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  1. PO
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    <p>Personally I never tried to call method of my class with keyword <code>class</code>. If we say that your class is named <code>Foo</code>, in your Main method you should write:</p> <pre><code>mzList = Foo.filreader("precursor",mzList); </code></pre> <p>In your first Main example, this doesn't make sense:</p> <pre><code>List mzList = new LinkedList(); mzList = new ArrayList(); </code></pre> <p>It should be either LinkedList() or ArrayList(), like so:</p> <p><code>List mzList = new LinkedList();</code> or <code>List mzList = new ArrayList();</code></p> <p>Next, you are passing file name "precursor", but in the first example you are using "./precursors" (but I think you are aware of that).</p> <p>Lastly you are assigning result of your method to variable <code>mzList</code>, and pass the same list instance as parameter. If you pass list as parameter, you don't have to return it back because it the very same list as created earlier in your code (read about references). You could use something like this:</p> <pre><code>public static void filereader (String filename, LinkedList someList) { FileInputStream input = new FileInputStream(filename); DataInputStream in = new DataInputStream(input); BufferedReader reader = new BufferedReader(new InputStreamReader(in)); String line; while ((line = reader.readLine()) != null) { if (line.equals("---")) { /* Do Nothing... */ } else { someList.add(line); } } in.close(); return(someList); } </code></pre> <p>and then simply (notice there is no assignment):</p> <pre><code>Foo.filreader("precursor",mzList); </code></pre> <p>As far I see, you are not making use of this input list in terms of reading data from it. Thus, you can initialize your list inside the method and return it, like so:</p> <pre><code>public static LinkedList filereader (String filename) { LinkedList someList = new LinkedList(); // notice list initialization FileInputStream input = new FileInputStream(filename); DataInputStream in = new DataInputStream(input); BufferedReader reader = new BufferedReader(new InputStreamReader(in)); String line; while ((line = reader.readLine()) != null) { if (line.equals("---")) { /* Do Nothing... */ } else { someList.add(line); } } in.close(); return(someList); } </code></pre> <p>and then simply call your method and assign your results:</p> <pre><code>mzList = Foo.filreader("precursor"); </code></pre>
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    1. POStruggling with methodizing my main program (a method that has a LinkedList as input and output specifically). Where am i going wrong with this?
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    1. USjjczopek
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    1. POStruggling with methodizing my main program (a method that has a LinkedList as input and output specifically). Where am i going wrong with this?
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    1. COThat makes sense indeed, i was still defining the list outside of the method which is rather unnecessary. I will try this now, and yes the class wasn't called class but i just used class.filereader to show abstractly how i called it, sorry for not being clear there.
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      1. USBas Jansen
    2. COIt confused me since `class` is a keyword in Java ;)
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    3. COYeah i realized that as soon i read your question :P Now... on to the curly braces bug fixing o.O
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