Changeset 29 for GSEXmlParser

Timestamp:

Apr 17, 2008, 2:04:16 PM (17 years ago)

Author:

sunny

Message:

1. add -f flag for xml and tsv file type
2. output tsv file format

Location:

GSEXmlParser

Files:

• GSEXmlParser.cpp (modified) (3 diffs)
• GSEXmlParser.h (modified) (2 diffs)
• GSEXmlParser.upp (modified) (1 diff)
• init (added)

GSEXmlParser/GSEXmlParser.cpp

@@ -24 +24 @@
                      XmlTag("Descriptions") (descs) 
                  );
+}
+
+String Data::ToTSV()
+{
+  String tsv, tab, nl;
+  tab = "\t";
+  nl = "\n";
+  tsv = source + tab + "Sample-iid" + tab + iid + nl +
+        source + tab + "Supplementary-Data:" + supp_type + tab + supp_data + nl;
+  for(int i = 0; i < desc.GetCount(); i++)      
+      tsv += source + tab + "Description:" + desc.GetKey(i) + tab + desc[i] + nl; 
+        
+  return tsv;
 }
 
@@ -91 +104 @@
 }
 
+String   GSEParser::ToTSV()
+{
+  String tsv, tab; 
+  tab = "\t";
+  tsv = "# rowkey" + tab + "columnkey" + tab + "value\n";
+  for (int i = 0; i < data.GetCount(); i++) {
+    tsv << data[i].ToTSV();
+  }
+  return tsv;
+}
+
 String TrimSpace(String str) {
   while (str.StartsWith(" ") && str.GetLength()) {
@@ -103 +127 @@
 CONSOLE_APP_MAIN
 {
-  String in, out, arg_flag;
+  String in, out, fmt, arg_flag;
+  /*
   in = "GSE2109_family.xml";
-  out = "GSEFamily.xml";
-  
+  out = "GSEFamily.tsv";
+  fmt = "tsv";
+  */
   const Vector<String>& cmdline = CommandLine();
+    
   for(int i = 0; i < cmdline.GetCount(); i++) {
     if (cmdline[i].StartsWith("-")){
       arg_flag = cmdline[i];      
     } else if (arg_flag.IsEqual("-i")) {
-      in = cmdline[i];
-      //Cout() << "in: " << in << "\n";
+      in = cmdline[i];    
     } else if (arg_flag.IsEqual("-o")) {
-      out = cmdline[i];
-      //Cout() << "out: " << out << "\n";
+      out = cmdline[i];     
+    } else if (arg_flag.IsEqual("-f")) {
+      fmt = cmdline[i];
+    } else if (arg_flag.StartsWith("-")) {
+      //Error argument
+      Cout() << "Usage Error: invalid argument "<< arg_flag << "\n";
+      exit(0);
     }
+  }
+  
+  if (cmdline.GetCount()==0 || in.IsEmpty() || out.IsEmpty() || fmt.IsEmpty()) {
+    Cout() << "Usage: GSEXmlParser.exe -f (xml|tsv) -i (input file) -o (output file)\n";
+    exit(0);  
   }
   
   GSEParser parser;
   parser.LoadXML(in);
-  SaveFile(out,parser.ToXML());
+  if (fmt.IsEqual("xml"))
+    SaveFile(out,parser.ToXML());
+  else if (fmt.IsEqual("tsv"))  {
+    SaveFile(out,parser.ToTSV());
+  }
+  
+  
   
 }

GSEXmlParser/GSEXmlParser.h

@@ -17 +17 @@
     String                    supp_data; //Supplementary-Data
     void   Dump();
-    String   ToXML();     
+    String   ToXML();
+    String   ToTSV();     
 };
 
@@ -24 +25 @@
   void     Dump();
     String   ToXML();
+    String   ToTSV();
     void     LoadXML(String filename);  
 };

GSEXmlParser/GSEXmlParser.upp

@@ +1 @@
+optimize_speed;
+
 uses
   Core;