how to apply a loaded properties class to a piece of text

http://www.javaalmanac.com/egs/java.util/Props.html
http://www.javaalmanac.com/egs/java.util/GetSetProps.html

Read each triplet then get the map value using the read triplet as the key:


class TripletReader {

      private FileReader in;
      
      public TripletReader(String fileName) {
            in = new FileReader(fileName);
      }
      
      public String readNextCode() throws IOException {
            int charsRead = in.read(codeBuffer);
            if (charsRead == 3) {
                  return new String(codeBuffer);
            }
            else if (charsRead < 3) {
                  throw new EOFException("Incorrect number of characters in source file");
            }

            else {
                  in.close();
                  return null;
            }
      }
      
      public void close() {
            try { in.close(); } catch(IOException e) { /* ignore */  }
      }
}      

ok so i have the read file stuff already implemented in a different class, but wondering how to decode each line?

thanks

objects: are u on here 24/7? lol

peace

(That is if i've got the right idea of

>>and i would like it to translate:

)

> objects: are u on here 24/7? lol

Its my job :)

> but wondering how to decode each line?

need to know the details of the format :)

well i think CHEJ might have it, but still not quite sure...

there are a couple complications:
each DNA string is not set to triplets, although each key is set to three chars.

for example

say i have a DNA strand like:

ATGGATTTATCTGCTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGT
GTCCCATCTGTCTGGAGTTGATCAAGGAACCTGTCTCCACAAAGTGTGACCACATATTTTGCAAATTTTG

-----

i have a start and stop code/key as well so at a certain triplet it should print start, and then go through and for every three it should print the corresponding protein value, and then when it reaches a stop codon, it should print stop, then look for the start codon again and repeat...

thanks

peace

sorry off topic, but a friend wants to sign up for EE but doesnt want to sign up on a time basis, but rather the point system?

is there still any way to do that?

thanks

peace

Is this the sort of thing? (Compile and run as Triplets.java)



import java.io.*;

public class Triplets {

      public static void main(String[] args) {

            try {
                  String triplets = "ATTGGCTCTTACCACTTGTCCCTCAAAACGACCACCCCATTGACTGGTGGCGATTGCGTCGACGGA";

                  TripletReader tr = new TripletReader(new StringReader(triplets));
                  String code = null;
                  while((code = tr.readNextCode()) != null) {
                        System.out.println(code);
                  }
                  tr.close();
                  }
                  catch(Exception e) {
                        e.printStackTrace();
                  }
      }

}


class TripletReader {

      private Reader in;
      private char[] codeBuffer;

      public TripletReader(Reader in) {
            this.in = in;
            codeBuffer = new char[3];
      }

      public String readNextCode() throws IOException {
            String code = null;
            int charsRead = in.read(codeBuffer);
            if (charsRead == 3) {
                  code = new String(codeBuffer);
            }
            else if (charsRead < 0) {
                  in.close();
            }
            else if (charsRead < 3) {
                  throw new EOFException("Incorrect number of characters in source file");
            }
            return code;

      }

      public void close() {
            try { in.close(); } catch(IOException e) { /* ignore */      }
      }
}

>>i have a start and stop code/key as well

What is this?

looks like:


ATG=Start

TAA=Stop
TAG=Stop
TGA=Stop

peace

CHEJ you are awesome!  

couple more things though,  how can i have that applied to the properties class?

i'm on Dr.Java right now and in the interactions pane i did" java Triplets"

and it separated that string into triplets and printed it out, and now i am just wondering how to set those triplets to the key i(we[you, objects, and zzynnx) made last night...

thanks

peace

OK, you could use the following. I've put a stop code at the end:

public static void main(String[] args) {

      try {
            java.util.Set stopCodes = new java.util.HashSet();
            stopCodes.add("TAA");
            stopCodes.add("TGA");
            stopCodes.add("TAG");


            String triplets = "ATTGGCTCTTACCACTTGTCCCTCAAAACGACCACCCCATTGACTGGTGGCGATTGCGTCGACGGATAG";

            TripletReader tr = new TripletReader(new StringReader(triplets));
            String code = null;
            while((code = tr.readNextCode()) != null) {
                  System.out.println(stopCodes.contains(code)? "(ignoring stop code)" : code);
            }
            tr.close();
            }
            catch(Exception e) {
                  e.printStackTrace();
            }
}

ummm nothing really changed....
also need it to read the string from a file rather than the above posted string... so can i just use a BufferedReader and use a JFileChooser to select a file and implement that instead of:

String triplets = "ATTGGCTCTTACCACTTGTCCCTCAAAACGACCACCCCATTGACTGGTGGCGATTGCGTCGACGGATAG";




also I really appreciate the help, but maybe post only some of the code, i dont want my professor to think that i just ripped off someone's code (which i am) but would also like to learn as well...please dont take any offense to this...

thanks

peace

oh and also its still not implementing the translation key

thanks

peace

> o can i just use a BufferedReader and use a JFileChooser to select a file and implement that instead of:

yes

if i do that though will i still be able to use a stringReader?

thanks

peace

no you would use code similiar to what I posted earlier and process the String directly, no need to create a StringReader

yeah thats what i ended up doing:

public class Separate {
  private static File inFile;

public static void main(String[] args) {
 

     try {
          java.util.Set stopCodes = new java.util.HashSet();
          stopCodes.add("TAA");
          stopCodes.add("TGA");
          stopCodes.add("TAG");
         
         
          GetFile g = new GetFile();
          g.openFile(inFile);


          //String triplets = "ATTGGCTCTTACCACTTGTCCCTCAAAACGACCACCCCATTGACTGGTGGCGATTGCGTCGACGGATAG";

          TripletReader tr = new TripletReader(new FileReader(inFile));
....

--------------------

and it compiles and when i try to run "java Separate"

it just hangs there... doesnt do anything....

thanks

peace

forgot to add that i have a GetFile class that basically is what u posted earlier

peace

Well not sure what you're doing ...

Use you're BufferedReader to read the file line by line, and then use the substring() method in String to iterate thru the triplets.

For a file, all you need to change is

TripletReader tr = new TripletReader(new FileReader(args[0])); // pass filename on command line

I saved that String several times to a file - it works just the same

sorry was trying to figure some things out...

here is what i did: i have the above posted code with GetFile, and in my GetFile class i have an openFile() method: which looks like:

    try{
      BufferedReader reader = new BufferedReader(new FileReader(inFile));
       line = reader.readLine();
      //System.out.println("The line : \"" +line+ "\"");
      while(line!=null){
        System.out.println("The next line is \"" +line+ "\"");
        line = reader.readLine();        
      }
    }

now when it prints, it doesnt print into triplets, like when i was using the string reader, but instead prints the while loop.... is there any way to bypass this and have it go to CEHJ's triplet reader class?

thanks

peace

command line?

peace

Use something like the following in a loop:

String triplet = line.substring(pos, pos+3);
pos += 3;

> I saved that String several times to a file - it works just the same

It will not necessarily work from a file.

You don't need to use a BufferedReader. The class i posted handles that. This is the output (from file or String):


ATT
GGC
TCT
TAC
CAC
TTG
TCC
CTC
AAA
ACG
ACC
ACC
CCA
TTG
ACT
GGT
GGC
GAT
TGC
GTC
GAC
GGA
(ignoring stop code)

right i implemented that but where do i input the file?

thanks

peace

public static void main(String[] args) {

      try {
            java.util.Set stopCodes = new java.util.HashSet();
            stopCodes.add("TAA");
            stopCodes.add("TGA");
            stopCodes.add("TAG");


            String triplets = "ATTGGCTCTTACCACTTGTCCCTCAAAACGACCACCCCATTGACTGGTGGCGATTGCGTCGACGGATAG";

            //TripletReader tr = new TripletReader(new StringReader(triplets));
            TripletReader tr = new TripletReader(new FileReader(args[0]));
            String code = null;
            while((code = tr.readNextCode()) != null) {
                  System.out.println(stopCodes.contains(code)? "(ignoring stop code)" : code);
            }
            tr.close();
            }
            catch(Exception e) {
                  e.printStackTrace();
            }
}

Pass it on the command line

> The class i posted handles that.

It doesn't handle it, it only supports single lines.

sorry i'm having a programming block... by command line do u mean the interactions pane?

or in the actual program?

thanks

peace

>>It doesn't handle it, it only supports single lines.

Why do you need lines in a file of codes? You don't - they just waste space


>>by command line do u mean the interactions pane?

java YourProgram yourcodefile.txt

>>do u mean the interactions pane?

If you are using some kind of IDE, you'll need to find out how to pass command line parameters. This is essential in a general sense too

> Why do you need lines in a file of codes? You don't - they just waste space

Cause thats the requirement ?????

> > Why do you need lines in a file of codes? You don't - they just waste space

So basically your saying first translate the file into one line, and then parse it.
A lot easier to just do one translation, instead of two.

1. Either the codes are in a file of their own
use FileReader

or

2. they're a line in a properties file

use StringReader

Which is it?

yeah that didnt work... got a filenotfound exception... it is in the same folder as the program folder....

thanks

peace

Use your BufferedReader code, and substring() to iterate thu the tokens.
Let me know if you need more details.

Can you clarify where exactly you want those code Strings?

well the DNA code is in a file that looks like this:

>ABC-1 [organism=Saccharomyces cerevisiae][strain=ABC][clone=1]
ATTGCGTTATGGAAATTCGAAACTGCCAAATACTATGTCACCATCATTGA
TGCACCTGGACACAGAGATTTCATCAAGAACATGATCACTGGTACTT
>ABC-2 [organism=Saccharomyces cerevisiae][strain=ABC][clone=2]
GATATTGCTTTATGGAAATTCGAAACTGCCAAATACTATGTCACCATCAT
TGATGCACCTGGACACAGAAATTTCATCAAGAACATGATCACTGGTACTT
>ABC-3 [organism=Saccharomyces cerevisiae][strain=ABC][clone=3]
ATTGCTTTATGGAAATTCGAAACTGCCAAATACTATGTTATGATGCACCT
GGACACAGAGATTTCATCAAAAACATGATCACTGGTACTT
>Xlae28S [organism=Xenopus laevis]
GGCTCGTGCGTCGATGAAGAACGCAGCAC

which didnt work so i tried copying just the strings into a separate txt file and it still didnt work...

i have a properties object but that is holding my translation table

AGT=A, etc

please hang in there with me, almost done with this project :)

thanks

peace

objects: yeah some more clarification would be nice, implementation wise

CEHJ:well basically i want to pass in the DNA code strings and have it translated through the tanslation table...

thanks

peace

> objects: yeah some more clarification would be nice, implementation wise

Let me know when you decide you need to use a BufferedReader and I'll walk u thru it.

I was under the impression that you just had the codes. It does work if the file only contains code triplets. You'd have to change the approach for that kind of file

ok... any ideas as to how i should change my approach?  ;)

thanks

peace

>  It does work if the file only contains code triplets.

It won't even work on the example file given (except of course if you edit it as you are suggesting)

> ok... any ideas as to how i should change my approach?  ;)

yes, use the approach I've been suggesting all thread ;)

ok if i HAVE to!  heheh j/k

umm still dont fully understand objects' method though (you are talking about the links u posted in the beginning right?)

i mean where should i put the buffered reader etc?

thanks

peace

If that's the file you have, then you should use a BufferedReader

yeah i am usings BufferedReader, but where should I put the BufferedReader?

and how should i parse the code file into the translated form?

thanks

peace

Now that CEHJ has finally understood that his suggestion would not work, heres a summary of the relavant pieces I've mentioned:

http://www.javaalmanac.com/egs/java.io/ReadLinesFromFile.html
http://www.javaalmanac.com/egs/java.util/Props.html
http://www.javaalmanac.com/egs/java.util/GetSetProps.html

Use something like the following in a loop to parse each line:

String triplet = line.substring(pos, pos+3);
pos += 3;

The startsWith() method of the String class will also be useful for determine which lines do and don't contain triplets.

ok so basically i have to get rid of CEHJ's above posted TripletReader and instead implement the loop?

where should i place the loop?

thanks

peace

also what are pos? IE what type?

thanks

peace

> i have to get rid of CEHJ's above posted TripletReader and instead implement the loop?

Yes its only good for handling single lines

> where should i place the loop?

inside the loop that is reading lines from file
ie. read a line from file and process it if it contains triplets

> also what are pos? IE what type?

an int

http://java.sun.com/j2se/1.4.2/docs/api/java/lang/String.html#substring(int, int)

ok so i tried that and it looks like this:

try{
      BufferedReader reader = new BufferedReader(new FileReader(inFile));
       line = reader.readLine();
      //System.out.println("The line : \"" +line+ "\"");
      while(line!=null){
        String triplet = line.substring(pos, pos+3);
        pos += 3;

but when i try running it, i get a string index outofbounds error (at runtime)

thanks

peace

you need a loop to read each line, not just the first line (see the example I posted earlier)
As a 1st step get it jusrt reading each line, then we can work on parsiung the lines read.

sorry which example you posted earlier?

thanks

peace

btw, thanks to everyone who contributed!

still not quite sure what to do though....

thanks

peace

oh also for when i parse through the DNA code file... is there a way that i can start at a specified code...

IE: @ ATG start the loop

thanks

peace

http://www.javaalmanac.com/egs/java.io/ReadLinesFromFile.html

well what should i implement in place of  "process" in the while loop?

thanks

peace

a loop to parse the line that was read.

ic but i dont really know how to do this...

any "tips" on how i can go about doing this?

thanks

peace

be something like:

int pos = 0;
while (pos<line.length()-3)
{
   String triplet = line.substring(pos, pos+3);
   System.out.println(triplet);
}

ok so then this goes in here:

  public void separate(File inFile){
    int pos = 0;
    while (pos<line.length()-3)
    {
      String triplet = line.substring(pos, pos+3);
      System.out.println(triplet);
    }
    //line = reader.readLine();
  }
--------
right?

thanks man!  ur a life saver!

peace

no it goes inside you loop that is reading file
ie. that loop is applied to each line (that contains triplets) read from file

it works but its only reading the first 2 characters and then printing that over and over again

peace

I'd suggest first getting the code to read the file line by line working.
then once that is done worry about parsing each line

YES!!  thank you so much!  now it parsing everything fine!

just need to figure out how to get it to read the properties object

thanks again!!

peace

http://www.javaalmanac.com/egs/java.util/GetSetProps.html

is there any way that instead of "a.b" i can have it set to key.value or something?

thanks

peace

"a.b" is the key, it can be whatever you like

In your case its the triplet (from memory)

but i mean that is the general form right?

how can i set it so that a = AGT, ATC, etc and b = A,T,R etc

and then "new value" = A,T,R etc

thank you!

peace

Sorry, not following what you mean

What does your properties file look like, and what do you want to get from it?

properties file looks like:
GCT=A
GCC=A
GCA=A
GCG=A

CGT=R
CGC=R
CGA=R
-----------

and i would like to have it so that the input file (my DNA code file, which is parsed into triplets) can be "decoded" according to the properties file:

ie: dna code: GCTGCCGCAGCGCGT -> AAAAR

thanks

peace

sorry been gone for a while...

objects: what is the variable line?  and where should i declare it?

thanks

peace

line is a String variable containing the last line read from file

so should i in the class decalre:

private String line;

?

thanks