Changeset 3240

Timestamp:

Apr 12, 2007, 1:01:22 PM (15 years ago)

Author:

dominic

Message:

added comments and close method

File:

• branches/tab2mage_ebi/src/plugins/core/net/sf/basedb/plugins/Tab2MageWriter.java (modified) (9 diffs)

branches/tab2mage_ebi/src/plugins/core/net/sf/basedb/plugins/Tab2MageWriter.java

@@ -2 +2 @@
 
 import java.io.BufferedWriter;
+import java.io.IOException;
 import java.io.OutputStreamWriter;
 import java.io.UnsupportedEncodingException;
@@ -55 +56 @@
       new BaseException(e);
     }
-    //statusOut.write(" Please check the messages below for the status of the export");
+    
   }
   
   /**
       writes the tab2mage file
-      @param experiment, the experiment to export which wasselected by the user on the GUI
-      @param protocols, the protocls used wthin the experiment
-      @param hybSectionHeader, a set containing the hybridization section headers
-      @param hybDataRows, list of hybridization data rows
-      @param job, the job parameter values
-      @param response, the reasponse object
-      @param dc, the client database control object
-   */
-  //  not checking for null parameters here, it is assumed it been catered for in the calling metthod
-  public static void writeTab2MageFile(Experiment experiment, Set<Protocol> protocols, Set<String> hybSectionHeader,  List<String> hybDataRows,
-                  ParameterValues job, Response response, DbControl dc)
+      @param experiment
+      @param protocols
+      @param hybSectionHeader
+      @param hybDataRows
+      @param job
+      @param response
+      @param dc
+   */
+  //  not checking for null parameters here, it is assumed it's been catered for in the calling method
+  public static void writeTab2MageFile(Experiment experiment, Set<Protocol> protocols, Set<String> hybSectionHeader,  
+                  List<String> hybDataRows, ParameterValues job, Response response, DbControl dc)
   {
     /*
@@ -89 +90 @@
     
   }
-  
+  /**
+    writes Tab2Mage experiment section
+    @param experiment, the experiment to write
+    @param response, the reponse object to reytun failures or expceptions
+    @param job, the job parameter values for the plugin
+   */
   private static void writeTab2MageExperimentSection(Experiment experiment, ParameterValues job, Response response)
   {
     try
     {
+      statusOut.write(" Please check the messages below for the status of the export"); //not part of experiment and may be moved elsewhere.
+      
       out.write("# This file contains an experiment exported in tab2mage specification from BASE\n\n");
       out.write("Experiment section \n");
@@ -123 +131 @@
       response.setError(ex.getMessage(), Arrays.asList(ex));
     }
-    finally
-    {
-      
-    }
-  }
-  
+  }
+  /**
+    writes Tab2Mage protocol section
+    @param protocols, list of protocols to write
+    @param response, the reponse object to return failures or exceptions
+    @param dc, database control object
+   */
   private static void writeTab2MageProtocolSection(Set<Protocol> protocols, DbControl dc, Response response)
   {
@@ -167 +176 @@
       response.setError(ex.getMessage(), Arrays.asList(ex));
     }
-    finally
-    {
-      
-    }
-  }
-  /**
-     Tab2Mage Hybridization  Header Section
+  }
+  /**
+     writes Tab2Mage hybridization  header section
      @param hybSectionHeader, the header to display
-     @param response, the reponse object to reytun failures
+     @param response, the reponse object to reytun failures or expceptions
    */
 
@@ -189 +194 @@
       }
       out.write("\n");
-    }
-    catch(Throwable ex)
-    {
-      response.setError(ex.getMessage(), Arrays.asList(ex));
-    }
-    
+      out.flush();
+    }
+    catch(Throwable ex)
+    {
+      response.setError(ex.getMessage(), Arrays.asList(ex));
+    }
   }
   
   /**
      Tab2Mage Hybridization  Channel Line Section
-     @param hybSectionHeader, the header to display
-     @param response, the reponse object to return failures
+     @param hybDataRow, the data rows to display
+     @param response, the reponse object to return failures or expceptions
    */
 
@@ -220 +225 @@
       }
       out.write("\n");
+      out.flush();
     }
     catch(Throwable ex)
@@ -227 +233 @@
     
   }
+  
+  /**
+    closes the file writers
+   */
+  public static void closeWriter()
+  {
+    try
+    {
+      if (out!= null) out.close();
+      if (statusOut!=null) statusOut.close();
+    }
+    catch(Throwable ex)
+    {
+      new IOException(ex.getMessage());
+    }
+  }
+  
   /**
    gets the file writer for the tab2mage file 
@@ -251 +274 @@
   }
   
-  
 }