Complement a DNA sequence in Java - java

//I trying to solve a problem I got from Codewars
// The question is as follows
/*Deoxyribonucleic acid (DNA) is a chemical found in the nucleus of cells and carries the "instructions" for the development and functioning of living organisms.
If you want to know more http://en.wikipedia.org/wiki/DNA
In DNA strings, symbols "A" and "T" are complements of each other, as "C" and "G". You have function with one side of the DNA (string, except for Haskell); you need to get the other complementary side. DNA strand is never empty or there is no DNA at all (again, except for Haskell).
*/
public class DnaStrand {
public static String makeComplement(String dna) {
StringBuilder builder = new StringBuilder();
for(int i=0;i<dna.length();i++){
char c = dna.charAt(i);
if(dna.charAt(i) == 'T'){
builder.append('A');
}
if(dna.charAt(i) == 'A'){
builder.append('T');
}
if(dna.charAt(i) == 'C'){
builder.append('G');
}
if(dna.charAt(i) == 'G'){
builder.append('T');
}
}
return builder.toString();
}
}
//This method seems to work correct
//But when I submit it, It shows that it is incorrect for various inputs from //code wars

Your code is...
if(dna.charAt(i) == 'G'){
builder.append('T');
}
The complement of 'G' is 'C' (not 'T'). So it should be...
if(dna.charAt(i) == 'G'){
builder.append('C');
}

Related

why am i getting this "the type of the expression must be an array type but resolved to string" in JAVA [duplicate]

I am getting the "Must be an array type but it resolved to string" error in my code. It also says that i (in the code below) cannot be resolved to a variable which I don't get.
public class DNAcgcount{
public double ratio(String dna){
int count=0;
for (int i=0;i<dna.length();i++);
if (dna[i]== "c"){
count+= 1;
if (dna[i]=="g"){
count+=1;
double answer = count/dna.length();
return answer;
}
}
}
}
Could you guys please help me figure out where the problem lies? I'm new to coding in Java so I am not entirely comfortable with the format yet.
Thanks a lot,
Junaid
You cannot access a String's character using subscript (dna[i]). Use charAt instead:
dna.charAt(i) == 'c'
Also, "c" is a String, 'c' is a char.
One more thing - integer division ( e.g. int_a / int_b ) results in an int, and so you lose accuracy, instead - cast one of the ints to double:
double answer = count/(double)dna.length();
Use {} to define the scope of the loop. Also, as others already pointed out, use charAt instead of [] and use ' for characters, and use floating point division for the ratio.
for (int i = 0; i < dna.length(); i++) {
if (dna.charAt(i) == 'c') {
count += 1;
}
if (dna.charAt(i) == 'g') {
count += 1;
}
}
Or a bit shorter, use || to or the two clauses together
if (dna.charAt(i) == 'c' || dna.charAt(i) == 'g') {
count += 1;
}
I think you are currently a bit weak at brackets , this is what i understood from your code and corrected it;
public class DNAcgcount{
public double ratio(String dna){
int count=0;
for (int i=0;i<dna.length();i++){
if (dna.charAt(i)== 'c')
count+= 1;
if (dna.charAt(i)=='g')
count+=1;
}
double answer = count/(double)dna.length();
return answer;
}
}
After if we have to close the brackets when what you want in if is finished . I think you wanted count to be the number of time c or g is present in the dna.
You also did some other mistakes like you have to use 'c' and 'g' instead of "c" and "g" if you are using .charAt(i) because it will be treated like a character and then only you can compare .
You may view this link
http://docs.oracle.com/javase/tutorial/java/nutsandbolts/if.html
http://docs.oracle.com/javase/tutorial/java/nutsandbolts/for.html
and you may also have a look at works you can do with string like charAt.
It seems like that you have a few problems with the main syntax of basic java functions like loops or if-else statement. Click here for a good tutorial on these.
You must correct your for-loop and your if-statement:
for(int i=0;i<dna.length();i++){
if(...){
...;
}
if(...){
...;
}
}
Now you wont get the Cant be resolved to a variable... exception.
Second thing is the usage of your string. You have to use it like this:
for(int i=0;i<dna.length();i++){
if(dna.charAt(i) == 'c'){
count += 1;
}
if(dna.charAt(i) == 'g'){
count += 1;
}
}
Now all your exceptions should be eleminated.
Your problem is with syntax dna[i], dna is a string and you access it as it would be an array by []. Use dna.charAt(i); instead.
You using String incorrectly. Instead of accessing via [] use dna.charAt(i).
Altough logically a string is an array of characters in Java a String type is a class (which means it has attributes and methods) and not a typical array.
And if you want to compare a single character to another enclose it with '' instead of "":
if (dna.charAt(i) == 'c')
.
.
There are two errors:
count should be double or should be casted do double answer = (double)count / dna.length();
and as mentioned above you should replace dna[i] with dna.charAt(i)

Tokenizing a String in Java

I am currently working on a project to parse strings into individual tokens. This is all and well, but I am stuck (obviously). I currently would like to test if a string matches a keyword (i.e. true, false, class, inherits, etc) and return that string as a token (please note I am not using the StringTokenizer that the Java API provides, IIRC).
Here is my code that pertains to the keywords:
if (isAlpha(ch)){
System.out.println("Current character:" + ch);
letters += ch;
charIndex--;
while(isDigit(nextChar()) || isAlpha(nextChar())){
Character c = nextChar();
System.out.println("C:" + c);
letters += c;
charIndex++;
System.out.println("After another character:" + letters);
}
if(letters == "class"){
token = new Token(token.CLASS, letters);
}
if(letters == "inherits"){
token = new Token(token.INHERIT, letters);
}
if(letters == "if"){
token = new Token(token.IF, letters);
} //etc etc
I have isolated the problem in my testing to strings that end in an alphabetic character (i.e. "funny"; this token/string would be an identifier). It keeps looping on the "y" and prints "Current character: y." It works with strings like "funny6" though. I may be missing the obvious (having to do with whitespace, perhaps), but any advice would be appreciated.
Thank you!

Constructor throwing runtime exception

I have a constructor that takes in a string as a parameter. I want to throw a runtime exception everytime the string that is passed into the constructor contains anything that is not either "A", "C", "G", or "T". Currently this is what my code looks like:
public DNAStrandNovice(String strand) {
passedStrand = strand;
if (passedStrand.contains("a") || passedStrand.contains("c")
|| passedStrand.contains("g") || passedStrand.contains("t")) {
throw new RuntimeException("Illegal DNA strand");
} else if (passedStrand.contains("1") || passedStrand.contains("2")
|| passedStrand.contains("3") || passedStrand.contains("4")
|| passedStrand.contains("5") || passedStrand.contains("6")
|| passedStrand.contains("7") || passedStrand.contains("8")
|| passedStrand.contains("9") || passedStrand.contains("0")) {
throw new RuntimeException("Illegal DNA Strand");
} else if (passedStrand.contains(",") || passedStrand.contains(".")
|| passedStrand.contains("?") || passedStrand.contains("/")
|| passedStrand.contains("<") || passedStrand.contains(">")) {
throw new RuntimeException("Illegal DNA Strand");
}
}
I feel like this could be implemented in a much more concise way, but I don't know how. Right now I'm just checking for every character that is not the capital letters "A", "C", "G", or "T" and throwing a run time exception but I feel like it's too tedious and bad programming style. Anyone have any ideas?
Check negatively, instead of positively.
for (int i = 0; i < str.length(); i++) {
if (str.charAt(i) != 'A' && str.charAt(i) != 'C'
&& str.charAt(i) != 'G' && str.charAt(i) != 'T') {
throw new IllegalArgumentException("Bad character " + str.charAt(i));
}
}
...or, even shorter,
for (int i = 0; i < str.length(); i++) {
if (!"ACGT".contains(str.charAt(i))) {
throw new IllegalArgumentException("Bad character " + str.charAt(i));
}
}
You can achieve this using regex (regular expressions):
public DNAStrandNovice(String strand) {
if (!strand.matches("[ACGT]+")) { //or [ACGT] <-- see note below
throw new RuntimeException("Illegal DNA strand");
}
passedStrand = strand;
}
The regular expression [ACGT]+ means the string must have one or more characters, and each of them must be one of A, C, G or T. The ! in front of strand.matches reverses the boolean value returned by matches, essentially meaning if the string does not match the regex, then throw RuntimeException.
Note: If you need the string to have exactly one character, use the regex [ACGT]. If you need to allow spaces, you can use [ACGT ]+ (then trim and check for empty) or [ACGT][ACGT ]+ (which ensures the first character is not a space).
You can even do much more complex and powerful regex checks such as patterns that should contain exactly four characters repeated with spaces in between (example ATCG TACG) or even where only certain characters appear in certain places, like only A and C can appear as first two characters, and only G and T can appear following it (example ACTG is correct while AGTC is wrong). I will leave all that as an exercise.
Recommend against using an exception. Define an Enum and pass that.
public enum DnaCode { A, C, G, T }
...
public DNAStrandNovice(List<DnaCode> strand) {
...
}
Or make it a DnaCode[] if you prefer. You can control the input and avoid dealing with interrupted control flow. Exceptions are rather expensive to throw and are not really intended for use as a method of flow control.
You can make the code slightly more efficient by manaully looping through the characters and checking for the letters either with ifs or a Set.
But honestly, unless performance is a problem, it's good how it. Very obvious and easy to maintain.
I was going to jump in with a possibility...
public boolean validateLetter(String letter){
HashMap<String, String> dna = new HashMap<String, String>();
dna.put("A", "A");
dna.put("C", "C");
dna.put("G", "G");
dna.put("T", "T");
if(dna.get(letter) == null){
System.out.println("fail");
return false;
} else {
return true;
}
}
I would also not put that code in the constructor, rather put it in its own method and call from the constructor.
public DNAStrandNovice(String strand){
if(strand.matches("^[A-Za-z]*[0-9]+[A-Za-z]*$") || strand.matches("^[a-zA-Z]*[^a-zA-Z0-9][a-zA-Z]*$") || strand.matches("^[A-Za-z]*[acgt]+[A-Za-z]*$")){
throw new RuntimeException("Illegal DNA strand");
}
}

String Symmetry Program

Hey I could use a little bit of help to figure out why my program isn't working. The question is to make a program using recursion that figures if it the text given is a palindrome or not after all the punctuation and white spaces are removed. While the program so far compiles, it returns every value as false. We are only allowed to change the isSymmetrical method. I could use whatever help possible trying to figure out how to make this work. Thank you.
public class StringSymmetry {
public static boolean isSymmetrical(String inputText)
{
if(inputText.length() == 0 || inputText.length() ==1)
return true;
if(inputText.charAt(0) == inputText.charAt(inputText.length()-1))
return isSymmetrical(inputText.substring(1,inputText.length()-1));
return false;
}
public static void main(String[] args) {
String[] sampleData =
{ "Don't nod",
"Dogma: I am God",
"Too bad - I hid a boot",
"Rats live on no evil star",
"No trace; not one carton",
"Was it Eliot's toilet I saw?",
"Murder for a jar of red rum",
"May a moody baby doom a yam?",
"Go hang a salami; I'm a lasagna hog!",
"Name is Bond, James Bond"
};
for (String s : sampleData)
{
System.out.println("isSymmetrical (" + s + ") returns " + isSymmetrical(s));
}
}
}
The problem is that you didn't include any checks for case or punctuation and white space.
One way you could do it is something like this. The specifics depend on what you're allowed to use for the assignment, but you're probably intended to do something along these lines.
Also, note that toLowerCase is problematic if you have the default locale set to something unusual like Turkey. For proper robustness, you need to specify a locale, but this isn't something you'll have to worry about in a homework assignment.
public static boolean isSymmetrical(String inputText)
{
inputText = inputText.toLowerCase();
if(inputText.length() == 0 || inputText.length() ==1)
return true;
if(!Character.isLetter(inputText.charAt(0)))
return isSymmetrical(inputText.substring(1,inputText.length()));
if(!Character.isLetter(inputText.charAt(inputText.length()-1)))
return isSymmetrical(inputText.substring(0,inputText.length()-1));
if(inputText.charAt(0) == inputText.charAt(inputText.length()-1))
return isSymmetrical(inputText.substring(1,inputText.length()-1));
return false;
}
Check the following function:
public static boolean isPalindrome(String str, int x) {
if(x == 0) return true;
if(str.charAt(0) == str.charAt((str.length() - 1)))
return isPalindrome(str.substring(1, str.length() - 1), x - 1);
return false;
}
Explanation:
A recursive function with the following parameter's:
str - a String object which will be tested for symmetry.
x - Integer that represent's the recursive tester parameter and decides for how far you want to iterate and check for two sided symmetry.
The base case is set to zero and return's true when you finished the desired iteration number.
The second if-condition statement is used to check the corner's of the string that is given, and its return statement will recursively enter another testing loop with shorter corner's of the original String( . . . corner's will be shorter by one).

regular expression for \" in java

I need to write a regular expression for string read from a file
apple,boy,cat,"dog,cat","time\" after\"noon"
I need to split it into
apple
boy
cat
dog,cat
time"after"noon
I tried using
Pattern pattern =
Pattern.compile("[\\\"]");
String items[]=pattern.split(match);
for the second part but I could not get the right answer,can you help me with this?
Since your question is more of a parsing problem than a regex problem, here's another solution that will work:
public class CsvReader {
Reader r;
int row, col;
boolean endOfRow;
public CsvReader(Reader r){
this.r = r instanceof BufferedReader ? r : new BufferedReader(r);
this.row = -1;
this.col = 0;
this.endOfRow = true;
}
/**
* Returns the next string in the input stream, or null when no input is left
* #return
* #throws IOException
*/
public String next() throws IOException {
int i = r.read();
if(i == -1)
return null;
if(this.endOfRow){
this.row++;
this.col = 0;
this.endOfRow = false;
} else {
this.col++;
}
StringBuilder b = new StringBuilder();
outerLoop:
while(true){
char c = (char) i;
if(i == -1)
break;
if(c == ','){
break;
} else if(c == '\n'){
endOfRow = true;
break;
} else if(c == '\\'){
i = r.read();
if(i == -1){
break;
} else {
b.append((char)i);
}
} else if(c == '"'){
while(true){
i = r.read();
if(i == -1){
break outerLoop;
}
c = (char)i;
if(c == '\\'){
i = r.read();
if(i == -1){
break outerLoop;
} else {
b.append((char)i);
}
} else if(c == '"'){
r.mark(2);
i = r.read();
if(i == '"'){
b.append('"');
} else {
r.reset();
break;
}
} else {
b.append(c);
}
}
} else {
b.append(c);
}
i = r.read();
}
return b.toString().trim();
}
public int getColNum(){
return col;
}
public int getRowNum(){
return row;
}
public static void main(String[] args){
try {
String input = "apple,boy,cat,\"dog,cat\",\"time\\\" after\\\"noon\"\nquick\"fix\" hello, \"\"\"who's there?\"";
System.out.println(input);
Reader r = new StringReader(input);
CsvReader csv = new CsvReader(r);
String s;
while((s = csv.next()) != null){
System.out.println("R" + csv.getRowNum() + "C" + csv.getColNum() + ": " + s);
}
} catch(IOException e){
e.printStackTrace();
}
}
}
Running this code, I get the output:
R0C0: apple
R0C1: boy
R0C2: cat
R0C3: dog,cat
R0C4: time" after"noon
R1C0: quickfix hello
R1C1: "who's there?
This should fit your needs pretty well.
A few disclaimers, though:
It won't catch errors in the syntax of the CSV format, such as an unescaped quotation mark in the middle of a value.
It won't perform any character conversion (such as converting "\n" to a newline character). Backslashes simply cause the following character to be treated literally, including other backslashes. (That should be easy enough to alter if you need additional functionality)
Some csv files escape quotes by doubling them rather than using a backslash, this code now looks for both.
Edit: Looked up the csv format, discovered there's no real standard, but updated my code to catch quotes escaped by doubling rather than backslashes.
Edit 2: Fixed. Should work as advertised now. Also modified it to test the tracking of row and column numbers.
First thing: String.split() uses the regex to find the separators, not the substrings.
Edit: I'm not sure if this can be done with String.split(). I think the only way you could deal with the quotes while only matching the comma would be by readahead and lookbehind, and that's going to break in quite a lot of cases.
Edit2: I'm pretty sure it can be done with a regular expression. And I'm sure this one case could be solved with string.split() -- but a general solution wouldn't be simple.
Basically, you're looking for anything that isn't a comma as input [^,], you can handle quotes as a separate character. I've gotten most of the way there myself. I'm getting this as output:
apple
boy
cat
dog
cat
time\" after\"noon
But I'm not sure why it has so many blank lines.
My complete code is:
String input = "apple,boy,cat,\"dog,cat\",\"time\\\" after\\\"noon\"";
Pattern pattern =
Pattern.compile("(\\s|[^,\"\\\\]|(\\\\.)||(\".*\"))*");
Matcher m = pattern.matcher(input);
while(m.find()){
System.out.println(m.group());
}
But yeah, I'll echo the guy above and say that if there's no requirement to use a regular expression, then it's probably simpler to do it manually.
But then I guess I'm almost there. It's spitting out ... oh hey, I see what's going on here. I think I can fix that.
But I'm going to echo the guy above and say that if there's no requirement to use a regular expression, it's probably better to do it one character at a time and implement the logic manually. If your regex isn't picture-perfect, then it could cause all kinds of unpredictable weirdness down the line.
I am not really sure about this but you could have a go at Pattern.compile("[\\\\"]");
\ is an escape character and to detect a \ in the expression, \\\\ could be used.
A similar thing worked for me in another context and I hope it solves your problem too.

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