latest working version

Assign3.java

import java.io.*; 
import java.util.*; 

public class stephsFork1 {
  
	public static void intro()    {//figure out what we want to say
		System.out.println("This program reports information about DNA");
		System.out.println("nucleotide sequences that may encode proteins.");
		System.out.println("(such as Captain Picards hair growth protein)");
		System.out.println("");
        }
    
    
    public static final int HOW_MANY_OF_EACH = 4;//AGCT-
   public static final int NUCS_IN_CODON = 3;//groups of 3
   public static final int PERCENT_MASS = 30;//min percent
   public static final int ARE_THERE_ENOUGH_CODONS = 5;//min num of codons
   
   public static void main(String[] args) throws FileNotFoundException {
	   Scanner console = new Scanner(System.in);
      
      intro();
      processFile();      
        
   } 
   private static void processFile() throws FileNotFoundException {
	     // whatFile(console);

	   Scanner console = new Scanner(System.in);  
	   File userFileAnswer = whatFile(console);
	      Scanner read1 = new Scanner(userFileAnswer); 
	      String nLine = read1.nextLine();
	      String nName = (""); //insert name into quotes
	      PrintStream output = new PrintStream(output(console));
	   while (read1.hasNextLine())   {
	          nName = nLine;
	         String nucsInARow = read1.nextLine().toUpperCase();//here's Chloe's toUpperCase statement
	         int[] numberOfNucs = howManyNucs(nucsInARow);
	         double[] massP = massPercentage(numberOfNucs);
	         String [] codon = codon(nucsInARow);
	         boolean IsItAProtein = isItAProtein(codon, massP);
	         outputToFile(nName, nucsInARow, numberOfNucs, massP, codon, 
	            output, IsItAProtein);
	         if (read1.hasNextLine())   {
	             nLine = read1.nextLine();
	         }
	   }     
	
}
public static File whatFile(Scanner console)    {//ask for file
      System.out.print("Input file name: "); 
      File answer = new File(console.nextLine());
      return  answer;
 }  
   public static File output(Scanner console)    {//where to send output
      System.out.print("Output file name: ");
      File fileName = new File (console.nextLine());
      return fileName;
   }
   
   
   public static int[] howManyNucs(String lineNucs)  {//counting all the nucleotides at the same time
      int[] nucCount = new int[HOW_MANY_OF_EACH];
      for (int i = 0; i < lineNucs.length(); i++)  {
         int index = "ACGT".indexOf(lineNucs.charAt(i));
         if (index >= 0)   {
            nucCount[index]++;
         }
      }
      return nucCount;
   }
   public static double[] massPercentage (int[] nucCount) {
      double[] mass = {135.128, 111.103, 151.128, 125.107};//total mass of string**not sure where to put the 'junk'
      double[] massOfEach = new double[HOW_MANY_OF_EACH];//mass of each nuc
      double[] massPercent = new double[HOW_MANY_OF_EACH];
      double massSum = 0;
      for (int m = 0; m < HOW_MANY_OF_EACH; m++) {
          massOfEach[m] = ((nucCount[m]) * (mass[m]));
         massSum = massOfEach[m]+ massSum;
         }
      for (int p = 0; p < HOW_MANY_OF_EACH; p++) {
         massPercent[p] = Math.round((massOfEach[p] / massSum) * 1000.0)/10.0;//percent mass of each nuc
      }
      return massPercent;  
   }
     public static String[] codon(String lineOfNucs) {//puts into groups of 3 (codons)
      String[] codon = new String [(lineOfNucs.length() / NUCS_IN_CODON)];
      int indexStart = 0;
      for (int c = 0; c < codon.length; c++)   {
         codon[c] = lineOfNucs.substring(indexStart, (indexStart + NUCS_IN_CODON));
         indexStart = indexStart + NUCS_IN_CODON;
      }
      return codon;
   }
   
   public static boolean isItAProtein(String[] codon, double[] massPercent)  {
     //is it a protein?
      if (!codon[0].equals("ATG")) {//start with ATG
         return false;
      }
      if ((!codon[codon.length-1].equals("TAA")) && (!codon[codon.length-1].equals("TAG")) && 
            (!codon[codon.length-1].equals("TGA"))) {
         return false;//end requirements
      }        
      if (codon.length < ARE_THERE_ENOUGH_CODONS)   {//is it long enough?
         return false;
      }      
      if ((massPercent[1] + massPercent[2]) < PERCENT_MASS) {
         return false;//percentage mass check
      }
      return true;
   }  //output
   public static void outputToFile (String nName, String nNucs, int[] nucCounts, 
         double[] massPercent,String[] codons, PrintStream output, boolean protein) {
      output.println("Name: " + nName);
      output.println("Nucleotides: " + nNucs);
      output.println("Nucleotide counts: " + Arrays.toString(nucCounts));
      output.println("Mass percentages: " + Arrays.toString(massPercent));
      output.println("Codons: " + Arrays.toString(codons));
      output.print("Encodes a protein: ");
      if (protein == true) {
         output.println("yes");
      } else {
         output.println("no");
      }
      output.println("");
   }

   
  
}

Only thing with this new part you added is that it doesn't have the processFile method that Stuart wrote in order for the file to be read.

I am updating it now with the processFile method, I noticed the model we're basing our code off has a lot going on in their main method so I'm going to streamline ours down and keep less work in main

As of now these two method calls:
intro();
processFile();
will run the program and save the output to a txt file. We still haven't figured out how to not calculate dashes - "junk" in the mass percentages

Ok that was weird, the last comment was by me but apparently Stephanie was still logged into my laptop. I'm back to being Stuart now

It's only asking for the input file name and output file name for me and then doesn't do anything. :/

I was a dummy and didn't see it was creating the file in my documents! P.S. I fixed the junk output and updated the code on my original!

That's cool, I didn't know it would create the file for you I thought we had to have a .txt file already saved before hand

Hello,

My name is Jonathan and I work with the introductory computer science courses at the University of Washington. This post contains solution code to a homework assignment that was adapted from one of our own.

This post's code is indexed by Google, enabling current students to easily find it and cheat on their assignments.

Would you please remove this post or make it secret in order to help us enforce our academic policy?

By removing this post, you would be removing a tool that our students could use in academic misconduct.

Thank you,
Jonathan Sanders
Intro Support, Computer Science & Engineering
University of Washington
jsanders@cs.washington.edu

More info on our course: http://courses.cs.washington.edu/courses/cse142/15au/