writing of annotation

* fix of wrinting
* tool for writing

matlabcode/FCS/writeAnnotationResfile2xml.m

+function writeAnnotationResfile2xml(resfile, FAsession)
+
+    if nargin < 1
+        [resfile, pathname] = uigetfile({'*.res'; '*.*'},'Select res file', '');
+        if ~resfile
+        return
+    end
+    resfile = fullfile(pathname, resfile);
+    end
+    [pathname, resbase, ext] = fileparts(resfile);
+    [tmp, dirname] = fileparts(pathname);
+    if nargin < 2
+        FAsession = resbase;
+        FAsession = '2c'
+    end 
+    restable = readtable(resfile, 'Delimiter', '\t', 'Header', 1, 'FileType', 'text', 'TreatAsEmpty',{'NA'});
+    xmlFAfiles = strrep(restable.FullPath, ['.zen'], ['.zen.' FAsession '.xml']);
+    for iD = 1:length(xmlFAfiles)
+        fprintf('%s Writing annotation of file %d/%d\n', resfile, iD, length(xmlFAfiles))
+        if ~exist(xmlFAfiles{iD})
+            % search locally
+            [m, iend] = regexp(xmlFAfiles{iD}, dirname, 'match', 'end');
+            xmlfile = fullfile(pathname, xmlFAfiles{iD}(iend+1:end));
+        else
+            xmlfile = xmlFAfiles{iD};
+        end
+        if ~exist(xmlfile)
+            error('Coul not find file');
+        end
+        node = xmlFA.readnode(xmlfile);
+%         [path1, fout, ext] = fileparts(xmlfile);
+%         [path, fout, ext] = fileparts(fout);
+%         
+%         fname_out = fullfile(path1, sprintf('%s.test.xml', fout));
+        if iscell(restable.Annotation)
+            ann = restable.Annotation{iD};
+        else
+            ann = restable.Annotation(iD);
+        end 
+             
+        if isnan(ann)
+           xmlFA.writeannotation(node, 32);
+        else
+           xmlFA.writeannotation(node, ann);
+        end
+        xmlFA.writenode(xmlfile, node);
+    end
+end

matlabcode/FCS/xmlFA.m

@@ -18,7 +18,7 @@ classdef xmlFA
                 node = nodes.item(i);
                 switch(char(node.item(1).getTextContent))
                     case 'm_nAnnotation'
-                        ann = str2num(node.item(3).getTextContent);
+                        ann = char(node.item(3).getTextContent);
                         break;
                 end
             end
@@ -31,8 +31,17 @@ classdef xmlFA
                 node = nodes.item(i);
                 switch(char(node.item(1).getTextContent))
                     case 'm_nAnnotation'
-                        node.item(3).setTextContent(num2str(ann));
-                        break;
+                        if isempty(ann)
+                             node.item(3).setTextContent('32');
+                             break
+                        else
+                            if ischar(ann)
+                                node.item(3).setTextContent(num2str(double(ann)));
+                            else
+                                node.item(3).setTextContent(num2str(ann));
+                            end
+                            break;
+                        end
                 end
             end
         end