coFindPaths.m

function [nobj numTwoHops]=coFindPaths(neuron1,neuron2,max_hops,verboseFlag,coStruct)
%COFINDPATHS(neuron1,neuron2,max_hops,verboseFlag)
%
%find all one or two hop pathways from neuron1 to neuron2
%in maxhops or fewer hops  (maxhops cannot exceed 3)
%
%**currently, output datastructure only includes direct paths, not multihop
% although these are given in the verbose command line output
%
%.if particular left or right suffix is not specified in neuron names,
%the search will be performed for all possible L/R combinations and
%output will be given as a struct array
%
%
%example: coFindPaths('ASH','AWC');
%will give pathways for ASHL->AWCL, ASHR->ASHR, ASHR->AWCL, and ASHL->AWCR
%
%.synapses can only be traversed in one direction, gap junctions in either
%
%.needs NeuronConnect.xls in same directory (get latest from WormAtlas.org)
%
%Saul Kato
%101201
%

if nargin<3 || isempty(max_hops)
    max_hops=2;
end

if nargin<1
    neuron1='AWCL'; 
end

if nargin<2
    neuron2='AIAL';
end

if nargin<4 || isempty(verboseFlag)
    verboseFlag=true;
end


if verboseFlag
    disp(' ');
    disp(['FINDING PATHS FOR ' neuron1 ' -> ' neuron2 ', max ' num2str(max_hops) ' hops.']);
    disp('(syn=synapse, syp=polyadic synapse, gap=gap junction)');
    disp(' ');
end


verblist={'syn','syp','gap'};


if nargin<4 || isempty(coStruct)
    
    
    %load database
    [num,txt,raw] = xlsread('NeuronConnect.xls','','','basic');


    %preprocess database
    txt(1,:)=[];  %delete header
    numrows=size(num,1);
    verb=zeros(numrows,1);
    for i=1:numrows
        if strcmp(txt{i,3},'S')  
            verb(i)=1;
        elseif strcmp(txt{i,3},'Sp')
            verb(i)=2;
        elseif strcmp(txt{i,3} ,'EJ')
            verb(i)=3;
        end
    end

    reverb=zeros(numrows,1);
    for i=1:numrows
        if strcmp(txt{i,3},'R')  
            reverb(i)=1;
        elseif strcmp(txt{i,3},'Rp')
            reverb(i)=2;
        elseif strcmp(txt{i,3} ,'EJ')
            reverb(i)=3;
        end
    end

 
    
else
 
    verb=coStruct.verb;
    reverb=coStruct.reverb;
    num=coStruct.num;
    txt=coStruct.txt;
    
    numrows=size(num,1);

end

neuron1L=[neuron1 'L'];
neuron2L=[neuron2 'L'];
neuron1R=[neuron1 'R'];
neuron2R=[neuron2 'R'];

    for i=1:numrows
        if strcmp(txt(i,1),neuron1)
            firstneuron={neuron1}; break;
        else
            firstneuron={};
        end
    end

    for i=1:numrows
        if strcmp(txt(i,1),neuron2)
            secondneuron={neuron2}; break;
        else
            secondneuron={};
        end
    end

    for i=1:numrows
        if strcmp(txt(i,1),neuron1L)
            firstneuron={firstneuron{:}, neuron1L}; break
        end
    end

    for i=1:numrows
         if strcmp(txt(i,1),neuron1R)
            firstneuron={firstneuron{:}, neuron1R}; break
        end
    end   

    for i=1:numrows
         if strcmp(txt(i,1),neuron1L)
            secondneuron={secondneuron{:}, neuron2L}; break
        end
    end   

    for i=1:numrows
         if strcmp(txt(i,1),neuron1R)
            secondneuron={secondneuron{:}, neuron2R}; break
        end
    end   
    
    
kk=1;
for ii=1:length(firstneuron)
    for jj=1:length(secondneuron)
        if verboseFlag
            disp(' ');
            disp('------------------------------');
            disp(['||       ' firstneuron{ii} ' -> ' secondneuron{jj} '       ||']);
        end
        nobj(kk)=FindPathsOneNeuron(firstneuron{ii},secondneuron{jj},max_hops);
        kk=kk+1;
    end
end

if ~exist('nobj') nobj=[]; end

%subfuncs

    function snobj=FindPathsOneNeuron(n1,n2,maxhops)

    snobj.n1=n1;
    snobj.n2=n2;
    
    m=1; 
    
    if verboseFlag
        disp('one hop paths:');
    end
    
    snobj.downjunction=[];
    snobj.downstrength=[];

    %find 1-hop paths
    for i=1:numrows
        if strcmp(n1,txt(i,1))
            if strcmp(n2,txt(i,2))
                if verb(i)~=0
                    p{m}=[txt{i,1} ' -' num2str(num(i)) verblist{verb(i)} '-> ' txt{i,2} ...
                      ];
                    numsyn(m)=num(i);
                    
                    if verboseFlag disp(p{m}); end
                    
                    %write into nobj
                    snobj.downjunction{m}=verblist{verb(i)};
                    snobj.downstrength(m)=num(i);
                    
                    
                    m=m+1;
                end
            end
        end
    end

    if verboseFlag
        if (m==1) disp('none'); else disp([num2str(m-1) ' 1-hop paths found.']); end;
    end

    %find 2-hop paths

   
    if maxhops>1  %2 hops
        numTwoHops=0;
        if verboseFlag
            disp(' ');
            disp('two hop paths:');
        end
        n=1;
        for i=1:numrows
            if strcmp(n1,txt(i,1))
                for j=1:numrows  
                    if strcmp(n2,txt(j,2)) && strcmp(txt(j,1),txt(i,2))
                        if verb(i)~=0 && verb(j)~=0
                            pp{n}=[txt{i,1} ' -' num2str(num(i)) verblist{verb(i)} '-> '...
                                txt{i,2}  ' -' num2str(num(j)) verblist{verb(j)} '-> ' txt{j,2}];
                            numpp1(n)=num(i);
                            numpp2(n)=num(j);
                            if verboseFlag disp(pp{n}); end
                            numTwoHops=numTwoHops+1;
                            n=n+1;
                        end
                    end
                end
            end
        end
        if verboseFlag
            if (n==1) disp('none');  else disp([num2str(n-1) ' 2-hop paths found.']); end;
        end
    end

    %find 3-hop paths

    if maxhops>2 %3 hops

        if verboseFlag
            disp(' ');
            disp('three hop paths:');
        end

        c2=1;
        for i=1:numrows
            if strcmp(n1,txt(i,1))
                if verb(i)~=0
                    ppp_2{c2}=txt(i,2);
                    ppp_12{c2}=[num2str(num(i)) verblist{verb(i)}];
                    c2=c2+1;
                end
            end
        end

        c3=1;
        for i=1:numrows
            if strcmp(n2,txt(i,2))
                if reverb(i)~=0
                    ppp_3{c3}=txt(i,1);
                    ppp_34{c3}=[num2str(num(i)) verblist{reverb(i)}];
                    c3=c3+1;
                end
            end
        end
        c2=c2-1;
        c3=c3-1;

        q=1;
        for c=1:c2
            for cc=1:c3
                for i=1:numrows
                    if strcmp(ppp_2{c},txt(i,1)) && strcmp(ppp_3{cc},txt(i,2))
                        if verb(i)~=0
                            ppp{q}=[n1 ' -' ppp_12{c} '-> ' txt{i,1} ...
                                ' -' num2str(num(i)) verblist{verb(i)} '-> ' txt{i,2} ...
                                ' -' ppp_34{cc} '-> ' n2];
                            if verboseFlag disp(ppp{q}); end
                            q=q+1;
                        end
                    end
                end   
            end
        end

        if verboseFlag
            if (q==1) disp('none'); else disp([num2str(q-1) ' 3-hop paths found.']); end;
        end
    end

    end 

end %main