[Biojava-l] (no subject)
Ramana
ramana@galainfotek.com
Fri, 17 Aug 2001 11:25:11 +0530
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Hello,
This is ramana from GalaInfotek
Now i am able to run the programmes.....
But i have another doubt .
In Following code:
in this code we must pass the Protein fasta file ,if i send DNA fasta =
file
it raise bioexception b'cause we are calling
SeqIOTools.readFastaProtein().
My problem is i want send a file wheather it is DNA fasta
or Protein fasta ,i want find the file type (DNA or Protein or GenBank) =
and
find the alphabet.
I found a method read(BufferedReader br) in AlignmentFormat if =
implementut
this interface raises a error ,could u plz tell me which classes i want =
to
import and solution....
bye
RAMANA
GalaInfotek
------------------------
import java.io.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
public class TestingSymbol
{
public static void main(String[] args)
{
try
{
if (args.length !=3D 1)
throw new Exception("usage: java GCContent filename.fa");
String fileName =3D args[0];
System.out.println("FileName"+fileName);
BufferedReader br=3Dnew BufferedReader(new
FileReader(fileName));
SequenceIterator str=3DSeqIOTools.readFastaProtein(br);
System.out.println("after sequence iterator");
while(str.hasNext())
{System.out.println("inside while");
Sequence seq=3Dstr.nextSequence();
int at=3D0;
for(int i=3D1;i<seq.length();i++)
{
System.out.println(seq.getAlphabet());
}
}
}catch(Exception ee){System.out.println("Error"+ee);}
}
}
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<DIV><FONT face=3DArial size=3D2>Hello,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>This is ramana from GalaInfotek<BR>Now =
i am able to=20
run the programmes.....<BR>But i have another doubt .<BR> In =
Following=20
code:<BR>in this code we must pass the Protein fasta file ,if i send DNA =
fasta=20
file<BR>it raise bioexception b'cause we are=20
calling<BR>SeqIOTools.readFastaProtein().<BR>My problem is i want =
send a=20
file wheather it is DNA fasta<BR>or Protein fasta ,i want find the file =
type=20
(DNA or Protein or GenBank) and<BR>find the alphabet.<BR>I found a =
method=20
read(BufferedReader br) in AlignmentFormat if implementut<BR>this=20
interface raises a error ,could u plz tell me which classes i want =
to<BR>import and=20
solution....<BR>bye<BR>RAMANA<BR>GalaInfotek<BR>------------------------<=
BR>import=20
java.io.*;<BR>import org.biojava.bio.symbol.*;<BR>import=20
org.biojava.bio.seq.*;<BR>import org.biojava.bio.seq.io.*;<BR>public =
class=20
TestingSymbol<BR>{<BR> public static void main(String[]=20
args)<BR> {<BR> try<BR> {<BR> if =
(args.length=20
!=3D 1)<BR> throw new Exception("usage: java GCContent =
filename.fa");<BR> String fileName =
=3D=20
args[0];<BR> =20
System.out.println("FileName"+fileName);<BR>  =
; =20
BufferedReader br=3Dnew=20
BufferedReader(new<BR>FileReader(fileName));<BR> &=
nbsp; =20
SequenceIterator =
str=3DSeqIOTools.readFastaProtein(br);<BR> =20
System.out.println("after sequence iterator");<BR> =20
while(str.hasNext())<BR> {System.out.println("inside=20
while");<BR> Sequence=20
seq=3Dstr.nextSequence();<BR> int=20
at=3D0;<BR> for(int=20
i=3D1;i<seq.length();i++)<BR> =20
{<BR> =20
System.out.println(seq.getAlphabet());<BR><BR> =20
}<BR><BR> =
}<BR> =20
}catch(Exception=20
ee){System.out.println("Error"+ee);}<BR> }<BR>}<BR><BR>-------------=
-------------<BR></DIV></FONT></BODY></HTML>
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