Merge branch 'master' of https://github.com/ProgrammingLife2016/PL4-2016

ProgrammingLife2016 · Jun 3, 2016 · bf51958 · bf51958
2 parents bdb529d + f5108c9
commit bf51958
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diff --git a/src/main/java/application/controllers/MainController.java b/src/main/java/application/controllers/MainController.java
@@ -61,8 +61,6 @@ public MainController() {
         this.count = -1;
         this.secondCount = -1;
 
-//        this.getRoot().getStylesheets().add("/css/main.css");
-
         ImageView imageView = new ImageView("/DART2N.png");
         imageView.fitWidthProperty().bind(this.getRoot().widthProperty());
         imageView.fitHeightProperty().bind(this.getRoot().heightProperty());

diff --git a/src/main/java/core/Parser.java b/src/main/java/core/Parser.java
@@ -92,34 +92,15 @@ private void processNextLine(String nextLine) {
         }
     }
 
-//    /**
-//     * Read gfa file as a resource in the jar.
-//     * @param input - the input.
-//     * @return - A HashMap containing the information from the .gfa file.
-//     */
-//    public final HashMap<Integer, Node> readGFAAsResource(final InputStream input){
-//        BufferedReader bReader;
-//        bReader = new BufferedReader(new InputStreamReader(input));
-//        return readGFA(bReader, null);
-//    }
-
     /**
      * Read gfa file from a filepath.
      * @param input - the input
      * @return - A HashMap containing the information from the .gfa file.
      * @throws IOException
      */
     public final HashMap<Integer, Node> readGFAAsString(final String input, List<Annotation> a) throws IOException{
-//        InputStream stream =
-//
-
-//        BufferedReader bReader;
-//        BufferedReader = new BufferedReader(new FileReader(input));
-//
         FileInputStream fileInputStream = new FileInputStream(input);
 
-//        InputStream inputStream = new InputStream(bReader);
-
         return readGFA(fileInputStream, a);
     }
 

diff --git a/src/main/java/core/graph/Graph.java b/src/main/java/core/graph/Graph.java
@@ -62,11 +62,6 @@ public Graph() {
 
         annotations = readCDSFilteredGFF(
                 getClass().getResourceAsStream("/decorationV5_20130412.gff"));
-
-//        startMap = getNodeMapFromFile();
-//        nodeIds = startMap.size();
-//        levelMaps = GraphReducer.createLevelMaps(startMap, 1);
-
     }
 
     /**
@@ -78,8 +73,6 @@ public Graph() {
     public HashMap<Integer, Node> getNodeMapFromFile(String s) {
         try {
             Parser parser = new Parser();
-            InputStream inputStream = getClass().getResourceAsStream("/TB10.gfa");
-            //startMap = parser.readGFA(inputStream, annotations);
 
             startMap = parser.readGFAAsString(s, annotations);
             nodeIds = startMap.size();