[Biojava-l] Running a java program on mac

[Elaine Forbes]

Hi there-

I am a geneticist who would like to run a java program to analyse some 
genomic sequences. So far i have downloaded Biojava 1.3 and my mac already 
has Java 1.4.2. Within 'Terminal' i can set my path so that it is looking in 
the directory which has my genomic seq files and the java program. I believe 
that firstly i have to compile the program therefore i am using the command 
javac followed by the name of the prog (ATcounter.java). unfortunately i am 
getting error messages (script attached below). Do i need to move my biojava 
folder to somewhere else. I have tried putting it in the same directory as 
the java prog- no difference.

If anyone can help or suggest anything it would be much appreciated....

biosc171:~/desktop/documents/projects/transcript-slip-programs elaineforbes$ 
javac ATcounter.java
ATcounter.java:17: package org.biojava.bio does not exist
import org.biojava.bio.*;
^
ATcounter.java:18: package org.biojava.bio.seq does not exist
import org.biojava.bio.seq.*;
^
ATcounter.java:19: package org.biojava.bio.seq.io does not exist
import org.biojava.bio.seq.io.*;
^
ATcounter.java:20: package org.biojava.bio.symbol does not exist
import org.biojava.bio.symbol.*;
^
ATcounter.java:124: cannot resolve symbol
symbol  : class Symbol
location: class ATcounter
  public void count(int[] theArray, Symbol sym){
                                    ^
ATcounter.java:157: cannot resolve symbol
symbol  : class Sequence
location: class ATcounter
  private Sequence seq;
          ^
ATcounter.java:158: cannot resolve symbol
symbol  : class Symbol
location: class ATcounter
  private Symbol current;
          ^
ATcounter.java:61: cannot resolve symbol
symbol  : class SequenceIterator
location: class ATcounter
          SequenceIterator si = SeqIOTools.readFastaDNA(br);
          ^
ATcounter.java:61: cannot resolve symbol
symbol  : variable SeqIOTools
location: class ATcounter
          SequenceIterator si = SeqIOTools.readFastaDNA(br);
                                ^
ATcounter.java:65: cannot resolve symbol
symbol  : class SequenceIterator
location: class ATcounter
          SequenceIterator fnaSi = SeqIOTools.readFastaDNA(fnaBr);
          ^
ATcounter.java:65: cannot resolve symbol
symbol  : variable SeqIOTools
location: class ATcounter
          SequenceIterator fnaSi = SeqIOTools.readFastaDNA(fnaBr);
                                   ^
ATcounter.java:79: cannot resolve symbol
symbol  : variable DNATools
location: class ATcounter
              count(ffnAarray, DNATools.a());
                               ^
ATcounter.java:80: cannot resolve symbol
symbol  : variable DNATools
location: class ATcounter
              count(ffnTarray, DNATools.t());
                               ^
ATcounter.java:91: cannot resolve symbol
symbol  : variable DNATools
location: class ATcounter
              count(fnaAarray, DNATools.a());
                               ^
ATcounter.java:92: cannot resolve symbol
symbol  : variable DNATools
location: class ATcounter
              count(fnaTarray, DNATools.t());
                               ^
15 errors


Thanks

Weelainy