Changeset 248

Timestamp:

Mar 28, 2007, 6:29:17 PM (16 years ago)

Author:

Johan Enell

Message:

major changes to basefile
some methods are deprecated and will be removed

Location:

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

Files:

• BASEFile.java (added)
• BASEFileAssaySection.java (modified) (4 diffs)
• BASEFileDataSection.java (added)
• BASEFileReader.java (modified) (4 diffs)
• BASEFileSection.java (modified) (13 diffs)
• BASEFileSpotSection.java (modified) (8 diffs)

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

@@ -28 +28 @@
 import java.util.List;
 
-public class BASEFileAssaySection extends BASEFileSection
+public class BASEFileAssaySection extends BASEFileDataSection
 {
   private final ArrayList<String> data;
-
-  private final int height;
-  
-  private final int width;
   
   private final HashMap<Integer, Integer> idIndex = new HashMap<Integer, Integer>();
@@ -40 +36 @@
   public BASEFileAssaySection(BASEFileSection bfs) throws BASEFileException
   {
-    if (!bfs.getType().equals("assays"))
+    super(bfs);
+    if (!bfs.isType("assays"))
     {
       throw new BASEFileException("Section must be of type 'assays' to create an assay section.");
@@ -49 +46 @@
     this.width = width;
     this.data = new ArrayList<String>(height*width);
-  }
-  
-  public final int getHeight()
-  {
-    return height;
-  }
-
-  public final int getWidth()
-  {
-    return width;
   }
   
@@ -95 +82 @@
     return this.findIntOpt("count");
   }
+
+  @Override
+  public int getDataLineLength()
+  {
+    return getColumns().size();
+  }
   
 }

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

@@ -60 +60 @@
    * @throws FileNotFoundException If the infile cant be found
    */
+  @Deprecated
   public BASEFileReader(File in) throws FileNotFoundException
   {
@@ -136 +137 @@
    */
   public <R, S> BASEFileSpotSection<R, S> readSpotSection()
-    throws BadFormatException, IOException
+    throws BASEFileException, IOException
   {
     while (section != null && !section.isType("spots"))
@@ -150 +151 @@
    * @param <S>
    * @return
-   * @throws BadFormatException 
    * @throws IOException 
    * @throws BadSectionException 
@@ -157 +157 @@
     throws BASEFileException, IOException
   {
+    section = readSection(false); 
     while (section != null && !section.isType("assays"))
     {
       section = readSection(false);
+    }
+    if (section == null)
+    {
+      throw new BASEFileException("Couldn't find assays section in file "+this.inFile.getAbsolutePath());
     }
     return new BASEFileAssaySection(section);

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

@@ -23 +23 @@
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 /**
@@ -56 +58 @@
 
   /**
+   * The type of this section. 
+   */
+  private String type;
+
+  private long pointer;
+
+  /**
    * Creates a new BASEFileSection.
    */
@@ -61 +70 @@
   {
     startLine = -1;
+    pointer = -1;
     dataStartLine = -1;
-    setHeader("section", "");
+    type = "";
+  }
+
+  public BASEFileSection(BASEFileSection bfs) throws BASEFileException
+  {
+    if (bfs == null)
+    {
+      throw new BASEFileException("Can't initiate an assay section with a null section.");
+    }
+    startLine = bfs.getStartLine();
+    pointer = bfs.getStartPointer();
+    dataStartLine = bfs.getDataStartLine();
+    type = bfs.getType();
+    setHeaders(bfs.getHeaders());
   }
 
@@ -224 +247 @@
   public final String setHeader(Object key, Object value)
   {
-    return headers.put(key.toString(), value.toString());
+    String ret = "";
+    if ("section".equals(key))
+    {
+      ret = this.getType();
+      this.setType(value.toString());
+    }
+    else
+    {
+      ret = headers.put(key.toString(), value.toString());
+    }
+    return ret;
   }
 
@@ -281 +314 @@
     return this.headers.get(key.toString());
   }
+  
+  public final Map<String, String> getHeaders()
+  {
+    return Collections.unmodifiableMap(this.headers);
+  }
 
   public final String removeHeader(Object key)
@@ -291 +329 @@
   }
 
-  final boolean setHeaders(HashMap<String, String> headers)
+  final boolean setHeaders(Map<String, String> headers)
   {
     if (headers == null)
@@ -300 +338 @@
     for (String key : headers.keySet())
     {
-      this.headers.put(key, headers.get(key));
+      this.setHeader(key, headers.get(key));
     }
     return true;
   }
+  
+  public int getColIndex(String header, String col) throws BASEFileException
+  {
+    List<String> l = this.findFieldList(header);
+    if (l == null) throw new BASEFileException("Can't find header "+header);
+    int index = l.indexOf(col);
+    if (index == -1) throw new BASEFileException("Can't find column "+col+" in header "+header);
+    return index;
+  }
 
   /**
@@ -312 +359 @@
   public final String getType()
   {
-    return headers.get("section");
-  }
-
-  /**
-   * @param string
-   * @return
+    return type;
+  }
+
+  /**
+   * Checks the type of this section.
+   * 
+   * @param string the type to test
+   * @return true if type matches string
    */
   public final boolean isType(String string)
@@ -323 +372 @@
     return getType().equals(string);
   }
+  
+  /**
+   * Sets the type of this section.
+   * 
+   * @return the new type
+   */
+  public final void setType(String type)
+  {
+    this.type = type;
+  }
 
   public final int getDataStartLine()
@@ -329 +388 @@
   }
 
+  @Deprecated
   public final void setDataStartLine(int dataStartLine)
   {
@@ -334 +394 @@
   }
 
+  public final void setStartPointer(long pointer)
+  {
+    this.pointer = pointer;
+  }
+
   public final int getStartLine()
   {
     return startLine;
   }
+  
+  public final long getStartPointer()
+  {
+    return pointer;
+  }
 
   public final void setStartLine(int startLine)
@@ -347 +417 @@
   {
     this.headers.clear();
-    setHeader("section", "");
     startLine = -1;
     dataStartLine = -1;
@@ -359 +428 @@
     for (String key : headers.keySet())
     {
-      if (!key.equals("section"))
-      {
-        ret += key + "\t" + headers.get(key) + "\n";
-      }
+      ret += key + "\t" + headers.get(key) + "\n";
     }
     ret += "%";

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

@@ -26 +26 @@
 import java.util.List;
 
-public class BASEFileSpotSection<R, S> extends BASEFileSection
+public class BASEFileSpotSection<R, S> extends BASEFileDataSection
 {
 
-  private final int height;
-  private final int width;
   private final ArrayList<S> spotData;
   private final ArrayList<R> reporterData;
-  
-  public BASEFileSpotSection(BASEFileSection bfs)
+    
+  public BASEFileSpotSection(BASEFileSection bfs) throws BASEFileException
   {
-    this.height = bfs.findIntOpt("count");
-    this.width = bfs.findStringOpts("assayFields").length * bfs.findStringOpts("assays").length + bfs.findStringOpts("columns").length - 1;
+    super(bfs);
+    if (!bfs.isType("spots"))
+    {
+      throw new BASEFileException("Section must be of type 'spots' to create an assay section.");
+    }
+    this.setHeight(bfs.findIntOpt("count"));
+    this.setWidth(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);
@@ -45 +48 @@
   public BASEFileSpotSection(int height, int width)
   {
+    this.setType("spots");
     this.height = height;
     this.width = width;
@@ -54 +58 @@
   public final void setDataMatrix(int height, int width)
   {
-    
+    this.height = height;
+    this.width = width;
+    this.spotData.ensureCapacity(height*width);
+    this.reporterData.ensureCapacity(height);
   }
   
@@ -97 +104 @@
     i = reporterData.indexOf(reporter) + i;
     return spotData.set(i, spot);
-    
   }
   
@@ -111 +117 @@
   }
 
+  public int getColumnsColIndex(String col) throws BASEFileException
+  {
+    return this.getColIndex("columns", col);
+  }
+
   public List<Integer> getAssaysHeader()
   {
@@ -116 +127 @@
   }
 
+  public int getAssaysColIndex(String col) throws BASEFileException
+  {
+    return this.getColIndex("assays", col);
+  }
+
   public List<String> getAssayFieldsHeader()
   {
     return this.findFieldList("assayFields");
+  }
+
+  public int getAssayFieldsColIndex(String col) throws BASEFileException
+  {
+    return this.getColIndex("assayFields", col);
   }
   
@@ -128 +149 @@
   public boolean isValid()
   {
-    if (!isType("spots")) return false;
     if (getColumnHeader() == null) return false;
     if (getAssayFieldsHeader() == null) return false;
     if (getAssaysHeader() == null) return false;
     return true;
-  }
-
-  public final int getHeight()
-  {
-    return height;
-  }
-
-  public final int getWidth()
-  {
-    return width;
   }
 
@@ -174 +184 @@
     return reporterData.size();
   }
+
+  @Override
+  public int getDataLineLength()
+  {
+    int length = this.getColumnHeader().size() -1;
+    length += this.getAssayFieldsHeader().size() * this.getAssaysHeader().size();
+    return length;
+  }
 }