gera_licht
Nieuwe gebruiker
- Lid geworden
- 8 mrt 2004
- Berichten
- 2
Hoi allemaal,
Ik ben een beginner op het gebied van java. Ik ben bezig met een programmaatje, maar ik krijg een "illegal character: \154". Dit gebeurt vanaf de tweede "/**". Deze fout zit vaak meerdere keren in een zin en ik krijg 100 van deze fouten.
code:
import java.io.*;
import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.symbol.*;
/**
* <p>Program to six-frame translate a nucleotide sequence</p>
*/
public class Hex {
/**
* Call this to get usage info, program terminates after call.
*/
public static void help() {
System.out.println(
"usage: java utils.Hex <file> <format eg fasta> <dna|rna>");
System.exit( -1);
}
public static void main(String[] args) throws Exception{
if (args.length != 3) {
help();
}
BufferedReader br = null;
String format = args[1];
String alpha = args[2];
try {
br = new BufferedReader(new FileReader(args[0]));
SequenceIterator seqi =
(SequenceIterator)SeqIOTools.fileToBiojava(format, alpha, br);
//for each sequence
while(seqi.hasNext()){
Sequence seq = seqi.nextSequence();
//for each frame
for (int i = 0; i < 3; i++) {
SymbolList prot;
Sequence trans;
//take the reading frame
SymbolList syms = seq.subList(
i+1,
seq.length() - (seq.length() - i)%3);
//if it is DNA transcribe it to RNA
if(syms.getAlphabet() == DNATools.getDNA()){
syms = RNATools.transcribe(syms);
}
//output forward translation to STDOUT
prot = RNATools.translate(syms);
trans = SequenceTools.createSequence(prot, "", seq.getName()+ "TranslationFrame: +"+i, Annotation.EMPTY_ANNOTATION);
SeqIOTools.writeFasta(System.out, trans);
//output reverse frame translation to STDOUT
syms = RNATools.reverseComplement(syms);
prot = RNATools.translate(syms);
trans = SequenceTools.createSequence(prot, "", seq.getName() + "TranslationFrame: -" + i, Annotation.EMPTY_ANNOTATION);
SeqIOTools.writeFasta(System.out, trans);
}
}
}
finally {
if(br != null){
br.close();
}
}
}
}
En dit zijn een paar van de fout meldingen:
Hex.java:13: illegal character: \154
/**
^
Hex.java:16: illegal character: \154
public static void help() {
^
Hex.java:17: illegal character: \154
System.out.println(
^
Hex.java:17: illegal character: \154
System.out.println(
^
Hex.java:17: illegal character: \154
System.out.println(
^
Hex.java:18: illegal character: \154
"usage: java utils.Hex <file> <format eg fasta> <dna|rna>");
^
Hex.java:18: illegal character: \154
"usage: java utils.Hex <file> <format eg fasta> <dna|rna>");
^
Hex.java:18: illegal character: \154
"usage: java utils.Hex <file> <format eg fasta> <dna|rna>");
^
Graag jullie hulp hierbij. Ik gebruik trouwens kwrite van linux.
Gera
Ik ben een beginner op het gebied van java. Ik ben bezig met een programmaatje, maar ik krijg een "illegal character: \154". Dit gebeurt vanaf de tweede "/**". Deze fout zit vaak meerdere keren in een zin en ik krijg 100 van deze fouten.
code:
import java.io.*;
import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.symbol.*;
/**
* <p>Program to six-frame translate a nucleotide sequence</p>
*/
public class Hex {
/**
* Call this to get usage info, program terminates after call.
*/
public static void help() {
System.out.println(
"usage: java utils.Hex <file> <format eg fasta> <dna|rna>");
System.exit( -1);
}
public static void main(String[] args) throws Exception{
if (args.length != 3) {
help();
}
BufferedReader br = null;
String format = args[1];
String alpha = args[2];
try {
br = new BufferedReader(new FileReader(args[0]));
SequenceIterator seqi =
(SequenceIterator)SeqIOTools.fileToBiojava(format, alpha, br);
//for each sequence
while(seqi.hasNext()){
Sequence seq = seqi.nextSequence();
//for each frame
for (int i = 0; i < 3; i++) {
SymbolList prot;
Sequence trans;
//take the reading frame
SymbolList syms = seq.subList(
i+1,
seq.length() - (seq.length() - i)%3);
//if it is DNA transcribe it to RNA
if(syms.getAlphabet() == DNATools.getDNA()){
syms = RNATools.transcribe(syms);
}
//output forward translation to STDOUT
prot = RNATools.translate(syms);
trans = SequenceTools.createSequence(prot, "", seq.getName()+ "TranslationFrame: +"+i, Annotation.EMPTY_ANNOTATION);
SeqIOTools.writeFasta(System.out, trans);
//output reverse frame translation to STDOUT
syms = RNATools.reverseComplement(syms);
prot = RNATools.translate(syms);
trans = SequenceTools.createSequence(prot, "", seq.getName() + "TranslationFrame: -" + i, Annotation.EMPTY_ANNOTATION);
SeqIOTools.writeFasta(System.out, trans);
}
}
}
finally {
if(br != null){
br.close();
}
}
}
}
En dit zijn een paar van de fout meldingen:
Hex.java:13: illegal character: \154
/**
^
Hex.java:16: illegal character: \154
public static void help() {
^
Hex.java:17: illegal character: \154
System.out.println(
^
Hex.java:17: illegal character: \154
System.out.println(
^
Hex.java:17: illegal character: \154
System.out.println(
^
Hex.java:18: illegal character: \154
"usage: java utils.Hex <file> <format eg fasta> <dna|rna>");
^
Hex.java:18: illegal character: \154
"usage: java utils.Hex <file> <format eg fasta> <dna|rna>");
^
Hex.java:18: illegal character: \154
"usage: java utils.Hex <file> <format eg fasta> <dna|rna>");
^
Graag jullie hulp hierbij. Ik gebruik trouwens kwrite van linux.
Gera