; This file holds the directory information for the java class BioProgramsProgram
; It is read every time the program is run
; It is rewritten every time the user updates the parameters through the GUI's settings panel
; Everything after the semi-colon on each line is ignored by the parser
; key-value pairs have EXACTLY one space between the key and the value
;
; Last updated: 22-Oct-02 18:18:41
;
;
alignEditorInDir d:/genexp; 
blastDatabaseDir d:/genexp/blastdb; 
blastExePath D:/bioPrograms/BLAST/blastall.exe; 
blastFastaFileDir d:/genexp/fasta; 
blastOutDir d:/genexp/blast; 
blastOutfileExt .blst; 
blastParserFilename parserOutfile.sum; 
blastParserInDir d:/genexp/blast; 
blastParserOutDir d:/genexp/parsed; 
blastParserOutfileExt .sum; 
blastTempDbDir d:/genexp/temp; 
blastTempDbFilename tempdb; 
blastTempSeqDir d:/genexp/temp; 
blastTempSeqFilename blast.tmp; 
chromtreeExeDir D:/bioPrograms/chromtree; 
chromtreeInDir d:/genexp; 
chromtreeOutDir d:/genexp/dist; 
chromtreeOutExt .dist; 
clustalExePath D:/bioPrograms/clustalw/clustalw.exe; 
clustalInDir d:/genexp/retSeq; 
clustalOutDir d:/genexp/clustal; 
clustalProfileDir d:/genexp/clustal; 
clustalTempDir d:/genexp/temp; 
clustalTempFilename chrom; 
defaultDir d:/genexp/temp; 
dianaInDir d:/genexp/fasta; 
dianaOutDir d:/genexp/fasta; 
dianaOutfileExt .di_out; 
evolveOutDir d:/genexp; 
fastaLineLength 80; 
fastacmdExePath D:/bioPrograms/BLAST/fastacmd.exe; 
fastacmdTempDir d:/genexp/temp; 
fastacmdTempFilename fastacmd.tmp; 
formatdbPath D:/bioPrograms/BLAST/formatdb.exe; 
genExpDocDir D:/work/java/genExpDocs; 
homolSearchGenomeDir d:/genexp; 
homolSearchHomolOutDir d:/genexp; 
homolSearchOutDir d:/genexp; 
homolSearchOutExt .homol; 
htmlDir d:/genexp/temp/html; 
htmlViewerExePath C:/Program Files/Internet Explorer/IEXPLORE.EXE; 
matrixInDir d:/genexp; 
matrixOutDir d:/genexp; 
phyDocDir D:/bioPrograms/phylip3.6a/doc; 
phyExeDir D:/bioPrograms/phylip3.6a/exe; 
phyInDir d:/genexp; 
phyOutDir d:/genexp; 
phyTempDir d:/genexp/temp; 
prionPartitionInDir d:/genexp; 
prionPartitionOutDir d:/genexp; 
resSearchInDir d:/genexp; 
resSearchOutDir d:/genexp; 
resSearchOutfileExt .resSearch; 
retrieveSeqInDir d:/genexp/retSeq; 
retrieveSeqOutDir d:/genexp/retSeq; 
retrieveSeqOutfileExt .retSeq; 
seqExtractInDir d:/genexp; 
seqExtractOutDir d:/genexp; 
seqExtractOutfileExt .names; 
treesDirInDir d:/genexp; 
treesInDir d:/genexp; 
treesOutDir d:/genexp;