Home > BiKEGG > UpdateDBase.m

UpdateDBase

PURPOSE ^

UpdateDBase(GUI)

SYNOPSIS ^

function varargout = UpdateDBase(varargin)

DESCRIPTION ^

 UpdateDBase(GUI)
 Updating the local database of BiKEGG for offline use.

 O. Jamialahmadi
 TMU, Chem. Eng. Dept., Biotech. Group 
 Mar. 2015

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SUBFUNCTIONS ^

SOURCE CODE ^

0001 function varargout = UpdateDBase(varargin)
0002 % UpdateDBase(GUI)
0003 % Updating the local database of BiKEGG for offline use.
0004 %
0005 % O. Jamialahmadi
0006 % TMU, Chem. Eng. Dept., Biotech. Group
0007 % Mar. 2015
0008 
0009 % Begin initialization code - DO NOT EDIT
0010 gui_Singleton = 1;
0011 gui_State = struct('gui_Name',       mfilename, ...
0012                    'gui_Singleton',  gui_Singleton, ...
0013                    'gui_OpeningFcn', @UpdateDBase_OpeningFcn, ...
0014                    'gui_OutputFcn',  @UpdateDBase_OutputFcn, ...
0015                    'gui_LayoutFcn',  [] , ...
0016                    'gui_Callback',   []);
0017 if nargin && ischar(varargin{1})
0018     gui_State.gui_Callback = str2func(varargin{1});
0019 end
0020 
0021 if nargout
0022     [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
0023 else
0024     gui_mainfcn(gui_State, varargin{:});
0025 end
0026 % End initialization code - DO NOT EDIT
0027 
0028 
0029 % --- Executes just before UpdateDBase is made visible.
0030 function UpdateDBase_OpeningFcn(hObject, eventdata, handles, varargin)
0031 % This function has no output args, see OutputFcn.
0032 % hObject    handle to figure
0033 % eventdata  reserved - to be defined in a future version of MATLAB
0034 % handles    structure with handles and user data (see GUIDATA)
0035 % varargin   command line arguments to UpdateDBase (see VARARGIN)
0036 
0037 % Choose default command line output for UpdateDBase
0038 handles.output = hObject;
0039 
0040 % Update handles structure
0041 guidata(hObject, handles);
0042 
0043 % UIWAIT makes UpdateDBase wait for user response (see UIRESUME)
0044 % uiwait(handles.figure1);
0045 
0046 
0047 % --- Outputs from this function are returned to the command line.
0048 function varargout = UpdateDBase_OutputFcn(hObject, eventdata, handles) 
0049 % varargout  cell array for returning output args (see VARARGOUT);
0050 % hObject    handle to figure
0051 % eventdata  reserved - to be defined in a future version of MATLAB
0052 % handles    structure with handles and user data (see GUIDATA)
0053 
0054 % Get default command line output from handles structure
0055 varargout{1} = handles.output;
0056 
0057 
0058 % --- Executes on button press in rxn2mappushbutton1.
0059 function rxn2mappushbutton1_Callback(hObject, eventdata, handles)
0060 % hObject    handle to rxn2mappushbutton1 (see GCBO)
0061 % eventdata  reserved - to be defined in a future version of MATLAB
0062 % handles    structure with handles and user data (see GUIDATA)
0063 TestLink='http://rest.kegg.jp';
0064 [~,Stat1]=urlread(TestLink);
0065 if ~Stat1
0066     msgbox({'This step requires a stable internet connection';...
0067         'Seemingly you are offline!'});
0068     return
0069 end
0070 
0071 Text1 = 'Updating rxn2map.txt...';
0072 fprintf(Text1)
0073 Data=urlread('http://rest.kegg.jp/link/path/rn');
0074 Pth1 = which ('Bigg2Kegg.m');
0075 tind = find(Pth1=='\',1,'last');
0076 Pth = Pth1(1:tind-1);
0077 Pth1 = [Pth,'\','rxn2map.txt'];
0078 Idf = fopen(Pth1,'w');
0079 fprintf(Idf,Data);
0080 fclose(Idf);
0081 waitfor(msgbox('rxn2map.txt was successfully updated!','Update'))
0082 for i =1:numel(Text1)
0083     fprintf('\b')
0084 end
0085 % --- Executes on button press in map2cpdpushbutton.
0086 function map2cpdpushbutton_Callback(hObject, eventdata, handles)
0087 % hObject    handle to map2cpdpushbutton (see GCBO)
0088 % eventdata  reserved - to be defined in a future version of MATLAB
0089 % handles    structure with handles and user data (see GUIDATA)
0090 TestLink='http://rest.kegg.jp';
0091 [~,Stat1]=urlread(TestLink);
0092 if ~Stat1
0093     msgbox({'This step requires a stable internet connection';...
0094         'Seemingly you are offline!'});
0095     return
0096 end
0097 Text1 = 'Updating map2cpd.txt...';
0098 fprintf(Text1)
0099 Data=urlread('http://rest.kegg.jp/link/cpd/path');
0100 Pth1 = which ('Bigg2Kegg.m');
0101 tind = find(Pth1=='\',1,'last');
0102 Pth = Pth1(1:tind-1);
0103 Pth1 = [Pth,'\','map2cpd.txt'];
0104 Idf = fopen(Pth1,'w');
0105 fprintf(Idf,Data);
0106 fclose(Idf);
0107 waitfor(msgbox('map2cpd.txt was successfully updated!','Update'))
0108 for i =1:numel(Text1)
0109     fprintf('\b')
0110 end
0111 
0112 % --- Executes on button press in KEGGmapspushbutton.
0113 function KEGGmapspushbutton_Callback(hObject, eventdata, handles)
0114 % hObject    handle to KEGGmapspushbutton (see GCBO)
0115 % eventdata  reserved - to be defined in a future version of MATLAB
0116 % handles    structure with handles and user data (see GUIDATA)
0117 TestLink='http://rest.kegg.jp';
0118 [~,Stat1]=urlread(TestLink);
0119 if ~Stat1
0120     msgbox({'This step requires a stable internet connection';...
0121         'Seemingly you are offline!'});
0122     return
0123 end
0124 Text1 = 'Updating KEGGmaps.txt...';
0125 fprintf(Text1)
0126 Data=urlread('http://rest.kegg.jp/list/pathway');
0127 Pth1 = which ('Bigg2Kegg.m');
0128 tind = find(Pth1=='\',1,'last');
0129 Pth = Pth1(1:tind-1);
0130 Pth1 = [Pth,'\','KEGGmaps.txt'];
0131 Idf = fopen(Pth1,'w');
0132 fprintf(Idf,Data);
0133 fclose(Idf);
0134 waitfor(msgbox('KEGGmaps.txt was successfully updated!','Update'))
0135 for i =1:numel(Text1)
0136     fprintf('\b')
0137 end
0138 
0139 % --- Executes on button press in KEGGcpdpushbutton.
0140 function KEGGcpdpushbutton_Callback(hObject, eventdata, handles)
0141 % hObject    handle to KEGGcpdpushbutton (see GCBO)
0142 % eventdata  reserved - to be defined in a future version of MATLAB
0143 % handles    structure with handles and user data (see GUIDATA)
0144 TestLink='http://rest.kegg.jp';
0145 [~,Stat1]=urlread(TestLink);
0146 if ~Stat1
0147     msgbox({'This step requires a stable internet connection';...
0148         'Seemingly you are offline!'});
0149     return
0150 end
0151 Text1 = 'Updating KEGGcpd.txt...';
0152 fprintf(Text1)
0153 Data=urlread('http://rest.kegg.jp/list/cpd');
0154 Pth1 = which ('Bigg2Kegg.m');
0155 tind = find(Pth1=='\',1,'last');
0156 Pth = Pth1(1:tind-1);
0157 Pth1 = [Pth,'\','KEGGcpd.txt'];
0158 Idf = fopen(Pth1,'w');
0159 fprintf(Idf,Data);
0160 fclose(Idf);
0161 waitfor(msgbox('KEGGcpd.txt was successfully updated!','Update'))
0162 for i =1:numel(Text1)
0163     fprintf('\b')
0164 end
0165 
0166 % --- Executes on button press in ec2rxnpushbutton.
0167 function ec2rxnpushbutton_Callback(hObject, eventdata, handles)
0168 % hObject    handle to ec2rxnpushbutton (see GCBO)
0169 % eventdata  reserved - to be defined in a future version of MATLAB
0170 % handles    structure with handles and user data (see GUIDATA)
0171 TestLink='http://rest.kegg.jp';
0172 [~,Stat1]=urlread(TestLink);
0173 if ~Stat1
0174     msgbox({'This step requires a stable internet connection';...
0175         'Seemingly you are offline!'});
0176     return
0177 end
0178 Text1 = 'Updating ec2rxn.txt...';
0179 fprintf(Text1)
0180 Data=urlread('http://rest.kegg.jp/link/rn/ec');
0181 Pth1 = which ('Bigg2Kegg.m');
0182 tind = find(Pth1=='\',1,'last');
0183 Pth = Pth1(1:tind-1);
0184 Pth1 = [Pth,'\','ec2rxn.txt'];
0185 Idf = fopen(Pth1,'w');
0186 fprintf(Idf,Data);
0187 fclose(Idf);
0188 waitfor(msgbox('ec2rxn.txt was successfully updated!','Update'))
0189 for i =1:numel(Text1)
0190     fprintf('\b')
0191 end
0192 
0193 % --- Executes on button press in cpd2weightpushbutton.
0194 function cpd2weightpushbutton_Callback(hObject, eventdata, handles)
0195 % hObject    handle to cpd2weightpushbutton (see GCBO)
0196 % eventdata  reserved - to be defined in a future version of MATLAB
0197 % handles    structure with handles and user data (see GUIDATA)
0198 TestLink='http://rest.kegg.jp';
0199 [~,Stat1]=urlread(TestLink);
0200 if ~Stat1
0201     msgbox({'This step requires a stable internet connection';...
0202         'Seemingly you are offline!'});
0203     return
0204 end
0205 Text1 = 'Updating cpd2weight.txt...';
0206 fprintf(Text1)
0207 Data=urlread('http://rest.kegg.jp/find/compound/1-9000/mol_weight');
0208 Pth1 = which ('Bigg2Kegg.m');
0209 tind = find(Pth1=='\',1,'last');
0210 Pth = Pth1(1:tind-1);
0211 Pth1 = [Pth,'\','cpd2weight.txt'];
0212 Idf = fopen(Pth1,'w');
0213 fprintf(Idf,Data);
0214 fclose(Idf);
0215 waitfor(msgbox('cpd2weight.txt was successfully updated!','Update'))
0216 for i =1:numel(Text1)
0217     fprintf('\b')
0218 end
0219 
0220 % --- Executes on button press in cpd2rxnpushbutton.
0221 function cpd2rxnpushbutton_Callback(hObject, eventdata, handles)
0222 % hObject    handle to cpd2rxnpushbutton (see GCBO)
0223 % eventdata  reserved - to be defined in a future version of MATLAB
0224 % handles    structure with handles and user data (see GUIDATA)
0225 TestLink='http://rest.kegg.jp';
0226 [~,Stat1]=urlread(TestLink);
0227 if ~Stat1
0228     msgbox({'This step requires a stable internet connection';...
0229         'Seemingly you are offline!'});
0230     return
0231 end
0232 Text1 = 'Updating cpd2rxn.txt...';
0233 fprintf(Text1)
0234 Data=urlread('http://rest.kegg.jp/link/rn/cpd');
0235 Pth1 = which ('Bigg2Kegg.m');
0236 tind = find(Pth1=='\',1,'last');
0237 Pth = Pth1(1:tind-1);
0238 Pth1 = [Pth,'\','cpd2rxn.txt'];
0239 Idf = fopen(Pth1,'w');
0240 fprintf(Idf,Data);
0241 fclose(Idf);
0242 waitfor(msgbox('cpd2rxn.txt was successfully updated!','Update'))
0243 for i =1:numel(Text1)
0244     fprintf('\b')
0245 end
0246 
0247 
0248 % --- Executes on button press in Donepushbutton8.
0249 function Donepushbutton8_Callback(hObject, eventdata, handles)
0250 % hObject    handle to Donepushbutton8 (see GCBO)
0251 % eventdata  reserved - to be defined in a future version of MATLAB
0252 % handles    structure with handles and user data (see GUIDATA)
0253 close(gcf)
0254 
0255 
0256 % --- Executes on button press in Weight4TransRxnspushbutton.
0257 function Weight4TransRxnspushbutton_Callback(hObject, eventdata, handles)
0258 % hObject    handle to Weight4TransRxnspushbutton (see GCBO)
0259 % eventdata  reserved - to be defined in a future version of MATLAB
0260 % handles    structure with handles and user data (see GUIDATA)
0261 TestLink='http://rest.kegg.jp';
0262 [~,Stat1]=urlread(TestLink);
0263 if ~Stat1
0264     msgbox({'This step requires a stable internet connection';...
0265         'Seemingly you are offline!'});
0266     return
0267 end
0268 Text1 = 'Updating W4TranRxns2.txt and W4TranRxns4.txt...';
0269 fprintf(Text1)
0270 fprintf('\n')
0271 Weight4TransRxns(2)
0272 fprintf('\n')
0273 Weight4TransRxns(4)
0274 fprintf('\n')
0275 waitfor(msgbox('W4TranRxns2.txt and W4TranRxns4.txt was successfully updated!','Update'))
0276 for i =1:numel(Text1)
0277     fprintf('\b')
0278 end
0279 clc
0280 
0281 % --- Executes on button press in getKGMLpushbutton.
0282 function getKGMLpushbutton_Callback(hObject, eventdata, handles)
0283 % hObject    handle to getKGMLpushbutton (see GCBO)
0284 % eventdata  reserved - to be defined in a future version of MATLAB
0285 % handles    structure with handles and user data (see GUIDATA)
0286 TestLink='http://rest.kegg.jp';
0287 [~,Stat1]=urlread(TestLink);
0288 if ~Stat1
0289     msgbox({'This step requires a stable internet connection';...
0290         'Seemingly you are offline!'});
0291     return
0292 end
0293 Text1 = 'Updating KEGGmaps folder...';
0294 fprintf([Text1,'\n'])
0295 getKGML
0296 waitfor(msgbox('KEGGmaps folder was successfully updated!','Update'))
0297 for i =1:numel(Text1)
0298     fprintf('\b')
0299 end
0300 
0301 % --- Executes on button press in MultiRxnpushbutton.
0302 function MultiRxnpushbutton_Callback(hObject, eventdata, handles)
0303 % hObject    handle to MultiRxnpushbutton (see GCBO)
0304 % eventdata  reserved - to be defined in a future version of MATLAB
0305 % handles    structure with handles and user data (see GUIDATA)
0306 TestLink='http://rest.kegg.jp';
0307 [~,Stat1]=urlread(TestLink);
0308 if ~Stat1
0309     msgbox({'This step requires a stable internet connection';...
0310         'Seemingly you are offline!'});
0311     return
0312 end
0313 Text1 = 'Updating OfflineRxnData folder...';
0314 fprintf(Text1)
0315 GetData4MultiRxns
0316 waitfor(msgbox('OfflineRxnData folder was successfully updated!','Update'))
0317 for i =1:numel(Text1)
0318     fprintf('\b')
0319 end
0320 clc
0321 
0322 % --- Executes on button press in Orgspushbutton.
0323 function Orgspushbutton_Callback(hObject, eventdata, handles)
0324 % hObject    handle to Orgspushbutton (see GCBO)
0325 % eventdata  reserved - to be defined in a future version of MATLAB
0326 % handles    structure with handles and user data (see GUIDATA)
0327 TestLink='http://rest.kegg.jp';
0328 [~,Stat1]=urlread(TestLink);
0329 if ~Stat1
0330     msgbox({'This step requires a stable internet connection';...
0331         'Seemingly you are offline!'});
0332     return
0333 end
0334 Text1 = 'Updating orgs.txt...';
0335 fprintf(Text1)
0336 Data=urlread('http://rest.kegg.jp/list/organism');
0337 Pth1 = which ('Precons.m');
0338 tind = find(Pth1=='\',1,'last');
0339 Pth = Pth1(1:tind-1);
0340 Pth1 = [Pth,'\','orgs.txt'];
0341 Idf = fopen(Pth1,'w');
0342 fprintf(Idf,Data);
0343 fclose(Idf);
0344 waitfor(msgbox('orgs.txt was successfully updated!','Update'))
0345 for i =1:numel(Text1)
0346     fprintf('\b')
0347 end
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