Notes for compiling Java source code from Don Gilbert,  August 2001

These include flybase/eugenes  programs of gnomap, Gene Ontology and Controlled Vocabulary
hierarchical data browser with gene and image links,
gene data reporters (fbreportj, eugenes report), readseq, seqpup and related.

These are specific to Readseq, but you can substitute the relevant
program package, using codewarrior projects (in XML) which specify the necessary
source code.


Find readseq source at 
  ftp://iubio.bio.indiana.edu/molbio/readseq/java/ 
as readseq-source.zip 
Find java source for the full set of flybase and eugenes programs at
  ftp://iubio.bio.indiana.edu/molbio/java/source/ 
as fbjava-source.zip
 
Find java source for SeqPup, Phylodendron and related at same folder
as  dclapjava-src.zip

For fbjava-source, find codewarrior project documents in the
  codewar.prjs/ folder

How to compile Readseq with Metrowerks Codewarrior

    1.Unzip/unjar readseq-source.zip 
      (unzip -a readseq-source.zip to convert newlines) 
    2.Package contents are currently: 
            rez/ -- Resource, properties files 
            rseq.mcp.xml -- Metrowerks Codewarrior project definition 
            src/ -- Java source code 
            ibm-xml4j-min.jar -- basic XML SAX parser 
            orgxml.jar -- XML class definitions 
    3.Import rseq.mcp.xml as the Codewarrior project. 

How to compile Readseq with Sun javac

    1.Follow step 1 above. 
    2.Find in src/split4javac.pl - a Perl program to convert
    multi-public java sources to single-public-named-same sources
    as required by javac.
    3.Run split4javac.pl as: 

          perl src/split4javac.pl -i rseq.mcp.xml -a src/split4javac.addlist -o splits/ \
             >& log.split

          -- This reads project sources from .xml and creates output .java in split4/ 
          It can also be run from MacPerl/BBEdit

    4.Compile with javac on unix as 

        find splits -name "*.java" -exec \
          javac -classpath ibm-xml4j-min.jar:orgxml.jar -sourcepath splits -d splits {} \;

        -- if there are javac errors related to missing source classes, add the missing
           class to the src/split4javac.addlist and rerun split4javac.pl
           
        -- test as
         java -cp .:splits:ibm-xml4j-min.jar:orgxml.jar run