Changeset 1023

Timestamp:

Apr 7, 2009, 12:35:48 AM (14 years ago)

Author:

Jari Häkkinen

Message:

Addresses #197. In anticipation of abort functionality the underlying binary cannot read/write too much information from standard streams. Now qQN can use files or cin/cout

File:

• plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/bin/qQN.cc (modified) (3 diffs)

plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/bin/qQN.cc

@@ -49 +49 @@
 {
   CommandLine cmd;
-  OptionArg<std::string> assay(cmd, "assay-data", "assay annotation file");
+  OptionArg<std::string> assay(cmd, "assay-data", "assay annotations", true);
+  OptionArg<std::string> indata(cmd, "in-data", "data to be normalized");
+  OptionArg<std::string> outdata(cmd, "out-data", "normalized data");
   OptionHelp help(cmd);
   help.synopsis()=(std::string("See ") +
@@ -77 +79 @@
   }
 
+  if (version.present()) {
+    std::cout << copyright.str();
+    return EXIT_SUCCESS;
+  }
+
+  std::ifstream* infile=NULL;
+  std::streambuf* cin_buffer=NULL;
+  if (indata.present()) {
+    infile=new std::ifstream(indata.value().c_str());
+    cin_buffer = std::cin.rdbuf(); // save cin's input buffer
+    std::cin.rdbuf(infile->rdbuf());
+  }
   Matrix m(std::cin,'\t');
+  if (indata.present()) {
+    std::cin.rdbuf(cin_buffer); // restore old input buffer
+    infile->close();
+    delete infile;
+  }
+
   std::vector<double> target(m.rows(),0);
   ( assay.present() ? create_target(target,m,assay.value()) :
@@ -85 +105 @@
   Matrix result(m.rows(),m.columns());
   cn(m,result);
+
+  std::ofstream* outfile=NULL;
+  std::streambuf* cout_buffer = std::cout.rdbuf();
+  if (outdata.present()) {
+    outfile=new std::ofstream(outdata.value().c_str());
+    cout_buffer = std::cout.rdbuf(); // save cout's output buffer
+    std::cout.rdbuf(outfile->rdbuf());
+  }
   std::cout << result << std::endl;
+  if (outdata.present()) {
+    std::cout.rdbuf(cout_buffer); // restore old output buffer
+    outfile->close();
+    delete outfile;
+  }
 
   return EXIT_SUCCESS;