varargout=ADAlignTrials(AlignEv,bn,minTrTime,varargin)

function varargout=ADAlignTrials(AlignEv,bn,minTrTime,varargin)
% function varargout=ADAlignTrials(AlignEv,bn,minTrTime,varargin)
%   
%   Aligns AD data matrices on a given event during the trial.
%   NOTE: This assumes a sampling rate of 1kHz for the AD Data, and that
%   all the times in bn and minTrTime are in ms. Also Note- The times in
%   AlignEv and bn and I think minTrTime too are assumed to be integers in
%   the input. If they are not input this way, each will be rounded
%   anyway. Both endpoints of bn are inclusive, so for example if you ask
%   to align from -5 to +5 ms from a given event, this will output 11
%   samples as it also assumes that everything is at 1 kHz.
%
%   Example of how this is called:
%   [AlX,AlY]=ADAlignTrials(LastLeaveFix_,[-300 300],0,EyeX_,EyeY_);
%
%   For every input AD data matrix in the varargin (nTr x nSampsPerTrial), 
%   this outputs the data in the corresponding in order in varargout in the
%   same format but aligned on AlignEv (nTr x 1), a vector of event times
%   in ms to align to.  bn is a 1x2 matrix of the minimum and maximum times
%   to output relative to AlignEv, such that the outputs in varargout will
%   be of size (nTr x bn(2)-bn(1)+1). minTrTime is the time relative to 
%   TrialStart_ (or conceivably some other event) of the first time sample 
%   in the input AD matrix in varargin. It's important that minTrTime and 
%   AlignEv are referenced to the same event, typically TrialStart_. 
%
%   This doesn't use a big for loop (across trials) and so should be fairly
%   quick.
%
%   Note: to plot this as an individual trace for each trial, all on one 
%   graph, it's simply- plot([bn(1):bn(2)],OutArg);
%
%   ***************** This will run into trouble if there are NAN's in your AlignEv... If
%   you run into trouble with this, that's a likely culprit
%
%   written 070711 by MJN

if nargin<4 error(['nargin is only: ' num2str(nargin) '. You need at least 4 arguments.']); end
AlignEv=round(AlignEv);     bn=round(bn);   minTrTime=round(minTrTime);

if size(AlignEv,1)>size(AlignEv,2)  AlignEv=AlignEv';   end
    
maxTrTime=minTrTime+size(varargin{1},2)-1;
nTrs=length(AlignEv);

TimeLims=minmax(AlignEv)+bn;
FrontPad=min([minTrTime TimeLims(1)]);
EndPad=max([maxTrTime TimeLims(2)]);
tmpnsamps=EndPad-FrontPad+1;

if FrontPad<minTrTime   disp('Warning- bn(1) went before AD sample for some trials. Padding beginning of these with NaN''s'); end
if EndPad>maxTrTime   disp('Warning- bn(2) went beyond AD sample for some trials. Padding ends of these with NaN''s'); end

t=repmat([FrontPad:EndPad]',1,nTrs)-repmat(AlignEv,tmpnsamps,1);
for iAD=1:nargin-3
    curAD=varargin{iAD}';
    if FrontPad<minTrTime
        curAD=[NaN*ones(minTrTime-FrontPad,nTrs); curAD];
    end
    if EndPad>maxTrTime
        curAD=[curAD; NaN*ones(EndPad-maxTrTime,nTrs)];
    end
                
    varargout{iAD}=reshape(curAD( t>=bn(1) & t<=bn(2) ),bn(2)-bn(1)+1,nTrs)';
end