--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/KinaMine-Galaxy-7-7/src/kinamine/KinaMineDriver.java	Tue Feb 20 14:31:15 2018 -0500
@@ -0,0 +1,152 @@
+/**
+ *****************************************************************************
+ * <p>
+ * Copyright (c) Regents of the University of Minnesota. All Rights Reserved.
+ * <p>
+ * Author: Kevin Murray University of Minnesota - (murra668@umn.edu)
+ * <p>
+ *****************************************************************************
+ */
+package kinamine;
+
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+
+/**
+ * Driver class for KinaMine. Processes arguments collected from GUI.
+ *
+ * @version 1.0
+ * @author murra668
+ */
+public class KinaMineDriver {
+
+    /**
+     * Main run method for KinaMine. Processes arguments and stores file
+     * contents for compiling a run.
+     *
+     * @param args
+     * @param debug
+     * @return
+     */
+    public static boolean run(String[] args, boolean debug) {
+
+        /** Process aruments. */
+        String pepPath = args[0];
+        String fastaPath = args[1];
+        String outPath = args[2];
+        double fdrScore = Double.valueOf(args[3]);
+        String outGroup = "output";
+
+        /** Read peptide report. */
+        ArrayList<String> peptides = retTabFile(pepPath);
+        peptides.remove(0);
+
+        ArrayList<String> proteins = new ArrayList<>();
+        
+        /** Read fasta database */
+        if (fastaPath.contains("fasta")){
+            proteins = retFastaFile(fastaPath);
+        } else {
+            proteins = retTabFile(fastaPath);
+        }
+        
+
+        /** Create new run. */
+        Run run = new Run(peptides, proteins, fdrScore);
+
+        /** Write run reports. */
+        Reporter.writeReports(run, outPath, outGroup);
+
+        return true;
+    }
+
+    /**
+     * Reads tabular files.
+     *
+     * @param path
+     * @return Arraylist of lines.
+     */
+    public static ArrayList<String> retTabFile(String path) {
+
+        /** Initialize lines */
+        ArrayList<String> lines = new ArrayList<>();
+
+        try {
+
+            /** Configure reader. */
+            FileReader fr = new FileReader(path);
+            BufferedReader br = new BufferedReader(fr);
+
+            /** Initialize first line, headers - discard */
+            String line = br.readLine();
+
+            /**
+             * Read each line in the configuration file and add each line to an
+             * array (to be returned)
+             */
+            while (line != null) {
+
+                /** If line is all tabs, end of file */
+                if (line.startsWith("\t")) {
+                    break;
+                }
+
+                /** Add line to list. */
+                lines.add(line);
+                line = br.readLine();
+            }
+
+            /** Close the file */
+            br.close();
+
+        } catch (FileNotFoundException filenotfoundexxption) {
+            System.out.println(path + ", does not exist");
+        } catch (IOException ioexception) {
+            ioexception.printStackTrace();
+        }
+
+        return lines;
+    }
+
+    public static ArrayList<String> retFastaFile(String path) {
+
+        /** Initialize lines */
+        ArrayList<String> lines = new ArrayList<>();
+
+        try {
+
+            /** Configure reader. */
+            FileReader fr = new FileReader(path);
+            BufferedReader br = new BufferedReader(fr);
+
+            String line = br.readLine();
+            String prot = "";
+
+            while (line != null) {
+                
+                if (line.startsWith(">")){
+                    String[] temp = line.split(" ");
+                    prot = temp[0].trim() + "\t \t";
+                } else {
+                    prot +=  line.trim();
+                    lines.add(prot);
+                }
+                
+                line = br.readLine();
+            }
+
+            br.close();
+
+        } catch (FileNotFoundException filenotfoundexxption) {
+            System.out.println(path + ", does not exist");
+        } catch (IOException ioexception) {
+            ioexception.printStackTrace();
+        }
+
+        return lines;
+    }
+
+}