%% AmPgui % a GUI to create 4 data-structures %% function AmPgui(action) % created 2020/06/05 by Bas Kooijman, modified 2020/08/14, 2021/08/03, 2021/08/21, 2026/07/01 %% Syntax % <../AmPgui.m *AmPgui*> %% Description % It writes 4 data-structures from scratch % % * data: structure with data % * auxData: structure with auxiliary data % * metaData: structure with metaData % * txtData: structure with text for data % % Input: no explicit input (facultative input is set by the function itself in multiple calls) % % Output: no explicit output, but global exit-flag infoAmPgui is set with % % - 0, species is in AmP, skip writing 4 source files % - 1, writing 4 source files with species recognized by CoL % - 2, writing 4 source files with species not recognized by CoL, but genus is in AmP % - 3, writing 4 source files with species not recognized by CoL, genus is not in AmP, but family is % - 4, writing 4 source files with species not recognized by CoL, family is not in AmP, but order is % - 5, writing 4 source files with species not recognized by CoL, order is not in AmP, but class is % - 6, writing 4 source files with species not recognized by CoL, class is not in AmP, but phylum is % - 7, writing 4 source files with species not recognized by CoL, phylum is not in AmP %% Remarks % % * Set metaData on global before use of this function. % * Files will be saved in your local directory, which should not contain results_my_pet.mat files, other than written by this function % * Use the cd command to the dir of your choice BEFORE running this function to save files in the desired place. % * All weights are set at default values in the resulting file; % * The first call to "species" in the gui uses automatised completions, % subsequent calls use handfilling; % * This function is called in AmPeps % * Font colors in main AmPgui mean: % % - red: editing required % - green: editing not necessary % - black: editing facultative % % Notice that font colors only represent internal consistency, irrespective of content. % txtData.bibkey.data_id specifies the bibkey for dataset data_id; metaData.biblist.bibkey specifies the bibitem for bibkey. % metaData.bibkey.Fi and Ci specify the bibkeys for facts Fi and discussion Di persistent dmydata hspecies hecoCode hT_typical hauthor hcurator hgrp hdiscussion hfacts hacknowledgment hlinks hbiblist hdata_0 hCOMPLETE global data auxData metaData txtData select_id id_links eco_types color infoAmPgui list_spec handfilled global dspecies Hspecies Hfamily Horder Hclass Hphylum Hcommon Hwarning HwarningOK HCOMPLETE Hwait global Hauthor Hemail Haddress HK HD HDb HF HFb HT Hlinks H0v H0T H0b H0c D1 Hb ddata_0 Db global Hclimate Hecozone Hhabitat Hembryo Hmigrate Hfood Hgender Hreprod %UIControl_FontSize_bak = get(0, 'DefaultUIControlFontSize'); % 8 set(0, 'DefaultUIControlFontSize', 9); %set(0, 'DefaultUIControlFontSize', UIControl_FontSize_bak); if nargin == 0 % initiate structures and create the GUI % initiation handfilled = false; % taxonomy is not handfilled; links set automatically if ~isfield(data, 'data_0'); data.data_0 = []; end if ~isfield(data, 'data_1'); data.data_1 = []; end if ~isfield(auxData, 'temp'); auxData.temp = []; end if ~isfield(txtData, 'units'); txtData.units = []; txtData.units.temp = []; end if ~isfield(txtData, 'label'); txtData.label = []; txtData.label.temp = []; end if ~isfield(txtData, 'bibkey'); txtData.bibkey = []; end % for data if ~isfield(metaData, 'species'); metaData.species = ''; end if ~isfield(metaData, 'species_en'); metaData.species_en = ''; end if ~isfield(metaData, 'family'); metaData.family = ''; end if ~isfield(metaData, 'order'); metaData.order = ''; end if ~isfield(metaData, 'class'); metaData.class = ''; end if ~isfield(metaData, 'phylum'); metaData.phylum = ''; end ecoCode = {'climate', 'ecozone', 'habitat', 'embryo', 'migrate', 'food', 'gender', 'reprod'}; if ~isfield(metaData, 'ecoCode'); metaData.ecoCode = []; n = length(ecoCode); for i=1:n metaData.ecoCode.(ecoCode{i}) = []; end end if ~isfield(metaData, 'T_typical'); metaData.T_typical = []; end if ~isfield(metaData, 'data_0'); metaData.data_0 = {}; end if ~isfield(metaData, 'data_1'); metaData.data_1 = {}; end if ~isfield(metaData, 'bibkey'); metaData.bibkey = []; end % for discussion, facts id_links = {'id_CoL', 'id_ITIS', 'id_EoL', 'id_Wiki', 'id_ADW', 'id_Taxo', 'id_WoRMS', ... 'id_molluscabase', 'id_scorpion', 'id_spider', 'id_collembola', 'id_orthoptera', 'id_phasmida', 'id_aphid', 'id_diptera', 'id_lepidoptera', ... 'id_fishbase', 'id_amphweb', 'id_ReptileDB', 'id_avibase', 'id_birdlife', 'id_MSW3', 'id_AnAge'}; if ~isfield(metaData, 'links'); metaData.links = []; n_id = length(id_links); for i=1:n_id; metaData.links.(id_links{i}) = ''; end select_id = true(1,n_id); end if ~isfield(metaData, 'author'); metaData.author = []; end if ~isfield(metaData, 'email'); metaData.email = []; end if ~isfield(metaData, 'address'); metaData.address = []; end if ~isfield(metaData, 'curator'); metaData.curator = []; end if ~isfield(metaData, 'COMPLETE'); metaData.COMPLETE = []; end if ~isfield(metaData, 'discussion'); metaData.discussion = []; end if ~isfield(metaData, 'facts'); metaData.facts = []; end if ~isfield(metaData, 'acknowledgment'); metaData.acknowledgment = []; end if ~isfield(metaData, 'biblist'); metaData.biblist = []; end if isempty(eco_types); get_eco_types; end if isempty(list_spec); list_spec = select; end % lists of taxon names in AmP if isempty(color) color.species = [1 0 0]; color.ecoCode = [1 0 0]; color.T_typical = [1 0 0]; color.author = [1 0 0]; color.curator = [1 0 0]; color.grp = [0 0 0]; color.discussion = [0 0 0]; color.facts = [0 0 0]; color.acknowledgment = [0 0 0]; color.links = [1 0 0]; color.biblist = [1 0 0]; color.data_0 = [1 0 0]; color.COMPLETE = [1 0 0]; end if isempty(infoAmPgui) infoAmPgui = ~isempty(metaData.species); % AmPgui exit flag end % setup gui dmydata = dialog('Position',[30 550 250 275], 'Name','AmPgui'); hspecies = uicontrol('Parent',dmydata, 'Callback','AmPgui species', 'Position',[10 230 100 20], 'String','species', 'Style','pushbutton'); hecoCode = uicontrol('Parent',dmydata, 'Callback','AmPgui ecoCode', 'Position',[10 205 100 20], 'String','ecoCode', 'Style','pushbutton'); hT_typical= uicontrol('Parent',dmydata, 'Callback','AmPgui T_typical', 'Position',[10 180 100 20], 'String','T_typical', 'Style','pushbutton'); hauthor = uicontrol('Parent',dmydata, 'Callback','AmPgui author', 'Position',[10 135 100 20], 'String','author', 'Style','pushbutton'); hcurator = uicontrol('Parent',dmydata, 'Callback','AmPgui curator', 'Position',[10 110 100 20], 'String','curator', 'Style','pushbutton'); hgrp = uicontrol('Parent',dmydata, 'Callback','AmPgui grp', 'Position',[10 65 100 20], 'String','group plots', 'Style','pushbutton'); hdiscussion = uicontrol('Parent',dmydata, 'Callback','AmPgui discussion', 'Position',[10 40 100 20], 'String','discussion', 'Style','pushbutton'); hfacts = uicontrol('Parent',dmydata, 'Callback','AmPgui facts', 'Position',[10 15 100 20], 'String','facts', 'Style','pushbutton'); hlinks = uicontrol('Parent',dmydata, 'Callback','AmPgui links', 'Position',[130 230 100 20], 'String','links', 'Style','pushbutton'); hbiblist = uicontrol('Parent',dmydata, 'Callback','AmPgui biblist', 'Position',[130 205 100 20], 'String','biblist', 'Style','pushbutton'); hacknowledgment = uicontrol('Parent',dmydata, 'Callback','AmPgui acknowledgment', 'Position',[130 180 100 20], 'String','acknowledgment', 'Style','pushbutton'); hdata_0 = uicontrol('Parent',dmydata, 'Callback','AmPgui data_0', 'Position',[130 135 100 20], 'String','0-var data', 'Style','pushbutton'); uicontrol('Parent',dmydata, 'Callback','AmPgui data_1', 'Position',[130 110 100 20], 'String','1-var data', 'Style','pushbutton'); hCOMPLETE = uicontrol('Parent',dmydata, 'Callback','AmPgui COMPLETE', 'Position',[130 65 100 20], 'String','COMPLETE', 'Style','pushbutton'); uicontrol('Parent',dmydata, 'Callback','AmPgui resume', 'Position',[130 40 100 20], 'String','resume', 'Style','pushbutton'); uicontrol('Parent',dmydata, 'Callback','AmPgui pause', 'Position',[130 15 100 20], 'String','pause/save', 'Style','pushbutton'); % set default colors set(hspecies, 'ForegroundColor', color.species); set(hecoCode, 'ForegroundColor', color.ecoCode); set(hT_typical, 'ForegroundColor', color.T_typical); set(hauthor, 'ForegroundColor', color.author); set(hcurator, 'ForegroundColor', color.curator); set(hgrp, 'ForegroundColor', color.grp); set(hdiscussion, 'ForegroundColor', color.discussion); set(hfacts, 'ForegroundColor', color.facts); set(hlinks, 'ForegroundColor', color.links); set(hbiblist, 'ForegroundColor', color.biblist); set(hacknowledgment, 'ForegroundColor', color.acknowledgment); set(hdata_0, 'ForegroundColor', color.data_0); else % fill fields switch(action) case 'species' dspecies = dialog('Position',[450 150 600 150], 'Name','species dlg'); Warning = ''; Hwarning = uicontrol('Parent',dspecies, 'Position',[110 60 350 20], 'Style','text', 'String',Warning); WarningOK = ''; HwarningOK = uicontrol('Parent',dspecies, 'Position',[110 40 350 20], 'Style','text', 'String',WarningOK); Hfamily = uicontrol('Parent',dspecies, 'Position',[ 50 110 150 20], 'Style','text', 'String',['family: ',metaData.family]); Horder = uicontrol('Parent',dspecies, 'Position',[200 110 150 20], 'Style','text', 'String',['order: ', metaData.order]); Hclass = uicontrol('Parent',dspecies, 'Position',[350 110 150 20], 'Style','text', 'String',['class: ', metaData.class]); Hphylum = uicontrol('Parent',dspecies, 'Position',[ 50 80 150 20], 'Style','text', 'String',['phylum: ',metaData.phylum]); Hcommon = uicontrol('Parent',dspecies, 'Position',[200 80 240 20], 'Style','text', 'String',['common name: ',metaData.species_en]); if ~handfilled Hspecies = uicontrol('Parent',dspecies, 'Callback',{@speciesCb,dspecies}, 'Position',[110 15 350 20], 'Style','edit', 'String',metaData.species); else set(Hfamily, 'String',''); set(Horder, 'String',''); set(Hclass, 'String',''); set(Hphylum, 'String',''); set(Hcommon, 'String',''); Hspecies = uicontrol('Parent',dspecies, 'Callback',{@OKspeciesCb,dspecies}, 'Position',[110 15 350 20], 'Style','edit', 'String',metaData.species); end case 'ecoCode' decoCode = dialog('Position',[550 250 500 270], 'Name','ecoCode dlg'); % climate uicontrol('Parent',decoCode, 'Position',[10 230 146 20], 'String','climate', 'Style','text'); Hclimate = uicontrol('Parent',decoCode, 'Position',[110 230 250 20], 'String',cell2str(metaData.ecoCode.climate)); uicontrol('Parent',decoCode, 'Callback',{@climateCb,Hclimate}, 'Position',[370 230 50 20], 'Style','pushbutton', 'String','edit'); % ecozone uicontrol('Parent',decoCode, 'Position',[10 200 146 20], 'String','ecozone', 'Style','text'); Hecozone = uicontrol('Parent',decoCode, 'Position',[110 200 250 20], 'String',cell2str(metaData.ecoCode.ecozone)); uicontrol('Parent',decoCode, 'Callback',{@ecozoneCb,Hecozone}, 'Position',[370 200 50 20], 'Style','pushbutton', 'String','edit'); % habitat uicontrol('Parent',decoCode, 'Position',[10 170 146 20], 'String','habitat', 'Style','text'); Hhabitat = uicontrol('Parent',decoCode, 'Position',[110 170 250 20], 'String',cell2str(metaData.ecoCode.habitat)); uicontrol('Parent',decoCode, 'Callback',{@habitatCb,Hhabitat}, 'Position',[370 170 50 20], 'Style','pushbutton', 'String','edit'); % embryo uicontrol('Parent',decoCode, 'Position',[10 140 146 20], 'String','embryo', 'Style','text'); Hembryo = uicontrol('Parent',decoCode, 'Position',[110 140 250 20], 'String',cell2str(metaData.ecoCode.embryo)); uicontrol('Parent',decoCode, 'Callback',{@embryoCb,Hembryo}, 'Position',[370 140 50 20], 'Style','pushbutton', 'String','edit'); % migrate uicontrol('Parent',decoCode, 'Position',[10 110 146 20], 'String','migrate', 'Style','text'); Hmigrate = uicontrol('Parent',decoCode, 'Position',[110 110 250 20], 'String',cell2str(metaData.ecoCode.migrate)); uicontrol('Parent',decoCode, 'Callback',{@migrateCb,Hmigrate}, 'Position',[370 110 50 20], 'Style','pushbutton', 'String','edit'); % food uicontrol('Parent',decoCode, 'Position',[10 80 146 20], 'String','food', 'Style','text'); Hfood = uicontrol('Parent',decoCode, 'Position',[110 80 250 20], 'String',cell2str(metaData.ecoCode.food)); uicontrol('Parent',decoCode, 'Callback',{@foodCb,Hfood}, 'Position',[370 80 50 20], 'Style','pushbutton', 'String','edit'); % gender uicontrol('Parent',decoCode, 'Position',[10 50 146 20], 'String','gender', 'Style','text'); Hgender = uicontrol('Parent',decoCode, 'Position',[110 50 250 20], 'String',cell2str(metaData.ecoCode.gender)); uicontrol('Parent',decoCode, 'Callback',{@genderCb,Hgender}, 'Position',[370 50 50 20], 'Style','pushbutton', 'String','edit'); % reprod uicontrol('Parent',decoCode, 'Position',[10 20 146 20], 'String','reprod', 'Style','text'); Hreprod = uicontrol('Parent',decoCode, 'Position',[110 20 250 20], 'String',cell2str(metaData.ecoCode.reprod)); uicontrol('Parent',decoCode, 'Callback',{@reprodCb,Hreprod}, 'Position',[370 20 50 20], 'Style','pushbutton', 'String','edit'); uicontrol('Parent',decoCode, 'Callback',{@OKCb,decoCode}, 'Position',[430 20 50 20], 'Style','pushbutton', 'String','OK'); case 'T_typical' dT_typical = dialog('Position',[300 250 300 100], 'Name','T_typical dlg'); uicontrol('Parent',dT_typical, 'Position',[10 50 200 20], 'String','Typical body temperature in C', 'Style','text'); HT = uicontrol('Parent',dT_typical, 'Callback',@T_typicalCb, 'Position',[200 50 50 20], 'Style','edit', 'String',num2str(K2C(metaData.T_typical))); uicontrol('Parent',dT_typical, 'Callback',{@OKCb,dT_typical}, 'Position',[100 20 20 20], 'String','OK', 'Style','pushbutton'); case 'author' Datevec = datevec(datenum(date)); metaData.date_subm = Datevec(1:3); dauthor = dialog('Position',[450 150 500 150], 'Name','author dlg'); uicontrol('Parent',dauthor, 'Position',[10 95 146 20], 'String','Name', 'Style','text'); Hauthor = uicontrol('Parent',dauthor, 'Callback',@authorCb, 'Position',[110 95 350 20], 'Style','edit', 'String',metaData.author); uicontrol('Parent',dauthor, 'Position',[10 70 146 20], 'String','email', 'Style','text'); Hemail = uicontrol('Parent',dauthor, 'Callback',@emailCb, 'Position',[110 70 350 20], 'Style','edit', 'String',metaData.email); uicontrol('Parent',dauthor, 'Position',[10 45 146 20], 'String','address', 'Style','text'); Haddress = uicontrol('Parent',dauthor, 'Callback',@addressCb, 'Position',[110 45 350 20], 'Style','edit', 'String',metaData.address); uicontrol('Parent',dauthor, 'Callback',{@OKCb,dauthor}, 'Position',[110 20 20 20], 'String','OK', 'Style','pushbutton'); case 'curator' curList = {'Starrlight Augustine', 'Mike Kearney', 'Bas Kooijman', 'Romain Lavaud', 'Dina Lika', 'Nina Marn', 'Goncalo Marques', 'Laure Peçquerie','Tan Tjui-Yeuw'}; emailList = {'starrlight@ecotechnics.edu', 'mrke@unimelb.edu.au', 'salm.kooijman@gmail.com', 'RLavaud@agcenter.lsu.edu', 'lika@uoc.gr' ,'nina.marn@gmail.com', 'goncalo.marques@tecnico.ulisboa.pt', 'laure.pecquerie@ird.fr', 'tan.tjuiyeuw@wur.nl'}; if ~isempty(metaData.curator) i = 1:9; i = i(ismember(curList, metaData.curator)); else i = 1; end i_cur = listdlg('ListString',curList, 'SelectionMode','single', 'Name','curator dlg', 'ListSize',[140 150], 'InitialValue',i); metaData.curator = curList{i_cur}; metaData.email_cur = emailList{i_cur}; Datevec = datevec(datenum(date)); metaData.date_acc = Datevec(1:3); case 'grp' sets = {{'tL_f', 'tL_m'}, {'tWw_f', 'tWw_m'}, {'tWd_f', 'tLWd_m'}, {'LWw_f', 'LWw_m'}, ... {'LWd_f', 'tWd_m'}, {'LdL_f', 'LdL_m'}}; comment = {'Data for females, males', 'Data for females, males', 'Data for females, males', 'Data for females, males', ... 'Data for females, males', 'Data for females, males'}; n_sets = length(sets); setsList = sets; sel_sets = false(n_sets,1); for i = 1:n_sets setsList{1} = cell2str(sets{i}); seti = sets{i}; if isfield(data.data_1, seti{1}) && isfield(data.data_1, seti{2}) sel_sets(1) = true; end end dgrp = dialog('Position',[450 150 350 250], 'Name','grp dlg'); uicontrol('Parent',dgrp, 'Position',[20 210 30 20], 'Callback',{@OKCb,dgrp}, 'String','OK'); if isempty(data.data_1) uicontrol('Parent',dgrp, 'Position',[70 210 250 20], 'String','no 1-variate data found'); elseif any(sel_sets) setsList = setsList(sel_sets); i_sets = listdlg('ListString',setsList, 'Name','grp dlg', 'ListSize',[200 80], 'InitialValue',1); n_sets = length(i_sets); for i=1:n_sets hight = 180 - i * 25; uicontrol('Parent',dgrp, 'Position',[ 20 hight 150 20], 'String',['set', num2str(i), ': ', setsList{i}]); uicontrol('Parent',dgrp, 'Position',[170 hight 175 20], 'String',['comment', num2str(i), ': ', comment{i}]); end metaData.grp.sets = sets(sel_sets); metaData.grp.comment = comment(sel_sets); else uicontrol('Parent',dgrp, 'Position',[70 210 250 20], 'String','no 1-variate data found that can be grouped'); end case 'discussion' ddiscussion = dialog('Position',[350 150 1000 550], 'Name','discussion dlg'); uicontrol('Parent',ddiscussion, 'Callback',{@OKCb,ddiscussion}, 'Position',[30 500 20 20], 'String','OK'); uicontrol('Parent',ddiscussion, 'Callback',{@addDiscussionCb,ddiscussion}, 'Position',[110 500 150 20], 'String','add discussion point', 'Style','pushbutton'); uicontrol('Parent',ddiscussion, 'Position',[790 500 146 20], 'String','bibkey', 'Style','text'); if ~isempty(metaData.discussion) fld = fields(metaData.discussion); n = length(fld); for i = 1:n hight = 475 - i * 25; uicontrol('Parent',ddiscussion, 'Position',[10, hight, 146, 20], 'String',fld{i}, 'Style','text'); HD(i) = uicontrol('Parent',ddiscussion, 'Callback',{@discussionCb, i}, 'Position',[110, hight, 650, 20], 'Style','edit', 'String',metaData.discussion.(fld{i})); if ~isfield(metaData.bibkey, fld{i}) metaData.bibkey.(fld{i}) = []; end HDb(i) = uicontrol('Parent',ddiscussion, 'Callback',{@discussionCb, i}, 'Position',[800, hight, 80, 20], 'Style','edit', 'String',metaData.bibkey.(fld{i})); uicontrol('Parent',ddiscussion, 'Callback',{@deleteCb,'discussion',i,ddiscussion}, 'Position',[920, hight, 20, 20], 'String','X', 'ForegroundColor',[1 0 0], 'FontWeight','bold'); end end case 'facts' dfacts = dialog('Position',[350 150 1000 550], 'Name','facts dlg'); uicontrol('Parent',dfacts, 'Callback',{@OKCb,dfacts}, 'Position',[30 500 20 20], 'String','OK'); HF = uicontrol('Parent',dfacts, 'Callback',{@addFactCb,dfacts}, 'Position',[110 500 150 20], 'String','add fact', 'Style','pushbutton'); uicontrol('Parent',dfacts, 'Position',[760 500 146 20], 'String','bibkey', 'Style','text'); if ~isempty(metaData.facts) fld = fields(metaData.facts); n = length(fld); for i = 1:n hight = 475 - i * 25; uicontrol('Parent',dfacts, 'Position',[10, hight, 146, 20], 'String',fld{i}, 'Style','text'); HF(i) = uicontrol('Parent',dfacts, 'Callback',{@factsCb, i}, 'Position',[110, hight, 650, 20], 'Style','edit', 'String',metaData.facts.(fld{i})); HFb(i) = uicontrol('Parent',dfacts, 'Callback',{@factsCb, i}, 'Position',[800, hight, 80, 20], 'Style','edit', 'String',metaData.bibkey.(fld{i})); uicontrol('Parent',dfacts, 'Callback',{@deleteCb,'facts',i,dfacts}, 'Position',[920, hight, 20, 20], 'String','X', 'ForegroundColor',[1 0 0], 'FontWeight','bold'); end end case 'acknowledgment' dacknowledgment = dialog('Position',[350 150 700 150], 'Name','acknowledgment dlg'); uicontrol('Parent',dacknowledgment, 'Position',[10 95 146 20], 'String','Text', 'Style','text'); uicontrol('Parent',dacknowledgment, 'Callback',{@OKCb,dacknowledgment}, 'Position',[110 70 20 20], 'String','OK'); HK = uicontrol('Parent',dacknowledgment, 'Callback',@acknowledgmentCb, 'Position',[110 95 550 20], 'Style','edit', 'String',metaData.acknowledgment); case 'links' dlinks = dialog('Position',[350 150 350 350],'Name','links dlg'); links = {... % general links 'https://www.catalogueoflife.org/col/' 'https://www.itis.gov/' 'https://eol.org/' 'https://en.wikipedia.org/wiki/' 'https://animaldiversity.org/' 'http://taxonomicon.taxonomy.nl/' 'https://marinespecies.org/' % taxon-specific links 'https://www.molluscabase.org/' 'https://www.ntnu.no/ub/scorpion-files/' 'https://wsc.nmbe.ch/' 'https://www.collembola.org/' 'http://Orthoptera.SpeciesFile.org' 'http://phasmida.speciesfile.org/' 'http://aphid.speciesfile.org/' 'https://diptera.info/' 'http://www.nhm.ac.uk/our-science/data/lepindex/' 'https://www.fishbase.org/' 'https://amphibiaweb.org/search/' 'https://reptile-database.reptarium.cz/' 'https://avibase.bsc-eoc.org/' 'http://datazone.birdlife.org/' 'https://www.departments.bucknell.edu/biology/resources/msw3/' 'https://genomics.senescence.info/'}; if ~handfilled % if taxonomy is handfilled include all websites and fill with empty select_id(1:7) = true; % general websites if isfield(metaData.links, 'id_CoL') && isempty(metaData.links.id_CoL) metaData.links.id_CoL = get_id_CoL(metaData.species); end if isfield(metaData.links, 'id_ITIS') && isempty(metaData.links.id_ITIS) % metaData.links.id_ITIS = get_id_ITIS(metaData.species); % the ITIS website is frequently not responding and holds progress end if isfield(metaData.links, 'id_EoL') && isempty(metaData.links.id_EoL) metaData.links.id_EoL = get_id_EoL(metaData.species); end if isfield(metaData.links, 'id_Wiki') && isempty(metaData.links.id_Wiki) metaData.links.id_Wiki = get_id_Wiki(metaData.species); end if isfield(metaData.links, 'id_ADW') && isempty(metaData.links.id_ADW) metaData.links.id_ADW = get_id_ADW(metaData.species); end if isfield(metaData.links, 'id_Taxo') && isempty(metaData.links.id_Taxo) metaData.links.id_Taxo = get_id_Taxo(metaData.species); end if isfield(metaData.links, 'id_WoRMS') && isempty(metaData.links.id_WoRMS) metaData.links.id_WoRMS = get_id_WoRMS(metaData.species); end select_id(8:23) = false; % taxon-specific websites if ~isempty(metaData.phylum) && ismember(metaData.phylum, 'Mollusca') && isempty(metaData.links.id_molluscabase) select_id(8) = true; metaData.links.id_molluscabase = get_id_molluscabase(metaData.species); end if ~isempty(metaData.order) && ismember(metaData.order, 'Scorpiones') && isempty(metaData.links.id_scorpion) select_id(9) = true; metaData.links.id_scorpion = get_id_scorpion(metaData.species); end if ~isempty(metaData.order) && ismember(metaData.order, 'Araneae') && isempty(metaData.links.id_spider) select_id(10) = true; metaData.links.id_spider = get_id_spider(metaData.species); end if ~isempty(metaData.class) && ismember(metaData.class, 'Entognatha') && isempty(metaData.links.id_collembola) select_id(11) = true; metaData.links.id_collembola = get_id_collembola(metaData.species); end if ~isempty(metaData.order) && ismember(metaData.order, 'Orthoptera') && isempty(metaData.links.id_orthoptera) select_id(12) = true; metaData.links.id_orthoptera = get_id_orthoptera(metaData.species); end if ~isempty(metaData.order) && ismember(metaData.order, 'Phasmatodea') && isempty(metaData.links.id_phasmida) select_id(13) = true; metaData.links.id_phasmida = get_id_phasmida(metaData.species); end if ~isempty(metaData.family) && ismember(metaData.family, 'Aphididae') && isempty(metaData.links.id_aphid) select_id(14) = true; metaData.links.id_aphid = get_id_aphid(metaData.species); end if ~isempty(metaData.order) && ismember(metaData.order, 'Diptera') && isempty(metaData.links.id_diptera) select_id(15) = true; metaData.links.id_diptera = get_id_diptera(metaData.species); end if ~isempty(metaData.order) && ismember(metaData.order, 'Lepidoptera') && isempty(metaData.links.id_lepidoptera) select_id(16) = true; metaData.links.id_lepidoptera = get_id_lepidoptera(metaData.species); end if ~isempty(metaData.class) && ismember(metaData.class, {'Cyclostomata', 'Chondrichthyes', 'Actinopterygii', 'Actinistia', 'Dipnoi'}) && isempty(metaData.links.id_fishbase) select_id(17) = true; metaData.links.id_fishbase = get_id_fishbase(metaData.species); end if ~isempty(metaData.class) && ismember(metaData.class, 'Amphibia') && isempty(metaData.links.id_amphweb) select_id(18) = true; metaData.links.id_amphweb = get_id_amphweb(metaData.species); end if ~isempty(metaData.class) && ismember(metaData.class, {'Reptilia','Squamata','Testudines','Crocodilia'}) && isempty(metaData.links.id_ReptileDB) select_id(19) = true; metaData.links.id_ReptileDB = get_id_ReptileDB(metaData.species); end if ~isempty(metaData.class) && ismember(metaData.class, 'Aves') && isempty(metaData.links.id_avibase) select_id(20) = true; metaData.links.id_avibase = get_id_avibase(metaData.species); end if ~isempty(metaData.class) && ismember(metaData.class, 'Aves') && isempty(metaData.links.id_birdlife) select_id(21) = true; metaData.links.id_birdlife = get_id_birdlife(metaData.species); end if ~isempty(metaData.class) && ismember(metaData.class, 'Mammalia') && isempty(metaData.links.id_MSW3) select_id(22) = true; metaData.links.id_MSW3 = get_id_MSW3(metaData.species); end if ~isempty(metaData.class) && ismember(metaData.class, {'Amphibia','Reptilia','Squamata','Testudines','Crocodilia','Aves','Mammalia'}) && isempty(metaData.links.id_AnAge) select_id(23) = true; metaData.links.id_AnAge = get_id_AnAge(metaData.species); end end select_id = logical(select_id); ID_links = id_links(select_id); Links = links(select_id); n_Links = length(ID_links); for i= 1:n_Links if i>1 && ~handfilled web(Links{i},'-browser'); end hight = 275 - i * 25; if ~isfield(metaData.links, ID_links{i}) metaData.links.(ID_links{i}) = []; end uicontrol('Parent',dlinks, 'Position',[0, hight, 146, 20], 'String',ID_links{i}, 'Style','text'); uicontrol('Parent',dlinks, 'Callback',{@OKCb,dlinks}, 'Position',[110 10 20 20], 'Style','pushbutton', 'String','OK'); if i == 1 && ~handfilled Hlinks(1) = uicontrol('Parent',dlinks, 'Position',[110, hight, 210, 20], 'Style','text', 'String',metaData.links.(ID_links{i})); else Hlinks(i) = uicontrol('Parent',dlinks, 'Callback',{@linksCb,ID_links,i}, 'Position',[110, hight, 210, 20], 'Style','edit', 'String',metaData.links.(ID_links{i})); end end case 'biblist' bibTypeList.article = {'author', 'title', 'journal', 'year', 'volume', 'pages', 'doi', 'url'}; bibTypeList.book = {'author', 'title', 'publisher', 'year', 'series', 'volume', 'isbn', 'url'}; bibTypeList.incollection = {'author', 'title', 'editor', 'booktitle', 'publisher', 'year', 'series', 'volume', 'isbn', 'url'}; bibTypeList.mastersthesis = {'author', 'title', 'school', 'year', 'address', 'doi', 'isbn', 'url'}; bibTypeList.phdthesis = {'author', 'title', 'school', 'year', 'address', 'doi', 'isbn', 'url'}; bibTypeList.techreport = {'author', 'title', 'institution', 'year', 'address', 'series', 'volume', 'doi', 'isbn', 'url'}; bibTypeList.misc = {'author', 'note', 'year', 'doi', 'isbn', 'url'}; dbiblist = dialog('Position',[350 100 250 700], 'Name','biblist dlg'); uicontrol('Parent',dbiblist, 'Position',[ 10 670 50 20], 'Callback',{@OKCb,dbiblist}, 'Style','pushbutton', 'String','OK'); uicontrol('Parent',dbiblist, 'Position',[70 670 100 20], 'Callback',{@addBibCb,dbiblist}, 'String','add bib item', 'Style','pushbutton'); if ~isempty(metaData.biblist) fld = fields(metaData.biblist); n = length(fld); for i = 1:n hight = 650 - i * 25; Hb(i) = uicontrol('Parent',dbiblist, 'Position',[ 10, hight, 100, 20], 'Style','text', 'String',fld{i}); % name uicontrol('Parent',dbiblist, 'Callback',{@DbCb,bibTypeList,i}, 'Position',[100, hight, 70 20], 'Style','pushbutton', 'String','edit'); uicontrol('Parent',dbiblist, 'Callback',{@deleteCb,'biblist',fld{i},dbiblist}, 'Position',[200, hight, 20, 20], 'String','X', 'ForegroundColor',[1 0 0], 'FontWeight','bold'); end end case 'data_0' code0 = { ... % code-name, units, temp-dependence, description 'ah', 'd', 1, 'age at hatch'; 'ab', 'd', 1, 'age at birth'; 'tx', 'd', 1, 'time since birth at weaning'; 't1', 'd', 1, 'time since birth at 1st instar'; 't2', 'd', 1, 'time since 1st instar at 2nd instar'; 't3', 'd', 1, 'time since 2nd instar at 3rd instar'; 't4', 'd', 1, 'time since 3rd instar at 4th instar'; 't5', 'd', 1, 'time since 4th instar at 5th instar'; 't6', 'd', 1, 'time since 5th instar at 6th instar'; 'tj', 'd', 1, 'time since birth at end acceleration'; 'tp', 'd', 1, 'time since birth at puberty'; 'tpm', 'd', 1, 'time since birth at puberty for males'; 'tR', 'd', 1, 'time since birth at first egg production'; 'te', 'd', 1, 'time since pupation at emergence'; 'am', 'd', 1, 'life span'; 'Lh', 'cm', 0, 'length at hatch'; 'Lb', 'cm', 0, 'length at birth' 'L1', 'cm', 0, 'length at 1st instar after birth' 'L2', 'cm', 0, 'length at 2nd instar' 'L3', 'cm', 0, 'length at 3rd instar' 'L4', 'cm', 0, 'length at 4th instar' 'L5', 'cm', 0, 'length at 5th instar' 'L6', 'cm', 0, 'length at 6th instar' 'Lx', 'cm', 0, 'length at weaning/fledging' 'Ls', 'cm', 0, 'length at start acceleration' 'Lj', 'cm', 0, 'length at end acceleration' 'Lp', 'cm', 0, 'length at puberty'; 'Lpm', 'cm', 0, 'length at puberty for males'; 'Li', 'cm', 0, 'ultimate length'; 'Lim', 'cm', 0, 'ultimate length for males'; 'Le', 'cm', 0, 'length of imago'; 'Ww0', 'g', 0, 'initial wet weight'; 'Wwh', 'g', 0, 'wet weight at hatch'; 'Wwb', 'g', 0, 'wet weight at birth'; 'Ww1', 'g', 0, 'wet weight at 1st instar after birth'; 'Ww2', 'g', 0, 'wet weight at 2nd instar'; 'Ww3', 'g', 0, 'wet weight at 3rd instar'; 'Ww4', 'g', 0, 'wet weight at 4th instar'; 'Ww5', 'g', 0, 'wet weight at 5th instar'; 'Ww6', 'g', 0, 'wet weight at 6th instar'; 'Wwx', 'g', 0, 'wet weight at weaning/fledging' 'Wws', 'g', 0, 'wet weight at start acceleration' 'Wwj', 'g', 0, 'wet weight at end acceleration'; 'Wwp', 'g', 0, 'wet weight at puberty'; 'Wwpm', 'g', 0, 'wet weight at puberty for males'; 'Wwi', 'g', 0, 'ultimate wet weight'; 'Wwim', 'g', 0, 'ultimate wet weight for males'; 'Wwe', 'g', 0, 'wet weight of imago'; 'Wdh', 'g', 0, 'dry weight at hatch'; 'Wdb', 'g', 0, 'dry weight at birth'; 'Wd1', 'g', 0, 'dry weight at 1st instar after birth'; 'Wd2', 'g', 0, 'dry weight at 2nd instar'; 'Wd3', 'g', 0, 'dry weight at 3rd instar'; 'Wd4', 'g', 0, 'dry weight at 4th instar'; 'Wd5', 'g', 0, 'dry weight at 5th instar'; 'Wd6', 'g', 0, 'dry weight at 6th instar'; 'Wdx', 'g', 0, 'dry weight at weaning/fledging' 'Wds', 'g', 0, 'dry weight at start acceleration' 'Wdj', 'g', 0, 'dry weight at end acceleration'; 'Wdp', 'g', 0, 'dry weight at puberty'; 'Wdpm', 'g', 0, 'dry weight at puberty for males'; 'Wdi', 'g', 0, 'ultimate dry weight'; 'Wdim', 'g', 0, 'ultimate dry weight for males'; 'Wde', 'g', 0, 'dry weight of imago'; 'E0', 'J', 0, 'initial energy content'; 'Ri', '#/d', 1, 'ultimate reproduction rate'; 'GSI', 'mol E_R/mol W', 1, 'Gonado-Somatic Index as fraction' }; ddata_0 = dialog('Position',[350 35 1050 620], 'Name','0-variate data dlg'); uicontrol('Parent',ddata_0, 'Position',[ 60 580 50 20], 'Callback',{@OKCb,ddata_0}, 'Style','pushbutton', 'String','OK'); uicontrol('Parent',ddata_0, 'Position',[400 580 150 20], 'Callback',{@add0Cb,code0,ddata_0}, 'String','add 0-var data', 'Style','pushbutton'); uicontrol('Parent',ddata_0, 'Position',[ 60 550 70 20], 'String','name', 'Style','text'); uicontrol('Parent',ddata_0, 'Position',[140 550 70 20], 'String','value', 'Style','text'); uicontrol('Parent',ddata_0, 'Position',[200 550 70 20], 'String','units', 'Style','text'); uicontrol('Parent',ddata_0, 'Position',[260 550 70 20], 'String','temp in C', 'Style','text'); uicontrol('Parent',ddata_0, 'Position',[390 550 70 20], 'String','label', 'Style','text'); uicontrol('Parent',ddata_0, 'Position',[550 550 70 20], 'String','bibkey', 'Style','text'); uicontrol('Parent',ddata_0, 'Position',[640 550 70 20], 'String','comment', 'Style','text'); if ~isempty(data.data_0) fld = fields(data.data_0); n = length(fld); for i = 1:n hight = 550 - i * 25; uicontrol('Parent',ddata_0, 'Position',[ 60, hight, 70, 20], 'Style','text', 'String',fld{i}); % name H0v(i) = uicontrol('Parent',ddata_0, 'Callback',{@d0Cb,i}, 'Position',[150, hight, 70, 20], 'Style','edit', 'String',num2str(data.data_0.(fld{i}))); % value H0u(i) = uicontrol('Parent',ddata_0, 'Position',[230, hight, 30, 20], 'Style','text', 'String',txtData.units.(fld{i})); % units if isfield(auxData.temp, fld{i}) H0T(i) = uicontrol('Parent',ddata_0, 'Callback',{@d0Cb,i}, 'Position',[270, hight, 40, 20], 'Style','edit', 'String',num2str(K2C(auxData.temp.(fld{i})))); % temp(C) else H0T(i) = uicontrol('Parent',ddata_0, 'Position',[270, hight, 40, 20], 'Style','text', 'String',''); end H0l(i) = uicontrol('Parent',ddata_0, 'Position',[320, hight, 220, 20], 'Style','text', 'String',txtData.label.(fld{i})); % label H0b(i) = uicontrol('Parent',ddata_0, 'Callback',{@d0Cb,i}, 'Position',[550, hight, 70, 20], 'Style','edit', 'String',cell2str(txtData.bibkey.(fld{i}))); % bibkey % if ~isfield(txtData.comment, fld{i}) % txtData.comment.(fld{i}) = []; % end H0c(i) = uicontrol('Parent',ddata_0, 'Callback',{@d0Cb,i}, 'Position',[650, hight, 300, 20], 'Style','edit', 'String',txtData.comment.(fld{i})); % comment uicontrol('Parent',ddata_0, 'Callback',{@deleteCb,'data_0',fld{i},ddata_0}, 'Position',[1000, hight, 20, 20], 'String','X', 'ForegroundColor',[1 0 0], 'FontWeight','bold'); end end case 'data_1' code1 = { ... % column 3 stands for yes-or-no temperature 'LWw', {'cm','g'}, 0, {'length','wet weight'}, ''; 'LWw_f', {'cm','g'}, 0, {'length','wet weight'}, 'Data for females'; 'LWw_m', {'cm','g'}, 0, {'length','wet weight'}, 'Data for males'; 'LWd', {'cm','g'}, 0, {'length','dry weight'}, ''; 'LWd_f', {'cm','g'}, 0, {'length','dry weight'}, 'Data for females'; 'LWd_m', {'cm','g'}, 0, {'length','dry weight'}, 'Data for males'; 'tL', {'d','cm'}, 1, {'time','length'}, ''; 'tL_f' {'d','cm'}, 1, {'time','length'}, 'Data for females'; 'tL_m' {'d','cm'}, 1, {'time','length'}, 'Data for males'; 'tWw', {'d', 'g'}, 1, {'time','wet weight'}, ''; 'tWw_f', {'d', 'g'}, 1, {'time','wet weight'}, 'Data for females'; 'tWw_m', {'d', 'g'}, 1, {'time','wet weight'}, 'Data for males'; 'tWd', {'d', 'g'}, 1, {'time','dry weight'}, ''; 'tWd_f', {'d', 'g'}, 1, {'time','dry weight'}, 'Data for females'; 'tWd_m', {'d', 'g'}, 1, {'time','dry weight'}, 'Data for males'; 'LdL', {'cm','cm/d'}, 1, {'length','change in length'}, ''; 'LdL_f', {'cm','cm/d'}, 1, {'length','change in length'}, 'Data for females'; 'LdL_m', {'cm','cm/d'}, 1, {'length','change in length'}, 'Data for males'; 'LN', {'cm','#'}, 1, {'length','yearly fecundity'}, ''; 'WwN', {'g','#'}, 1, {'wet weight','yearly fecundity'}, ''; 'WdN', {'g','#'}, 1, {'dry weight','yearly fecundity'}, ''; 'LR', {'cm','#/d'}, 1, {'length','reproduction rate'}, ''; 'WwR', {'g','#/d'}, 1, {'wet weight','reproduction rate'}, ''; 'WdR', {'g','#/d'}, 1, {'dry weight','reproduction rate'}, ''; 'LJO', {'cm','mol/d'}, 1, {'length','O2 consumption'}, ''; 'WwJO', {'g','mol/d'}, 1, {'wet weight','O2 consumption'}, ''; 'WdJO', {'g','mol/d'}, 1, {'dry weight','O2 consumption'}, ''; }; ddata_1 = dialog('Position',[350 35 520 800], 'Name','1-variate data dlg'); uicontrol('Parent',ddata_1, 'Position',[ 10 780 50 20], 'Callback',{@OKCb,ddata_1}, 'Style','pushbutton', 'String','OK'); uicontrol('Parent',ddata_1, 'Position',[150 780 150 20], 'Callback',{@add1Cb,code1,ddata_1}, 'String','add 1-var data', 'Style','pushbutton'); uicontrol('Parent',ddata_1, 'Position',[ 10 750 60 20], 'String','name', 'Style','text'); uicontrol('Parent',ddata_1, 'Position',[100 750 90 20], 'String','x-label', 'Style','text'); uicontrol('Parent',ddata_1, 'Position',[200 750 90 20], 'String','y-label', 'Style','text'); if ~isempty(data.data_1) fld = fields(data.data_1); n = length(fld); for i = 1:n hight = 750 - i * 25; uicontrol('Parent',ddata_1, 'Position',[ 10, hight, 70, 20], 'Style','text', 'String',fld{i}); % name label = txtData.label.(fld{i}); uicontrol('Parent',ddata_1, 'Position',[100, hight, 100, 20], 'Style','text', 'String',label{1}); % x-label uicontrol('Parent',ddata_1, 'Position',[200, hight, 100, 20], 'Style','text', 'String',label{2}); % y-label D1(i) = uicontrol('Parent',ddata_1, 'Callback',{@D1Cb,fld{i},i}, 'Position',[380, hight, 70 20], 'Style','pushbutton', 'String','edit'); uicontrol('Parent',ddata_1, 'Callback',{@deleteCb,'data_1',fld{i},ddata_0}, 'Position',[480, hight, 20, 20], 'String','X', 'ForegroundColor',[1 0 0], 'FontWeight','bold'); end end case 'COMPLETE' c = 'COMPLETE levels for data: Each level includes previous levels (from LikaKear2011)'; c0 = ' 0 Maximum length and body weight; weight as function of length'; c1 = ' 1 Age, length and weight at birth and puberty for one food level; mean life span (due to ageing)'; c2 = ' 2 Growth (curve) at one food level: length and weight as functions of age at constant (or abundant) food level'; c3 = ' 3 Reproduction and feeding as functions of age, length and/or weight at one food level'; c4 = ' 4 Growth (curve) at several (>1) food levels; age, length and weight at birth and puberty at several food levels'; c5 = ' 5 Reproduction and feeding as functions of age, length and/or weight at several (>1) food levels'; c6 = ' 6 Respiration as function of length or weight and life span at several (>1) food levels'; c7 = ' 7 Elemental composition at one food level, survival due to ageing as function of age'; c8 = ' 8 Elemental composition at several (>1) food levels, including composition of food'; c9 = ' 9 Elemental balances for C, H, O and N at several body sizes and several food levels'; c10 = '10 Energy balance at several body sizes and several food levels (including heat)'; dCOMPLETE = dialog('Position',[450 200 620 400], 'Name','COMPLETE dlg'); uicontrol('Parent',dCOMPLETE, 'Position',[ 10 365 600 20], 'Style','text', 'HorizontalAlignment','left', 'String',c, 'FontSize',11); uicontrol('Parent',dCOMPLETE, 'Position',[ 10 325 600 20], 'Style','text', 'HorizontalAlignment','left', 'String',c0); uicontrol('Parent',dCOMPLETE, 'Position',[ 10 300 600 20], 'Style','text', 'HorizontalAlignment','left', 'String',c1); uicontrol('Parent',dCOMPLETE, 'Position',[ 10 275 600 20], 'Style','text', 'HorizontalAlignment','left', 'String',c2); uicontrol('Parent',dCOMPLETE, 'Position',[ 10 250 600 20], 'Style','text', 'HorizontalAlignment','left', 'String',c3); uicontrol('Parent',dCOMPLETE, 'Position',[ 10 225 600 20], 'Style','text', 'HorizontalAlignment','left', 'String',c4); uicontrol('Parent',dCOMPLETE, 'Position',[ 10 200 600 20], 'Style','text', 'HorizontalAlignment','left', 'String',c5); uicontrol('Parent',dCOMPLETE, 'Position',[ 10 175 600 20], 'Style','text', 'HorizontalAlignment','left', 'String',c6); uicontrol('Parent',dCOMPLETE, 'Position',[ 10 150 600 20], 'Style','text', 'HorizontalAlignment','left', 'String',c7); uicontrol('Parent',dCOMPLETE, 'Position',[ 10 125 600 20], 'Style','text', 'HorizontalAlignment','left', 'String',c8); uicontrol('Parent',dCOMPLETE, 'Position',[ 10 100 600 20], 'Style','text', 'HorizontalAlignment','left', 'String',c9); uicontrol('Parent',dCOMPLETE, 'Position',[ 10 75 600 20], 'Style','text', 'HorizontalAlignment','left', 'String',c10); HCOMPLETE = uicontrol('Parent',dCOMPLETE, 'Position',[ 10 40 50 20], 'Callback',@COMPLETECb, 'Style','edit', 'String',metaData.COMPLETE); uicontrol('Parent',dCOMPLETE, 'Position',[ 110 40 50 20], 'Callback',{@OKCb,dCOMPLETE}, 'Style','pushbutton', 'String','OK'); case 'resume' if ismac || isunix list = strsplit(ls); list(end) = []; else list = cellstr(ls); end list_res = list(Contains(list,'results_')); n_res = length(list_res); list_backup = list_res(Contains(list_res,'_backup')); n_backup = length(list_backup); if n_backup > 0 load(list_backup{1}) AmPgui('setColors') elseif (n_res - n_backup) == 1 load(list_res{1}); AmPgui('setColors') elseif n_res == 0 fprintf('Warning from AmPgui: no results_my_pet.mat found\n'); else fprintf('Warning from AmPgui: more than a single file results_my_pet.mat found, remove the wrong ones first\n'); end case 'pause' nm = ['results_', metaData.species, '.mat']; %save(nm, 'data', 'auxData', 'metaData', 'txtData', 'color', 'select_id', 'id_links', 'eco_types'); save(nm, 'data', 'auxData', 'metaData', 'txtData', 'color', 'select_id', 'id_links', 'handfilled'); dpause = dialog('Position',[350 150 500 150],'Name','pause dlg'); uicontrol('Parent',dpause, 'Position',[ 50 95 400 20], 'String',['File ', nm, ' has been written'], 'Style','text'); uicontrol('Parent',dpause, 'Position',[80 60 150 20], 'Callback',{@stayCb,dpause}, 'String','stay in AmPgui', 'Style','pushbutton'); HAmPeps = uicontrol('Parent',dpause, 'Position',[250 60 200 20], 'Callback',{@proceedCb,dpause}, 'String','quit AmPgui, continue with AmPeps', 'Style','pushbutton'); Hquit = uicontrol('Parent',dpause, 'Position',[140 30 200 20], 'Callback',{@quitCb,{dpause,dmydata}}, 'String','quit AmPgui and AmPeps', 'Style','pushbutton'); set(HAmPeps, 'ForegroundColor',[0 0.6 0]); set(Hquit, 'ForegroundColor',[1 0 0]); end end % color settings: run this part only with AmPgui('setColors') try; close(Hwait); catch; end % close any wait warnings; function isvalid requires Toolbox Image Acquisition, Instrument control or OPC figure(dmydata); % bring the main dialog window to the front if ~any([isempty(metaData.species), isempty(metaData.family), isempty(metaData.order), isempty(metaData.class), isempty(metaData.phylum)]) color.species = [0 .6 0]; set(hspecies, 'ForegroundColor', color.species); end if any([isempty(metaData.ecoCode.climate), isempty(metaData.ecoCode.ecozone), isempty(metaData.ecoCode.habitat), ... isempty(metaData.ecoCode.embryo), isempty(metaData.ecoCode.food), isempty(metaData.ecoCode.gender), isempty(metaData.ecoCode.reprod)]) color.ecoCode = [1 0 0]; set(hecoCode, 'ForegroundColor', color.ecoCode); else color.ecoCode = [0 0.6 0]; set(hecoCode, 'ForegroundColor', color.ecoCode); end if ~isempty(metaData.T_typical) color.T_typical = [0 .6 0]; set(hT_typical, 'ForegroundColor', color.T_typical); end if isfield(metaData, 'author') && ~isempty(metaData.author) color.author = [0 .6 0]; set(hauthor, 'ForegroundColor', color.author); end if isfield(metaData, 'curator') && ~isempty(metaData.curator) color.curator = [0 .6 0]; set(hcurator, 'ForegroundColor', color.curator); end fld_male_0 = {'tpm', 'Lpm', 'Lim', 'Wwpm', 'Wwim', 'Wdpm', 'Wdim'}; fld_male_1 = {'tL_m', 'tWw_m', 'tWd_m', 'LWw_m', 'LWd_m', 'LdL_m'}; if isempty(metaData.discussion) if ~isempty(data.data_0) && any(ismember(fields(data.data_0),fld_male_0)) color.discussion = [1 0 0]; elseif ~isempty(data.data_1) && any(ismember(fields(data.data_1),fld_male_1)) color.discussion = [1 0 0]; else color.discussion = [0 0 0]; end else color.discussion = [0 0.6 0]; end set(hdiscussion, 'ForegroundColor', color.discussion); if isfield(metaData, 'facts') && ~isempty(metaData.facts) fld = fields(metaData.facts); n_fld = length(fld); color.facts = [0 .6 0]; for i = 1:n_fld if ~isfield(metaData.bibkey, fld{i}) && ~isempty(metaData.bibkey.(fld{i})) color.facts = [1 0 0]; end end end set(hfacts, 'ForegroundColor', color.facts); if isfield(metaData, 'acknowledgment') && ~isempty(metaData.acknowledgment) color.acknowledgment = [0 .6 0]; set(hacknowledgment, 'ForegroundColor', color.acknowledgment); end if ~isempty(select_id) color.links = [0 .6 0]; set(hlinks, 'ForegroundColor', color.links) end if ~isempty(data.data_0) color.data_0 = [0 0.6 0]; set(hdata_0, 'ForegroundColor', color.data_0); end if ~isempty(metaData.COMPLETE) color.COMPLETE = [0 0.6 0]; set(hCOMPLETE, 'ForegroundColor', color.COMPLETE); end if isfield(metaData, 'biblist') && ~isempty(metaData.biblist) bibitems = fields(metaData.biblist); else bibitems = {}; end bibkeys = {}; if ~isempty(data.data_0) fld = fields(data.data_0); n_fld = length(fld); for i=1:n_fld addbibkey = txtData.bibkey.(fld{i}); if iscell(addbibkey) bibkeys = [bibkeys, addbibkey{:}]; else bibkeys = [bibkeys, addbibkey]; end end bibkeys = unique(bibkeys); end if ~isempty(data.data_1) fld = fields(data.data_1); n_fld = length(fld); for i=1:n_fld addbibkey = txtData.bibkey.(fld{i}); if iscell(addbibkey) bibkeys = [bibkeys, addbibkey{:}]; else bibkeys = [bibkeys, addbibkey]; end end bibkeys = unique(bibkeys); end if ~isempty(metaData.bibkey) fld = fields(metaData.bibkey); n_fld = length(fld); for i=1:n_fld addbibkey = metaData.bibkey.(fld{i}); if iscell(addbibkey) bibkeys = [bibkeys, addbibkey{:}]; else bibkeys = [bibkeys, addbibkey]; end end bibkeys = unique(bibkeys); end bibkeys = unique(bibkeys); bibkeys_missing = bibkeys(~ismember(bibkeys,[bibitems; 'guess'])); if ~isempty(bibkeys_missing) color.biblist = [1 0 0]; fprintf(['Warning from AmPgui: missing bibitems are ', cell2str(bibkeys_missing),'\n']); else color.biblist = [0 0.6 0]; end set(hbiblist, 'ForegroundColor', color.biblist); end %% callback functions function speciesCb(~, ~, dspecies) % fill lineage automatically, see OKspeciesCb global metaData Hspecies hspecies Hfamily Horder Hclass Hphylum Hcommon Hwarning HwarningOK global color dmydata infoAmPgui list_spec handfilled lin % my_pet_lineage my_pet = strrep(get(Hspecies, 'string'), ' ', '_'); metaData.species = my_pet; handfilled = true; % don't call speciesCb again, but OKspeciesCb instead if ismember(my_pet,list_spec) % species is already in AmP set(Hfamily,'String',''); set(Horder,'String',''); set(Hclass,'String',''); set(Hphylum,'String',''); set(Hcommon,'String',''); set(Hwarning, 'String', 'species is already in AmP'); set(HwarningOK, 'String','OK proceeds to post-editing phase of AmPeps'); hleave = uicontrol('Parent',dspecies, 'Position',[40 15 20 20], 'Callback',{@leaveCb,{dspecies,dmydata}}, 'Style','pushbutton', 'String','OK'); infoAmPgui = 0; set(hleave, 'ForegroundColor', [1 0 0]); return end [id, id_txt, my_pet_acc, lin, rank] = get_id(my_pet); n_id = length(id); for i=1:n_id; metaData.links.(id_txt{i}) = id{i}; end for i=1:4; metaData.(rank{i}) = lin{i}; end if ~strcmp(my_pet_acc,my_pet); fprinf('Warning from AmPgui: species name is not accepted\n'); end nms = {}; % common name: prefer CoL, then Taxo if ~isempty(metaData.links.id_CoL); nms = get_common_CoL(metaData.links.id_CoL); end if isempty(nms) && ~isempty(metaData.links.id_Taxo); nms = get_common_Taxo(metaData.links.id_Taxo); end if isempty(nms) metaData.species_en = 'no_english_name'; else metaData.species_en = nms{1}; end set(Hfamily, 'String',metaData.family); set(Horder, 'String',metaData.order); set(Hclass, 'String',metaData.class); set(Hphylum, 'String',metaData.phylum); set(Hcommon, 'String',metaData.species_en); color.species = [0 0.6 0]; set(hspecies, 'ForegroundColor', color.species); frames = java.awt.Frame.getFrames(); frames(end).setAlwaysOnTop(1); frames(end-1).setAlwaysOnTop(1); infoAmPgui = 1; close(dspecies); AmPgui('setColors') AmPgui('species') % repeat case species, but now with run OKspeciesCb because handfilled is true end function OKspeciesCb(~, ~, dspecies) % fill/correct lineage manually global metaData Hspecies Hfamily Horder Hclass Hphylum Hcommon Hwarning HwarningOK %handfilled %handfilled = true; % taxonomy handfilled, links also filled manually my_pet = strrep(get(Hspecies, 'string'), ' ', '_'); metaData.species = my_pet; uicontrol('Parent',dspecies, 'Position',[10 110 60 20], 'Style','text', 'String','family: '); Hfamily = uicontrol('Parent',dspecies, 'Callback',@familyCb, 'Position',[70 110 90 20], 'Style','edit', 'String',metaData.family); uicontrol('Parent',dspecies, 'Position',[160 110 60 20], 'Style','text', 'String','order: '); Horder = uicontrol('Parent',dspecies, 'Callback',@orderCb, 'Position',[220 110 90 20], 'Style','edit', 'String',metaData.order); uicontrol('Parent',dspecies, 'Position',[310 110 60 20], 'Style','text', 'String','class: '); Hclass = uicontrol('Parent',dspecies, 'Callback',@classCb, 'Position',[370 110 140 20], 'Style','edit', 'String',metaData.class); uicontrol('Parent',dspecies, 'Position',[10 80 60 20], 'Style','text', 'String','phylum: '); Hphylum = uicontrol('Parent',dspecies, 'Callback',@phylumCb, 'Position',[80 80 90 20], 'Style','edit', 'String',metaData.phylum); uicontrol('Parent',dspecies, 'Position',[200 80 120 20], 'Style','text', 'String','common name: '); Hcommon = uicontrol('Parent',dspecies, 'Callback',@species_enCb, 'Position',[350 80 160 20], 'Style','edit', 'String',metaData.species_en); Hspecies = uicontrol('Parent',dspecies, 'Callback',{@speciesCb,dspecies}, 'Position',[110 15 350 20], 'Style','edit', 'String',metaData.species); set(Hwarning, 'String',''); set(HwarningOK, 'String',''); uicontrol('Parent',dspecies, 'Position',[40 15 20 20], 'Callback',{@OKlineageCb,dspecies}, 'Style','pushbutton', 'String','OK'); AmPgui('setColors') end function OKlineageCb(~, ~, dspecies) % check manually-filled lineage persistent list_genus list_family list_order list_class list_phylum global metaData Hwarning HwarningOK infoAmPgui Hwait lin % the lowest level in the manually filled dialog window dspecies that is in AmP is used; % higher levels are overwritten by those in the AmP lineage set(Hwarning, 'String','checking lineage, see Matlab window'); Hwait = waitbar(0,'Please wait for checking lineage ...'); if isempty(list_genus) list_genus = list_taxa('',3); waitbar(0.2,Hwait); list_family = list_taxa('',4); waitbar(0.4,Hwait); list_order = list_taxa('',5); waitbar(0.6,Hwait); list_class = list_taxa('',6); waitbar(0.8,Hwait); list_phylum = list_taxa('',7); waitbar(1.0,Hwait); end genus = strsplit(metaData.species,'_'); genus = genus{1}; if ismember(genus, list_genus) fprintf(['Genus "', genus, '" is present in AmP\n']) infoAmPgui = 2; metaData.family = lin{4}; metaData.order = lin{3}; metaData.class = lin{2}; metaData.phylum = lin{1}; elseif ismember(metaData.family, list_family) fprintf(['Genus is not present in AmP, but family "', metaData.family, '" is\n']) infoAmPgui = 3; list_lin = lineage_short(metaData.family); metaData.order = list_lin{4}; metaData.class = list_lin{3}; metaData.phylum = list_lin{2}; elseif ismember(metaData.order, list_order) fprintf(['Family is not present in AmP, but order "', metaData.order, '" is\n']) infoAmPgui = 4; list_lin = lineage(metaData.order); metaData.class = cell2str(list_class(ismember(list_class,list_lin))); metaData.phylum = cell2str(list_phylum(ismember(list_phylum,list_lin))); elseif ismember(metaData.class, list_class) fprintf(['Order is not present in AmP, but class "', metaData.class, '" is\n']) infoAmPgui = 5; list_lin = lineage(metaData.class); metaData.phylum = cell2str(list_phylum(ismember(list_phylum,list_lin))); elseif ismember(metaData.phylum, list_phylum) fprintf(['Class is not present in AmP, but phylum "', metaData.phylum, '" is\n']) infoAmPgui = 6; else fprintf(['Phylum "', metaData.phylum, '" is not present in AmP!\n']) infoAmPgui = 7; end close(dspecies); AmPgui('color') end function familyCb(~, ~) global metaData Hfamily metaData.family = get(Hfamily, 'string'); end function orderCb(~, ~) global metaData Horder metaData.order = get(Horder, 'string'); end function classCb(~, ~) global metaData Hclass metaData.class = get(Hclass, 'string'); end function phylumCb(~, ~) global metaData Hphylum metaData.phylum = get(Hphylum, 'string'); end function species_enCb(~, ~) global metaData Hcommon metaData.species_en = get(Hcommon, 'string'); end function climateCb(~, ~, Hclimate) global metaData eco_types hclimateLand hclimateSea set(hclimateLand,'Position',[250 20 1200 850]); % climate figure large size set(hclimateSea,'Position',[250 20 1200 850]); % climate figure large size climateCode = fields(eco_types.climate); n_climate = length(climateCode); if isempty(metaData.ecoCode.climate) i_climate = 1; else i_climate = 1:n_climate; sel_climate = ismember(climateCode,metaData.ecoCode.climate); i_climate = i_climate(sel_climate); end i_climate = listdlg('ListString',climateCode, 'Name','climate dlg', 'ListSize',[205 450], 'InitialValue',i_climate); metaData.ecoCode.climate = climateCode(i_climate); set(Hclimate, 'String', cell2str(metaData.ecoCode.climate)); set(hclimateLand,'Position',[300 450 500 300]); % climate figure normal size set(hclimateSea, 'Position',[900 450 500 300]); % climate figure normal size AmPgui('setColors') end function ecozoneCb(~, ~, Hecozone) global metaData eco_types hecozones hoceans set(hecozones,'Position',[250 20 1200 850]); % ecozone figures large size set(hoceans, 'Position',[250 20 1200 850]); % ecozone figures large size ecozoneCode = fields(eco_types.ecozone); n_ecozone = length(ecozoneCode); ecozoneCodeList = ecozoneCode; for i=1:n_ecozone ecozoneCodeList{i} = [ecozoneCodeList{i}, ': ', eco_types.ecozone.(ecozoneCode{i})]; end if isempty(metaData.ecoCode.ecozone) i_ecozone = 1; else i_ecozone = 1:n_ecozone; sel_ecozone = ismember(ecozoneCode,metaData.ecoCode.ecozone); i_ecozone = i_ecozone(sel_ecozone); end i_ecozone = listdlg('ListString', ecozoneCodeList,'Name', 'ecozone dlg','ListSize',[450 500], 'InitialValue',i_ecozone); metaData.ecoCode.ecozone = ecozoneCode(i_ecozone); set(Hecozone, 'String', cell2str(metaData.ecoCode.ecozone)); set(hecozones,'Position',[300 50 500 300]); % ecozone figures normal size set(hoceans, 'Position',[900 50 500 300]); % ecozone figures normal size AmPgui('setColors') end function habitatCb(~, ~, Hhabitat) global metaData eco_types habitatCode = fields(eco_types.habitat); n_habitat = length(habitatCode); habitatCodeList = habitatCode; for i=1:n_habitat habitatCodeList{i} = [habitatCodeList{i}, ': ', eco_types.habitat.(habitatCode{i})]; end if isempty(metaData.ecoCode.habitat) i_habitat = 1; else code = metaData.ecoCode.habitat; n_code = length(code); for i = 1:n_code; Code = code{i}; code{i} = Code(3:end); end % remove stage codes i_habitat = 1:n_habitat; i_habitat = i_habitat(i_habitat(ismember(habitatCode,code))); end i_habitat = listdlg('ListString',habitatCodeList, 'Name','habitat dlg', 'ListSize',[400 500], 'InitialValue',i_habitat); habitatCode = prependStage(i_habitat, habitatCode, habitatCodeList, 'habitat'); metaData.ecoCode.habitat = habitatCode; set(Hhabitat, 'String', cell2str(metaData.ecoCode.habitat)); AmPgui('setColors') end function embryoCb(~, ~, Hembryo) global metaData eco_types embryoCode = fields(eco_types.embryo); n_embryo = length(embryoCode); embryoCodeList = embryoCode; for i=1:n_embryo embryoCodeList{i} = [embryoCodeList{i}, ': ', eco_types.embryo.(embryoCode{i})]; end if isempty(metaData.ecoCode.embryo) i_embryo = 1; else i_embryo = 1:n_embryo; i_embryo = i_embryo(i_embryo(ismember(embryoCode,metaData.ecoCode.embryo))); end i_embryo = listdlg('ListString',embryoCodeList, 'Name','embryo dlg', 'ListSize',[450 500], 'InitialValue',i_embryo); metaData.ecoCode.embryo = embryoCode(i_embryo); set(Hembryo, 'String', cell2str(metaData.ecoCode.embryo)); AmPgui('setColors') end function migrateCb(~, ~, Hmigrate) global metaData eco_types migrateCode = fields(eco_types.migrate); n_migrate = length(migrateCode); migrateCodeList = migrateCode; for i=1:n_migrate migrateCodeList{i} = [migrateCodeList{i}, ': ', eco_types.migrate.(migrateCode{i})]; end migrateCode = [' '; migrateCode]; migrateCodeList = [' no migration/torpor'; migrateCodeList]; if isempty(metaData.ecoCode.migrate) i_migrate = 1; else i_migrate = 1:n_migrate; i_migrate = i_migrate(i_migrate(ismember(migrateCode,metaData.ecoCode.migrate))); end i_migrate = listdlg('ListString',migrateCodeList, 'Name','migrate dlg', 'ListSize',[600 180], 'InitialValue',i_migrate); metaData.ecoCode.migrate = migrateCode(i_migrate); set(Hmigrate, 'String', cell2str(metaData.ecoCode.migrate)); AmPgui('setColors') end function foodCb(~, ~, Hfood) global metaData eco_types foodCode = fields(eco_types.food); n_food = length(foodCode); foodCodeList = foodCode; for i=1:n_food foodCodeList{i} = [foodCodeList{i}, ': ', eco_types.food.(foodCode{i})]; end if isempty(metaData.ecoCode.food) i_food = 1; else code = metaData.ecoCode.food; n_code = length(code); for i = 1:n_code; Code = code{i}; code{i} = Code(3:end); end; % remove stage codes i_food = 1:n_food; i_food = i_food(i_food(ismember(foodCode,code))); end i_food = listdlg('ListString',foodCodeList, 'Name','food dlg', 'ListSize',[600 500], 'InitialValue',i_food); foodCode = prependStage(i_food, foodCode, foodCodeList, 'food'); metaData.ecoCode.food = foodCode; set(Hfood, 'String', cell2str(metaData.ecoCode.food)); AmPgui('setColors') end function genderCb(~, ~, Hgender) global metaData eco_types genderCode = fields(eco_types.gender); n_gender = length(genderCode); genderCodeList = genderCode; for i=1:n_gender genderCodeList{i} = [genderCodeList{i}, ': ', eco_types.gender.(genderCode{i})]; end if isempty(metaData.ecoCode.gender) i_gender = 1; else i_gender = 1:n_gender; i_gender = i_gender(i_gender(ismember(genderCode,metaData.ecoCode.gender))); end i_gender = listdlg('ListString',genderCodeList, 'Name','gender dlg', 'ListSize',[600 190], 'InitialValue',i_gender); metaData.ecoCode.gender = genderCode(i_gender); set(Hgender, 'String', cell2str(metaData.ecoCode.gender)); AmPgui('setColors') end function reprodCb(~, ~, Hreprod) global metaData eco_types reprodCode = fields(eco_types.reprod); n_reprod = length(reprodCode); reprodCodeList = reprodCode; for i=1:n_reprod reprodCodeList{i} = [reprodCodeList{i}, ': ', eco_types.reprod.(reprodCode{i})]; end if isempty(metaData.ecoCode.reprod) i_reprod = 1; else i_reprod = 1:n_reprod; i_reprod = i_reprod(i_reprod(ismember(reprodCode,metaData.ecoCode.reprod))); end i_reprod = listdlg('ListString',reprodCodeList, 'Name','reprod dlg', 'ListSize',[600 120], 'InitialValue',i_reprod); metaData.ecoCode.reprod = reprodCode(i_reprod); set(Hreprod, 'String', cell2str(metaData.ecoCode.reprod)); AmPgui('setColors') end function T_typicalCb(~, ~) global metaData HT metaData.T_typical = C2K(str2double(get(HT, 'string'))); AmPgui('setColors') end function authorCb(~, ~) global metaData Hauthor metaData.author = str2cell(get(Hauthor, 'string')); AmPgui('setColors') end function emailCb(~, ~) global metaData Hemail metaData.email = get(Hemail, 'string'); end function addressCb(~, ~) global metaData Haddress metaData.address = get(Haddress, 'string'); end function addDiscussionCb(~, ~, ddiscussion) global metaData if isfield(metaData.discussion, 'D1') n = 1 + length(fields(metaData.discussion)); else n = 1; end nm = ['D', num2str(n)]; metaData.discussion.(nm) = []; metaData.bibkey.(nm) = []; delete(ddiscussion) AmPgui('discussion') end function discussionCb(~, ~, i) global metaData HD HDb nm = ['D', num2str(i)]; metaData.discussion.(nm) = get(HD(i), 'string'); metaData.bibkey.(nm) = str2cell(get(HDb(i), 'string')); end function addFactCb(~, ~, dfacts) global metaData if isfield(metaData.facts, 'F1') n = 1 + length(fields(metaData.facts)); else n = 1; end nm = ['F', num2str(n)]; metaData.facts.(nm) = []; metaData.bibkey.(nm) = []; delete(dfacts) AmPgui('facts') end function factsCb(~, ~, i) global metaData HF HFb nm = ['F', num2str(i)]; metaData.facts.(nm) = get(HF(i), 'string'); metaData.bibkey.(nm) = str2cell(get(HFb(i), 'string')); end function acknowledgmentCb(~, ~) global metaData HK metaData.acknowledgment = get(HK, 'string'); end function linksCb(~, ~, id_links,i) global metaData Hlinks metaData.links.(id_links{i}) = get(Hlinks(i), 'string'); end function addBibCb(~, ~, dbiblist) % create new bibitem in biblist with bibkey "new" global metaData metaData.biblist.new = []; delete(dbiblist) AmPgui('biblist') end function DbCb(~, ~, bibTypeList, i_bibkey) % present bibitem to allow filling of fields global metaData Dbb Dbi Db bibkey = fields(metaData.biblist); bibkey = bibkey{i_bibkey}; Db = dialog('Position',[350 320 800 320], 'Name','bibitem dlg'); uicontrol('Parent',Db, 'Position',[ 20 280 50 20], 'Callback',{@OKCb,Db}, 'Style','pushbutton', 'String','OK'); uicontrol('Parent',Db, 'Position',[100 280 50 20], 'Style','text', 'String','bibkey: '); Dbb = uicontrol('Parent',Db, 'Position',[160 280 80 20], 'Callback',{@bibkeyCb,bibTypeList,bibkey,i_bibkey}, 'Style','edit', 'String',bibkey); if ~isempty(metaData.biblist) && ~strcmp(bibkey, 'new') uicontrol('Parent',Db, 'Position',[300 280 150 20], 'String',['type: ',metaData.biblist.(bibkey).type], 'Style','text'); fld = bibTypeList.(metaData.biblist.(bibkey).type); n_fld = length(fld); for i=1:n_fld hight = 260 - i * 25; if ~isfield(metaData.biblist.(bibkey), fld{i}) metaData.biblist.(bibkey).(fld{i}) = []; end str = metaData.biblist.(bibkey).(fld{i}); uicontrol('Parent',Db, 'Position',[20 hight 80 20], 'Style','text', 'String',[fld{i},': ']); Dbi(i) = uicontrol('Parent',Db, 'Position',[100 hight 680 20], 'Callback',{@bibitemFldCb,bibkey,fld{i},i}, 'Style','edit', 'String',str); end end end function bibkeyCb(~, ~, bibTypeList, bibkey, i_bibkey) global metaData Dbb Db Hb bibkeyNew = get(Dbb, 'string'); metaData.biblist = renameStructField(metaData.biblist, bibkey, bibkeyNew); if strcmp(bibkey, 'new') % set type and fill fields with empty if existing bibkey was new fld = fields(bibTypeList); i_type = listdlg('ListString',fields(bibTypeList), 'Name','biblist dlg', 'ListSize',[100 150], 'SelectionMode','single', 'InitialValue',1); metaData.biblist.(bibkeyNew).type = fld{i_type}; fld = bibTypeList.(fld{i_type}); n_fld = length(fld); for i=1:n_fld metaData.biblist.(bibkeyNew).(fld{i}) = []; end end set(Hb(i_bibkey), 'String',bibkeyNew); delete(Db); DbCb([], [], bibTypeList, i_bibkey) AmPgui('color'); end function bibitemFldCb(~, ~, bibkey, fld, i) % fill a field of a bibitem global metaData Dbi metaData.biblist.(bibkey).(fld) = get(Dbi(i), 'string'); end function add0Cb(~, ~, code0, ddata_0) % add 0-var data set to data_0 % code0: array of possible 0-var data sets: name, description % ddata_0: handle for data_0 dialog global data txtData auxData metaData n_code0 = size(code0,1); codeList0 = code0(:,1); for i = 1:n_code0 codeList0{i} = [code0{i,1}, ': ', code0{i,4}]; end i_code0 = listdlg('ListString',codeList0, 'Name','0-var data dlg', 'ListSize',[300 400], 'InitialValue',n_code0); code0 = code0(i_code0,:); if ~isempty(data.data_0) data_0 = fields(data.data_0); code0 = code0(~ismember(code0(:,1), data_0),:); end n = size(code0,1); for i = 1:n data.data_0.(code0{i,1}) = []; txtData.units.(code0{i,1}) = code0{i,2}; txtData.label.(code0{i,1}) = code0{i,4}; txtData.bibkey.(code0{i,1}) = []; txtData.comment.(code0{i,1}) = ''; if code0{i,3} auxData.temp.(code0{i,1}) = []; end metaData.data_0 = [metaData.data_0; code0{i,1}]; end delete(ddata_0); AmPgui('data_0'); end function d0Cb(~, ~, i) % fill fields for 0-var data set i global data auxData txtData H0v H0T H0b H0c fld = fields(data.data_0); data.data_0.(fld{i}) = str2double(get(H0v(i), 'string')); if isfield(auxData.temp, fld{i}) auxData.temp.(fld{i}) = C2K(str2double(get(H0T(i), 'string'))); txtData.units.temp.(fld{i}) = 'K'; txtData.label.temp.(fld{i}) = 'temperature'; end txtData.bibkey.(fld{i}) = str2cell(get(H0b(i), 'string')); txtData.comment.(fld{i}) = get(H0c(i), 'string'); end function add1Cb(~, ~, code1, ddata_1) global data txtData auxData metaData n_code1 = size(code1,1); codeList1 = code1(:,1); for i = 1:n_code1 codeList1{i} = [code1{i,1}, ': ', cell2str(code1{i,4})]; end i_code1 = listdlg('ListString',codeList1, 'Name','1-var data dlg', 'ListSize',[300 350], 'InitialValue',n_code1); code1 = code1(i_code1,:); if ~isempty(data.data_1) data_1 = fields(data.data_1); code1 = code1(~ismember(code1(:,1), data_1),:); end n = size(code1,1); for i = 1:n data.data_1.(code1{i,1}) = []; txtData.units.(code1{i,1}) = code1{i,2}; txtData.label.(code1{i,1}) = code1{i,4}; txtData.bibkey.(code1{i,1}) = []; txtData.comment.(code1{i,1}) = []; if code1{i,3} auxData.temp.(code1{i,1}) = []; end metaData.data_1 = [metaData.data_1; code1{i,1}]; end delete(ddata_1); AmPgui('data_1'); end function D1Cb(~, ~, fld, i) global data auxData txtData D1 H1v H1T H1b H1c D1(i) = dialog('Position',[150 35 475 500], 'Name','1-variate data set dlg'); units = txtData.units.(fld); label = txtData.label.(fld); uicontrol('Parent',D1(i), 'Position',[ 20 480 50 20], 'Callback',{@OKCb,D1(i)}, 'Style','pushbutton', 'String','OK'); uicontrol('Parent',D1(i), 'Position',[ 80 480 150 20], 'String',['name: ', fld], 'Style','text'); uicontrol('Parent',D1(i), 'Position',[225 480 100 20], 'String',['units: ', units{1},' , ',units{2}], 'Style','text'); H1v(i) = uicontrol('Parent',D1(i), 'Min',0, 'Max',300, 'Position',[20 20 200 450], 'Callback',{@d1Cb,fld,i}, 'String',num2str(data.data_1.(fld)), 'Style','edit'); uicontrol('Parent',D1(i), 'Position',[225 400 100 20], 'String','x-label:', 'Style','text'); uicontrol('Parent',D1(i), 'Position',[245 375 200 20], 'String',label{1}, 'Style','text'); uicontrol('Parent',D1(i), 'Position',[225 350 100 20], 'String','y-label:', 'Style','text'); uicontrol('Parent',D1(i), 'Position',[245 325 200 20], 'String',label{2}, 'Style','text'); if isfield(auxData.temp,(fld)) uicontrol('Parent',D1(i), 'Position',[225 300 100 20], 'String','temperature in C', 'Style','text'); H1T(i) = uicontrol('Parent',D1(i), 'Position',[325 300 50 20], 'Callback',{@d1TCb,fld,i}, 'String', num2str(K2C(auxData.temp.(fld))), 'Style','edit'); end uicontrol('Parent',D1(i), 'Position',[225 275 100 20], 'String','bibkey', 'Style','text'); H1b(i) = uicontrol('Parent',D1(i), 'Position',[300 275 100 20], 'Callback',{@d1bCb,fld,i}, 'String',txtData.bibkey.(fld), 'Style','edit'); uicontrol('Parent',D1(i), 'Position',[225 250 70 20], 'String','comment', 'Style','text'); H1c(i) = uicontrol('Parent',D1(i), 'Position',[225 225 240 20], 'Callback',{@d1cCb,fld,i}, 'String',txtData.comment.(fld), 'Style','edit'); end function d1Cb(~, ~, fld, i) global data H1v data.data_1.(fld) = str2num(get(H1v(i), 'string')); end function d1TCb(~, ~, fld, i) global auxData txtData H1T auxData.temp.(fld) = C2K(str2double(get(H1T(i), 'string'))); txtData.units.temp.(fld) = 'K'; txtData.label.temp.(fld) = 'temperature'; end function d1bCb(~, ~, fld, i) global txtData H1b txtData.bibkey.(fld) = str2cell(get(H1b(i), 'string')); end function d1cCb(~, ~, fld, i) global txtData H1c txtData.comment.(fld) = get(H1c(i), 'string'); end function COMPLETECb(~, ~) global metaData HCOMPLETE metaData.COMPLETE = str2double(get(HCOMPLETE, 'string')); AmPgui('setColors') end function stayCb(~, ~, H) OKCb([], [], H); end function proceedCb(~, ~, H) global infoAmPgui data metaData txtData auxData color select_id id_links eco_types % do all data_0 have bibkeys? check_bibkey0 = false; if ~isempty(data.data_0) fld_0 = fields(data.data_0); n = length(fld_0); check_bibkey0 = false(n,1); for i= 1:n if ~isfield(txtData.bibkey, fld_0{i}) fprintf(['Warning from AmPeps: please enter a bibkey for dataset ', fld_0{i}, '\n']); check_bibkey0{i} = true; end end end % do all data_1 have bibkeys? check_bibkey1 = false; if ~isempty(data.data_1) fld_1 = fields(data.data_1); n = length(fld_1); check_bibkey1 = false(n,1); for i= 1:n if ~isfield(txtData.bibkey, fld_1{i}) fprintf(['Warning from AmPeps: please enter a bibkey for dataset ', fld_1{i}, '\n']); check_bibkey1{i} = true; end end end % do all facts have bibkeys? check_bibkeyF = false; if ~isempty(metaData.facts) fld_F = fields(metaData.facts); n = length(fld_F); check_bibkeyF = false(n,1); for i= 1:n if ~isfield(metaData.bibkey, fld_F{i}) fprintf(['Warning from AmPeps: please enter a bibkey for fact ', fld_F{i}, '\n']); check_bibkeyF(i) = true; end end end % do all bibkeys have bibitems? check_bibitem = false; if ~isempty(txtData.bibkey) && ~isempty(metaData.biblist) bibkeys = {}; dataNm = fields(txtData.bibkey); n_data = length(dataNm); check_bibitem = false(n_data,1); for i = 1:n_data addbibkey = txtData.bibkey.(dataNm{i}); if iscell(addbibkey) bibkeys = [bibkeys; addbibkey(:)]; else bibkeys = [bibkeys; addbibkey]; end end if ~isempty(metaData.bibkey) % bibkeys for facts and discussion points fld = fields(metaData.bibkey); n_fld = length(fld); for i=1:n_fld addbibkey = metaData.bibkey.(fld{i}); if iscell(addbibkey) bibkeys = [bibkeys; addbibkey(:)]; else bibkeys = [bibkeys; addbibkey]; end end end bibkeys = unique(bibkeys); bibkeys = bibkeys(~ismember(bibkeys, [fields(metaData.biblist); 'guess'; 'Kooy2010'])); if ~isempty(bibkeys) fprintf('Warning from AmPeps: the following bibkeys were not found in the biblist, please complete\n'); bibkeys check_bibitem = true; end end % are all ecoCodes filled, except migrate? eco = {'climate', 'ecozone', 'habitat', 'embryo', 'food', 'gender', 'reprod'}; n_eco = length(eco); check_eco = false(n_eco,1); for i = 1 : n_eco check_eco(i) = isempty(metaData.ecoCode.(eco{i})); end % first check that all required fields are filled, if so proceed to AmPeps if isempty(metaData.author); fprintf('Warning from AmPeps: please enter author details\n') OKCb([], [], H); AmPgui('author'); elseif isempty(metaData.curator); fprintf('Warning from AmPeps:select curator\n') OKCb([], [], H); AmPgui('curator'); elseif isempty(metaData.species); fprintf('Warning from AmPeps: please enter species name\n') OKCb([], [], H); AmPgui('species'); elseif any(check_eco) fprintf('Warning from AmPeps: empty ecoCodes ', cell2str(eco(check_eco)),'\n'); OKCb([], [], H); AmPgui('ecoCode') elseif isempty(metaData.T_typical); fprintf('Warning from AmPeps: please specify typical body temperature\n') OKCb([], [], H); AmPgui('T_typical'); elseif isempty(metaData.COMPLETE); fprintf('Warning from AmPeps: please specify COMPLETE\n') OKCb([], [], H); AmPgui('COMPLETE'); elseif isempty(data.data_0) | isempty(txtData.units.temp) fprintf('Warning from AmPeps: please enter at least one 0-variate data point that is time-dependent\n'); OKCb([], [], H); AmPgui('data_0'); elseif isempty(metaData.biblist) fprintf('Warning from AmPeps: empty biblist, please complete\n'); OKCb([], [], H); AmPgui('biblist'); elseif any(check_bibkeyF) OKCb([], [], H); AmPgui('facts'); elseif any(check_bibkey0) OKCb([], [], H); AmPgui('data_0'); elseif any(check_bibkey1) OKCb([], [], H); AmPgui('data_1'); elseif check_bibitem OKCb([], [], H); AmPgui('biblist'); else save(['results_', metaData.species, '.mat'], 'data', 'auxData', 'metaData', 'txtData', 'color', 'select_id', 'id_links', 'eco_types', 'infoAmPgui'); OKCb([], [], H); AmPeps(infoAmPgui); end end function leaveCb(~, ~, H) global infoAmPgui OKCb([], [], H); AmPeps(infoAmPgui); end function quitCb(~, ~, H) OKCb([], [], H); close all; end function OKCb(~, ~, H) if iscell(H) n = length(H); for i = 1:n close(H{i}); end else close(H); end end function deleteCb(~, ~, type, id, handle) global data metaData txtData switch type case 'facts' fact = ['F', num2str(id)]; metaData.facts = rmfield(metaData.facts, fact); metaData.bibkey = rmfield(metaData.bibkey, fact); if isfield(metaData.facts, ['F', num2str(id+1)]) n = length(fields(metaData.facts)) - id + 2; for i = 1:n metaData.facts = renameStructField(metaData.facts,['F', num2str(i + 1)], ['F', num2str(i)]); metaData.bibkey = renameStructField(metaData.bibkey,['F', num2str(i + 1)], ['F', num2str(i)]); end end close(handle); AmPgui('facts'); case 'discussion' disc = ['D', num2str(id)]; metaData.discussion = rmfield(metaData.discussion, disc); metaData.bibkey = rmfield(metaData.bibkey, disc); if isfield(metaData.discussion, ['D', num2str(id+1)]) n = length(fields(metaData.discussion)) - id + 2; for i = 1:n metaData.discussion = renameStructField(metaData.discussion,['D', num2str(i + 1)], ['D', num2str(i)]); metaData.bibkey = renameStructField(metaData.bibkey,['D', num2str(i + 1)], ['D', num2str(i)]); end end close(handle); AmPgui('discussion'); case 'biblist' metaData.biblist = rmfield(metaData.biblist, id); close(handle); AmPgui('biblist'); case 'data_0' data.data_0 = rmfield(data.data_0, id); txtData.bibkey = rmfield(txtData.bibkey, id); delete(handle); AmPgui('data_0'); case 'data_1' data.data_1 = rmfield(data.data_1, id); txtData.bibkey = rmfield(txtData.bibkey, id); close(handle); AmPgui('data_1'); end end %% other support functions function str = cell2str(cell) if isempty(cell) str = []; return end if ~iscell(cell) str = cell; return end n = length(cell); str = []; for i=1:n str = [str, cell{i}, ',']; end str(end) = []; end function c = str2cell(str) if isempty(str) c = {}; return elseif iscell(str) c = str; return end str = strsplit(str, ','); n = length(str); c = cell(1,n); for i=1:n c{i} = str{i}; end end function stageCode = prependStage(ind, code, codeList, type) stageList = { ... '0b', '0j', ... '0x stage ij is the period', ... '0p between events i and j', ... '0i', ... 'bj 0: start', ... 'bx b: birth', ... 'bp j: metamorphosis', ... 'bi x: weaning/fledge', ... 'jp p: puberty', ... 'ji i: death', ... % this spacing gives the best outlining on the screen 'xp', 'xi', 'pi'}; stageCode = code(ind); n = length(ind); switch type case 'habitat' init = 5; % stageCode 0i case 'food' init = 9; % stageCode bi end for i = 1:n fprintf(['Prepend stage for code ', code{ind(i)},'\n']); name = ['stage code for ', codeList{ind(i)}]; i_stage = listdlg('ListString',stageList, 'Name',name, 'SelectionMode','single', 'ListSize',[600 250], 'InitialValue',init); stage = stageList{i_stage}; stageCode{i} = [stage(1:2), code{ind(i)}]; end end function sel = Contains(nm, str) % this fuction is the same as Matlab built-in-function contains, but the R2016a version does not work with cell input n = length(nm); sel = true(n,1); for i=1:n sel(i) = ~isempty(strfind(nm{i}, str)); end end