Changeset 1014

Timestamp:

Mar 30, 2009, 6:40:55 PM (14 years ago)

Author:

Jari Häkkinen

Message:

Fixes #191. Added standard options and also assay annotation data file option.

Location:

plugins/base2/net.sf.basedb.normalizers/trunk/src

Files:

• c++/bin/qQN.cc (modified) (3 diffs)
• net/sf/basedb/plugins/qQuantileNormalization.java (modified) (1 diff)

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

@@ -23 +23 @@
 */
 
-#include "yat/normalizer/ColumnNormalizer.h"
-#include "yat/normalizer/qQuantileNormalizer.h"
+#include <config.h> // this header file is created by configure
 
-#include "yat/utility/Matrix.h"
+#include <yat/normalizer/ColumnNormalizer.h>
+#include <yat/normalizer/qQuantileNormalizer.h>
 
+#include <yat/utility/CommandLine.h>
+#include <yat/utility/Matrix.h>
+#include <yat/utility/OptionArg.h>
+#include <yat/utility/OptionHelp.h>
+#include <yat/utility/OptionSwitch.h>
+
+#include <cstdlib>
 #include <fstream>
 #include <iostream>
@@ -36 +43 @@
 {  
   using namespace normalizer;
+  using namespace utility;
 
-  utility::Matrix m(std::cin,'\t');
-  utility::Matrix result(m.rows(),m.columns());
+  CommandLine cmd;
+  OptionArg<std::string> dir(cmd, "assay-data", "assay annotation file");
+  OptionHelp help(cmd);
+  help.synopsis()=(std::string("See ") +
+                   "http://baseplugins.thep.lu.se/net.sf.basedb.normalizers " +
+                   "for\ndetails on this program\n");
+  OptionSwitch version(cmd, "version", "output version and exit");
+  std::stringstream copyright;
+  copyright << cmd.program_name() << VERSION << '\n'
+            << "Copyright (C) 2009 Jari Häkkinen\n\n"
+            << "This is free software see the source for copying "
+            << "conditions. There is NO\nwarranty; not even for "
+            << "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n";
+  try {
+    cmd.parse(argc, argv);
+  }
+  catch (cmd_error& e) {
+    if (version.present()) {
+      std::cout << copyright.str();
+      return EXIT_SUCCESS;
+    }
+    std::cout << e.what() << std::endl;
+    return EXIT_FAILURE;
+  }  
+  if (version.present()) {
+    std::cout << copyright.str();
+    return EXIT_SUCCESS;
+  }
+
+  Matrix m(std::cin,'\t');
+  Matrix result(m.rows(),m.columns());
   qQuantileNormalizer qqn(m.begin_column(0), m.end_column(0),100);
   ColumnNormalizer<qQuantileNormalizer> cn(qqn);
@@ -44 +81 @@
   std::cout << result << std::endl;
 
-  return 0;
+  return EXIT_SUCCESS;
 }

plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/qQuantileNormalization.java

@@ -214 +214 @@
     assaydata="assay.data";
     exportData();
-    String[] cmd = { "qQN" };
+    String[] cmd = { "qQN", "--assay-data", assaydata };
     execute(cmd);
   }