From cc8cefc83ca7216594d937b839673efafeee68f4 Mon Sep 17 00:00:00 2001
From: Michael Andreen <harv@ruin.nu>
Date: Mon, 30 Jul 2007 10:07:13 +0000
Subject: [PATCH] adding command line options

---
 src/CMakeLists.txt |  6 +++++-
 src/main.cpp       | 47 ++++++++++++++++++++++++++++++++++++++++++----
 2 files changed, 48 insertions(+), 5 deletions(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 16e2936..88e33de 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -2,7 +2,11 @@ PROJECT(GeneSort)
 
 SET(CMAKE_VERBOSE_MAKEFILE OFF)
 
-ADD_DEFINITIONS(-Wall -g)
+ADD_DEFINITIONS(-Wall -pedantic -g -D_GLIBCXX_DEBUG)
+
+#INCLUDE(CheckCXXSourceCompiles)
+
+#CheckCXXSourceCompiles(test HAVE_TR1)
 
 INCLUDE_DIRECTORIES(.)
 ADD_LIBRARY(GeneSort geneorder genealgorithms modelidentifier genesorter)
diff --git a/src/main.cpp b/src/main.cpp
index 5e6a5c9..34ac34f 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -2,8 +2,12 @@
 #include <vector>
 #include <queue>
 #include <iterator>
+#include <fstream>
+
 using namespace std;
 
+#include <unistd.h>
+
 #include "geneorder.h"
 #include "modelidentifier.h"
 #include "genesorter.h"
@@ -11,16 +15,51 @@ using namespace std;
 
 typedef pair<ModelIdentifier::Model,double> modelpair;
 
-int main(){
+int main(int argc, char** argv){
+
+	string ann = "default.ann";
 
+	int opt;
+	while ((opt = getopt(argc, argv, "n:h")) != -1) {
+		switch (opt) {
+			case 'n':
+				ann = optarg;
+				break;
+			case 'h':
+				cout << "Usage: " << argv[0] << " [OPTION] [FILE]" << endl
+					<< endl << "  -n <ann>   Specifies which artificial neural network to use for identification. '" << ann << "' is used by default"
+					<< endl << "  -h         Prints this help message"
+					<< endl << endl
+					<< "With no FILE, or if FILE is '-', stdin will be used"
+					<< endl;
+				exit(EXIT_SUCCESS);
+				break;
+			default: /* '?' */
+				cerr << "Usage:  " << argv[0] << " [-n <ann>] [-h] [FILE]" << endl;
+				exit(EXIT_FAILURE);
+		}
+	}
+
+	istream* in;
+	ifstream file;
+	if (optind == argc || *argv[optind] == '-'){
+		in = &cin;
+	}else{
+		file.open(argv[optind]);
+		if (file.fail()){
+			cerr << "Could not open file: '" << argv[optind] << "'" << endl;
+			exit(EXIT_FAILURE);
+		}
+		in = &file;
+	}
 	//TODO: Parse
 	vector<Gene> g;
-	copy(istream_iterator<int>(cin), istream_iterator<int>(),
+	copy(istream_iterator<int>(*in), istream_iterator<int>(),
 		     back_inserter(g));   
 	GeneOrder go(g.begin(),g.end());
 
 	//TODO: Identify
-	ModelIdentifier mi("default.ann");
+	ModelIdentifier mi(ann);
 	map<ModelIdentifier::Model,double> scores = mi.identify(go);
 	for (map<ModelIdentifier::Model,double>::iterator m = scores.begin();
 			m != scores.end(); ++m){
@@ -32,5 +71,5 @@ int main(){
 	//TODO: Sort
 	GeneSorter::ActionList al = so.sort(go);
 	//TODO: Print result
-	return 0;
+	return EXIT_SUCCESS;
 }
-- 
2.39.2