Looking-to-cue-sides-and-modulation-of-value-in-OFC/code/support_functions/getSpikeSequences.m

function [spkdata] = getSpikeSequences(subjdata,sesn,timeStartAlgn,timeEndAlgn)

if nargin < 4
    if nargin < 3
        if nargin < 2
            if nargin< 1
                error('Provide subject data.');
            end
            sesn='all';
        end
        timeStartAlgn='offer1';
    end
    timeEndAlgn='choicemade';
end

if strcmpi(sesn,'all')
    sesn=1:length(subjdata);
end

spkdata_str{sesn}.spikeseqs=[];


for sn=sesn
    for tr=1:size(subjdata{sn}.spikeseqs,1)
        curroff1ref=round(subjdata{sn}.timings(tr).appearOffer1Time);
        
        if strcmpi(timeStartAlgn,'offer1')
            timeStartBin=0;
        elseif strcmpi(timeStartAlgn,'delay1')
            timeStartBin=round(subjdata{sn}.timings(tr).disappearOffer1Time)-curroff1ref;
        elseif strcmpi(timeStartAlgn,'offer2')
            timeStartBin=round(subjdata{sn}.timings(tr).appearOffer2Time)-curroff1ref;
        elseif strcmpi(timeStartAlgn,'delay2')
            timeStartBin=round(subjdata{sn}.timings(tr).disappearOffer2Time)-curroff1ref;
        elseif strcmpi(timeStartAlgn,'fixdot')
            timeStartBin=round(subjdata{sn}.timings(tr).appearFixDotTime)-curroff1ref;
        elseif strcmpi(timeStartAlgn,'choicego')
            timeStartBin=round(subjdata{sn}.timings(tr).choiceGoTime)-curroff1ref;
        elseif strcmpi(timeStartAlgn,'feedback')
            timeStartBin=round(subjdata{sn}.timings(tr).feedbackTime)-curroff1ref;
        elseif strcmpi(timeStartAlgn,'startfix')
            timeStartBin=round(subjdata{sn}.timings(tr).fixStartFixnDotTime)-curroff1ref;
        elseif strcmpi(timeStartAlgn,'choicemade')
            timeStartBin=round(subjdata{sn}.timings(tr).choiceMadeTime)-curroff1ref;
        elseif strcmpi(timeStartAlgn,'choicesacc')
            timeStartBin=round(min([subjdata{sn}.timings(tr).fixStartRightOfferTime subjdata{sn}.timings(tr).fixStartLeftOfferTime]))-curroff1ref;
        elseif strcmpi(timeStartAlgn,'preoffer1')
            timeStartBin=-3000;
        end
        
        
        if strcmpi(timeEndAlgn,'offer1')
            timeEndBin=0;
        elseif strcmpi(timeEndAlgn,'delay1')
            timeEndBin=round(subjdata{sn}.timings(tr).disappearOffer1Time)-curroff1ref;
        elseif strcmpi(timeEndAlgn,'offer2')
            timeEndBin=round(subjdata{sn}.timings(tr).appearOffer2Time)-curroff1ref;
        elseif strcmpi(timeEndAlgn,'delay2')
            timeEndBin=round(subjdata{sn}.timings(tr).disappearOffer2Time)-curroff1ref;
        elseif strcmpi(timeEndAlgn,'fixdot')
            timeEndBin=round(subjdata{sn}.timings(tr).appearFixDotTime)-curroff1ref;
        elseif strcmpi(timeEndAlgn,'choicego')
            timeEndBin=round(subjdata{sn}.timings(tr).choiceGoTime)-curroff1ref;
        elseif strcmpi(timeEndAlgn,'feedback')
            timeEndBin=round(subjdata{sn}.timings(tr).feedbackTime)-curroff1ref;
        elseif strcmpi(timeEndAlgn,'startfix')
            timeEndBin=round(subjdata{sn}.timings(tr).fixStartFixnDotTime)-curroff1ref;
        elseif strcmpi(timeEndAlgn,'choicemade')
            timeEndBin=round(subjdata{sn}.timings(tr).choiceMadeTime)-curroff1ref;
        elseif strcmpi(timeEndAlgn,'choicesacc')
            timeEndBin=round(min([subjdata{sn}.timings(tr).fixStartRightOfferTime subjdata{sn}.timings(tr).fixStartLeftOfferTime]))-curroff1ref;
        elseif strcmpi(timeEndAlgn,'trialend')
            timeEndBin=7000;
        end
        
        currsnspksq{tr}.currtrspksq(:,1:(timeEndBin-timeStartBin))=subjdata{sn}.spikeseqs(tr,:,(timeStartBin+1:timeEndBin)+3000);
    end
    maxntp=max(arrayfun(@(tr) size(currsnspksq{tr}.currtrspksq,2),1:size(currsnspksq,2)));
    spkdata_str{sn}.spikeseqs=nan(size(subjdata{sn}.spikeseqs,1),size(subjdata{sn}.spikeseqs,2),maxntp);
    for tr=1:size(subjdata{sn}.spikeseqs,1)
        spkdata_str{sn}.spikeseqs(tr,:,1:size(currsnspksq{tr}.currtrspksq,2))=currsnspksq{tr}.currtrspksq;
    end
    clearvars currsnspksq
end

maxntp=max(arrayfun(@(xx) size(spkdata_str{xx}.spikeseqs,3),sesn));

spkdata.spikeseqs=[];
for sn=sesn
    spkdata.spikeseqs=cat(1,spkdata.spikeseqs,cat(3,spkdata_str{sn}.spikeseqs,...
        nan([size(spkdata_str{sn}.spikeseqs,1:2), maxntp-size(spkdata_str{sn}.spikeseqs,3)]))); 
end

spkdata.starttime=timeStartAlgn;
spkdata.endtime=timeEndAlgn;

end