[Biojava-l] blast parser alignment middle line

Hello! Is there a way to get the middle line of an alignment that I parse out of the blast output? In the example below, it would be the "S++VGTR..." line. In the Alignment of the SeqSimilaritySearchSubHit, I only find a Sequence entry for Query and Sbjct. Query: 2 SFEVGTRCWYPHKELGWIGAEVIKNEFN

[Biojava-l] Blast Parser oddity

Hi! I am currently evaluating the XML output of NCBI Blast, and the ability of BioJava to parse this output. For this purpose, I have done twice the identical blastp and blastn (i.e. the same sequence against the same database with the same parameters), one time with the standard output, and o

[Biojava-l] cvs.biojava.org down?

Hi! I can't access the host cvs.biojava.org via ping and http. Maybe the machine is down? Christian ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

[Biojava-l] Missing ProcessTools class

Hi! I just found that the class org.biojava.utils.ProcessTools is not part of the source and binary distribution of BioJava 1.3.1, but they are part of the biojava-live CVS. Are they missing by accident? By the way, what is the recommended way to compile BioJava 1.3.1, since biojava-1.3.1.tar.