; SeqPup.prefs 
; default preferences for application

[version=5]
; increase version # each time this is edited to get app to update
; prefs.  You can add a new [version=6] section at the end and
; any new values after that will replace version=5 values.

[general]
gOptionIsOn=1
gShortFolder=0



[windows]
fgLockText=1
fgUseColor=1
fgWinRect=211 87 781 389
gRichDocRect=10 34 500 404

[fonts]
gNameFontName=Times
gNameFontSize=10
gNameStyle=0
gBaseFontName=Courier
gBaseFontSize=10
gBaseStyle=0
gIndexFontName=Times
gIndexFontSize=9
gIndexStyle=0
gSeqFontName=Courier
gSeqFontSize=10
gSeqStyle=2
gTextFontName=Courier
gTextFontSize=10

[seqprint]
gNameLeft=0
gNameRight=1
gIndexLeft=1
gIndexRight=1
gIndexTop=1
gColored=0
gShowComplement=1
gThreeLetAA=0
gShowAA1=1
gShowAA2=1
gShowAA3=1
gShowCompAA1=1
gShowCompAA2=1
gShowCompAA3=1
gOnlyORF=0
gBasesPerLine=60

[remap]
gShowAllZymes=1
gShowCutpoints=1
gShowNoncutters=1
gShowExcludedCutters=1
gREMinCuts=1
gREMaxCuts=999



[version=6]
; updates for release 0.4i, aug'95

[seqdoc]
gWriteMasks=1
gMinCommonPercent=70
fgStartDoc=1
fgViewMode=0
fgSire=SPup


[version=11]
; updates for release 0.5a, jan'96

[paths]
; can use UNIX standard path descriptions here. DCLAP converts to local OS
; e.g., /root/path/to/somewhere   -- full path from a root disk
; or,  relative/path/to/somewhere -- relative path from app folder
; okay to use local OS conventions, but avoid "/" in path if not UNIX
temp=
tables=tables
apps=apps
help=help

[data]
codon=tables:codon.table
renzyme=tables:renzyme.table
color=tables:color.table

[menus]
menubar=file,edit,seq,inet,childapp,window
file=File,New/N,Open.../O,Close/W,-,Save/S,Save As...,-,Print,Help/H,Quit/Q
edit=Edit,Undo/U,-,Cut/X,Copy/C,Paste/V,Clear,-,Select All/A
seq=Sequence
inet=Internet
apps=ChildApp
window=Windows

[apps]
clustal=ClustalW Multiple align...
cap=CAP Contig assembly...
fastdnaml=FastDNAml...
lsadt=DeSoete LSADTree...
drawtree=Draw unrooted Tree...
drawgram=Draw Cladogram...
autoseq=AutoSeq base calling...
dnaml
;dnaml=Phylip DNAML...

[autoseq]
form=$apps:autoseq.html

[drawgram]
form=$apps:drawgram.html

[drawtree]
form=$apps:drawtree.html

[lsadt]
form=$apps:lsadt.html

[clustal]
form=$apps:clustalw.html

[cap]
form=$apps:cap2.html

[fastdnaml]
form=$apps:fastdnaml.html

[dnaml]
form=$apps:dnaml.html


[version=63]
; new for version 0.6c, june 1996

[apps]
autoseq=AutoSeq base calling...

[autoseq]
form=$apps:autoseq.html

[inet]
bop_title=[BOP servers]
gcg_map=GCG Map...
gcg_blast=GCG Blast...
gcg_pepstruc=GCG Peptide Struct...
gcg_motifs=GCG Motifs...
gcg_fasta=GCG FastA...
gcg_prime=GCG Prime...
gcg_mfold=GCG MFold...
gcg_pileup=GCG Pileup...

[gcg_map]
form=$apps:gcg_map.html
[gcg_blast]
form=$apps:gcg_blast.html
[gcg_pepstruc]
form=$apps:gcg_pepstruc.html
[gcg_motifs]
form=$apps:gcg_motifs.html
[gcg_fasta]
form=$apps:gcg_fasta.html
[gcg_prime]
form=$apps:gcg_prime.html
[gcg_mfold]
form=$apps:gcg_mfold.html
[gcg_pileup]
form=$apps:gcg_pileup.html

[version=64]
; cap software is not 'cap2' but cap version 1 w/ a few changes
; new cap2 by X. Huang is a different program (and not freely available)
[cap]
form=$apps:cap.html