lib/ms/ident/pepxml.rb in ms-ident-0.0.3 vs lib/ms/ident/pepxml.rb in ms-ident-0.0.17

@@ -41,22 +41,49 @@
     xml_stylesheet = Nokogiri::XML::ProcessingInstruction.new(doc, "xml-stylesheet", %Q{type="text/xsl" href="#{location}"})
     doc.root.add_previous_sibling  xml_stylesheet
     doc
   end
   
-  # writes xml file named msms_pipeline_analysis.summary_xml into the msms_run_summary.base_name directory
-  def to_xml_file
-    to_xml(File.dirname(msms_pipeline_analysis.msms_run_summary.base_name) + '/' + msms_pipeline_analysis.summary_xml)
-  end
+  # if no options are given, an xml string is returned.  If either :outdir or
+  # :outfile is given, the xml is written to file and the output filename is returned.
+  # A single string argument will be interpreted as :outfile if it ends in
+  # '.xml' and the :outdir otherwise.  In this case, update_summary_xml is still true
+  #
+  # options:
+  #     
+  #     arg                    default
+  #     :outdir             => nil   write to disk using this outdir with summary_xml basename
+  #     :outfile            => nil   write to this filename (overrides outdir)
+  #     :update_summary_xml => true  update summary_xml attribute to point to the output file true/false
+  #
+  # set outdir to
+  # File.dirname(pepxml_obj.msms_pipeline_analysis.msms_run_summary.base_name)
+  # to write to the same directory as the input search file.
+  def to_xml(opts={})
+    opts ||= {}
+    if opts.is_a?(String) 
+      opts = ( opts.match(/\.xml$/) ?  {:outfile => opts} : {:outdir => opts } )
+    end
+    opt = {:update_summary_xml => true, :outdir => nil, :outfile => nil}.merge(opts)
 
-  # if no outfile is given, an xml string is returned.  summary_xml should
-  # have already been set and is not influenced by the outfile given here.
-  def to_xml(outfile=nil)
+    if opt[:outfile]
+      outfile = opt[:outfile]
+    elsif opt[:outdir]
+      outfile = File.join(opt[:outdir], msms_pipeline_analysis.summary_xml.split(/[\/\\]/).last)
+    end
+    self.msms_pipeline_analysis.summary_xml = File.expand_path(outfile) if (opt[:update_summary_xml] && outfile)
+
     builder = Nokogiri::XML::Builder.new(:encoding => XML_ENCODING)
     msms_pipeline_analysis.to_xml(builder)
     add_stylesheet(builder.doc, Ms::Ident::Pepxml::XML_STYLESHEET_LOCATION)
     string = builder.doc.to_xml
-    outfile ? File.open(outfile,'w') {|out| out.print(string) } : string
+
+    if outfile 
+      File.open(outfile,'w') {|out| out.print(string) }
+      outfile
+    else
+      string
+    end
   end
 end