Changeset 250

Timestamp:

Mar 30, 2007, 5:09:34 PM (16 years ago)

Author:

Johan Enell

Message:

there were some buggs ...

Location:

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

Files:

• BASEFile.java (modified) (3 diffs)
• BASEFileAssaySection.java (modified) (4 diffs)
• BASEFileDataSection.java (modified) (3 diffs)
• BASEFileSection.java (modified) (7 diffs)
• BASEFileSpotSection.java (modified) (9 diffs)

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

@@ -26 +26 @@
 import java.io.File;
 import java.io.IOException;
+import java.io.PrintWriter;
 import java.io.RandomAccessFile;
 import java.util.ArrayList;
-import java.util.List;
+import java.util.HashMap;
 
 public class BASEFile<R, S>
 {
+  private final File file;
   private final RandomAccessFile raf;
-  private BASEFileAssaySection assaySection;
-  private List<BASEFileSpotSection<R, S>> spotSections;
-  private List<BASEFileSection> sections;
+  private final boolean write;
+  private BASEFileAssaySection assaySection = null;
+  private ArrayList<BASEFileSpotSection<R, S>> spotSections = new ArrayList<BASEFileSpotSection<R,S>>();
+  private ArrayList<BASEFileSection> sections = new ArrayList<BASEFileSection>();
+  private HashMap<Integer, long[]> sectionPointers = new HashMap<Integer, long[]>();
+  
   private BASEFileSection currentSection = null;
   
-  public BASEFile(File file) throws BASEFileException
-  {
-    try
-    {
-      this.raf = new RandomAccessFile(file, "r");
+  @SuppressWarnings("unchecked")
+  public BASEFile(File file, String mode) throws BASEFileException
+  {
+    try
+    {
+      this.file = file;
+      if ("r".equals(mode))
+      {
+        write = false;
+        raf = new RandomAccessFile(file, "r");
+        String line = raf.readLine();
+        if (!"BASEfile".equals(line))
+        {
+          throw new BASEFileException("File "+file.getAbsolutePath()+" is no basefile. First line must be 'BASEfile'");
+        }
+        BASEFileSection bfs = readSection();
+        while (bfs != null)
+        {
+          if (bfs instanceof BASEFileAssaySection)
+          {
+            if (assaySection != null)
+            {
+              throw new BadFormatException("This basefile already has an assay section");
+            }
+            assaySection = (BASEFileAssaySection) bfs;
+          }
+          else if (bfs instanceof BASEFileSpotSection)
+          {
+            spotSections.add((BASEFileSpotSection<R, S>) bfs);
+          }
+          else
+          {
+            sections.add(bfs);
+          }
+          bfs = readSection();
+        }
+      }
+      else if("rw".equals(mode))
+      {
+        write = true;
+        raf = new RandomAccessFile(file, "rwd");
+      }
+      else
+      {
+        throw new IllegalArgumentException("Mode must be 'r' or 'rw'");
+      }
+    }
+    catch (IOException e)
+    {
+      throw new BASEFileException(e);
+    }
+  }
+
+  private BASEFileSection readSection() throws BASEFileException
+  {
+    try
+    {
       String line = raf.readLine();
-      if (!"BASEFile".equals(line))
-      {
-        throw new BASEFileException("File "+file.getAbsolutePath()+" is no basefile. First line must be 'BASEFile'.");
-      }
-      spotSections = new ArrayList<BASEFileSpotSection<R,S>>();
-      sections = new ArrayList<BASEFileSection>();
-      BASEFileSection bfs = readSection();
-      while (bfs != null)
-      {
-        if (bfs.isType("assays"))
-        {
-          this.assaySection = new BASEFileAssaySection(bfs);
-          this.assaySection.setDataPointer(raf.getFilePointer());
-        }
-        else if (bfs.isType("spots"))
-        {
-          BASEFileSpotSection<R, S> spotSection = new BASEFileSpotSection<R, S>(bfs);
-          spotSection.setDataPointer(raf.getFilePointer());
-          this.spotSections.add(new BASEFileSpotSection<R, S>(bfs));
-        }
-        else
-        {
-          this.sections.add(bfs);
-        }
-        
-        bfs = readSection();
-      }
-    }
-    catch (IOException e)
-    {
-      throw new BASEFileException(e);
-    }
-  }
-
-  private BASEFileSection readSection() throws IOException
-  {
-    long pointer = raf.getFilePointer();
-    String line = raf.readLine();
-    BASEFileSection bfs = null;
-    while(line == null)
-    {
-      String[] head = line.split("\t", 2);
-      if(head[0].equals("section") && head.length == 2)
-      {
-        bfs = new BASEFileSection();
-        bfs.setStartPointer(pointer);
-        bfs.setType(head[1]);
-      }
-      else if (head[0].equals("%") && bfs != null)
-      {
-        return bfs;
-      }
-      else if (bfs != null && head.length == 2)
-      {
-        bfs.setHeader(head[0], head[1]);
-      }
-      pointer = raf.getFilePointer();
-      line = raf.readLine();
+      BASEFileSection bfs = null;
+      while(line != null)
+      {
+        String[] head = line.split("\t", 2);
+        if(head[0].equals("section") && head.length == 2)
+        {
+          bfs = newSection(head[1]);
+          sectionPointers.put(bfs.hashCode(), new long[]{raf.getFilePointer(), -1L});
+        }
+        else if (head[0].equals("%") && bfs != null)
+        {
+          bfs.init();
+          if (bfs instanceof BASEFileDataSection)
+          {
+            sectionPointers.get(bfs.hashCode())[1] = raf.getFilePointer();
+          }
+          return bfs;
+        }
+        else if (bfs != null && head.length == 2)
+        {
+          bfs.setHeader(head[0], head[1]);
+        }
+        line = raf.readLine();
+      }
+    }
+    catch (IOException e)
+    {
+      throw new BASEFileException(e);
     }
     return null;
   }
-
+  
+  public final void addSpotSection(BASEFileSpotSection<R, S> bfss) throws BASEFileException
+  {
+    if (!write)
+      throw new BASEFileException("Onlu aloud to set assaysection in write mode");
+    spotSections.add(bfss);
+  }
+
+  private BASEFileSection newSection(String type)
+  {
+    if (type.equals("assays"))
+    {
+      return new BASEFileAssaySection();
+    }
+    else if (type.equals("spots"))
+    {
+      return new BASEFileSpotSection();
+    }
+    else
+    {
+      return new BASEFileSection(type);
+    }
+  }
+  
   /**
    * Get the assay section.
@@ -122 +172 @@
    * @return a spot section.
    */
-  public BASEFileSpotSection<R, S> getSpotSection()
-  {
-    return spotSections.get(0);
-  }
-
+  public BASEFileSpotSection<R, S> getSpotSection() throws BASEFileException
+  {
+    if (spotSections.size() == 0)
+    {
+      throw new BASEFileException("No spot section avalible");
+    }
+    return getSpotSection(0);
+  }
+
+  public BASEFileSpotSection<R, S> getSpotSection(int i)
+  {
+    return spotSections.get(i);
+  }
+
+  public final void setAssaySection(BASEFileAssaySection bfas) throws BASEFileException
+  {
+    if (assaySection != null)
+      throw new BASEFileException("Assaysection is already set");
+    if (!write)
+      throw new BASEFileException("Only aloud to set assaysection in write mode");
+      
+    assaySection = bfas;
+  }
+  
   /**
-   * Sets the current section two this section and sets the reading pointer to 
+   * Sets the current section to this section and sets the reading pointer to 
    * the data pointer of this section if it is a data section. If it an ordinary 
    * section the reading pointer is set to the start point.
    * 
    * @param bfs the section
+   * @throws BASEFileException if thee isn't part of this basefile or if the section
+   *  lacks filepointer
    */
   public void setCurrentSection(BASEFileSection bfs) throws BASEFileException
   {
-    this.currentSection = bfs;
-    try
-    {
-      if (bfs instanceof BASEFileDataSection)
-      {
-        this.raf.seek(((BASEFileDataSection) bfs).getDataPointer());
+    try
+    {
+      long[] pointers = sectionPointers.get(bfs.hashCode());
+      if (pointers == null)
+      {
+        throw new BASEFileException("This section is not part of this basefile");
+      }
+      currentSection = bfs;
+      if (pointers[1] != -1)
+      {
+        raf.seek(pointers[1]);
+      }
+      else if (pointers[0] != -1)
+      {
+        raf.seek(pointers[0]);
       }
       else
       {
-        this.raf.seek(bfs.getStartPointer());
+        throw new BASEFileException("This section has no file pointer");
       }
     }
@@ -177 +257 @@
       if (line == null || line.equals(""))
       {
-        this.currentSection = null;
+        currentSection = null;
+        raf.seek(0);
         return null;
       }
       else
       {
-        return line.split("\t", bfds.getDataLineLength());
-      }
-    }
-    catch (IOException e)
-    {
-      throw new BASEFileException(e);
-    }
-    
+        String[] ret = line.split("\t", -1);
+        if (ret.length != bfds.getDataLineLength())
+        {
+          throw new BASEFileException("Dataline must have "+bfds.getDataLineLength()+" fields");
+        }
+        return ret;
+      }
+    }
+    catch (IOException e)
+    {
+      throw new BASEFileException(e);
+    }
+  }
+  
+  public void validate() throws BASEFileException
+  {
+    assaySection.validate();
+    for (BASEFileSpotSection<R, S> bfss : spotSections)
+    {
+      bfss.validate();
+    }
+    for (BASEFileSection bfs : sections)
+    {
+      bfs.validate();
+    }
+  }
+
+  public void write() throws BASEFileException
+  {
+    if (!write)
+      throw new BASEFileException("This basefile isn't writable");
+    try
+    {
+      validate();
+      
+      PrintWriter out = new PrintWriter(file);
+      out.println("BASEfile");
+      if (assaySection != null)
+      {
+        out.println(assaySection);
+        for (int i = 0; i < assaySection.getHeight(); ++i)
+        {
+          assaySection.getDataLine(i);
+        }
+        out.println();
+      }
+      for (BASEFileSpotSection<R, S> bfss : spotSections)
+      {
+        out.println(bfss.toString());
+        out.println("DATA");
+        out.println();
+      }
+      out.close();
+    }
+    catch (IOException e)
+    {
+      throw new BASEFileException(e);
+    }
   }
 }

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

@@ -30 +30 @@
 public class BASEFileAssaySection extends BASEFileDataSection
 {
-  private final ArrayList<String> data;
+  private final ArrayList<String> data = new ArrayList<String>();
   
   private final HashMap<Integer, Integer> idIndex = new HashMap<Integer, Integer>();
+  
+  public BASEFileAssaySection()
+  {
+    super("assays");
+  }
   
   public BASEFileAssaySection(BASEFileSection bfs) throws BASEFileException
@@ -41 +46 @@
       throw new BASEFileException("Section must be of type 'assays' to create an assay section.");
     }
-    int height = bfs.findIntOpt("count");
-    int width = bfs.findStringOpts("columns").length;
-    this.height = height;
-    this.width = width;
-    this.data = new ArrayList<String>(height*width);
+    init();
   }
   
@@ -68 +69 @@
   }
   
+  public final int getDataSize()
+  {
+    return data.size();
+  }
+  
   public final List<String> getAnnotationColumns()
   {
-    return this.findFieldList("annotationColumns");
+    return findFieldList("annotationColumns");
+  }
+  
+  public final int getAnnotationColumnsColIndex(String col) throws BASEFileException
+  {
+    return getColIndex("annotationColumns", col);
   }
   
   public final List<String> getColumns()
   {
-    return this.findFieldList("columns");
+    return findFieldList("columns");
   }
   
-  @Override
-  public final int getCount()
+  public final int getColumnsColIndex(String col) throws BASEFileException
   {
-    return this.findIntOpt("count");
+    return getColIndex("columns", col);
   }
 
+  public final String setColumns(Object... values)
+  {
+    return setHeader("columns", values);
+  }
+
+  public final String setAnnotationColumns(Object... values)
+  {
+    return setHeader("annotationColumns", values);
+  }
+  
   @Override
   public int getDataLineLength()
@@ -89 +109 @@
     return getColumns().size();
   }
+
+  @Override
+  public String getDataLine(int i)
+  {
+    int index = i * getWidth();
+    String line = data.get(index);
+    for (int j = 1; j < getWidth(); ++j)
+    {
+      line += "\t" + data.get(index + j);
+    }
+    return line;
+  }
+
+  @Override
+  protected void init() throws BASEFileException
+  {
+    super.init();
+    setHeight(getCount());
+    setWidth(getColumns().size());
+    data.ensureCapacity(getHeight()*getWidth());
+  }
+
+  @Override
+  public void addData(Object... data)
+    throws BASEFileException
+  {
+    super.addData(data);
+    addData((String[]) data);
+  }
   
+  public void addData(String... data) throws BASEFileException
+  {
+    super.addData((Object[]) data);
+    if (data.length != getWidth())
+    {
+      throw new BASEFileException("The data line must contain "+getWidth()+" items");
+    }
+    int idcol = getColumnsColIndex("id");
+    int namecol = getColumnsColIndex("name");
+    idIndex.put(new Integer(data[idcol]), this.data.size() + namecol - 1);
+    for (String s : data)
+    {
+      this.data.add(s);
+    }
+  }
+
+  @Override
+  public void validate()
+    throws BASEFileException
+  {
+    super.validate();
+    if (getHeader("annotationColumns") == null) throw new BadSectionException("Data section must contain annotationColumns header");
+    if (getHeader("columns") == null) throw new BadSectionException("Data section must contain columns header");
+    if (getDataSize() != getHeight() * getWidth()) throw new BadSectionException("The size of the data list is missmatch");
+  }
 }

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

@@ -30 +30 @@
   
   protected int width;
-
-  private long dataPointer;
-  
-  protected BASEFileDataSection()
-  {
-    super();
-    dataPointer = -1;
-  }
   
   public BASEFileDataSection(BASEFileSection bfs) throws BASEFileException
   {
     super(bfs);
-    dataPointer = -1;
   }
   
   public BASEFileDataSection(BASEFileDataSection bfds) throws BASEFileException
   {
-    super(bfds);
-    dataPointer = bfds.getDataPointer();
+    this((BASEFileSection)bfds);
+    this.setWidth(bfds.getWidth());
+    this.setHeight(bfds.getHeight());
   }
   
+  protected BASEFileDataSection(String type)
+  {
+    super(type);
+  }
+
   public int getCount()
   {
     return this.findIntOpt("count");
-  }
-  
-  public long getDataPointer()
-  {
-    return this.dataPointer;
   }
 
@@ -70 +62 @@
     return width;
   }
-
-  public void setDataPointer(long pointer)
+  
+  public final String setCount(int c)
   {
-    this.dataPointer = pointer;
+    return setHeader("count", c);
   }
 
@@ -87 +79 @@
 
   public abstract int getDataLineLength();
+  
+  public abstract String getDataLine(int i);
+  
+  public void addData(Object... data)
+    throws BASEFileException
+  {
+    if (!isInitiated())
+    {
+      init();
+    }
+  }
+
+  @Override
+  protected void init() throws BASEFileException
+  {
+    super.init();
+  }
+
+  @Override
+  public void validate() throws BASEFileException
+  {
+    super.validate();
+    if (getHeader("count") == null) throw new BadSectionException("Data section must contain count header");
+  }
 }

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

@@ -62 +62 @@
   private String type;
 
-  private long pointer;
+  private boolean init = false;
 
   /**
    * Creates a new BASEFileSection.
    */
+  @Deprecated
   public BASEFileSection()
   {
     startLine = -1;
-    pointer = -1;
     dataStartLine = -1;
     type = "";
   }
 
+  /**
+   * Creates a new BASEFileSection.
+   */
+  public BASEFileSection(String type)
+  {
+    startLine = -1;
+    dataStartLine = -1;
+    this.type = type;
+  }
+  
   public BASEFileSection(BASEFileSection bfs) throws BASEFileException
   {
@@ -82 +92 @@
     }
     startLine = bfs.getStartLine();
-    pointer = bfs.getStartPointer();
     dataStartLine = bfs.getDataStartLine();
     type = bfs.getType();
@@ -361 +370 @@
     return type;
   }
+  
+  protected boolean isInitiated()
+  {
+    return init;
+  }
 
   /**
@@ -378 +392 @@
    * @return the new type
    */
+  @Deprecated
   public final void setType(String type)
   {
@@ -393 +408 @@
     this.dataStartLine = dataStartLine;
   }
-
-  public final void setStartPointer(long pointer)
-  {
-    this.pointer = pointer;
-  }
-
   public final int getStartLine()
   {
@@ -404 +413 @@
   }
   
-  public final long getStartPointer()
-  {
-    return pointer;
-  }
-
   public final void setStartLine(int startLine)
   {
@@ -434 +438 @@
     return ret;
   }
+
+  protected void init() throws BASEFileException
+  {
+    if (init)
+    {
+      throw new BASEFileException("This section has already been initiated");
+    }
+    init  = true;
+  }
+
+  public void validate() throws BASEFileException
+  {}
 }

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

@@ -29 +29 @@
 {
 
-  private final ArrayList<S> spotData;
-  private final ArrayList<R> reporterData;
-    
+  private final ArrayList<S> spotData = new ArrayList<S>();
+  private final ArrayList<R> reporterData = new ArrayList<R>();
+  
+  public BASEFileSpotSection()
+  {
+    super("spots");
+  }
+  
   public BASEFileSpotSection(BASEFileSection bfs) throws BASEFileException
   {
@@ -39 +44 @@
       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);
+    init();
   }
   
@@ -48 +50 @@
   public BASEFileSpotSection(int height, int width)
   {
-    this.setType("spots");
+    this();
     this.height = height;
     this.width = width;
-    this.spotData = new ArrayList<S>(height*width);
-    this.reporterData = new ArrayList<R>(height);
   }
   
@@ -78 +78 @@
     return spotData.iterator();
   }
-
-  public boolean addData(R reporter, S... spots)
-  {
-    if (spotData == null || reporterData == null) return false;
-    if (spots.length != width) return false;
-    return reporterData.add(reporter) && spotData.addAll(Arrays.asList(spots));
+  
+  @SuppressWarnings("unchecked")
+  @Override
+  public void addData(Object... data)
+    throws BASEFileException
+  {
+    super.addData(data);
+    if (data.length < 2)
+    {
+      throw new BASEFileException("Must have at least two objects to add");
+    }
+    S[] spots = (S[]) new Object[data.length - 1];
+    System.arraycopy(data, 1, spots, 0, spots.length);
+    reporterData.add((R) data[0]);
+    spotData.addAll(Arrays.asList(spots));
+  }
+
+  public void addData(R reporter, S... spots) throws BASEFileException
+  {
+    Object[] data = new Object[spots.length + 1];
+    data[0] = reporter;
+    System.arraycopy(spots, 0, data, 1, spots.length);
+    addData(data);
   }
   
@@ -112 +129 @@
   }
   
-  public List<String> getColumnHeader()
+  public List<String> getColumns()
   {
     return this.findFieldList("columns");
@@ -122 +139 @@
   }
 
-  public List<Integer> getAssaysHeader()
+  public List<Integer> getAssays()
   {
     return this.findFieldIntList("assays");
@@ -132 +149 @@
   }
 
-  public List<String> getAssayFieldsHeader()
+  public List<String> getAssayFields()
   {
     return this.findFieldList("assayFields");
@@ -142 +159 @@
   }
   
-  public int getCountHeader()
-  {
-    return this.findIntOpt("count");
-  }
-  
   public boolean isValid()
   {
-    if (getColumnHeader() == null) return false;
-    if (getAssayFieldsHeader() == null) return false;
-    if (getAssaysHeader() == null) return false;
+    if (getColumns() == null) return false;
+    if (getAssayFields() == null) return false;
+    if (getAssays() == null) return false;
     return true;
   }
@@ -185 +197 @@
   }
 
+  public final int getChannels()
+  {
+    return findIntOpt("channels");
+  }
+  
+  public final String setChannels(int channels)
+  {
+    return setHeader("channels", channels);
+  }
+
+  public final String setExtraFloats(Object... values)
+  {
+    return setHeader("setExtraFloats", values);
+  }
+
+  public final String setAssayFields(Object... values)
+  {
+    return setHeader("assayFields", values);
+  }
+
+  public final String setColumns(Object... values)
+  {
+    return setHeader("columns", values);
+  }
+
+  public final String setAssays(Integer... values)
+  {
+    return setHeader("assays", (Object[]) values);
+  }
+
   @Override
   public int getDataLineLength()
   {
-    int length = this.getColumnHeader().size() -1;
-    length += this.getAssayFieldsHeader().size() * this.getAssaysHeader().size();
+    int length = this.getColumns().size() -1;
+    length += this.getAssayFields().size() * this.getAssays().size();
     return length;
   }
+
+  @Override
+  public String getDataLine(int i)
+  {
+    
+    return null;
+  }
+
+  @Override
+  protected void init() throws BASEFileException
+  {
+    super.init();
+    setHeight(getCount());
+    setWidth(getAssays().size());
+    spotData.ensureCapacity(getHeight()*getWidth());
+    reporterData.ensureCapacity(getHeight());
+  }
+
+  @Override
+  public void validate() throws BASEFileException
+  {
+    super.validate();
+    if (getHeader("channels") == null) throw new BadSectionException("Data section must contain channels header");
+    if (getHeader("assays") == null) throw new BadSectionException("Data section must contain assays header");
+    if (getHeader("assayFields") == null) throw new BadSectionException("Data section must contain assayFields header");
+    if (getHeader("columns") == null) throw new BadSectionException("Data section must contain columns header");
+    if (getHeader("setExtraFloats") != null)
+    {
+      List<String> assayFields = getAssayFields();
+      for (String s : findFieldList("setExtraFloats"))
+      {
+        if (!assayFields.contains(s))
+        {
+          throw new BadSectionException("Header assayFields must contain "+s);
+        }
+      }
+    }
+    if (getReporterSize() != getHeight()) throw new BadSectionException("The size of the reporter list and height doesn't match");
+    if (getSpotSize() != getHeight()*getWidth()) throw new BadSectionException("The size of the spot list and height*width doesn't match");
+  }
 }