Re: handling gap symbols

Hi Andreas, List,

On 21-05-10 03:56, Andreas Dräger wrote:
> Hi Wim,
>
> Yes, you are absolutely right. The alignment used two different Gap
> Symbols. I do not remember the details on this exactly, because the
> implementation has been massively changed in the mean time. So, if you
> can check out the latest code from the repository, you will find a
> version of the alignment algorithms that does use only one kind of Gap
> Symbol. The old version cannot be changed or further developed anymore,
> sorry. Many changes were necessary to finally ensure that the Alignment
> will be gathered in a useful data structure. I strongly recomment not to
> use the Alignment from the currently available release of BioJava but to
> use the latest version from the SVN repository. You can do an anonymeous
> check out by following the instructions of this web site:
> http://biojava.org/wiki/CVS_to_SVN_Migration

I've checked out the latest code from the git repository, but I'm having 
some trouble getting it to compile properly. I hope this is the right 
place to ask more questions.

My first question is whether I really need all of the modules for this 
simple alignment, or whether I can just stick to one of them (sequence? 
alignment?).

The first problem I'm having to build the full package is a test failing 
in structure (testFilterDuplicateAFPs) and in the das module 
(testUniProtServer, testParseSourcesResponse). Skipping those I also 
found a small file encoding bug (a source file is encoded as ISO-8859-1 
and the compiler is using either the platform encoding or default 
UTF-8), I've attached a small patch for this.

The second problem (after skipping the tests) is apparently a reference 
problem to the core module from DNATools. I keep getting:
.../sequence/sequence-dna/src/main/java/org/biojava3/seq/dna/DNATools.java:[29,31] 
package org.biojava3.core.symbol does not exist

Indeed, the biojava-3 module doesn't contain that package.

thanks for any help,
Wim
-- 
Wim De Smet
http://www.straininfo.net/

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diff --git a/das/src/main/java/org/biojava/bio/program/das/dasalignment/DASException.java b/das/src/main/java/org/biojava/bio/program/das/dasalignment/DASException.java
index 78718d5..9ca87e0 100644
--- a/das/src/main/java/org/biojava/bio/program/das/dasalignment/DASException.java
+++ b/das/src/main/java/org/biojava/bio/program/das/dasalignment/DASException.java
@@ -26,7 +26,7 @@ import org.biojava.bio.BioException;
 /**
  * An exception of one of the DAS classes.
  *
- * @author Andreas Prlic, Thomas Down, Benjamin Schuster-Böckler
+ * @author Andreas Prlic, Thomas Down, Benjamin Schuster-Böckler
  */
 
 public class DASException extends BioException {