From e5c815342378614d1050b7468150feccebf981f3 Mon Sep 17 00:00:00 2001
From: ksiadzrobak <xiadzrobak@protonmail.com>
Date: Tue, 19 Jun 2018 21:06:27 +0200
Subject: [PATCH] Alignment of -c and -a

---
 jplag/src/main/java/jplag/Program.java        | 39 ++++++++++++-------
 .../jplag/options/CommandLineOptions.java     |  4 +-
 2 files changed, 27 insertions(+), 16 deletions(-)

diff --git a/jplag/src/main/java/jplag/Program.java b/jplag/src/main/java/jplag/Program.java
index deb3d20df..58e0dec53 100644
--- a/jplag/src/main/java/jplag/Program.java
+++ b/jplag/src/main/java/jplag/Program.java
@@ -429,19 +429,23 @@ private Vector<Submission> createSubmissions(File f, SubmissionType type) throws
         return result;
     }
 
-	private void createSubmissionsFileList() throws jplag.ExitException {
-		submissions = new Vector<Submission>();
-		File f = null;
-		if (options.root_dir != null) {
-			f = new File(options.root_dir);
-			if (!f.isDirectory()) {
-				throw new jplag.ExitException(options.root_dir + " is not a directory!");
-			}
-		}
-		for (String file : options.fileList){
-			submissions.addElement(new Submission(file, f, this, get_language(), SubmissionType.REGULAR));
-		}
-	}
+    private Vector<Submission> createSubmissionsFileList() throws jplag.ExitException {
+        Vector<Submission> result = new Vector<Submission>();
+        File f = null;
+
+        if (options.root_dir != null) {
+            f = new File(options.root_dir);
+            if (!f.isDirectory()) {
+                throw new jplag.ExitException(options.root_dir + " is not a directory!");
+            }
+        }
+
+        for (String file : options.fileList){
+            result.addElement(new Submission(file, f, this, get_language(), SubmissionType.REGULAR));
+        }
+
+        return result;
+    }
 
     private Submission createBasecodeSubmission() throws jplag.ExitException {
         if (!options.useBasecode)
@@ -1162,7 +1166,8 @@ public void run() throws jplag.ExitException {
         readExclusionFile();
 
         if (options.fileListMode) {
-	        createSubmissionsFileList();
+            submissions = createSubmissionsFileList();
+            basecodeSubmission = createBasecodeSubmission();
         } else if (options.include_file == null) {
             submissions = createSubmissions(new File(options.root_dir), SubmissionType.REGULAR);
             basecodeSubmission = createBasecodeSubmission();
@@ -1170,6 +1175,12 @@ public void run() throws jplag.ExitException {
         } else
             createSubmissionsExp();
 
+        if (options.useArchivalSubmissions) {
+            archivalSubmissions = createSubmissions(new File(options.archivalSubmissions),
+                SubmissionType.ARCHIVAL);
+            System.out.println(archivalSubmissions.size() + " archival submissions\n");
+        }
+
         if (!options.skipParse) {
             try {
                 parseAll(submissions);
diff --git a/jplag/src/main/java/jplag/options/CommandLineOptions.java b/jplag/src/main/java/jplag/options/CommandLineOptions.java
index e1fad3a83..e28467b39 100644
--- a/jplag/src/main/java/jplag/options/CommandLineOptions.java
+++ b/jplag/src/main/java/jplag/options/CommandLineOptions.java
@@ -237,7 +237,7 @@ else if (tmp.equals("avr"))
             else 
                 throw new jplag.ExitException("Illegal clustertype: \"" + tmp
                         + "\"\nAvailable types are 'min', 'max' and 'avr'!");
-			
+
             System.out.println("Clustering activated; type: "
                     + args[i + 1].toUpperCase());
             i++;
@@ -325,7 +325,7 @@ else if (tmp.equals("avr"))
             }
             this.title = args[i + 1];
             i++;
-        } else if (arg.equals("-c") && i + 2 < args.length){
+        } else if (arg.equals("-c") && i + 1 < args.length) {
             this.fileListMode = true;
             while (i + 1 < args.length){
                 this.fileList.add(args[i + 1]);