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Diffstat (limited to 'Master/texmf-dist/tex/latex/texshade/texshade.def')
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1 files changed, 167 insertions, 0 deletions
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.def b/Master/texmf-dist/tex/latex/texshade/texshade.def new file mode 100644 index 00000000000..be63e0f7c69 --- /dev/null +++ b/Master/texmf-dist/tex/latex/texshade/texshade.def @@ -0,0 +1,167 @@ + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%% %%%%% +%%%%% Default parameter settings for the LaTeX ``TeXshade'' package %%%%% +%%%%% %%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%% %%%%% +%%%%% This example file contains all standard settings of the TeXshade %%%%% +%%%%% package. It can be used as a template for the creation of perso- %%%%% +%%%%% nal parameter files. All TeXshade user commands are allowed and %%%%% +%%%%% functional when specified here. %%%%% +%%%%% %%%%% +%%%%% To activate these settings for your alignment load this file by %%%%% +%%%%% naming it as optional parameter at the beginning of the texshade %%%%% +%%%%% environment, e.g. %%%%% +%%%%% %%%%% +%%%%% \begin{texshade}[myparameterfile]{alignmentfile} %%%%% +%%%%% . %%%%% +%%%%% . %%%%% +%%%%% \end{texshade} %%%%% +%%%%% %%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +\shadingmode{identical} % Shade identical residues only +\shadingcolors{blues} % Select the blue color scheme for shading +\constoallseqs % Calculate consensus considering all seqs +\threshold{50} % Consensus threshold percentage is 50 +\residuesperline{999} % As many residues as possible per line +\numberingwidth{9999} % Assign space for 4 digit numbering +\charstretch{1.15} % Stretch character width 1.15fold +\linestretch{1} % Do not stretch lines +\gapchar{.} % . is printed in sequence gaps +\gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt +\gapcolors{Black}{White} % Gap symbols appear `Black on White' +\numberingcolor{Black} % Numbering color is `Black' +\shownumbering{left} % Show sequence numbering on the left +\namescolor{Black} % Names' color is `Black' +\shownames{right} % Show sequence names on the right +\consensuscolors{Black}{White} % All consensus symbols/letters + {Black}{White} % appear `Black on White' + {Black}{White} % +\showconsensus{bottom} % Show consensus line at bottom with +\defconsensus{{}}{*}{!} % Blank =no match; * =match; ! =all match +\rulercolor{Black} % Ruler's color is `Black' +\hideruler % Do not show the ruler +\showleadinggaps % Show gap symbols before sequence start +\rulersteps{10} % Ruler ticks every 10 residues +\legendcolor{Black} % Legend text color is `Black' +\hidelegend % Do not show the legend +\alignment{center} % Center alignment on page +\medsepline % Medium height if separation line is on +\medblockskip % Medium skip between sequence blocks +\flexblockspace % Use optimized space between blocks +\featurerule{0.5ex} % Set feature rule thickness to 1/5 ex +\bargraphstretch{1} % Do not stretch bars in feature graphs +\colorscalestretch{1} % Do not stretch color scales in features +\backtranstext{horizontal} % Horizontal triplets in feature texts +\backtranslabel{alternating} % Alternating triplets in feature styles +\setfamily{residues}{tt} % Use typewriter family for residues +\setseries{residues}{md} % Use normal series for residues +\setshape {residues}{up} % Use upright shape for residues +\setsize {residues}{normalsize} % Use normal size for residues +\setfamily{numbering}{tt} % Use typewriter family for numbering +\setseries{numbering}{md} % Use normal series for numbering +\setshape {numbering}{up} % Use upright shape for numbering +\setsize {numbering}{normalsize} % Use normal size for numbering +\setfamily{names}{tt} % Use typewriter family for names +\setseries{names}{md} % Use normal series for names +\setshape {names}{up} % Use upright shape for names +\setsize {names}{normalsize} % Use normal size for names +\setfamily{features}{rm} % Use roman family for feature texts +\setseries{features}{md} % Use normal series for feature texts +\setshape {features}{it} % Use italics shape for feature texts +\setsize {features}{normalsize} % Use normal size for feature texts +\setfamily{legend}{tt} % Use typewriter family for legend texts +\setseries{legend}{md} % Use normal series for legend texts +\setshape {legend}{up} % Use upright shape for legend texts +\setsize {legend}{normalsize} % Use normal size for legend texts +\tintdefault{medium} % Use medium tint intensity +\emphdefault{it} % Use italics to emphasize regions +\showonPHDsec{alpha,beta} % Show helices and strands (PHD input) +\showonPHDtopo{internal,external,TM}% Show int., ext. and TM's (PHD input) +\showonHMMTOP{TM} % Show TM's (not int/ext on HMMTOP input) +\showonSTRIDE{alpha,3-10,pi,beta} % Show helices and strands (STRIDE input) +\showonDSSP{alpha,3-10,pi,beta} % Show helices and strands (DSSP input) +\secondcolumnDSSP % Use numbering from 2. column in DSSP +\appearance{PHDtopo}{internal} % \ + {bottom}{'-'} % \ + {int.\ \Alphacount} % | +\appearance{PHDtopo}{external} % | + {top}{,-,} % | + {ext.\ \Alphacount} % | +\appearance{PHDtopo}{TM}{top} % | + {box[LightGray]:TM\numcount}{} % | +\appearance{HMMTOP}{internal} % | + {bottom}{---} % | + {int.\ \Alphacount} % | +\appearance{HMMTOP}{external} % | + {top}{---} % | + {ext.\ \Alphacount} % | +\appearance{HMMTOP}{TM}{top} % | + {helix}{TM\numcount} % | +\appearance{PHDsec}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | +\appearance{PHDsec}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{STRIDE}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | Definitions for the appearance of +\appearance{STRIDE}{3-10}{top} % \ + {fill:$\circ$}{3$_{10}$} % > secondary structures included from| +\appearance{STRIDE}{pi} % / + {top}{---}{$\pi$} % | PHD-, STRIDE-, or DSSP-files. +\appearance{STRIDE}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{STRIDE}{bridge} % | + {top}{fill:$\uparrow$}{} % | +\appearance{STRIDE}{turn} % | + {top}{,-,}{turn} % | +\appearance{DSSP}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | +\appearance{DSSP}{3-10}{top} % | + {fill:$\circ$}{3$_{10}$} % | +\appearance{DSSP}{pi} % | + {top}{---}{$\pi$} % | +\appearance{DSSP}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{DSSP}{bridge} % | + {top}{fill:$\uparrow$}{} % | +\appearance{DSSP}{turn} % | + {top}{,-,}{turn} % | +\appearance{DSSP}{bend}{top} % / + {fill:$\diamond$}{} % / + +\pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ} % Amino acid grouping due to similarity + +\pepsims{F}{YW} % Y and W are similar to F +\pepsims{Y}{WF} % W and F are similar to Y +\pepsims{W}{YF} % Y and F are similar to W + +\pepsims{I}{LVM} % L, V and M are similar to I +\pepsims{L}{VMI} % V, M and I are similar to L +\pepsims{V}{MIL} % M, I and L are similar to V + +\pepsims{R}{KH} % K and H are similar to R +\pepsims{K}{HR} % H and R are similar to K +\pepsims{H}{RK} % R and K are similar to H + +\pepsims{A}{GS} % G and S are similar to A +\pepsims{G}{A} % A (but not S) is similar to G + +\pepsims{S}{TA} % T and A are similar to S +\pepsims{T}{S} % S (but not A) is similar to T + +\pepsims{D}{EN} % E and N (but not Q) are similar to D +\pepsims{E}{DQ} % D and Q (but not N) are similar to E +\pepsims{N}{QD} % Q and D (but not E) are similar to N +\pepsims{Q}{NE} % N and E (but not D) are similar to Q + +\DNAgroups{GAR,CTY} % Nucleotide grouping due to similarity + +\DNAsims{A}{GR} % G and R are similar to A +\DNAsims{G}{AR} % A and R are similar to G +\DNAsims{R}{AG} % A and G are similar to R + +\DNAsims{C}{TY} % T and Y are similar to C +\DNAsims{T}{CY} % C and Y are similar to T +\DNAsims{Y}{CT} % C and T are similar to Y |