Changeset 247

Timestamp:

Mar 27, 2007, 5:19:44 PM (16 years ago)

Author:

Johan Enell

Message:

Added BASEFileAssaySection

Location:

trunk/se/lu/onk/BaseFile/src/basefile

Files:

• BASEFileAssaySection.java (added)
• BASEFileReader.java (modified) (1 diff)
• BASEFileSpotSection.java (modified) (2 diffs)

trunk/se/lu/onk/BaseFile/src/basefile/BASEFileReader.java

@@ -134 +134 @@
    * @throws BadFormatException 
    * @throws IOException 
+   */
+  public <R, S> BASEFileSpotSection<R, S> readSpotSection()
+    throws BadFormatException, IOException
+  {
+    while (section != null && !section.isType("spots"))
+    {
+      section = readSection(false);
+    }
+    return new BASEFileSpotSection<R, S>(section);
+  }
+  
+  /**
+   * TODO: Write javadoc for readSpotSection()
+   * @param <R>
+   * @param <S>
+   * @return
+   * @throws BadFormatException 
+   * @throws IOException 
    * @throws BadSectionException 
    */
-  @SuppressWarnings("unchecked")
-  public <R, S> BASEFileSpotSection<R, S>  readSpotSection()
-    throws BadFormatException, IOException
-  {
-    section = new BASEFileSpotSection<R, S>();
-    while (section != null && !section.isType("spots"))
+  public BASEFileAssaySection readAssaySection()
+    throws BASEFileException, IOException
+  {
+    while (section != null && !section.isType("assays"))
     {
       section = readSection(false);
     }
-    return (BASEFileSpotSection<R, S>) section;
+    return new BASEFileAssaySection(section);
   }
 

trunk/se/lu/onk/BaseFile/src/basefile/BASEFileSpotSection.java

@@ -29 +29 @@
 {
 
-  private int height;
-  private int width;
-  private ArrayList<S> spotData;
-  private ArrayList<R> reporterData;
+  private final int height;
+  private final int width;
+  private final ArrayList<S> spotData;
+  private final ArrayList<R> reporterData;
   
-  public BASEFileSpotSection()
+  public BASEFileSpotSection(BASEFileSection bfs)
   {
-    super();
+    this.height = bfs.findIntOpt("count");
+    this.width = bfs.findStringOpts("assayFields").length * bfs.findStringOpts("assays").length + bfs.findStringOpts("columns").length - 1;
+    this.spotData = new ArrayList<S>(height*width);
+    this.reporterData = new ArrayList<R>(height);
   }
-
-  public void setDataMatrix(int height, int width)
+  
+  @Deprecated
+  public BASEFileSpotSection(int height, int width)
   {
     this.height = height;
@@ -45 +49 @@
     this.spotData = new ArrayList<S>(height*width);
     this.reporterData = new ArrayList<R>(height);
+  }
+  
+  @Deprecated
+  public final void setDataMatrix(int height, int width)
+  {
+    
   }