home *** CD-ROM | disk | FTP | other *** search
/ Celestin Apprentice 4 / Apprentice-Release4.iso / Source Code / Libraries / DCLAP 4j / SeqPups / SeqPup.prefs < prev   
Encoding:
Windows Setup INFormation  |  1995-12-17  |  2.8 KB  |  147 lines  |  [TEXT/R*ch]
  1. ; SeqPup.prefs 
  2. ; default preferences for application
  3.  
  4. [version=5]
  5. ; increase version # each time this is edited to get app to update
  6. ; prefs.  You can add a new [version=6] section at the end and
  7. ; any new values after that will replace version=5 values.
  8.  
  9. [general]
  10. gOptionIsOn=1
  11. gShortFolder=0
  12.  
  13. [paths]
  14. temp=
  15. tables=tables
  16. apps=apps
  17. help=help
  18.  
  19. [data]
  20. codon=tables:codon.table
  21. renzyme=tables:renzyme.table
  22. color=tables:color.table
  23.  
  24. [menus]
  25. menubar=file,edit,seq,inet,childapp,window
  26. file=File,New/N,Open.../O,Close/W,-,Save/S,Save As...,-,Print,Help/H,Quit/Q
  27. edit=Edit,Undo/U,-,Cut/X,Copy/C,Paste/V,Clear,-,Select All/A
  28. seq=Sequence
  29. inet=Internet
  30. childapp=ChildApp
  31. window=Windows
  32.  
  33. [apps]
  34. clustal=ClustalW Multiple align...
  35. cap=CAP Contig assembly...
  36. fastdnaml=FastDNAml...
  37. ;dnaml=Phylip DNAML...
  38.  
  39. [clustal]
  40. desc=A multiple sequence alignment application
  41. path=$apps:clustalw
  42. help=$apps:clustalw.doc
  43. ;cmd=/infile=$temp:clustal.inseq /outfile=$temp:clustal.outseq /output=gcg /align
  44. cmd=/infile=clustal.inseq /outfile=clustal.outseq /output=gcg /align
  45. infile=$apps:clustal.inseq
  46. seqformat=nbrf
  47. minseq=2
  48. outfile1=$apps:clustal.outseq    biosequence/msf
  49. outfile2=$apps:clustal.dnd    biotree/newick
  50.  
  51. [cap]
  52. desc=A gel contig assembly application
  53. path=$apps:cap2
  54. help=$apps:cap2.doc
  55. ;cmd=$temp:cap.inseq $temp:cap.outseq 20 85
  56. cmd=cap.inseq cap.outseq 20 85
  57. infile=$apps:cap.inseq
  58. seqformat=fasta
  59. minseq=2
  60. outfile1=$apps:cap.outseq    biosequence/fasta
  61. dlog1=input name=minoverlap value="20" title="Min. number bases overlap"
  62. dlog2=input name=pctmatch value="85" title="Percent match"
  63.  
  64. [fastdnaml]
  65. desc=A faster DNA max likelihood phylogeny estimator
  66. path=$apps:fastDNAml
  67. help=$apps:fastDNAml.doc
  68. cmd=
  69. infile=$apps:infile
  70. seqformat=phylip
  71. minseq=2
  72. outfile1=$apps:outfile    text/plain
  73. outfile2=$apps:checkpoint.0    text/plain
  74.  
  75. [dnaml]
  76. desc=A DNA max likelihood phylogeny estimator, from Phylip
  77. path=$apps:dnaml
  78. help=$apps:dnaml.doc
  79. cmd=< $temp:dnaml.inseq
  80. infile=$temp:dnaml.inseq
  81. seqformat=phylip
  82. minseq=2
  83. outfile1=$apps:outfile    text/plain
  84. outfile2=$apps:treefile    biotree/newick
  85.  
  86. [windows]
  87. fgLockText=1
  88. fgUseColor=1
  89. fgWinRect=211 87 781 389
  90. gRichDocRect=10 34 500 404
  91.  
  92. [fonts]
  93. gNameFontName=Times
  94. gNameFontSize=10
  95. gNameStyle=0
  96. gBaseFontName=Courier
  97. gBaseFontSize=10
  98. gBaseStyle=0
  99. gIndexFontName=Times
  100. gIndexFontSize=9
  101. gIndexStyle=0
  102. gSeqFontName=Courier
  103. gSeqFontSize=10
  104. gSeqStyle=2
  105. gTextFontName=Courier
  106. gTextFontSize=10
  107.  
  108. [seqprint]
  109. gNameLeft=0
  110. gNameRight=1
  111. gIndexLeft=1
  112. gIndexRight=1
  113. gIndexTop=1
  114. gColored=0
  115. gShowComplement=1
  116. gThreeLetAA=0
  117. gShowAA1=1
  118. gShowAA2=1
  119. gShowAA3=1
  120. gShowCompAA1=1
  121. gShowCompAA2=1
  122. gShowCompAA3=1
  123. gOnlyORF=0
  124. gBasesPerLine=60
  125.  
  126. [remap]
  127. gShowAllZymes=1
  128. gShowCutpoints=1
  129. gShowNoncutters=1
  130. gShowExcludedCutters=1
  131. gREMinCuts=1
  132. gREMaxCuts=999
  133.  
  134.  
  135.  
  136. [version=6]
  137. ; updates for release 0.4i, aug'95
  138.  
  139. [seqdoc]
  140. gWriteMasks=1
  141. gMinCommonPercent=70
  142. fgStartDoc=1
  143. fgViewMode=0
  144.  
  145.  
  146.  
  147.