[Biojava-l] biojava demo code

Xuefeng Bruce Ling ling@ling.ipc.net
Thu, 25 Jan 2001 15:57:55 -0800 

--=====================_29342512==_.ALT
Content-Type: text/plain; charset="us-ascii"

Hi,

Initially I tried to use CVS and biojava-live to build according to the README,
it just did not work.  See in my previous email.

I poked around the biojava FTP site and I found that they have jan 12 and 19
jar file and the source code of jan 19. It turns out that the jan 19 code is
with biojava-live directory.  Personally I think that is not good software
release style.  If you want to release the jar file at certain release, then
the code has to be in sync with that.  Another thing is that for the software
release, can you put the win zip version there as well?  Not everyone programs
on unix especially for JAVA.

I tried that and to my disappointment, some of the demon code works and some
cannot even be compiled.  These are the errors when I tried to compile the code
under demos/seq.  Some of the domon code works under that directory and the
ones show below doesn't work.

See the following errors coming: 

javac *java
count = 0, total = 25
count = 0, total = 25
SimpleAssemblyTest.java:19: Class seq.SimpleSequence not found.
        Sequence seq1 = new SimpleSequence(dna1, "seq1", "seq1",
                            ^
SimpleAssemblyTest.java:23: Class seq.SimpleSequence not found.
        Sequence seq2 = new SimpleSequence(dna2, "seq2", "seq2",
                            ^
TestGenbank.java:18: Incompatible type for declaration. Explicit cast needed to
convert org.biojava.bio.seq.io.GenbankFormat to
org.biojava.bio.seq.io.SequenceFormat.
      SequenceFormat gFormat = new GenbankFormat();
                     ^
TestGenbank.java:21: Class seq.SimpleSequenceFactory not found.
      SequenceFactory sFact = new SimpleSequenceFactory();
                                  ^
TestGenbank.java:25: Incompatible type for constructor. Explicit cast needed to
convert org.biojava.bio.seq.SequenceFactory to
org.biojava.bio.seq.io.SequenceBuilderFactory.
        new StreamReader(gReader, gFormat, rParser, sFact);
                                                    ^
TestTranslation.java:11: Can't access class
org.biojava.bio.symbol.ReverseSymbolList. Class or interface must be public, in
same package, or an accessible member class.
      SymbolList rev = new ReverseSymbolList(randomSeq);
                           ^
TestTranslation.java:13: Can't access class
org.biojava.bio.symbol.WindowedSymbolList. Class or interface must be public,
in same package, or an accessible member class.
      SymbolList codons = new WindowedSymbolList(revComp, 3);
                              ^
TestTranslation.java:14: Can't access class
org.biojava.bio.symbol.TranslatedSymbolList. Class or interface must be public,
in same package, or an accessible member class.
      SymbolList translation = new TranslatedSymbolList(
                                   ^
TestTranslation.java:16: Undefined variable or class name: GeneticCode
        GeneticCode.UNIVERSAL
        ^
9 errors


--=====================_29342512==_.ALT
Content-Type: text/html; charset="us-ascii"

<html>
Hi,<br>
<br>
Initially I tried to use CVS and biojava-live to build according to the
README, it just did not work.&nbsp; See in my previous email.<br>
<br>
I poked around the biojava FTP site and I found that they have jan 12 and
19 jar file and the source code of jan 19. It turns out that the jan 19
code is with biojava-live directory.&nbsp; Personally I think that is not
good software release style.&nbsp; If you want to release the jar file at
certain release, then the code has to be in sync with that.&nbsp; Another
thing is that for the software release, can you put the win zip version
there as well?&nbsp; Not everyone programs on unix especially for
JAVA.<br>
<br>
I tried that and to my disappointment, some of the demon code works and
some cannot even be compiled.&nbsp; These are the errors when I tried to
compile the code under demos/seq.&nbsp; Some of the domon code works
under that directory and the ones show below doesn't work.<br>
<br>
See the following errors coming: <br>
<br>
<font face="Courier New, Courier">javac *java<br>
count = 0, total = 25<br>
count = 0, total = 25<br>
SimpleAssemblyTest.java:19: Class seq.SimpleSequence not found.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Sequence seq1 = new
SimpleSequence(dna1, &quot;seq1&quot;, &quot;seq1&quot;,<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;
^<br>
SimpleAssemblyTest.java:23: Class seq.SimpleSequence not found.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Sequence seq2 = new
SimpleSequence(dna2, &quot;seq2&quot;, &quot;seq2&quot;,<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;
^<br>
TestGenbank.java:18: Incompatible type for declaration. Explicit cast
needed to convert org.biojava.bio.seq.io.GenbankFormat to
org.biojava.bio.seq.io.SequenceFormat.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SequenceFormat gFormat = new
GenbankFormat();<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
^<br>
TestGenbank.java:21: Class seq.SimpleSequenceFactory not found.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SequenceFactory sFact = new
SimpleSequenceFactory();<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;
^<br>
TestGenbank.java:25: Incompatible type for constructor. Explicit cast
needed to convert org.biojava.bio.seq.SequenceFactory to
org.biojava.bio.seq.io.SequenceBuilderFactory.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; new StreamReader(gReader,
gFormat, rParser, sFact);<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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
^<br>
TestTranslation.java:11: Can't access class
org.biojava.bio.symbol.ReverseSymbolList. Class or interface must be
public, in same package, or an accessible member class.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SymbolList rev = new
ReverseSymbolList(randomSeq);<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;
^<br>
TestTranslation.java:13: Can't access class
org.biojava.bio.symbol.WindowedSymbolList. Class or interface must be
public, in same package, or an accessible member class.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SymbolList codons = new
WindowedSymbolList(revComp, 3);<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;
^<br>
TestTranslation.java:14: Can't access class
org.biojava.bio.symbol.TranslatedSymbolList. Class or interface must be
public, in same package, or an accessible member class.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SymbolList translation = new
TranslatedSymbolList(<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;&nbsp;
^<br>
TestTranslation.java:16: Undefined variable or class name:
GeneticCode<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; GeneticCode.UNIVERSAL<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ^<br>
9 errors<br>
<br>
</font></html>

--=====================_29342512==_.ALT--