Thread: Converting Two dimensional array into an Array list

So I am working on a homework assignment. I say that ahead of time so no one thinks i am being sneaky or what not. However My teacher is asking us to take our two dimensional array we built and rewrite the code so instead of storing the data into the two dimensional array, it will store it into a arraylist and then we will transfer the array list into another class called "Protein". I will post the assignment below so you can get a better understanding of what he is asking. I am a little less then a month new to the language, and the teacher is going way to fast for me to really learn the material. The people in this community have been more then helpful in filling the space my teacher is leaving.
So here is the assignment

Assignment 2

Parsing Biological Data

Implementing the Protein Class

Your task is to create a Protein class that holds important protein data and performs basic
operations on proteins. Below is the same uniprot sample from the rst assignment

ID HBA_HUMAN Reviewed; 142 AA.
AC P69905; P01922; Q1HDT5; Q3MIF5; Q53F97; Q96KF1; Q9NYR7; Q9UCM0;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 28-JUL-2009, entry version 75.
DE RecName: Full=Hemoglobin subunit alpha;
DE AltName: Full=Hemoglobin alpha chain;
DE AltName: Full=Alpha-globin;
GN Name=HBA1;
GN and
GN Name=HBA2;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
....
SQ SEQUENCE 142 AA; 15258 MW; 15E13666573BBBAE CRC64;
MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG
KKVADALTNA VAHVDDMPNA LSALSDLHAH KLRVDPVNFK LLSHCLLVTL AAHLPAEFTP
AVHASLDKFL ASVSTVLTSK YR
//

In addition to the primary accession number and sequence, the Protein class will hold the
description of the protein as well as the source organism. In the sample above, the descrip-
tion and source organism are Hemoglobin subunit alpha and Homo sapiens (Human). In
order to access and modify this information, your class must implement getter and setter
methods for each private instance variable. In addition to these methods, you must override
(implement) the following class methods:

public String toString(): Implementing this method will allow us to directly print
useful information about proteins using System.out.println(protein). This method
should return a String formatted as follows:

AC: <the primary accession number>
DE: <the description>
OS: <the source organism>
SQ: <the sequence>

public boolean equals(Protein otherProtein): When the equals method is called
(e.g. myProtein.equals(otherProtein)), it should return true only if myProtein
and otherProtein are the same protein. Implementing this method correctly will require
us to use the keyword this which we will discuss in lab.

Extending the Parser class

Your next task is to enhance the parser so that it can read in every uniprot le that lives in
some directory (folder). In particular, you must implement the following:

public class Parser{
//global variable that stores all of the proteins.
private ArrayList<Protein> protein_database = new ArrayList<Protein>();
.
.
.
/*
fills the protein_database arraylist with all the proteins
defined in the uniprot files that exist inside the directoryName folder.
*/
public static void parseAll(String directoryName){
//CODE GOES HERE
}


You will need Java's ArrayList and File class to correctly implement the recursive method
parseAll. File methods such as isDirectory, exists, list, and listFiles will be quite
helpful. In a nutshell, an ArrayList is an expandable array that allows us to add elements
without knowing the size of the array in advance.
Since we are no longer concerned with outputting to a le, the main method of your Parser
class must be as follows:

public static void main(String[] args){
//outputs a list of all the proteins defined in the uniprot files
//that reside in the folderName folder
String folderName = args[0];
parseAll(folderName);
System.out.println(protein_database);
}

Specications, notes, and hints

The name of the source code les must be Parser.java and Protein.java . The program
should be executable as: java Parser uniprotDirectory where uniprotDirectory is
the name of the directory (folder) that contains the uniprot les.

Since we are now interested in holding more protein data (other than AC and SQ),
you will need to adjust your parse method to extract this new data.

Do not assume that only uniprot les live in uniprotDirectory. You may assume that
all uniprot les will end in .dat.

ArrayLists will allow you to make your parse method simpler.

Sorry it is such a long explanation.
Also if someone could help me understand WHAT he is wanting me to do in this assignment that would be appreciated. He does not explain very clearly what he is asking.

Ok so here is my assignment as of now. The only part i have added for assignment two is looking for the "DE" and the "OS" in the while loop in the method "extract_data"

import java.util.*;
import java.io.*;
 
public class Parser 
{
	    public static void main(String[] args) throws IOException
	    {	
	    	PrintWriter out = new PrintWriter("fastaFile");
	    	String[][] extractedInfo = extract_info();
		int n = count_entries();
 
	    	for(int i = 0; i < n; i++)
	    	{
			out.write("<"+extractedInfo[i][1]+"\n"+extractedInfo[i][0]+"\n"
						 +extractedInfo[i][2]+"\n"+extractedInfo[i][3]+"\n");
	    	}
 		out.close();	        
	    }
 
 
	    public static String[][] extract_info() throws IOException 
	    {
		String[][] extractedData = new String[count_entries()][4];
	    	File uniprot = new File ("uniprotFile");
	    	Scanner uniprotScanner = new Scanner (uniprot);
	    	int i = 0;
	    	boolean foundAC = false; //stored in [i][1]
	    	boolean SQMode = false; //stored in [i][0]
	    	String sequence = "";
	    	boolean foundDE = false; //stored in [i][2]
	    	boolean foundOS = false; //stored in [i][3]
 
	    	while (uniprotScanner.hasNextLine())
	    	{
	    		String currentLine = uniprotScanner.nextLine();
	    		String[] tokens = currentLine.split(" ");
 
	    		if ( tokens [0].equals("AC") && !foundAC )
	    		{
	    			extractedData[i][1] = tokens[3];
	    			foundAC = true;
	    		}
	    			else if (tokens [0].equals("SQ") && !SQMode)
	    			{
	    				SQMode = true;
	    			}
	    			else if (tokens [0].equals("DE") && !foundDE)
	    			{	
	    				extractedData[i][2] = currentLine;
	    				foundDE = true;
	    			}
	    			else if (tokens [0].equals("OS") && !foundOS)
	    			{
	    				extractedData[i][3] = currentLine;
	    				foundOS = true;
	    			}
	    				else if (currentLine.startsWith("//"))
	    				{
	    					SQMode = foundAC = foundDE = foundOS = false;
	    					extractedData[i][0] = sequence; 
	    					sequence = "";
	    					i++;
	    				}	
	    					else if (SQMode)
	    					{
	    						sequence += currentLine.replaceAll(" ", "");
	    					}	    		    					
	    	}	
	    	return extractedData;
	    }
 
	    public static int count_entries() throws IOException
	    {
	    	int entriesCount = 0;
	    	File uniprot = new File ("uniprotFile");
	    	Scanner uniprotScanner = new Scanner (uniprot);
	    while (uniprotScanner.hasNextLine())
	    { 
	    	String currentLine = uniprotScanner.nextLine();
	    	String[] tokens = currentLine.split(" ");
 
	    	if (tokens [0].equals("//"))
	    	{
	    		entriesCount++;
	    	} 
	    }
	    return entriesCount;
	    }
 }

Now in this code I am saving the data I have found into a two dimensional array. Now he wants us to change that so it is saving into an arraylist and then save that array list into another class called "Protein".

I would much rather just save the two dimensional array into an arraylist. How can this be achieved.

I know I am asking alot of this community and have presented alot of information, but I thank anyone who is willing to spend the time to provide me some clarification

The array list would have to be formatted

public String toString(): Implementing this method will allow us to directly print
useful information about proteins using System.out.println(protein). This method
should return a String formatted as follows:

AC: <the primary accession number>
DE: <the description>
OS: <the source organism>
SQ: <the sequence>

I changed my code around actually so this is the new code

import java.util.*;
import java.io.*;
 
public class Parser 
{
	private static ArrayList<Protein> protein_database = new ArrayList<Protein>();
 
	    public static void main(String[] args) throws IOException
	    {	
	    	PrintWriter out = new PrintWriter("fastaFile");
	    	String[][] extractedInfo = extract_info();
		int n = count_entries();
 
	    	for(int i = 0; i < n; i++)
	    	{
			out.write("<"+extractedInfo[i][1]+"\n"+extractedInfo[i][0]+"\n"
						 +extractedInfo[i][2]+"\n"+extractedInfo[i][3]+"\n");
	    	}
 		out.close();	        
	    }
 
	    public static void parseAll(String directoryName)
	    {
 
	    }
 
	    public static void extracted_info(String s) throws IOException 
	    {
		String extractedData = new String();
	    	File uniprot = new File (s);
	    	Scanner uniprotScanner = new Scanner (uniprot);
	    	boolean foundAC = false; //stored in [i][1]
	    	boolean SQMode = false; //stored in [i][0]
	    	String sequence = "";
	    	String ACline = "";
	    	String DEline = "";
	    	String OSline = "";
	    	boolean foundDE = false; //stored in [i][2]
	    	boolean foundOS = false; //stored in [i][3]
 
 
	    	while (uniprotScanner.hasNextLine())
	    	{
	    		String currentLine = uniprotScanner.nextLine();
	    		String[] tokens = currentLine.split(" ");
 
	    		if ( tokens [0].equals("AC") && !foundAC )
	    		{
	    			ACline = tokens[3];
	    			foundAC = true;
	    		}
	    			else if (tokens [0].equals("SQ") && !SQMode)
	    			{
	    				SQMode = true;
	    			}
	    			else if (tokens [0].equals("DE") && !foundDE)
	    			{	
	    				DEline = currentLine;
	    				foundDE = true;
	    			}
	    			else if (tokens [0].equals("OS") && !foundOS)
	    			{
	    				OSline = currentLine;
	    				foundOS = true;
	    			}
	    				else if (currentLine.startsWith("//"))
	    				{
	    					SQMode = foundAC = foundDE = foundOS = false;
	    					Protein info = new Protein(ACline, sequence, DEline, OSline);
	    					protein_database.add(info);
	    					sequence = "";
 
	    				}	
	    					else if (SQMode)
	    					{
	    						sequence += currentLine.replaceAll(" ", "");
	    					}	    		    					
	    	}	
 
	    }
 
	    public static int count_entries() throws IOException
	    {
	    	int entriesCount = 0;
	    	File uniprot = new File ("uniprotFile");
	    	Scanner uniprotScanner = new Scanner (uniprot);
	    while (uniprotScanner.hasNextLine())
	    { 
	    	String currentLine = uniprotScanner.nextLine();
	    	String[] tokens = currentLine.split(" ");
 
	    	if (tokens [0].equals("//"))
	    	{
	    		entriesCount++;
	    	} 
	    }
	    return entriesCount;
	    }
 }

and this is the "Protein" Class as well

public class Protein {
	private String proteinAC;
	private String proteinSQ;
	private String proteinDE;
	private String proteinOS;
 
 
	public Protein(String proteinAC, String proteinSQ, String proteinDE,
			String proteinOS) {
		super();
		this.proteinAC = proteinAC;
		this.proteinSQ = proteinSQ;
		this.proteinDE = proteinDE;
		this.proteinOS = proteinOS;
	}
	public String getProteinAC() {
		return proteinAC;
	}
	public void setProteinAC(String proteinAC) {
		this.proteinAC = proteinAC;
	}
	public String getProteinSQ() {
		return proteinSQ;
	}
	public void setProteinSQ(String proteinSQ) {
		this.proteinSQ = proteinSQ;
	}
	public String getProteinDE() {
		return proteinDE;
	}
	public void setProteinDE(String proteinDE) {
		this.proteinDE = proteinDE;
	}
	public String getProteinOS() {
		return proteinOS;
	}
	public void setProteinOS(String proteinOS) {
		this.proteinOS = proteinOS;
	}
 
	public boolean equals(Protein otherProtein)
	{
		if (otherProtein.proteinSQ.equals(this.proteinSQ))
		{
			return true;
		}
		else return false;
	}
 
}

So in my method that extracts the data i now have it just reading into strings and then reading those into the Protein class. So i figured that out. My issue is how to format the Class to output the string like the format above.
And also I have to write a recursive method to find every ".dat" file in a folder (which contains sub folders and other files that are not ".dat")
How to do the recursive method I am still very confused on he told me to use

public static void parseAll(String directoryName)
	    {
 
	    }

This which is the method he wants to find the ".dat" files but i do not know how to check a set of folders to do that. So help on this portion would also be appreciated.
Thanks again for responding. I know this is alot of information but I am very new to Java and this teacher is teaching us by "throwing us in the water and hoping we learn how to swim" method and i can not learn like that very easily.

Thanks again

I appreciate the quick reply. So what i am curious is with are two things at the moment

first: Is how to write this recursive method to check all files, because all i know is that these methods call themselves until the base case is reach, however i do not know the "Skeleton" on how to do this
Second: How do i format each string inside the:

Protein info = new Protein(ACline, sequence, DEline, OSline);
	   protein_database.add(info);

so when we do the println on the proteins they print in the format stated above

Ok so the recursive method also needs to check each directory for files ending in ".dat" so how would i be able to:
first: call the file name in to be "recursed"
second: make each name in first folder be Strings so i can then run the

string.endsWith(".dat"); command on it?

last: continue into each individual folder inside because the first folder will have multiple folder that need to be checked individually. i feel that this method would just check one set of folders and then end

So for instance i could do

protein.toString("AC: " + ACline +"\n" +"SQ: " + SQline +"\n" + "DE: " + DEline + "\n" + "OS: " + OSline + "\n");

also how would i get it to display in this method if my teacher were to call a println command? Would the above code store it in that way? or would it have to be printed that way?

Ok so what is a good command that can even open a file or find a folder on a desktop? I don't know how to do that at all. And i read an article that discusses the "Tree" set of data which this would be if im correct. So would the method have to check down one entire set of folders and then check through the other branch? Or would it go folder layer by folder layer (if that makes sense).
Finally are you saying that I need to create a method that prints out the protein?
my assignment shows this way

public String toString():

but in the parameters of that would i do what i did above by printing it out? Or would i do that inside the method itself?

SO what i have to do in this program. Is read in a folder (of the users choose run through command line) then once that is open find all the ".dat" files inside each folder inside (each folder CAN contain more folders and coan contain files that are not .dat) Once i find each file I am to find the required information out of each filer (I have done that) and save each into the Protein Class (which i have also done) From there I need to follow this (taken directly from my assignment)

public String toString(): Implementing this method will allow us to directly print
useful information about proteins using System.out.println(protein). This method
should return a String formatted as follows:
AC: <the primary accession number>
DE: <the description>
OS: <the source organism>
SQ: <the sequence>

So this is where I am confused. How do i do the above so when they print it out it is formatted as such.