 Peter Johansson
+# Copyright (C) 2010, 2011 Peter Johansson
 #
 # This file is part of the yat library, http://dev.thep.lu.se/yat
@@ -25 +25 @@
 libomic_la_SOURCES += DNA.cc
 libomic_la_SOURCES += GenomicPosition.cc
+libomic_la_SOURCES += GFF.cc
+libomic_la_SOURCES += GFF2.cc
+libomic_la_SOURCES += GFF3.cc
 
 include_omicdir = $(includedir)/yat/omic
@@ -32 +35 @@
 include_omic_HEADERS += DNA.h
 include_omic_HEADERS += GenomicPosition.h
+include_omic_HEADERS += GFF.h
+include_omic_HEADERS += GFF2.h
+include_omic_HEADERS += GFF3.h
 
 DISTCLEANFILES = doxygen.mk