staden-common 2.0.0+b11-2 / usr / share / staden / etc / spinrc

This file is indexed.

/usr/share/staden/etc/spinrc is in staden-common 2.0.0+b11-2.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below. 

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#-----------------------------------------------------------------------------
# Packages required
#-----------------------------------------------------------------------------
load_package tk_utils
load_package spin
load_package sip
load_package nip

package require tablelist

#-----------------------------------------------------------------------------
# Menus
#-----------------------------------------------------------------------------
set_menu seq_menu
add_menu File				1 0 left
add_menu View				1 0 left
add_menu Options			1 0 left
add_menu Sequences			1 0 left
add_menu Statistics			1 0 left
add_menu "Translation"			1 0 left
add_menu "Search"			1 0 left
#add_menu Lists				1 0 left
add_menu Comparison			1 0 left
add_menu Help				1 0 right

# The menu state bit enable/disable patterns are as follows
# Bit 0: Startup and no sequences loaded  1
# Bit 1: Busy mode                        2
# Bit 2: Sequences loaded  		  4

add_cascade     {File.Load sequence}                    1 0
add_command     {File.Load sequence.Simple}             1 0 {CreateSimpleBrowser}
add_command     {File.Load sequence.Personal search}    1 0 {CreatePersonalBrowser}
add_command	{File.Save}				4 4 {file_save_d}
add_command	{File.Change directory}			1 0 {ChangeDir}
add_command	{File.Sequence manager}			4 4 {SequenceManager}
#if {$tcl_platform(platform) == "unix"} {
#    add_command	{File.Send to}				4 4 {SendTo}
#}
add_command	{File.Exit}				1 0 {seq_exit}

add_command	{View.Results manager}			4 4 {rasterResultsManager {show_help spin {SPIN-Result-Manager}}}

#add_command	{View.Sequence display}		4 4 {SeqedDisplay 1 \[get_active_seq_id\]}

add_command	{View.Sequence display}		4 4 {SeqedDisplay_d}

add_command	{Options.Change protein score matrix} 		1 0 \
			{ChangeScoreMatrix}
add_command	{Options.Set protein alignment symbols} 	1 0 \
			{SetAlignmentSymbols}
add_command	{Options.Configure matches}	1 0 {ConfigMatches}

add_check	{Options.Hide duplicate matches} 1 0 rem_dup {set_remove_dup \$rem_dup}
add_command	{Options.Set fonts}		1 0 {SetFonts}
if { $tcl_platform(platform) != "windows" } {
  add_command	{Options.Colours}		1 0 {ConfigureColours}
  #add_command	{Options.Sequence library}	1 0 {SetSequenceLibrary}
}

add_command	{Sequences.Horizonal}		4 4 {set_horizontal_d}
add_command	{Sequences.Vertical}		4 4 {set_vertical_d}
add_command	{Sequences.Set range}		4 4 {set_range_d}
add_command     {Sequences.Copy}                4 4 {copy_range_d}
add_command	{Sequences.Complement}		4 4 {complement_d}
add_command	{Sequences.Interconvert t and u} 4 4 {interconvert_d}
add_command     {Sequences.Translate} 		4 4 {translate_d}
add_command	{Sequences.Scramble}		4 4 {scramble_d}
add_cascade     {Sequences.Sequence type}     4 4
add_command     {Sequences.Sequence type.Linear}  4 4 {set_structure_d 0}
add_command     {Sequences.Sequence type.Circular} 4 4 {set_structure_d 1}
add_command	{Sequences.Rotate}		4 4 {rotate_d}
add_separator	Sequences.S1
add_command	{Sequences.Save}		4 4 {file_save_d}
add_command	{Sequences.Delete}		4 4 {file_delete_d}

add_command	{Statistics.Count sequence composition} 4 4 {CountBaseComp}
add_command	{Statistics.Count dinucleotide frequencies} 4 4 {CountDinucFreq}
add_command	{Statistics.Plot base composition} 4 4 {PlotBaseComp}

add_command	{Translation.Set genetic code}      4 4 {SetGeneticCode}
add_command	{Translation.Translate} 4 4 {NipTranslate}
add_cascade	{Translation.Find open reading frames}  4 4
add_command 	{Translation.Calculate and write codon table to disk} 4 4 {CodonUsage}

add_command 	{Translation.Find open reading frames.write as feature table} 4 4 {TranslateFT}
add_command 	{Translation.Find open reading frames.write protein as fasta file} 4 4 {TranslateFasta}

add_cascade	{Search.Protein genes}	 	4 4
add_command	{Search.tRNA genes}             4 4 {trnaSearch}
add_command	{Search.Search for string (DNA)}	4 4 {NipStringSearch}
add_command	{Search.Restriction enzyme map} 4 4 {NipRestrictionEnzymeDialogue}

add_command	{Search.Protein genes.codon pref}    4 4 {CodonPref}
add_command	{Search.Protein genes.author test}   4 4 {AuthorTest}
add_command	{Search.Protein genes.base bias}     4 4 {BaseBias}

add_command 	{Search.Plot start codons} 4 4 {NipStartCodons}
add_command 	{Search.Plot stop codons} 4 4 {NipStopCodons}

add_command 	{Search.Search for splice junctions} 4 4 {SpliceSearch}
add_command	{Search.Search using weight matrix (DNA)}  4 4 {NipWtMatrixSearch}

add_command	{Lists.Edit}			1 2 {EditListDialog}
add_command	{Lists.Create}			1 2 {CreateListDialog}
add_command	{Lists.Delete}			1 2 {DeleteListDialog}
add_command	{Lists.Copy}			1 2 {CopyListDialog}
add_command	{Lists.Load}			1 2 {LoadListDialog}
add_command	{Lists.Save}			1 2 {SaveListDialog}
add_command	{Lists.Print}			1 2 {PrintListDialog}

add_command	{Comparison.Find similar spans}	 4 4 {CompareSpans}
add_command	{Comparison.Find matching words} 4 4 {SipIdentities}
add_command	{Comparison.Find best diagonals} 4 4 {QuickScan}
add_command	{Comparison.Align sequences}	 4 4 {AlignSeqs}
add_command     {Comparison.Local alignment}     4 4 {SimAlign}

add_command	{Help.Contents}		1 0 {show_help spin Contents}
add_command	{Help.Introduction}	1 0 {show_help spin SPIN-Introduction}
add_command	{Help.Output Window}	1 0 {show_help interface {UI-Output}}
add_separator	{Help.S1}
add_command	{Help.Index}		1 0 {show_help spin Index}

#-----------------------------------------------------------------------------
# Global variables
#-----------------------------------------------------------------------------
set_def OUTPUT_SCROLL		1
set_def GENETIC_CODE_DIR	$env(STADTABL)/gcodes
set_def GENETIC_CODE		code_1

set_def SEQ.WIN 		.seq
set_def SEQ_WIN_WIDTH           7  

set_def SEQ.CURSOR.LINE_WIDTH   2

set_def SEQ_DISP.WIN            .sequence_pair_display
set_def SEQ_DISP.PLOT_WIDTH     80

set_def GRAPH.CURSOR.SENSITIVE    5
set_def GRAPH.RASTER.BORDERWIDTH  2

set_def DOT.CURSOR.SENSITIVE    5
set_def DOT.RASTER.BORDERWIDTH  2

set_def   CURSOR.COLOUR.0	"#0000ff"; #blue
set_def   CURSOR.COLOUR.1	"#8b8b00"; #yellow4 
set_def   CURSOR.COLOUR.2	"#ff0000"; #red
set_def   CURSOR.COLOUR.3	"#228b22"; #forestgreen
set_def   CURSOR.COLOUR.4	"#5f9ea0"; #cadetblue
set_def   CURSOR.COLOUR.5	"#4b0082"; #indigo
set_def   CURSOR.COLOUR.6	"#a52a2a"; #brown
set_def   CURSOR.COLOUR.7	"#ffa500"; #orange
set_def   CURSOR.COLOUR.8	"#00c0c0"; #turquoise(ish)
set_def   CURSOR.COLOUR.9	"#d02090"; #violet red

set_def   RASTER.COLOUR.0	"#0000ff"; #blue
set_def   RASTER.COLOUR.1	"#8b8b00"; #yellow4 
set_def   RASTER.COLOUR.2	"#ff0000"; #red
set_def   RASTER.COLOUR.3	"#228b22"; #forestgreen
set_def   RASTER.COLOUR.4	"#5f9ea0"; #cadetblue
set_def   RASTER.COLOUR.5	"#4b0082"; #indigo
set_def   RASTER.COLOUR.6	"#a52a2a"; #brown
set_def   RASTER.COLOUR.7	"#ffa500"; #orange
set_def   RASTER.COLOUR.8	"#00c0c0"; #turquoise(ish)
set_def   RASTER.COLOUR.9	"#d02090"; #violet red

#-----------------------------------------------------------------------------
# Local variables
#-----------------------------------------------------------------------------
set_def SEQED.AMINO_ACID_MODE		0

#-----------------------------------------------------------------------------
# SEQED
#-----------------------------------------------------------------------------
#save
set_def SEQED.SAVE.RANGE.NAME		"Range"
set_def SEQED.SAVE.LINE_LEN.NAME	"Line length"
set_def SEQED.SAVE.LINE_LEN.VALUE	60
set_def SEQED.SAVE.FILENAME.NAME	"File name"
set_def SEQED.SAVE.FILENAME.VALUE	""

set_def SEQED.SEARCH.DIRECTION.NAME	Direction
set_def SEQED.SEARCH.DIRECTION.VALUE	1
set_def SEQED.SEARCH.DIRECTION.BUTTON.1	forward
set_def SEQED.SEARCH.DIRECTION.BUTTON.2	backward
set_def SEQED.SEARCH.MATCH.NAME		"Minimum percent match"
set_def SEQED.SEARCH.MATCH.VALUE	75.0
set_def SEQED.SEARCH.STRAND.NAME	Strand
set_def SEQED.SEARCH.STRAND.VALUE	1
set_def SEQED.SEARCH.STRAND.BUTTON.1	forward
set_def SEQED.SEARCH.STRAND.BUTTON.2	reverse
set_def SEQED.SEARCH.STRING.NAME	"Search string"
set_def SEQED.SEARCH.STRING.VALUE	""
set_def SEQED.SEARCH.USE_IUB.NAME               "Search algorithm"
set_def SEQED.SEARCH.USE_IUB.VALUE              1
set_def SEQED.SEARCH.USE_IUB.BUTTON1.NAME       "iub codes"
set_def SEQED.SEARCH.USE_IUB.BUTTON2.NAME       literal
set_def SEQED.SEARCH.USE_IUB.BUTTON1.VALUE      1
set_def SEQED.SEARCH.USE_IUB.BUTTON2.VALUE      0

# For the file loading dialogues
set_def SIMPLE.WIN              .simple
set_def PERSONAL.WIN            .personal

#-----------------------------------------------------------------------------
#emboss definitions
#-----------------------------------------------------------------------------

set_def EMBOSS.MAX_MENU_ITEMS 40
set_def EMBOSS.L_WIDTH  0

set_def EMBOSS.RASTER.GRAPH.TITLE       "graph"
set_def EMBOSS.RASTER.GRAPH.PLOT_HEIGHT 200
set_def EMBOSS.RASTER.GRAPH.PLOT_WIDTH  500
set_def EMBOSS.RULER.GRAPH.PLOT_HEIGHT   40
set_def EMBOSS.RULER.GRAPH.PLOT_WIDTH   100
set_def EMBOSS.RASTER.SINGLE.PLOT_HEIGHT 60

set_def EMBOSS.RASTER.DOT.TITLE "dot plot"
set_def EMBOSS.RASTER.DOT.PLOT_HEIGHT 400
set_def EMBOSS.RASTER.DOT.PLOT_WIDTH  400
set_def EMBOSS.RULER.DOT.PLOT_HEIGHT   40
set_def EMBOSS.RULER.DOT.PLOT_WIDTH   100

set_def EMBOSS.TYPE     ""

load_package %L/spin_emboss	 {}	 spin_emboss 0

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