Changeset 579

Timestamp:

Feb 8, 2008, 2:52:54 PM (15 years ago)

Author:

Martin Svensson

Message:

Fixes #98 Implement validator and metadata extractor plug-in for BGX files

File:

• trunk/net/sf/basedb/illumina/src/net/sf/basedb/illumina/filehandler/BgxFileHandler.java (modified) (6 diffs)

trunk/net/sf/basedb/illumina/src/net/sf/basedb/illumina/filehandler/BgxFileHandler.java

@@ -97 +97 @@
   }
 
-  /*  
-      @see net.sf.basedb.core.filehandler.DataFileMetadataReader#extractMetadata(net.sf.basedb.core.DbControl)
+  /**   
+      Extracts the number of controls that is defined in the [HEADINGS] section.
+      @param dc DbControl used when accessing the database.
    */
   @Override
@@ -119 +120 @@
   }
 
-  /*
-      @see net.sf.basedb.core.filehandler.DataFileMetadataReader#resetMetadata(net.sf.basedb.core.DbControl)
+  /**
+      Sets the number of features in file to '0'
+      @param dc DbControl used when accessing the database.
    */
   @Override
@@ -130 +132 @@
   
   /*
-    Gets a right type of input stream depending on if 
-    it comes from a packed or unpacked file.
+    Gets the right type of input stream depending if it comes
+    from a compressed file(GZIP) or none-compressed file. 
    */
   private InputStream wrapInputStream (InputStream in)
@@ -152 +154 @@
     Takes a file, packed(gzip) or not packed and parse certain amount of lines.
     Parsed heading lines will be stored in a list.
-    If one of [Probes] or [Controls] section is found, the next line in file will 
-    be checked. 
-    It must contain required (by the feature importer and reporter importer) columns.
+    The file considers to be valid if the [Probes] section is found and next line
+    contains of at least the columns: Probe_Id and Array_Address_Id.
    */
   private List<String> parseHeadings(File bgxFile, int range)
@@ -186 +187 @@
         line = reader.readLine();
         headings.add(line);
-        if (line.matches("\\[Probes\\]") || line.matches("\\[Controls\\]"))
+        if (line.matches("\\[Probes\\]"))
         {
           line = reader.readLine();
@@ -208 +209 @@
   }
   
+  /*
+    Gets the number of controls - defined in the headings section.
+   */
   private int getNumFeatures(List<String> headings)
   {
     int numControls = 0;
-    if (headings != null && !(headings.size()<1))
+    if (headings != null && !(headings.size() < 1))
     {   
       for (String s : headings)