In article <36CC2FD1.D7A98FF0 at Genetik.Uni-Bielefeld.DE> Frank-Joerg Vorhoelter <Frank.Vorhoelter at Genetik.Uni-Bielefeld.DE> writes:
>I am using Staden 1998. Every time I start a Contig Edior, I am changing
>some settings the same way. I want to see the Reading Quality and the
>Consensus Quality. And usually I want to Set Default Confidences. I
>guess there is some way to do this automatically. But I could not find
>out how.
You've spotted one of our weak points!
Yes, it can be done, although not with a single button click.
Almost everything in the editor is user-configurable in a permanent
manner, including several things which aren't possible from the GUI
(eg colours).
The key is to look at the $STADENROOT/tables/gaprc file, pick out the
fields you want to modify, and to write them back to your own ~/.gaprc
file. The next time Gap4 starts up it will read that file and override
the system defaults.
For simplicity, I've listed the full lot here. (NB: from the 1999.0
distribution, the 1998.0 may have a few minor differences)
James
set_def CONTIG_EDITOR.LIST_CONFIDENCE.ONLY_NUM_ERRS 1
set_def CONTIG_EDITOR.CUTOFF_COLOUR grey70
set_def CONTIG_EDITOR.BASE_COLOUR black
set_def CONTIG_EDITOR.AUTO_DISPLAY_TRACES 0
set_def CONTIG_EDITOR.AUTO_SAVE 0
set_def CONTIG_EDITOR.AMINO_ACID_MODE 0
set_def CONTIG_EDITOR.TEMPLATE_GROUP 0
set_def CONTIG_EDITOR.SHOW_QUALITY 0
set_def CONTIG_EDITOR.SHOW_CONSENSUS_QUALITY 0
set_def CONTIG_EDITOR.FONT {sheet_font}
set_def CONTIG_EDITOR.FONT_MB {menu_font}
set_def CONTIG_EDITOR.MAX_HEIGHT 30
set_def CONTIG_EDITOR.NAMES_WIDTH 23
set_def CONTIG_EDITOR.SE_INS_ANY 0
set_def CONTIG_EDITOR.SE_DEL_READ 0
set_def CONTIG_EDITOR.SE_DEL_DASH_CONS 1
set_def CONTIG_EDITOR.SE_DEL_ANY_CONS 0
set_def CONTIG_EDITOR.SE_REPLACE_CONS 0
set_def CONTIG_EDITOR.SE_READ_SHIFT 0
set_def CONTIG_EDITOR.SE_TRANS_ANY 0
set_def CONTIG_EDITOR.SE_UPPERCASE 1
set_def CONTIG_EDITOR.SE_EDIT_MODE 0
set_def CONTIG_EDITOR.SE_SET.1 {0 0 0 1 0 0 0 0 1 1}
set_def CONTIG_EDITOR.SE_SET.2 {1 1 1 1 0 1 1 0 1 1}
set_def CONTIG_EDITOR.INSERTION_CONFIDENCE 100
set_def CONTIG_EDITOR.REPLACE_CONFIDENCE 100
set_def CONTIG_EDITOR.TRACE_DIFF 0
set_def CONTIG_EDITOR.TRACE_CONS_MATCH 1
set_def CONTIG_EDITOR.TRACE_CONS_SELECT 1
set_def CONTIG_EDITOR.TRACE_DIFF_ALGORITHM 0
set_def CONTIG_EDITOR.TRACE_DIFF_SCALE 0
set_def CONTIG_EDITOR.TRACE_LOCK 1
set_def CONTIG_EDITOR.DISAGREEMENTS 0
set_def CONTIG_EDITOR.DISAGREE_MODE 1
set_def CONTIG_EDITOR.DISAGREE_CASE 1
set_def CONTIG_EDITOR.DIFF_COLOUR "#00ac00"
set_def CONTIG_EDITOR.COMPARE_STRANDS 0
set_def CONTIG_EDITOR.SHOW_EDITS 0
set_def CONTIG_EDITOR.EDIT_DEL_COLOUR "red"
set_def CONTIG_EDITOR.EDIT_BASE_COLOUR "#ff9090"
set_def CONTIG_EDITOR.EDIT_PAD_COLOUR "#90ee90"
set_def CONTIG_EDITOR.EDIT_CONF_COLOUR "#6060ff"
set_def CONTIG_EDITOR.QUAL0_COLOUR "#494949"
set_def CONTIG_EDITOR.QUAL1_COLOUR "#696969"
set_def CONTIG_EDITOR.QUAL2_COLOUR "#898989"
set_def CONTIG_EDITOR.QUAL3_COLOUR "#a9a9a9"
set_def CONTIG_EDITOR.QUAL4_COLOUR "#b9b9b9"
set_def CONTIG_EDITOR.QUAL5_COLOUR "#c9c9c9"
set_def CONTIG_EDITOR.QUAL6_COLOUR "#d9d9d9"
set_def CONTIG_EDITOR.QUAL7_COLOUR "#e0e0e0"
set_def CONTIG_EDITOR.QUAL8_COLOUR "#e8e8e8"
set_def CONTIG_EDITOR.QUAL9_COLOUR "#f0f0f0"
set_def CONTIG_EDITOR.QUAL_IGNORE "#ff5050"
set_def CONTIG_EDITOR.SEARCH.POSITION_DEF ""
set_def CONTIG_EDITOR.SEARCH.ANNO_DEF ""
set_def CONTIG_EDITOR.SEARCH.SEQUENCE_DEF ""
set_def CONTIG_EDITOR.SEARCH.CONSQUALITY_DEF 10
set_def CONTIG_EDITOR.SEARCH.FILE_DEF ""
set_def CONTIG_EDITOR.SEARCH.NAME_DEF ""
set_def CONTIG_EDITOR.SEARCH.DISCREPANCY_DEF 20
set_def CONTIG_EDITOR.STATUS_STRAND 0
set_def CONTIG_EDITOR.STATUS_FRAME1P 0
set_def CONTIG_EDITOR.STATUS_FRAME2P 0
set_def CONTIG_EDITOR.STATUS_FRAME3P 0
set_def CONTIG_EDITOR.STATUS_FRAME1M 0
set_def CONTIG_EDITOR.STATUS_FRAME2M 0
set_def CONTIG_EDITOR.STATUS_FRAME3M 0
set_def TRACE_DISPLAY.CUTOFF_COLOUR grey70
set_def TRACE_DISPLAY.BACKGROUND $normal_bg
set_def TRACE_DISPLAY.XMAG 150
set_def TRACE_DISPLAY.DIRECTION bottom
set_def TRACE_DISPLAY.TRACE_HEIGHT 150
set_def TRACE_DISPLAY.NUM_TRACES 5
set_def CONTIG_EDITOR.AUTO_DISPLAY_TRACES_CONF "+ - +d -d"
set_def CONTIG_EDITOR.TAGS {*}
--
James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/
