File changes are not being recorded

I have two files.

1. run_matlab.sh

2. drawdendrograms.m

I have update the drawdendrograms.m file with the proper color.mat file information. But still when I run MATLAB script, it is reading the older file path and not the changed one.

~~~~~~~~~~~~~~

cat run_matlab.sh

#!/bin/sh
# script for execution of deployed applications
#
# Sets up the MCR environment for the current $ARCH and executes 
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
  echo Usage:
  echo    $0 \<deployedMCRroot\> args
else
  echo Setting up environment variables
  MCRROOT="$1"
  echo ---
  TMPDIR=/data/cache/temp${RANDOM};
  mkdir $TMPDIR;
  export MCR_CACHE_ROOT=$TMPDIR;
  LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
  MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; 
  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;  
  XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
  export LD_LIBRARY_PATH;
  export XAPPLRESDIR;
  echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
  shift 1
  args=
  while [ $# -gt 0 ]; do
      token=`echo "$1" | sed 's/ /\\\\ /g'`   # Add blackslash before each blank
      args="${args} ${token}" 
      shift
  done
 ##eval "${exe_dir}"/makeViz /usr/local/matlab-compiler/v711 $args
eval "${exe_dir}"/makeViz  $args
fi
rm -rf $TMPDIR;
exit

~~~

cat drawdendrograms.m

function [] = drawExpressionAndDendograms(dir)
% 1) reads the expression values (counts of mirs in sample)(vals_fn), 
% reads the names of the mirs/samples(mirs_labels, sample_labels_fn), 
% reads the dendrograms information - the distances as they have been computed. 
% 2) computes the frequences: log2(mirs count/total mirs counts per sample)
% (if the value in the paranthesis is 0 then the log2(0) is replaced with -15)
% 3) draw the expression matrix, the dendrograms and the labels 
% 4) exports the image as png, eps and pdf

% arguments 

% input dir and file names
%dir                     = input('directory= ', 's');
sample_dendr_fn         = '/sample_dendrogram';
mirs_dendr_fn           = '/mirs_dendrogram';
vals_fn                 = '/selcount.vals';
mirs_labels_fn          = '/out.names';
sample_labels_fn        = '/out.header';
output_fn               = '/expressionDendrogramsInMatlab';
total_mirs_per_sample_fn   = '/total_mirs_per_sample.count';

% graphical parameters
% used for the dendrogram representation
sample_scale            = 0.01; %50;
mirs_scale              = 0.00007;
border                  = 0.5;
image_scale             = 12;
negative_infinity       = -22; % old: -17  %Value used to denote -infinity obtained in log(0)
                                %Also used when zero padding is done (at the right
                                %of the expression matrix) 

% load the input files
EXPR                    = load([dir vals_fn]);
TOTAL_MIRS_PER_SAMPLE   = load([dir total_mirs_per_sample_fn]);
LabelsMirs              = importdata([dir mirs_labels_fn]);
LabelsTissues           = importdata([dir sample_labels_fn]);

%MB added to handle sample labeled with numbers
if (~iscell(LabelsTissues))
    LabelsTissues=num2str(LabelsTissues);
    LabelsTissues=cellstr(LabelsTissues);
    LabelsTissues=strtrim(LabelsTissues);
end

if  (size(EXPR,1)>1 && size(EXPR,2)>1)
    SAMPLE_DENDR            = load([dir sample_dendr_fn]);
    MIRS_DENDR              = load([dir mirs_dendr_fn]);
end;

% get the length of the longest miRNA/Sample Label
mirsLabelMaxLen         = size(char(LabelsMirs),2)-4;
sampleLabelMaxLen       = size(char(LabelsTissues),2)-5;

% space for the labels
sample_shift            = sampleLabelMaxLen;
mirs_shift              = mirsLabelMaxLen;

% get the dimensions
cols                    = size(LabelsTissues,1);
rows                    = size(LabelsMirs,1);

if  (size(EXPR,1)>1 && size(EXPR,2)>1)
    sampleDendHeight        = max(SAMPLE_DENDR(:,3));
    mirsDendHeight          = max(MIRS_DENDR(:,3));
else
    sampleDendHeight        = 0;
    mirsDendHeight          = 0;
end

if (mirs_scale * mirsDendHeight > 90)
    mirs_scale = 90 / mirsDendHeight;
end

if (sampleDendHeight * sample_scale > 10)
    sample_scale = 10 / sampleDendHeight;
end
if (mirs_scale * mirsDendHeight < 2)
    mirs_scale = 2 / mirsDendHeight;
end

if (sampleDendHeight * sample_scale < 10)
    sample_scale = 10 / sampleDendHeight;
end

%XLim, YLim
xMin                    = border-mirs_scale*mirsDendHeight-mirs_shift-1; %measured in points; <0
xMax                    = cols+border;
yMin                    = border-sample_scale*sampleDendHeight-sample_shift-1; %measured in points; <0
yMax                    = rows+border+1;

%Graphical options
width                   = (-xMin + xMax)*image_scale;
height                  = (-yMin + yMax)*image_scale;

figure;
set(gcf,...
    'visible','off',...                     % the figure is not shown
    'PaperUnits', 'points',...              % The unit is points
    'PaperSize',[width height],...         % the size of the paper is given by weight and height   
    'Position',[0 0 width height],...
    'PaperPositionMode','auto',...          % Keeps the ratio between height/weight
    'InvertHardcopy','on');

% load the colormap
load('/home/smiRNADB_colormap.mat','mycmap');
colormap(mycmap);

% compute and draw dendograms 
if  (size(EXPR,1)>1 && size(EXPR,2)>1)
   [H1,T1,sample_perm] = dendrogramInSamePlot(SAMPLE_DENDR,sample_shift,sample_scale,'orientation','top'); % perm contains the permutation of the elements
   hold on;
   [H2,T2,mirs_perm]   = dendrogramInSamePlot(MIRS_DENDR,mirs_shift,mirs_scale,'orientation','right'); % perm contains the permutation of the elements
   hold on;

    % permute the cols oF the expression matrix according to sample_perm
    EXPR1=EXPR(:,sample_perm);
    EXPR_Perm = EXPR1(mirs_perm,:);
    TOTAL_MIRS_PER_SAMPLE = TOTAL_MIRS_PER_SAMPLE(:,sample_perm);
    colTotal = sum(EXPR_Perm);
  else
    %sample_perm = 1:size(EXPR,2);
    %mirs_perm   = 1:size(EXPR,1); 
    %EXPR_Perm   = EXPR;

    %one sample
    if size(EXPR,2)==1
       [EXPR_Perm, mirs_perm]   = sort(EXPR(:,1),'descend');
       sample_perm = 1;
       colTotal = sum(EXPR_Perm);
    end 

    %one mirs
    if size(EXPR,1)==1
       sample_perm = 1:size(EXPR,2);
       mirs_perm   = 1;
       EXPR_Perm   = EXPR;
    end;

end

for iRowIndex = 1:size(EXPR_Perm,1)
    for iColIndex = 1:size(EXPR_Perm,2)
  EXPR_Perm(iRowIndex,iColIndex) = getFrequence(EXPR_Perm(iRowIndex,iColIndex),TOTAL_MIRS_PER_SAMPLE(iColIndex),negative_infinity);
    end;
end;

%one mirs
if size(EXPR,1)==1
  [EXPR_Perm, sample_perm] = sort(EXPR_Perm(1,:),'descend');
  colTotal = EXPR_Perm;
  TOTAL_MIRS_PER_SAMPLE = TOTAL_MIRS_PER_SAMPLE(:,sample_perm);
end;

rest = TOTAL_MIRS_PER_SAMPLE-colTotal;
for iColIndex = 1:size(rest,2)
   rest(iColIndex) = getFrequence(rest(iColIndex),TOTAL_MIRS_PER_SAMPLE(iColIndex),negative_infinity);
end;

% plot the expression matrix
image([EXPR_Perm; rest],'CDataMapping','scaled')

xlim([xMin xMax]);
ylim([yMin yMax]);
set(gca,...
    'YDir','reverse');

% write the labels
for i=1:rows
   rw=mirs_perm(i);
   %rw = i;
   text(0,i,LabelsMirs(rw,1),'HorizontalAlignment','right','VerticalAlignment','middle','FontSize',image_scale-1, 'Interpreter','none','FontName','FixedWidth');
   %text((from+to)/2,-2,descr,'Rotation',90);    
end
% the all other label
text(0,rows+1,'all-other mirs','HorizontalAlignment','right','VerticalAlignment','middle','FontSize',image_scale-1, 'Interpreter','none','FontName','FixedWidth');

for i=1:cols
   cw=sample_perm(i);
   %cw = i;

text(i,0,LabelsTissues(cw,1),'HorizontalAlignment','left','VerticalAlignment','middle','FontSize',image_scale-1,'Rotation',90,'Interpreter','none','FontName','FixedWidth')

end

% axes
set(gca,...
    'Position',[0.01 0.01 0.98 0.98],...          % position of the ases inside the figure
    'DataAspectRatio',[1 1 1],...                 % when resizing keep the ratio constant  
    'Visible','off');
%createcolorbar(gca,[0.02, 0.93, 0.03, 0.065]);

bar_height = (sample_scale*sampleDendHeight+sample_shift)*image_scale;
bar_width  = 20;
bar_border = border*image_scale;
createcolorbar(gca,[bar_border, height-bar_border-bar_height, bar_width, bar_height]);

set(0,'DefaultFigureRenderer','Painters');  % Default renderer (choice between OpenGL and ...)

%export files
print('-depsc2','-r0','-loose',[dir output_fn '.eps']) 
print('-dpng','-r0',[dir output_fn '.png'])
%print('-dpdf','-r0','-loose',[dir output_fn '.pdf'])
%exit;

%------------------------------------------------------------------------
function createcolorbar(axes1,position)
%CREATECOLORBAR(AXES1)
%  AXES1:  colorbar axes

%%Create colorbar
colorbar1 = colorbar('peer', axes1,...
    'Units','pixels',...
    'Position',position,...
    'Box','on',...
    'XLim',[-0.5 1.5]);

%-------------------------------------------------------------------------
function freq = getFrequence(value,total,negativeInf)
%choose 1e-6 instead of 0 to evoit cases where value is ~ 0 (e.g. 1e-12) 
%when log(value/total) < negativeInf; this happens when computing the freq 
%of the rest of mirs

%if value > 1e-6
%  freq =  log(value/total)/log(2);
%else
%  freq = negativeInf;
%end

if total > 0 && log2(value/total) > negativeInf 
  freq =  log2(value/total);
else
  freq = negativeInf;
end

On line 110 above, the load function is not reading the proper mat file, it is reading the path before the changes have been made. Any help is appreciated.

I am new to MATLAB, so I am guessing I have to flush the cache or something.

Thanks in advance.