Program now runs according to command line arguments.

Author: ybalcanci

hw3/Makefile

@@ -1,2 +1,2 @@
 all:
-	g++ -o out readFile.cpp writeToFile.cpp needleman_wunsch.cpp smith_waterman.cpp main.cpp
+	g++ -o allalign readFile.cpp writeToFile.cpp needleman_wunsch.cpp smith_waterman.cpp main.cpp

hw3/README.txt

@@ -0,0 +1,2 @@
+Type "make" to compile source files.
+Type "./allalign <NECESSARY OPTIONS>" to run the program.

hw3/main.cpp

@@ -2,6 +2,7 @@
 #include <string>
 #include <bits/stdc++.h> 
 #include "unistd.h"
+#include <getopt.h>
 
 using namespace std;
 
@@ -12,19 +13,68 @@ int needleman_wunsch(string sequence1Name, string sequence1, string sequence2Nam
 					int gapopen, int gapext, int matchScore, int mismatchPenalty);
 
 int main(int argc, char *argv[]) {
-	if (argc < 2) {
-		fprintf(stderr, "usage: ./out <textFileName patternFileName>\n"); 
-		return -1; 
-	}
+	int c;
+	string mode;
+	string fileName;
+	int gapopen;
+	int gapext;
+	while (1) {
+		static struct option long_options[] = {
+			{"mode",     required_argument,       0, 'm'},
+			{"input",  required_argument,       0, 'i'},
+			{"gapopen",  required_argument, 0, 'o'},
+			{"gapext",  required_argument, 0, 'e'},
+			{0, 0, 0, 0}
+		};
+		/* getopt_long stores the option index here. */
+		int option_index = 0;
+	
+		c = getopt_long (argc, argv, "m:i:o:e:",
+						long_options, &option_index);
+	
+		/* Detect the end of the options. */
+		if (c == -1)
+		break;
+	
+		switch (c) {
+        case 'm':
+			mode = optarg;
+			break;
+	
+        case 'i':
+			fileName = optarg;
+			break;
 
-	vector<string> sequences = readFile(argv[1]);
+        case 'o':
+			gapopen = atoi(optarg);
+			break;
 
-	int gapopen = -5;
-	int gapext = -2;
+        case 'e':
+			gapext = atoi(optarg);
+			break;
+        case '?':
+			/* getopt_long already printed an error message. */
+			return 1;
+			break;
+
+        default:
+			abort ();
+        }
+    }
+	
+	vector<string> sequences = readFile(fileName);
+
 	int matchScore = 2;
 	int mismatchPenalty = -3;
-		
-	needleman_wunsch(sequences[0], sequences[1], sequences[2], sequences[3], gapopen, gapext, matchScore, mismatchPenalty);
+	if(mode.compare("global") == 0){
+		needleman_wunsch(sequences[0], sequences[1], sequences[2], sequences[3], 0, gapopen, matchScore, mismatchPenalty);
+	} else if(mode.compare("aglobal") == 0){
+		needleman_wunsch(sequences[0], sequences[1], sequences[2], sequences[3], gapopen, gapext, matchScore, mismatchPenalty);
+	} else if(mode.compare("local") == 0){
+		smith_waterman(sequences[0], sequences[1], sequences[2], sequences[3], 0, gapopen, matchScore, mismatchPenalty);
+	} else if(mode.compare("alocal") == 0){
+		smith_waterman(sequences[0], sequences[1], sequences[2], sequences[3], gapopen, gapext, matchScore, mismatchPenalty);
+	}
 
-	smith_waterman(sequences[0], sequences[1], sequences[2], sequences[3], gapopen, gapext, matchScore, mismatchPenalty);
+	return 0;
 }