Programming Forums > Application Development > Java

BungalowBill · Nov 9th, 2006, 11:16 AM

Im writing a program to find out if a protein sequence has a turn in it (don't ask) and this is what i want to do.

I need to enter a sequence, at the terminal, i.e. CAENBVWGKL or something then i need to convert this string into an array to separate it all up and give each letter its own place in the array. The rest becomes very complicated biology stuff so i won't bore you with it. I just need to crack this part.

(Toggle Plain Text)

ArrayList sequence = new ArrayList

//hopefully, eventually a list like this will be made somewhere.

sequence[] = ["C","A","E","N" etc.]

So if i tried to get sequence[2] i would get "A" back.

It seems like it should be pretty straightforward but i can't figure it out.

Does anyone know of any good resources where i can see examples of this kind of thing? I feel like i'm going round in circles with google searching for "converting strings to arrayList" and various similar conbinations.

Any help?

Kaja Fumei · Nov 9th, 2006, 11:34 AM

Do you really need an ArrayList? Is sequence actually going to modified once it has been read? If not, it seems like a waste to use an ArrayList. If all you need is to be able to look up an index in the sequence you can the String class's charAt(index) method on your input string.

xavier · Nov 9th, 2006, 12:55 PM

you could also look into ToCharArray() function that will convert a string into a character array. Wich seems to be exactly what you need.

It doesn't apear like you need an arraylist.

Iftikhar · Nov 9th, 2006, 2:03 PM

You can convert striung to charcters array as suggested by xavier like this
[code]
char [] chrArray = strBiologyStuff.ToCharArray();
[\code]
Then still you want each chracter in arrayList then you can loop throught this array list using

(Toggle Plain Text)

foreach(char chr in chrArray)
 arrList.Add(chr);

titaniumdecoy · Nov 9th, 2006, 5:52 PM

I would use Python rather than Java for this sort of task.

In Java, however, you should only use an ArrayList over a char[] array if you will be adding/removing elements after you initially create the collection.

@Iftikhar: You miscapitalized "ToCharArray" in your code (it should be "toCharArray"). As for your enhanced for loop, the keyword is still "for", not "foreach", and the separator is a colon, not "in". Also, the add method for an ArrayList is "add", not "Add". Next time please ensure that your code compiles and runs successfully before posting.

(Toggle Plain Text)

// The original sequence as a String
String sequence = "CAENBVWGKL";

// Convert it to an array of char
char[] seqChars = sequence.toCharArray();

// Now you can easily access each character
System.out.println(seqChars[0]);

// If you want an ArrayList instead
ArrayList<Character> seqList = new ArrayList<Character>();
for (char c : seqChars)
    seqList.add(c); // Add each character to the list

Jimbo · Nov 9th, 2006, 11:24 PM

Quote:

Originally Posted by titaniumdecoy

@Iftikhar: ...

Damn that C#, eh? :beard:

On subject, you could either do it with the ArrayList or a char[] as suggested, but if you eventually want to look at substrings as well (e.g. see if ABAB occurred), you might consider keeping it as a string and using charAt(). That way you can use substring() for finding the substrings, rather than selecting a subset of an array[list].

BungalowBill · Nov 10th, 2006, 6:55 AM

Alright thanks for that guys. The reason i was going to use an arraylist was that later on im gonna have to make similar lists for indivdual amino acids which include ints and i thought it would be better to use arraylists which could handle both strings and integers. For example:-

the amino acid Alanine, just A for short would have a list like this.

A[142,83,66,0.06,0.076,0.035,0.058]

(If you're interested about what those numbers are, the first one is the P(a) which is the propensity of this particular ammino acid to participate in alpha helices. The next is P(b), beta sheets and it goes on like that.

I plan to have 20 of these lists, one for each of the most common amino acids which i want to mantipulate to pick out certain values for formulas.

Could i just declare each list at the start of the file? ie

(Toggle Plain Text)

ArrayList A = new ArrayList
ArrayList R = new ArrayList
etc..

A[142,83,66,0.06,0.076,0.035,0.058]
R[98,93,95,0.07,0.106,0.099,0.085]
etc..

then access the different values as i wish with if statements?

(Toggle Plain Text)

if(i.equals("A")) {
  x = A[1]; 
}

which would hopefully set the x value to 142, to be used in a later calulation.
What do you guys think?

titaniumdecoy · Nov 10th, 2006, 2:58 PM

You could use a map to associate each letter with an array of numbers, as demonstrated below. This way there is no need to use if statements to extract values. You might also consider reading the values from a file rather than hard-coding them to make the program more flexible.

(Toggle Plain Text)

HashMap<Character, double[]> map = new HashMap<Character, double[]>();

map.put('A', new double[] { 142,83,66,0.06,0.076,0.035,0.058 });
map.put('R', new double[] { 98,93,95,0.07,0.106,0.099,0.085 });

double x = map.get('A')[0]; // Sets x to the first value in A (142)
double y = map.get('R')[2]; // Sets y to the third value in R (95)

lectricpharaoh · Nov 11th, 2006, 7:08 AM

Another thing you could do is write a class to represent amino acids. It would have methods to get the values associated with a particular amino acid (or you could just expose them as public final constants), an enum definition for the various acids (so that you could not construct an object except for a valid amino acid), and a variable storing the enum value for this particular instance. Assuming you implement the proper interfaces, such as Comparable, you could then create an array of the suckers, and sort, search, etc the array.

Iftikhar · Nov 11th, 2006, 12:19 PM

I think some one already the language I used is C Sharp. Pretty much like Java

. That is a good thing also.

Nov 9th, 2006, 11:16 AM	#1
BungalowBill Programmer Join Date: Dec 2005 Posts: 40 Rep Power: 0	ArrayLists Im writing a program to find out if a protein sequence has a turn in it (don't ask) and this is what i want to do. I need to enter a sequence, at the terminal, i.e. CAENBVWGKL or something then i need to convert this string into an array to separate it all up and give each letter its own place in the array. The rest becomes very complicated biology stuff so i won't bore you with it. I just need to crack this part. (Toggle Plain Text) ArrayList sequence = new ArrayList //hopefully, eventually a list like this will be made somewhere. sequence[] = ["C","A","E","N" etc.] ArrayList sequence = new ArrayList //hopefully, eventually a list like this will be made somewhere. sequence[] = ["C","A","E","N" etc.] So if i tried to get sequence[2] i would get "A" back. It seems like it should be pretty straightforward but i can't figure it out. Does anyone know of any good resources where i can see examples of this kind of thing? I feel like i'm going round in circles with google searching for "converting strings to arrayList" and various similar conbinations. Any help?

Nov 9th, 2006, 12:55 PM	#3
xavier Professional Programmer Join Date: Oct 2004 Location: .ro Posts: 383 Rep Power: 4	you could also look into ToCharArray() function that will convert a string into a character array. Wich seems to be exactly what you need. It doesn't apear like you need an arraylist. __________________ Don't take life too seriously, it's not permanent !

Nov 9th, 2006, 2:03 PM	#4
Iftikhar Programmer Join Date: Oct 2006 Location: London Posts: 40 Rep Power: 0	You can convert striung to charcters array as suggested by xavier like this [code] char [] chrArray = strBiologyStuff.ToCharArray(); [\code] Then still you want each chracter in arrayList then you can loop throught this array list using (Toggle Plain Text) foreach(char chr in chrArray) arrList.Add(chr); foreach(char chr in chrArray) arrList.Add(chr); __________________ Iftikhar Ahmed Khan For doing an experiment on programmer's mood please visit http://uxisfyp1.brunel.ac.uk/cspgiak

Nov 9th, 2006, 5:52 PM	#5
titaniumdecoy Expert Programmer Join Date: Nov 2005 Posts: 856 Rep Power: 3	I would use Python rather than Java for this sort of task. In Java, however, you should only use an ArrayList over a char[] array if you will be adding/removing elements after you initially create the collection. @Iftikhar: You miscapitalized "ToCharArray" in your code (it should be "toCharArray"). As for your enhanced for loop, the keyword is still "for", not "foreach", and the separator is a colon, not "in". Also, the add method for an ArrayList is "add", not "Add". Next time please ensure that your code compiles and runs successfully before posting. (Toggle Plain Text) // The original sequence as a String String sequence = "CAENBVWGKL"; // Convert it to an array of char char[] seqChars = sequence.toCharArray(); // Now you can easily access each character System.out.println(seqChars[0]); // If you want an ArrayList instead ArrayList<Character> seqList = new ArrayList<Character>(); for (char c : seqChars) seqList.add(c); // Add each character to the list // The original sequence as a String String sequence = "CAENBVWGKL"; // Convert it to an array of char char[] seqChars = sequence.toCharArray(); // Now you can easily access each character System.out.println(seqChars[0]); // If you want an ArrayList instead ArrayList<Character> seqList = new ArrayList<Character>(); for (char c : seqChars) seqList.add(c); // Add each character to the list

Nov 10th, 2006, 6:55 AM	#7
BungalowBill Programmer Join Date: Dec 2005 Posts: 40 Rep Power: 0	Alright thanks for that guys. The reason i was going to use an arraylist was that later on im gonna have to make similar lists for indivdual amino acids which include ints and i thought it would be better to use arraylists which could handle both strings and integers. For example:- the amino acid Alanine, just A for short would have a list like this. A[142,83,66,0.06,0.076,0.035,0.058] (If you're interested about what those numbers are, the first one is the P(a) which is the propensity of this particular ammino acid to participate in alpha helices. The next is P(b), beta sheets and it goes on like that. I plan to have 20 of these lists, one for each of the most common amino acids which i want to mantipulate to pick out certain values for formulas. Could i just declare each list at the start of the file? ie (Toggle Plain Text) ArrayList A = new ArrayList ArrayList R = new ArrayList etc.. A[142,83,66,0.06,0.076,0.035,0.058] R[98,93,95,0.07,0.106,0.099,0.085] etc.. ArrayList A = new ArrayList ArrayList R = new ArrayList etc.. A[142,83,66,0.06,0.076,0.035,0.058] R[98,93,95,0.07,0.106,0.099,0.085] etc.. then access the different values as i wish with if statements? (Toggle Plain Text) if(i.equals("A")) { x = A[1]; } if(i.equals("A")) { x = A[1]; } which would hopefully set the x value to 142, to be used in a later calulation. What do you guys think?

Nov 9th, 2006, 11:34 AM	#2
Kaja Fumei Hobbyist Programmer Join Date: Oct 2005 Posts: 134 Rep Power: 3	Do you really need an ArrayList? Is sequence actually going to modified once it has been read? If not, it seems like a waste to use an ArrayList. If all you need is to be able to look up an index in the sequence you can the String class's charAt(index) method on your input string.

Nov 10th, 2006, 2:58 PM	#8
titaniumdecoy Expert Programmer Join Date: Nov 2005 Posts: 856 Rep Power: 3	You could use a map to associate each letter with an array of numbers, as demonstrated below. This way there is no need to use if statements to extract values. You might also consider reading the values from a file rather than hard-coding them to make the program more flexible. (Toggle Plain Text) HashMap<Character, double[]> map = new HashMap<Character, double[]>(); map.put('A', new double[] { 142,83,66,0.06,0.076,0.035,0.058 }); map.put('R', new double[] { 98,93,95,0.07,0.106,0.099,0.085 }); double x = map.get('A')[0]; // Sets x to the first value in A (142) double y = map.get('R')[2]; // Sets y to the third value in R (95) HashMap<Character, double[]> map = new HashMap<Character, double[]>(); map.put('A', new double[] { 142,83,66,0.06,0.076,0.035,0.058 }); map.put('R', new double[] { 98,93,95,0.07,0.106,0.099,0.085 }); double x = map.get('A')[0]; // Sets x to the first value in A (142) double y = map.get('R')[2]; // Sets y to the third value in R (95)

Nov 11th, 2006, 7:08 AM	#9
lectricpharaoh Caffeinated Neural Net Join Date: Jun 2005 Location: Dry west coast of Canada Posts: 1,036 Rep Power: 5	Another thing you could do is write a class to represent amino acids. It would have methods to get the values associated with a particular amino acid (or you could just expose them as public final constants), an enum definition for the various acids (so that you could not construct an object except for a valid amino acid), and a variable storing the enum value for this particular instance. Assuming you implement the proper interfaces, such as Comparable, you could then create an array of the suckers, and sort, search, etc the array. __________________ And once again, Probability proves itself willing to sneak into a back alley and service Drama as would a copper-piece harlot. - Vaarsuvius, Order of the Stick

Nov 11th, 2006, 12:19 PM	#10
Iftikhar Programmer Join Date: Oct 2006 Location: London Posts: 40 Rep Power: 0	I think some one already the language I used is C Sharp. Pretty much like Java . That is a good thing also. __________________ Iftikhar Ahmed Khan For doing an experiment on programmer's mood please visit http://uxisfyp1.brunel.ac.uk/cspgiak

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Programming Forums > Application Development > Java

ArrayLists