Changeset 1146 for plugins/base2

Timestamp:

Jul 31, 2009, 2:00:28 PM (14 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #239: BGX reporter/feature importer auto-detection matches any files with at least two sections

Location:

plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins

Files:

• BgxFeatureImporter.java (modified) (1 diff)
• BgxReporterImporter.java (modified) (1 diff)

plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BgxFeatureImporter.java

@@ -168 +168 @@
   }
   
+  /**
+    The default {@link #isImportable()} method only looks in the first
+    section. In BGX files data is in the second section. So, if the
+    last found line is the [Probes] section we should continue to
+    parse and check if we find the data header.
+    @since 1.4
+  */
+  @Override
+  protected boolean isImportable(FlatFileParser ffp) 
+    throws IOException 
+  {
+    boolean importable = false;
+    Line last = ffp.getLine(ffp.getLineCount()-1);
+    if (last.type() == FlatFileParser.LineType.SECTION && 
+        Section.getByName(last.name()) == Section.PROBES)
+    {
+      importable = ffp.parseHeaders() == FlatFileParser.LineType.DATA_HEADER;
+    }
+    return importable;
+  }
+  
   @Override
   protected void handleSection(Line line) 

plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BgxReporterImporter.java

@@ -186 +186 @@
 
   /**
+    The default {@link #isImportable()} method only looks in the first
+    section. In BGX files data is in the second section. So, if the
+    last found line is the [Probes] section we should continue to
+    parse and check if we find the data header.
+    @since 1.4
+  */
+  @Override
+  protected boolean isImportable(FlatFileParser ffp) 
+    throws IOException 
+  {
+    boolean importable = false;
+    Line last = ffp.getLine(ffp.getLineCount()-1);
+    if (last.type() == FlatFileParser.LineType.SECTION && 
+        Section.getByName(last.name()) == Section.PROBES)
+    {
+      importable = ffp.parseHeaders() == FlatFileParser.LineType.DATA_HEADER;
+    }
+    return importable;
+  }
+  
+  /**
     When we get to the [Controls] section, we change configuration parameters
     for the parser and column mappings.