add help for rna_structure and output_Varna

Scripts/RNAstructure/rna_structure.m

@@ -2,8 +2,32 @@
 % [structure, bpp, SHAPE_out ] = rna_structure( sequence, area_shape, offset, seqpos, EX, NUM_BOOTSTRAP, cmd...
 %                                               temperature, shape_intercept, shape_slope, maxdist);
 %
-% make sure to set your path in get_exe_dir.m
+% Run RNAstructure data-drive secstr prediction with bootstrapping.
+% **Make sure to set your path in get_exe_dir.m
 %
+% [Input]
+% sequence          Required            RNA sequence
+% area_shape        Optional            1D bonus data, same length as sequence
+% offset            Optional            Sequence numbering offset
+% seqpos            Optional            Sequence position used to filter area_shape
+% EX                Optional            2D bonus data, same dimension as sequence
+% NUM_BOOTSTRAP     Optional            Number of bootstrap runs, in addition to run with original data. Default 0 (no bootstrap).
+% cmd_pk            Optional            RNAstructure executable flag: 0 for Fold, 1 for ShapeKnot. Default 0.
+% area_dms          Optional            1D bonus data for DMS
+% tempertature      Optional            Folding temperature, use Celcius. Default 24.
+% shape_intercept   Optional            1D bonus SHAPE intercept, default based on RNAstructure version
+% shape_slope       Optional            1D bonus SHAPE slope, default based on RNAstructrue version
+% maxdist           Optional            Max pairing distance, default none
+%
+% [Output]
+% structure         Prediction result secstr (using original data, no bootstrap)
+% bpp               Base-pairing probability matrix, summarized from bootstraping runs into percentages.
+% SHAPE_out         Filtered 1D bonus data
+%
+% by T47, 2015
+%
+
+if nargin == 0;  help( mfilename ); return; end;
 
 if ~exist( 'area_shape','var' ); area_shape = []; end;
 if ~exist( 'area_dms','var' ); area_dms = []; end;

Scripts/VARNA/output_varna_html.m

@@ -1,7 +1,39 @@
-function  [special_base_pairs, special_colors] = output_varna_html(varna_file, sequence, display_structure, native_structure, modeled_structure, offset, mutpos, crystpos, shape, bpp, color_mode)
-
-if ~exist('mutpos','var') || isempty(mutpos);  mutpos = [1:length(sequence)] + offset; end;
-if ~exist('crystpos','var') || isempty(crystpos);  crystpos = [1:length(sequence)] + offset; end;
+function [special_base_pairs, special_colors] = output_varna_html(varna_file, sequence, display_structure, native_structure, modeled_structure, offset, mutpos, crystpos, shape, bpp, color_mode)
+% [special_base_pairs, special_colors] = output_varna_html( ...
+%                               varna_file, sequence, display_structure, native_structure, modeled_structure, 
+%                               offset, mutpos, crystpos, shape, bpp, color_mode); 
+%
+% Generate HTML file with VARNA applet for RNA secstr visualziation.
+% **Make sure to set your path in get_varna.m
+%
+% [Input]
+% varna_file            Required            HTML file name
+% sequence              Required            RNA sequence for display
+% display_structure     Required            RNA secstr for display
+% native_structure      Optional            Reference/native secstr used for secstr comparison.
+% modeled_structure     Optional            Predicted/new secstr used for secstr comparison.
+% offset                Optional            Sequence numbering offset, default 0.
+% mutpos                Optional            [?]
+% crystpos              Optional            [?]
+% shape                 Optional            SHAPE reactivity profile for nucleotide coloring, default none.
+% bpp                   Optional            Base-pairing probability matrix for helix-wise confidence score.
+% color_mode            Optional            Secstr comparison line color set, default 1.
+%
+% [Output]
+% special_base_pairs    Index of base-pairs that differ between native_structure and modeled_structure
+% special_colors        Secstr comparison color set
+%
+% by T47, 2013-2015
+%
+
+if nargin == 0;  help( mfilename ); return; end;
+
+if ~exist('native_structure','var') || isempty(native_structure); native_structure = display_structure; end;
+if ~exist('modeled_structure','var') || isempty(modeled_structure); modeled_structure = display_structure; end;
+
+if ~exist('offset','var') || isempty(offset); offset = 0; end;
+if ~exist('mutpos','var') || isempty(mutpos); mutpos = [1:length(sequence)] + offset; end;
+if ~exist('crystpos','var') || isempty(crystpos); crystpos = [1:length(sequence)] + offset; end;
 if ~exist('color_mode', 'var') || isempty(color_mode); color_mode = 1; end;
 
 mutpos = sort(mutpos);