Contig Editor: How can I save changed settings

James Bonfield jkb at mrc-lmb.cam.ac.uk
Fri Feb 19 04:56:37 EST 1999


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/



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