378 lines
12 KiB
Mathematica
378 lines
12 KiB
Mathematica
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function baps5(varargin)
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% This is the machine-generated representation of a Handle Graphics object
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% and its children. Note that handle values may change when these objects
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% are re-created. This may cause problems with any callbacks written to
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% depend on the value of the handle at the time the object was saved.
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%
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% To reopen this object, just type the name of the M-file at the MATLAB
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% prompt. The M-file and its associated MAT-file must be on your path.
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% NEW: script version was added. 09.07.2007
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% Script function has been added by Lu Cheng, 11.03.2010
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% The script function is designed for semi-supervised clustering in the
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% trained clustering module, it adopts a codon linkage model for the DNA
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% sequence data
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% The calling command: baps5 -semi script_file
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global PARAMETERS; PARAMETERS = [];
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global SCRIPT_MODE; SCRIPT_MODE = [];
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if nargin == 1 % script version
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readScript(varargin{1});
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return
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else if nargin==2
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%----------------added by Lu Cheng, 11.03.2010
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if isequal(varargin{1},'-semi');
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script_file = varargin{2};
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PARAMETERS = semiReadScript(script_file);
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SCRIPT_MODE = true;
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trainedMix
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SCRIPT_MODE = [];
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PARAMETERS = [];
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else
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disp(cat(2,'Unknown option: ',varargin{1}));
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end
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return
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%---------------------------------------------
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end
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end
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% load baps4
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% Base frame
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h0 = figure('Color',[0.8 0.8 0.8], ...
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'MenuBar','none', ...
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'Position',[364 175 750 500], ...
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'Resize','on', ...
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'Tag','base_figure',...
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'Name','Bayesian Analysis of Population Structure',...
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'NumberTitle','off',...
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'Color',[.7 .9 .7]);
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% File menu
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h1 = uimenu('Parent',h0, ...
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'Label','File', ...
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'Tag','file_menu');
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h2 = uimenu('Parent',h1, ...
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'Label','Load Result', ...
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'Tag','load_menu');
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h3 = uimenu('Parent',h2, ...
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'Callback','baps4cbf load_mixture_menu', ...
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'Label','Mixture result', ...
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'Tag','mixture_menu');
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h3 = uimenu('Parent',h2, ...
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'Callback','baps4cbf load_spatial_menu', ...
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'Label','Spatial mixture result', ...
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'Tag','spatialmixture_menu');
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h3 = uimenu('Parent',h2, ...
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'Callback','baps4cbf load_admixture_menu', ...
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'Label','Admixture result', ...
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'Tag','admixture_menu');
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h2 = uimenu('Parent',h1, ...
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'Enable','on',...
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'Label','Compare Results', ...
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'Tag','compare_menu');
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h3 = uimenu('Parent',h2, ...
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'Callback','baps4cbf compare_menu', ...
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'Label','Mixture results', ...
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'Tag','compare_menu');
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h3 = uimenu('Parent',h2, ...
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'Callback','baps4cbf compare_admix_menu', ...
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'Label','AdMixture results', ...
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'Tag','compare_admix_menu');
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h2 = uimenu('Parent',h1, ...
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'Enable','off',...
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'Callback','baps4cbf close_menu', ...
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'Label','Close Results', ...
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'Tag','close_menu');
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h2 = uimenu('Parent',h1, ...
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'Label','Output File', ...
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'Tag','output_menu');
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h3 = uimenu('Parent',h2, ...
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'Callback','baps4cbf output_menu', ...
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'Label','Set', ...
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'Tag','set_menu');
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h3 = uimenu('Parent',h2, ...
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'Callback','baps4cbf remove_outputfile_menu', ...
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'Label','Remove', ...
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'Tag','remove_menu');
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h2 = uimenu('Parent',h1, ...
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'Callback','baps4cbf exit_menu', ...
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'Label','Exit', ...
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'Tag','exit_menu');
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% Distances menu
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h1 = uimenu('Parent',h0, ...
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'Enable','off',...
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'Label','Distances', ...
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'Tag','distances_menu');
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h2 = uimenu('Parent',h1, ...
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'Callback','baps4cbf calculate_kl', ...
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'Label','KL distance', ...
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'Tag','kl_menu');
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h2 = uimenu('Parent',h1, ...
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'Callback','baps4cbf calculate_nei', ...
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'Label','Nei distance', ...
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'Tag','nei_menu');
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h2 = uimenu('Parent',h1, ...
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'Callback','baps4cbf calculate_hamming', ...
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'Label','Hamming distance', ...
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'Tag','hamming_menu');
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% Graph menu
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h1 = uimenu('Parent',h0, ...
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'Enable','off', ...
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'Label','Graph', ...
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'Tag','graph_menu');
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h2 = uimenu('Parent',h1, ...
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'Enable','off', ...
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'Callback','baps4cbf plot_coordinates_menu', ...
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'Label','Plot Coordinates', ...
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'Tag','plot_coordinates_menu');
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h2 = uimenu('Parent',h1, ...
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'Enable','off', ...
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'Callback','baps4cbf partitio_menu', ...
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'Label','View Partition', ...
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'Tag','partitio_menu');
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h2 = uimenu('Parent',h1, ...
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'Enable','off', ...
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'Callback','baps4cbf admix_menu', ...
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'Label','View Admixture Results', ...
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'Tag','admix_menu');
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h2 = uimenu('Parent',h1, ...
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'Enable','off', ...
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'Callback','baps4cbf likelihood_menu', ...
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'Label','Changes of Log Likelihood', ...
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'Tag','likelihood_menu');
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h2 = uimenu('Parent',h1, ...
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'Enable','off', ...
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'Callback','baps4cbf energy_menu', ...
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'Label','Energy landscape', ...
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'Tag','energy_menu');
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h2 = uimenu('Parent',h1, ...
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'Enable','off', ...
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'Callback','baps4cbf geneflow_menu', ...
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'Label','Plot Gene Flow', ...
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'Tag','geneflow_menu');
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h2 = uimenu('Parent',h1, ...
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'Enable','off', ...
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'Callback','baps4cbf voronoi_menu', ...
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'Label','Voronoi Tessellation', ...
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'Tag','voronoi_menu');
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h2 = uimenu('Parent',h1, ...
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'Enable','off', ...
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'Callback','baps4cbf varmuus_menu', ...
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'Label','Local Uncertainty', ...
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'Tag','varmuus_menu');
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h2 = uimenu('Parent',h1, ...
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'Enable','off', ...
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'Callback','baps4cbf phylogeny_menu', ...
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'Label','Phylogeny', ...
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'Tag','phylogeny_menu');
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h3 = uimenu('Parent',h2, ...
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'Enable','off', ...
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'Callback','baps4cbf upgma_menu',...
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'Label', 'UPGMA', ...
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'Tag','upgma_menu');
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h3 = uimenu('Parent',h2, ...
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'Enable','off', ...
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'Callback','baps4cbf nj_menu',...
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'Label', 'Neighbor-Joining', ...
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'Tag','nj_menu');
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h2 = uimenu('Parent',h1, ...
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'Enable','off', ...
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'Callback','baps4cbf mutationplot_menu', ...
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'Label','Mutation Plot', ...
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'Tag','mutationplot_menu');
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% Tools menu
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h1 = uimenu('Parent',h0, ...
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'Label','Tools', ...
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'Tag','tools_menu');
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h2 = uimenu('Parent',h1, ...
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'Callback','baps4cbf fixk_menu', ...
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'Label','Enable Fixed-K Clustering', ...
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'Tag','fixk_menu', ...
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'Userdata', 0);
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h2 = uimenu('Parent',h1, ...
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'Callback','baps4cbf partitioncompare_menu', ...
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'Label','Partition Compare', ...
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'Tag','partitioncompare_menu', ...
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'Userdata', []);
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h2 = uimenu('Parent',h1, ...
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'Callback','baps4cbf loadfigure_menu', ...
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'Label','Load Figure', ...
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'Tag','loadfigure_menu');
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h2 = uimenu('Parent',h1, ...
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'Callback','baps4cbf changecolor_menu',...
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'Label', 'Change BAPS Color', ...
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'Tag','changecolor_menu');
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% Help menu
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h1 = uimenu('Parent',h0, ...
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'Label','Help', ...
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'Tag','help_menu');
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h2 = uimenu('Parent',h1, ...
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'Callback','baps4cbf helpdoc', ...
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'Enable','on', ...
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'Label','Help contents (doc)', ...
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'Tag','helpman_menu');
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h2 = uimenu('Parent',h1, ...
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'Callback','baps4cbf helponline', ...
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'Enable','on', ...
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'Label','BAPS on the web', ...
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'Tag','online_menu');
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h2 = uimenu('Parent',h1, ...
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'Callback','baps4cbf about', ...
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'Enable','on', ...
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'Label','About', ...
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'Tag','about_menu');
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% uicontrol
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'BackgroundColor',[0.82 0.82 0.77], ...
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'ListboxTop',0, ...
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'Position',[38.25 154.268575851393 381 148.721320743034], ...
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'Style','frame', ...
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'Tag','mix_frame');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'BackgroundColor',[0.82 0.82 0.77], ...
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'ListboxTop',0, ...
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'Position',[38.25 56 381 79.721320743034], ...
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'Style','frame', ...
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'Tag','admix_frame');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'BackgroundColor',[0.82 0.82 0.77], ...
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'ListboxTop',0, ...
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'Position',[156.75 279.545624148607 158 11.9465944272446], ...
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'String','Population mixture analysis', ...
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'Style','text', ...
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'Tag','mix_text');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'BackgroundColor',[0.82 0.82 0.77], ...
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'ListboxTop',0, ...
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'Position',[156.75 111.545624148607 138 11.9465944272446], ...
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'String','Population admixture analysis', ...
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'Style','text', ...
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'Tag','admix_text');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'Callback','baps4cbf mix1_button', ...
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'ListboxTop',0, ...
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'Position',[51.75 245.412497213622 163.5 22.7554179566563], ...
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'String','Clustering of individuals', ...
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'Tag','mix1_button');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'Callback','baps4cbf mix2_button', ...
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'ListboxTop',0, ...
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'Position',[51.75 212.75 163.5 23.25], ...
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'String','Clustering of groups of individuals', ...
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'Tag','mix2_button');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'Callback','baps4cbf trained_button', ...
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'ListboxTop',0, ...
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'Position',[51.75 178.284055727554 163.5 22.7554179566563], ...
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'String','Trained clustering', ...
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'Tag','trained_button');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'Callback','baps4cbf admix1_button', ...
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'ListboxTop',0, ...
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'Position',[51.7 75.412497213622 163.5 22.7554179566563], ...
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'String','Admixture based on mixture clustering', ...
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'Tag','admix1_button');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'Callback','baps4cbf admix2_button', ...
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'ListboxTop',0, ...
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'Position',[245.75 75.412497213622 163.5 22.7554179566563], ...
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'String','Admixture based on pre-defined populations', ...
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'Tag','admix2_button');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'BackgroundColor',[.7 .9 .7], ...
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'FontSize',10, ...
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'HorizontalAlignment','left', ...
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'ListboxTop',0, ...
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'Position',[36 28.5 100.75 14.25], ...
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'String','Data File:', ...
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'Style','text', ...
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'Tag','datafile_text');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'BackgroundColor',[.7 .9 .7], ...
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'FontSize',10, ...
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'HorizontalAlignment','left', ...
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'ListboxTop',0, ...
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'Position',[36 9.75 51 14.25], ...
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'String','Output File:', ...
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'Style','text', ...
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'Tag','outputfile_text');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'BackgroundColor',[.7 .9 .7], ...
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'FontSize',10, ...
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'HorizontalAlignment','left', ...
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'ListboxTop',0, ...
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'Position',[140.75 28.5 314.5 14.25], ...
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'Style','text', ...
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'Tag','filename1_text');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'BackgroundColor',[.7 .9 .7], ...
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'FontSize',10, ...
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'HorizontalAlignment','left', ...
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'ListboxTop',0, ...
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'Position',[93.75 9.75 314.5 14.25], ...
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'Style','text', ...
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'Tag','filename2_text');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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'Callback','baps4cbf spatial_button', ...
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'ListboxTop',0, ...
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'Position',[245.75 245.412497213622 163.5 22.7554179566563], ...
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'String','Spatial clustering of individuals', ...
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'Tag','spatial_button');
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h1 = uicontrol('Parent',h0, ...
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'Units','points', ...
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||
|
|
'Callback','baps4cbf spatial2_button', ...
|
||
|
|
'ListboxTop',0, ...
|
||
|
|
'Position',[245.75 212.75 163.5 23.25], ...
|
||
|
|
'String','Spatial clustering of groups', ...
|
||
|
|
'Tag','spatial2_button');
|
||
|
|
h1 = uicontrol('Parent',h0, ...
|
||
|
|
'Units','points', ...
|
||
|
|
'Callback','baps4cbf linkage_button', ...
|
||
|
|
'ListboxTop',0, ...
|
||
|
|
'Position',[245.75 178.284055727554 163.5 23.25], ...
|
||
|
|
'String','Clustering with linked loci', ...
|
||
|
|
'Tag','linkage_button');
|
||
|
|
|
||
|
|
% Starting text in the log window:
|
||
|
|
disp('**********************************************************');
|
||
|
|
disp('********************** BAPS 6.0 *************************');
|
||
|
|
disp('**********************************************************');
|
||
|
|
disp(' ');
|
||
|
|
disp('Closing this window will end the execution of the program.');
|
||
|
|
disp('However, it is recommended that you use ''Exit'' on the ''File''');
|
||
|
|
disp('menu of the main window or use the close-button in the upper');
|
||
|
|
disp('right-hand corner of the main window to exit the program.');
|
||
|
|
disp(' ');
|
||
|
|
|
||
|
|
if strcmp(computer,'PCWIN') || strcmp(computer,'PCWIN64')
|
||
|
|
if nargout > 0, fig = h0; end
|
||
|
|
drawnow
|
||
|
|
% seticon(h0, ['baps5.ico']);
|
||
|
|
end
|
||
|
|
% uimenufcn(gcf,'WindowCommandWindow')
|
||
|
|
|