mSpecifyQueryforGUI reads the entries in the GUI to set query constraints
0001 % mSpecifyQueryforGUI reads the entries in the GUI to set query constraints 0002 0003 % The variable Query has several fields: 0004 % xSpecifyQuery returns the description of a model motif 0005 % The variable Query has several fields: 0006 % Query.Filename a string like 1s72 0007 % Query.NTList list of nucleotide numbers 0008 % Query.ChainList list of chains, to uniquely identify NTs from numbers 0009 % Query.Mask a mask for which nucleotides to allow 0010 % Query.AngleWeight weights to put on the angles 0011 % Query.DistanceWeight weights to put on nucleotide distances 0012 % Query.DiscCutoff discrepancy cutoff D_0 0013 % Query.RelCutoff relaxed cutoff D_1 0014 % Query.Diff maximum difference between sorted nucleotide 0015 % indices; use with Sequential = 1 to screen for sequential constraints 0016 % Query.Geometric set to 0 to ignore geometry, only use screens. 0017 % Default is 1. 0018 % Query.ExcludeOverlap set to 1 to eliminate highly redundant motifs with 0019 % larger discrepancies; often, you get the same candidate with one or two 0020 % nucleotides different but much higher discrepancy. Default is 1 when 0021 % Query.NumNT > 6. 0022 %Added: Query.Config 0023 0024 for i=1:NTlen 0025 h=findobj('Tag',strcat('Config',num2str(i))); 0026 v=get(h,'Value'); 0027 s=get(h,'String'); 0028 Query.Config(i)=s(v); %use curly baracelets here {} because Query.Mask must be a character array, not a cell array. The (1) means that only first letter is taken (what is after it may be just description) 0029 end 0030 %%%End Read Query.ChainList from GUI 0031 0032 DiscCutoff=str2num(get(handles.GuarCutoff,'String')); %%%GuarCutoff name changed into DiscCutoff 0033 if ~isempty(DiscCutoff) 0034 Query.DiscCutoff = DiscCutoff; 0035 end 0036 0037 RelCutoff=str2num(get(handles.RelCutoff,'String')); 0038 if ~isempty(RelCutoff) 0039 Query.RelCutoff = RelCutoff; 0040 end 0041 0042 v=get(handles.Overlap,'Value'); 0043 if v==1 0044 Query.ExcludeOverlap=1; 0045 else 0046 Query.ExcludeOverlap=0; 0047 end 0048 0049 Query.Name=get(handles.SearchName,'String'); 0050 desc=get(handles.SearchDescription,'String'); 0051 if ~isempty(desc) && ~strcmp(desc,'-') 0052 Query.Description=desc; 0053 end 0054 0055 if get(handles.Geometric,'Value') == 1 0056 Query.Geometric=1; 0057 else 0058 Query.Geometric=0; 0059 end 0060 0061 %%%Read Query.Diagonal from GUI 0062 % Query.Diagonal includes Mask information and also some other info 0063 for i=1:NTlen 0064 h=findobj('Tag',strcat('Diagonal',num2str(i))); 0065 s=get(h,'String'); 0066 Query.Diagonal{i}=s; 0067 end 0068 %%%End Read Query.Diagonal from GUI 0069 0070 0071 %%%Read Query.Diff from GUI 0072 % Query.Diff = [4 4]; 0073 for i=1:NTlen 0074 for j=1:(i-1) 0075 h=findobj('Tag',strcat('Diff',num2str(i),num2str(j))); 0076 s=get(h,'String'); 0077 Query.Diff{i,j}=s; 0078 end 0079 end 0080 0081 for i=1:NTlen 0082 for j=(i+1):NTlen 0083 h=findobj('Tag',strcat('BPType',num2str(i),num2str(j))); 0084 s=get(h,'String'); 0085 Query.Edges{i,j}= regexprep(s,',',' '); %users can enter , instead of spaces between interaction codes 0086 end 0087 end 0088 0089