[Biojava-l] help for installation

Fri, 22 Mar 2002 10:18:19 +1100

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Dear Biojava friends

I have donwnloaded the three files biojava-1.21jar, bytecode-0.90.jar and 
xerces.ar on my windows2000 machine. I put them in the 
directory  c:\biojava. I set up the class path 
CLASSPATH=C:\biojava.jar;C:\xerces.jar;C:\bytecode.jar;.using control panel 
, system, user variables.
when I compile a demo progra GCContent.java , I get compile err,

biojava/GCContent.java [3:1] package org.biojava.bio.seq does not exist
import org.biojava.bio.seq.*;
^
biojava/GCContent.java [4:1] package org.biojava.bio.seq.io does not exist
import org.biojava.bio.seq.io.*;
^
biojava/GCContent.java [18:1] cannot resolve symbol
symbol  : class SequenceIterator
location: class GCContent
         SequenceIterator stream = SeqIOTools.readFastaDNA(br);
         ^
biojava/GCContent.java [18:1] cannot resolve symbol
symbol  : variable SeqIOTools
location: class GCContent
         SequenceIterator stream = SeqIOTools.readFastaDNA(br);
                                   ^
biojava/GCContent.java [23:1] cannot resolve symbol
symbol  : class Sequence
location: class GCContent
             Sequence seq = stream.nextSequence();
             ^
biojava/GCContent.java [26:1] cannot resolve symbol
symbol  : class Symbol
location: class GCContent
                 Symbol sym = seq.symbolAt(pos);
                 ^
biojava/GCContent.java [27:1] cannot resolve symbol
symbol  : variable DNATools
location: class GCContent
                 if (sym == DNATools.g() || sym == DNATools.c())
                            ^
biojava/GCContent.java [27:1] cannot resolve symbol
symbol  : variable DNATools
location: class GCContent
                 if (sym == DNATools.g() || sym == DNATools.c())
                                                   ^
9 errors
Errors compiling GCContent.

I would like to get some help to solve the problem. I am newcomer in java

Dr Yizhou Chen
Room 546 Gunn Building(B19)
Centre for Advanced Technologies in Animal Genetics and Reproduction 
(Reprogen)
School of Veterinary Science
University of Sydney
Sydney NSW 2006
Phone 61 2 9351 3154
Fax 61 2 9351 2114
email: yizhouc@vetsci.usyd.edu.eu
http://www.usyd.edu.au/vetfac/reprogen/
xerces
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<html>
Dear Biojava friends 
I have donwnloaded the three files biojava-1.21jar, bytecode-0.90.jar and
xerces.ar on my windows2000 machine. I put them in the directory&nbsp;
c:\biojava. I set up the class path
CLASSPATH=C:\biojava.jar;C:\xerces.jar;C:\bytecode.jar;.using control
panel , system, user variables. 
when I compile a demo progra GCContent.java , I get compile err,
 
biojava/GCContent.java [3:1] package org.biojava.bio.seq does not
exist 
import org.biojava.bio.seq.*; 
^ 
biojava/GCContent.java [4:1] package org.biojava.bio.seq.io does not
exist 
import org.biojava.bio.seq.io.*; 
^ 
biojava/GCContent.java [18:1] cannot resolve symbol 
symbol&nbsp; : class SequenceIterator&nbsp; 
location: class GCContent 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SequenceIterator stream =
SeqIOTools.readFastaDNA(br); 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ^ 
biojava/GCContent.java [18:1] cannot resolve symbol 
symbol&nbsp; : variable SeqIOTools&nbsp; 
location: class GCContent 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SequenceIterator stream =
SeqIOTools.readFastaDNA(br); 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
^ 
biojava/GCContent.java [23:1] cannot resolve symbol 
symbol&nbsp; : class Sequence&nbsp; 
location: class GCContent 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Sequence seq = stream.nextSequence(); 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
^ 
biojava/GCContent.java [26:1] cannot resolve symbol 
symbol&nbsp; : class Symbol&nbsp; 
location: class GCContent 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Symbol sym = seq.symbolAt(pos); 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
^ 
biojava/GCContent.java [27:1] cannot resolve symbol 
symbol&nbsp; : variable DNATools&nbsp; 
location: class GCContent 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
if (sym == DNATools.g() || sym == DNATools.c()) 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
^ 
biojava/GCContent.java [27:1] cannot resolve symbol 
symbol&nbsp; : variable DNATools&nbsp; 
location: class GCContent 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
if (sym == DNATools.g() || sym == DNATools.c()) 
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
^ 
9 errors 
Errors compiling GCContent. 
 
I would like to get some help to solve the problem. I am newcomer in
java 
 
<x-sigsep></x-sigsep>
Dr Yizhou Chen 
Room 546 Gunn Building(B19) 
Centre for Advanced Technologies in Animal Genetics and Reproduction
(Reprogen) 
School of Veterinary Science 
University of Sydney 
Sydney NSW 2006 
Phone 61 2 9351 3154 
Fax 61 2 9351 2114 
email: yizhouc@vetsci.usyd.edu.eu 
<a href="http://www.usyd.edu.au/vetfac/reprogen/" eudora="autourl">http://www.usyd.edu.au/vetfac/reprogen/</a> 
xerces</html>

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