Hi Biojava,
I am entirely new to Biojava and have limited Java experience (C is more
my thing), and so this is almost certainly a dumb question, but I cannot
seem to find an answer in the online docs. I am running debian 4 linux
and have:
java version "1.6.0_06"
Java(TM) SE Runtime Environment (build 1.6.0_06-b02)
Java HotSpot(TM) Server VM (build 10.0-b22, mixed mode)
I have downloaded the biojava code, unpacked it, and set the CLASSPATH
in bashrc :
BIOJAVA_BASE=/home/peter/bin/biojava/biojava-live_1.6
export CLASSPATH=${BIOJAVA_BASE}/biojava.jar
export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/commons-cli.jar
export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/commons-collections-2.1.jar
export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/bytecode.jar
export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/commons-dbcp-1.1.jar
export CLASSPATH=${CLASSPATH}:${BIOJAVA_BASE}/commons-pool-1.1.jar
export CLASSPATH=${CLASSPATH}:.
This also goes through without error from the command line. However,
when I try to compile one of the test programs as instructed on the page:
http://biojava.org/wiki/BioJava:GetStarted
[EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ javac seq/TestEmbl.java
I get a bunch of errors, apparently javac cannot find the imports it needs.
(see bottom of this mail).
I would greatly appreciate any tips how to get started here!
Thanks, Peter
[EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ javac seq/TestEmbl.java
seq/TestEmbl.java:25: package org.biojavax does not exist
import org.biojavax.Namespace;
^
seq/TestEmbl.java:26: package org.biojavax does not exist
import org.biojavax.RichObjectFactory;
^
seq/TestEmbl.java:27: package org.biojavax.bio.seq does not exist
import org.biojavax.bio.seq.RichSequence;
^
seq/TestEmbl.java:28: package org.biojavax.bio.seq does not exist
import org.biojavax.bio.seq.RichSequenceIterator;
^
seq/TestEmbl.java:48: cannot find symbol
symbol : class Namespace
location: class seq.TestEmbl
Namespace ns = RichObjectFactory.getDefaultNamespace();
^
seq/TestEmbl.java:48: cannot find symbol
symbol : variable RichObjectFactory
location: class seq.TestEmbl
Namespace ns = RichObjectFactory.getDefaultNamespace();
^
seq/TestEmbl.java:50: cannot find symbol
symbol : class RichSequenceIterator
location: class seq.TestEmbl
RichSequenceIterator seqI =
^
seq/TestEmbl.java:51: package RichSequence does not exist
RichSequence.IOTools.readEMBLDNA(br, ns);
^
seq/TestEmbl.java:54: cannot find symbol
symbol : class RichSequence
location: class seq.TestEmbl
RichSequence seq = seqI.nextRichSequence();
^
seq/TestEmbl.java:57: package RichSequence does not exist
RichSequence.IOTools.writeEMBL(System.out, seq, ns);
^
10 errors
[EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ java -version
java version "1.6.0_06"
Java(TM) SE Runtime Environment (build 1.6.0_06-b02)
Java HotSpot(TM) Server VM (build 10.0-b22, mixed mode)
[EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$ javac seq/TestEmbl.java
seq/TestEmbl.java:25: package org.biojavax does not exist
import org.biojavax.Namespace;
^
seq/TestEmbl.java:26: package org.biojavax does not exist
import org.biojavax.RichObjectFactory;
^
seq/TestEmbl.java:27: package org.biojavax.bio.seq does not exist
import org.biojavax.bio.seq.RichSequence;
^
seq/TestEmbl.java:28: package org.biojavax.bio.seq does not exist
import org.biojavax.bio.seq.RichSequenceIterator;
^
seq/TestEmbl.java:48: cannot find symbol
symbol : class Namespace
location: class seq.TestEmbl
Namespace ns = RichObjectFactory.getDefaultNamespace();
^
seq/TestEmbl.java:48: cannot find symbol
symbol : variable RichObjectFactory
location: class seq.TestEmbl
Namespace ns = RichObjectFactory.getDefaultNamespace();
^
seq/TestEmbl.java:50: cannot find symbol
symbol : class RichSequenceIterator
location: class seq.TestEmbl
RichSequenceIterator seqI =
^
seq/TestEmbl.java:51: package RichSequence does not exist
RichSequence.IOTools.readEMBLDNA(br, ns);
^
seq/TestEmbl.java:54: cannot find symbol
symbol : class RichSequence
location: class seq.TestEmbl
RichSequence seq = seqI.nextRichSequence();
^
seq/TestEmbl.java:57: package RichSequence does not exist
RichSequence.IOTools.writeEMBL(System.out, seq, ns);
^
10 errors
[EMAIL PROTECTED]:~/bin/biojava/biojava-live_1.6/demos$
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