Changeset 3022

Timestamp:

Dec 12, 2006, 10:57:50 AM (16 years ago)

Author:

dominic

Message:

 

File:

• branches/tab2mage_ebi/src/plugins/core/net/sf/basedb/plugins/Tab2MageExporter.java (modified) (40 diffs)

branches/tab2mage_ebi/src/plugins/core/net/sf/basedb/plugins/Tab2MageExporter.java

@@ -3 +3 @@
   Copyright (C) Authors contributing to this file.
 
+  This file is for NutriBASE - Nutrigenomics BioArray Software Environment.
+  A customisation of the BASE SOFTWARE.
+  
   BASE is free software; you can redistribute it and/or
   modify it under the terms of the GNU General Public License
@@ -18 +21 @@
   Boston, MA  02111-1307, USA.
 */
-package net.sf.basedb.plugins;
-
+package com.plugin;
 
 import java.io.BufferedWriter;
 import java.io.OutputStreamWriter;
 import java.io.Writer;
+import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -29 +32 @@
 import java.util.Date;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.LinkedHashSet;
+import java.util.LinkedHashMap; 
 import java.util.LinkedList;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeSet;
+import java.text.DateFormat;
+import java.util.TreeMap;
 
-import net.sf.basedb.core.Affymetrix;
+import utils.Values;
+import net.sf.basedb.core.plugin.About;
+import net.sf.basedb.core.plugin.AbstractPlugin;
+import net.sf.basedb.core.plugin.GuiContext;
+import net.sf.basedb.core.plugin.InteractivePlugin;
+import net.sf.basedb.core.plugin.AboutImpl;
+import net.sf.basedb.core.plugin.Plugin;
+import net.sf.basedb.core.plugin.Request;
+import net.sf.basedb.core.plugin.Response;
+import net.sf.basedb.core.plugin.Plugin.MainType;
+import net.sf.basedb.core.query.Annotations;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Orders;
+import net.sf.basedb.core.query.Restrictions;
+import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.Annotatable;
 import net.sf.basedb.core.Annotation;
 import net.sf.basedb.core.AnnotationSet;
 import net.sf.basedb.core.AnnotationType;
-import net.sf.basedb.core.Application;
 import net.sf.basedb.core.ArrayDesign;
 import net.sf.basedb.core.BaseException;
+import net.sf.basedb.core.BioMaterial;
 import net.sf.basedb.core.BioMaterialEvent;
+import net.sf.basedb.core.BooleanParameterType;
 import net.sf.basedb.core.BioSource;
-import net.sf.basedb.core.BooleanParameterType;
+import net.sf.basedb.core.Client;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Experiment;
@@ -51 +75 @@
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.Hybridization;
-import net.sf.basedb.core.Include;
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemAlreadyExistsException;
@@ -57 +80 @@
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.ItemResultList;
+import net.sf.basedb.core.Label;
 import net.sf.basedb.core.LabeledExtract;
+import net.sf.basedb.core.MeasuredBioMaterial;
+import net.sf.basedb.core.ParameterType;
 import net.sf.basedb.core.Path;
 import net.sf.basedb.core.PathParameterType;
+import net.sf.basedb.core.PlateMapping;
 import net.sf.basedb.core.PluginParameter;
 import net.sf.basedb.core.ProgressReporter;
@@ -68 +95 @@
 import net.sf.basedb.core.Scan;
 import net.sf.basedb.core.StringParameterType;
+import net.sf.basedb.core.Type;
 import net.sf.basedb.core.User;
-import net.sf.basedb.core.plugin.About;
-import net.sf.basedb.core.plugin.AboutImpl;
-import net.sf.basedb.core.plugin.AbstractPlugin;
-import net.sf.basedb.core.plugin.GuiContext;
-import net.sf.basedb.core.plugin.InteractivePlugin;
-import net.sf.basedb.core.plugin.Plugin;
-import net.sf.basedb.core.plugin.Request;
-import net.sf.basedb.core.plugin.Response;
-import net.sf.basedb.core.query.Hql;
-import net.sf.basedb.core.query.Orders;
-import net.sf.basedb.util.Values;
+import net.sf.basedb.core.Include;
+import net.sf.basedb.core.ArraySlide;
+import net.sf.basedb.core.Application;
+import net.sf.basedb.core.Affymetrix;
 
 /**
   A plugin that exports an experiment in tab2mage specification for submission to ArrayExpress public repository.
   @author Dominic 
-  @version 2.0
+  @version 1.0
   @base.modified $Date$
 */
@@ -253 +274 @@
     DbControl dc=null;
     Set<Protocol> protocols = new LinkedHashSet<Protocol>(); //to get protocols as they are entered
+      
     Set<String> hybSectionHeader= new LinkedHashSet<String>();
     Set<String>  protocolHybSectionHeader= new LinkedHashSet<String>();
     Set<String>  parameterHybSectionHeader= new LinkedHashSet<String>();
-    Map<AnnotationType, Annotation> factorValues= new HashMap<AnnotationType,Annotation>();
+    
+    //Map<String, String> bioMaterials= new LinkedHashMap<String, String>();
+    //Map<String, String> arrayDataInfo= new LinkedHashMap<String,String>();
     List<String> protocolRefId= new LinkedList<String>();
     List<String> hybridizationDataRows=new LinkedList<String>();
     List<String> parameterValues= new LinkedList<String>();
+    
     List<Annotation> expFactorValues= new LinkedList<Annotation>();
-    
-    List<String> twoColorHybDataRowsFirstSection=new LinkedList<String>();
-    List<String> twoColorHybDataRowsSecondSection=new LinkedList<String>();
-  
-    
+    Map<AnnotationType, Annotation> factorValues= new HashMap<AnnotationType,Annotation>();
+    List<String> twoColorHybDataRows=new LinkedList<String>();
+    List<String> twoColorParameterValues=new LinkedList<String>();
+    List<String> twoColorFirstParameterValues=new LinkedList<String>();
+    List<String> twoColorProtocolRefId= new LinkedList<String>();
+    List<String> twoColorFirstProtocolRefId= new LinkedList<String>();
+        
     boolean overwrite = false;
     boolean twoColorHyb= false; 
@@ -301 +328 @@
       Writer out= new BufferedWriter(new OutputStreamWriter(file.getUploadStream(false),"ISO-8859-1")); 
       
-      // Header section
+      /*
+        Tab2Mage Header section
+       */ 
       out.write("# This file contains an experiment exported in tab2mage specification from BASE2\n\n");
-      // Experiment Section
+      
+      /*
+        Tab2Mage Experiment Section
+       */
       out.write("Experiment section \n");
       out.write("domain\t"+Application.getHostName()+"\n");
@@ -327 +359 @@
       out.write("\n");
       out.flush();
-      
-      
+          
       // Get all protocols and hybs   
       ItemQuery<RawBioAssay> rawBioAssaysQuery = experiment.getRawBioAssays();
@@ -335 +366 @@
       for (RawBioAssay rba : rawBioAssays)
       {
-        twoColorHybDataRowsFirstSection.add("-done-"); //initialise the twocolor hyb row with -done- as the delimeter
+        twoColorHybDataRows.add("-done-"); //initialise the twocolor hyb row with -done- as the delimeter
         /*
           Data files and array information section//
@@ -348 +379 @@
           hybSectionHeader.add("File[raw]");
           hybridizationDataRows.add(celFile.getName());
-          twoColorHybDataRowsFirstSection.add(celFile.getName());
+          twoColorHybDataRows.add(celFile.getName());
           hybSectionHeader.add("File[cdf]");
           hybridizationDataRows.add(cdfFile.getName());
-          twoColorHybDataRowsFirstSection.add(cdfFile.getName());
+          twoColorHybDataRows.add(cdfFile.getName());
         }
         else
@@ -357 +388 @@
           hybSectionHeader.add("File[raw]");
           hybridizationDataRows.add(rba.getName());
-          twoColorHybDataRowsFirstSection.add(rba.getName());
+          twoColorHybDataRows.add(rba.getName());
         }
         hybSectionHeader.add("Array[accession]");
         hybridizationDataRows.add(arrayDesign.getName());
-        twoColorHybDataRowsFirstSection.add(arrayDesign.getName());
+        twoColorHybDataRows.add(arrayDesign.getName());
         
-            //Raw BioAssay protocol
+            //Raw BioAssay protocol and parameters
         protocolRefId.add(getFormattedProtocolId(rba.getProtocol()));
+        twoColorFirstProtocolRefId.add(getFormattedProtocolId(rba.getProtocol()));
         protocolHybSectionHeader.add("Protocol[image_analysis]");
-        //if (rba.getProtocol()!=null)
-        //{
-          protocols.add(rba.getProtocol()); //rawbioassay protocol
-          
-        //  System.out.println("raw bioassay protocol: P-BASE-"+rba.getProtocol().getId());
-        //}
+        protocols.add(rba.getProtocol()); //rawbioassay protocol
         if (rba.isAnnotated())
         {
@@ -383 +410 @@
               for (int i=0; i<annotation.getValues().size(); i++)
               {
-                parameterValues.add(annotation.getValues().get(i).toString());
+                if (annotation.getValues().get(i)!=null)
+                {
+                  parameterValues.add(annotation.getValues().get(i).toString());
+                  //twoColorParameterValues.add(annotation.getValues().get(i).toString());
+                  twoColorFirstParameterValues.add(annotation.getValues().get(i).toString());
+                }
+                else
+                {
+                  System.out.println("Here becuase the annotation value for parameter at raw bioassay  is null");
+                  parameterValues.add("\t");
+                }
               }
             }
-            //else
-            //{
-            //  parameterValues.add("\t");
-            //}
+            
           }
         } 
-          //Scanning and Protocol 
+          //Scanning Protocol and Parameters 
         Scan scan= rba.getScan();
         Protocol scanProtocol =scan.getProtocol();
         protocolRefId.add(getFormattedProtocolId(scanProtocol));
+        twoColorFirstProtocolRefId.add(getFormattedProtocolId(scanProtocol));
         protocolHybSectionHeader.add("Protocol[scanning]");
-        protocols.add(scanProtocol);  //scaning protocol
+        protocols.add(scanProtocol);  //scanning protocol
         if (scan.isAnnotated())
         {
@@ -409 +444 @@
               for (int i=0; i<annotation.getValues().size(); i++)
               {
-                parameterValues.add(annotation.getValues().get(i).toString());
+                if (annotation.getValues().get(i)!=null)
+                {
+                  parameterValues.add(annotation.getValues().get(i).toString());
+                  //if (twoColorHyb)twoColorParameterValues.add(annotation.getValues().get(i).toString());
+                  twoColorFirstParameterValues.add(annotation.getValues().get(i).toString());
+                }
+                else
+                {
+                  parameterValues.add("\t");
+                  twoColorFirstParameterValues.add("\t");
+                }
               }
             }
-            //else
-            //{
-          //    parameterValues.add("\t");
-          //  }
+            
           }
         }
         
-        //Hybridization
+          //Hybridization
         Hybridization hyb= scan.getHybridization();
         hybSectionHeader.add("Array[serial]");
         hybridizationDataRows.add(hyb.getArraySlide().getName());
-        twoColorHybDataRowsFirstSection.add(hyb.getArraySlide().getName());     
+        twoColorHybDataRows.add(hyb.getArraySlide().getName());     
         /*
           Names of materials and processes section
@@ -429 +471 @@
         hybSectionHeader.add("Hybridization");
         hybridizationDataRows.add(hyb.getName());
-        twoColorHybDataRowsFirstSection.add(hyb.getName()); 
+        twoColorHybDataRows.add(hyb.getName()); 
         
         System.out.println("The number of scans: "+hyb.countScans()); // count scans that created the hyb
@@ -437 +479 @@
         protocols.add(hybProtocol); 
         protocolRefId.add(getFormattedProtocolId(hybProtocol));
+        twoColorFirstProtocolRefId.add(getFormattedProtocolId(hybProtocol));
         protocolHybSectionHeader.add("Protocol[hybridization]");
         if (hyb.isAnnotated())
@@ -450 +493 @@
               {
                 parameterValues.add(annotation.getValues().get(i).toString());
+                //if (twoColorHyb)twoColorParameterValues.add(annotation.getValues().get(i).toString());
+                twoColorFirstParameterValues.add(annotation.getValues().get(i).toString());
               }
             }
@@ -463 +508 @@
         int hybsize=labeledExtracts.size();
         int count=1;
-        //STOPPED HERE (LAST CODE) TRYING TO IMPLEMENT TWO COLOR HYBS
-        //if (hybsize==2 && !hybridizationDataRows.contains("-done-")) 
-        //{
-        //  twoColorHybDataRowsFirstSection.addAll(hybridizationDataRows); //create anew data row for 2 color experiment
-        //  twoColorHybDataRowsSecondSection.addAll(hybridizationDataRows);
-        //  twoColorHyb=true;
-        //}else if(hybsize==2 && twoColorHyb )
-        //{ //NOTE THE OUTPUT SHOWS THAT i AM ADDING THE LAST INFORMATION, SO FIX THIS
-        //  twoColorHybDataRowsFirstSection.addAll(twoColorHybDataRowsSecondSection);
-        //}
-        // END OF LAST CODE
-        System.out.println("The size of the two color data hyb data row before the labeled extract section: " +twoColorHybDataRowsFirstSection.size());
-        System.out.println("The size of the hyb data row before adding to tow color hyb row: " +hybridizationDataRows.size());
+        System.out.println("The size of the two color data hyb data row before the labeled extract section: " +twoColorHybDataRows.size());
+        System.out.println("The size of the tow color param value before adding the labeled extract section is: " +twoColorFirstParameterValues.size());
         System.out.println(hybsize ==1 ? "Affy Expriment. Hyb size:"+hybsize :"2 - color Expreriment. Hyb size : "+hybsize );
         for (LabeledExtract labeledExtract :labeledExtracts) // can have more than one labeled extract (2 color experiments)
         {
-          
             //  labeled extract
           hybSectionHeader.add("LabeledExtract");
-          if (count<hybsize)
-          {
-            hybridizationDataRows.add(labeledExtract.getName());
-          }
-          else if (count==2)
-          {
-            twoColorHyb=true;
-            twoColorHybDataRowsFirstSection.add(labeledExtract.getName());
-          }
-        
+          protocolHybSectionHeader.add("Protocol[labeling]");
           Protocol lbExtractProtocol= labeledExtract.getCreationEvent().getProtocol();
           protocols.add(lbExtractProtocol); // labeled extract protocol
-          protocolRefId.add(getFormattedProtocolId(lbExtractProtocol));
-          protocolHybSectionHeader.add("Protocol[labeling]");
+          if (count<hybsize || count==1)
+          {
+            hybridizationDataRows.add(labeledExtract.getName());
+            protocolRefId.add(getFormattedProtocolId(lbExtractProtocol));
+      
+          }
+          else if (count==2)
+          {
+            twoColorHyb=true;
+            twoColorHybDataRows.add(labeledExtract.getName());
+            twoColorProtocolRefId.add(getFormattedProtocolId(lbExtractProtocol));
+          }
           if (labeledExtract.isAnnotated())
           {
@@ -507 +541 @@
                 for (int i=0; i<annotation.getValues().size(); i++)
                 {
-                  parameterValues.add(annotation.getValues().get(i).toString());
+                  if (count < hybsize || count==1)
+                  {
+                    parameterValues.add(annotation.getValues().get(i).toString());
+                  }
+                  else if(count==2)
+                  {
+                    twoColorParameterValues.add(annotation.getValues().get(i).toString());
+                  }
                 }
               }
@@ -516 +557 @@
             }
           }
+            // Label 
           String labelName= labeledExtract.getLabel().getName(); // the name of the label
           hybSectionHeader.add("Dye");
@@ -524 +566 @@
           else if (count==2)
           {
-            twoColorHybDataRowsFirstSection.add(labelName);
+            twoColorHybDataRows.add(labelName);
           }
             //  Extract
@@ -533 +575 @@
           {
             hybSectionHeader.add("Extract");
-            if (count < hybsize)
-            {
-              hybridizationDataRows.add(extract.getName());
-            }
-            else if (count==2)
-            {
-              twoColorHybDataRowsFirstSection.add(extract.getName());
-            }
-            
+            protocolHybSectionHeader.add("Protocol[extraction]");
             Protocol extractProtocol =extract.getCreationEvent().getProtocol(); //extract protocol
             protocols.add(extractProtocol); 
-            protocolRefId.add(getFormattedProtocolId(extractProtocol));
-            protocolHybSectionHeader.add("Protocol[extraction]");
+            if (count < hybsize || count==1)
+            {
+              hybridizationDataRows.add(extract.getName());
+              protocolRefId.add(getFormattedProtocolId(extractProtocol));
+            }
+            else if (count==2)
+            {
+              twoColorHybDataRows.add(extract.getName());
+              twoColorProtocolRefId.add(getFormattedProtocolId(extractProtocol));
+            }
+            
             if (extract.isAnnotated())
             {
@@ -558 +601 @@
                   {
                     System.out.println("The extract protocol parameter is :" + annotation.getValues().get(i).toString());
-                    parameterValues.add(annotation.getValues().get(i).toString());
+                    if (count < hybsize || count==1)
+                    {
+                      parameterValues.add(annotation.getValues().get(i).toString());
+                    }
+                    else if(count==2)
+                    {
+                      twoColorParameterValues.add(annotation.getValues().get(i).toString());
+                    }
                   }
                 }
@@ -570 +620 @@
           
             //Sample
-          Set<Annotatable>sampleOrPooledExtract= extract.getAnnotatableParents(); //get the sample or pooled extract
+          //Set<Annotatable>sampleOrPooledExtract= extract.getAnnotatableParents(); //get the sample or pooled extract
           Sample sample =extract.getSample(); // The sample, extract is created from
           if (sample != null)
           {
             hybSectionHeader.add("Sample");
-            if (count < hybsize)
+            protocolHybSectionHeader.add("Protocol[treatment]");
+            Protocol sampleProtocol=sample.getCreationEvent().getProtocol();      //sampling protocol
+            protocols.add(sampleProtocol); 
+            if (count < hybsize || count==1)
             {
               hybridizationDataRows.add(sample.getName());
+              protocolRefId.add(getFormattedProtocolId(sampleProtocol));
             }
             else if (count==2)
             {
-              twoColorHybDataRowsFirstSection.add(sample.getName());
+              twoColorHybDataRows.add(sample.getName());
+              twoColorProtocolRefId.add(getFormattedProtocolId(sampleProtocol));
             }
             
-            Protocol sampleProtocol=sample.getCreationEvent().getProtocol();      //sampling protocol
-            protocols.add(sampleProtocol);  
-            protocolRefId.add(getFormattedProtocolId(sampleProtocol));
-            protocolHybSectionHeader.add("Protocol[treatment]");
-              // sample protocol parameter
+              // sampling protocol parameter
             if (sample.isAnnotated())
             {
               ItemQuery<Annotation> annotationsQuery = sample.getAnnotationSet().getAnnotations();
+              annotationsQuery.include(Include.MINE,Include.IN_PROJECT, Include.SHARED);
               ItemResultList<Annotation> annotations= annotationsQuery.list(dc);
               for (Annotation annotation: annotations)
               {
+                
                 if (sampleProtocol.isParameter(annotation.getAnnotationType()))
                 {
@@ -600 +653 @@
                   for (int i=0; i<annotation.getValues().size(); i++)
                   {
-                    System.out.println("The sample protocl parameter is :" + annotation.getValues().get(i).toString());
-                    parameterValues.add(annotation.getValues().get(i).toString());
+                    System.out.println("The sample protocol parameter is :" + annotation.getValues().get(i).toString());
+                    if (annotation.getValues().get(i)!=null)
+                    {
+                      if (count < hybsize || count==1)
+                      {
+                        parameterValues.add(annotation.getValues().get(i).toString());
+                      }
+                      else if(count==2)
+                      {
+                        twoColorParameterValues.add(annotation.getValues().get(i).toString());
+                      }
+                    }
+                    else if(annotation.getValues().get(i)!=null)
+                    {
+                      System.out.println(annotation.getAnnotationType().getName()+ " is not a PARAMETER");
+                      parameterValues.add("\t");
+                    }
+                    
                   }
                 }
                 //else
                 //{
-                //  parameterValues.add("\t");
+                  //System.out.println(annotation.getAnnotationType().getName()+ " is not a PARAMETER");
+                  //parameterValues.add("\t");
                 //}
               }
@@ -618 +688 @@
             
             hybSectionHeader.add("Biosource");
-            if (count < hybsize)
+            if (count < hybsize || count==1)
             {
               hybridizationDataRows.add(bioSource.getName());
@@ -624 +694 @@
             else if(count==2)
             {
-              twoColorHybDataRowsFirstSection.add(bioSource.getName());
+              twoColorHybDataRows.add(bioSource.getName());
             }
             AnnotationSet bsAnnotationSet =bioSource.getAnnotationSet();
@@ -637 +707 @@
                 for (int i=0; i<annotation.getValues().size(); i++)
                 {
-                  if (count < hybsize)
+                  if (count < hybsize || count==1)
                   {
                     hybridizationDataRows.add(annotation.getValues().get(i).toString());
@@ -643 +713 @@
                   else if(count==2)
                   {
-                    twoColorHybDataRowsFirstSection.add(annotation.getValues().get(i).toString());
+                    twoColorHybDataRows.add(annotation.getValues().get(i).toString());
                   }
-                  
                 }
               }
@@ -655 +724 @@
         } //end of labeled extract loop
         
-        System.out.println("THE VALUE OF COUNT IS: "+ count);
-        //for (String protcolId : protocolRefId) //add protocol id
-        //{
+        //System.out.println("THE VALUE OF COUNT IS: "+ count);
+          // add protocol hyb ref ids
+        for (String protcolId : protocolRefId) //add protocol id
+        {
           //System.out.println("----Test protocol id added----");
           //System.out.println("Id: "+protcolId);
-        /// hybridizationDataRows.add(protcolId);
-        //}
-        //for (String paramValue : parameterValues ) //add parameter values
-        //{
+          hybridizationDataRows.add(protcolId);
+        }
+        if (twoColorHyb)
+        {
+          twoColorFirstProtocolRefId.addAll(twoColorProtocolRefId);
+          for (String protocolId : twoColorFirstProtocolRefId )
+          {
+            twoColorHybDataRows.add(protocolId);
+          }
+        }
+          //  add parameter values
+        for (String paramValue : parameterValues ) 
+        {
           //System.out.println("----Test parametervalue added----");
-        //  hybridizationDataRows.add(paramValue);
-        //}
+          hybridizationDataRows.add(paramValue);
+        }
+        if (twoColorHyb)
+        {
+          twoColorFirstParameterValues.addAll(twoColorParameterValues);
+          for (String paramValue : twoColorFirstParameterValues  ) 
+          {
+            twoColorHybDataRows.add(paramValue);
+          }
+        }
+        
         /*
           Experimental Factor Section
@@ -678 +766 @@
             {
               hybridizationDataRows.add(Values.getEmptyStringIfNull(value.getValues().get(i).toString()).toString());
+              if (twoColorHyb) twoColorHybDataRows.add(Values.getEmptyStringIfNull(value.getValues().get(i).toString()).toString());
             }
           }
@@ -683 +772 @@
           {
             hybridizationDataRows.add("\t");
-          }
-        }
-        if (twoColorHyb)
-        {
-          //twoColorHybDataRowsFirstSection.add("-done-");
-          hybridizationDataRows.addAll(twoColorHybDataRowsFirstSection);
-          //hybridizationDataRows.add("-done-");
-        }
+            if (twoColorHyb) twoColorHybDataRows.add("\t");
+          }
+        }
+        
+        if (twoColorHyb)hybridizationDataRows.addAll(twoColorHybDataRows);
+        // clear all necessary data holder for reuse
         protocolRefId.clear();
         parameterValues.clear();
         factorValues.clear();
-        if (!twoColorHybDataRowsFirstSection.isEmpty()) 
-        {
-          twoColorHybDataRowsFirstSection.clear();
+        twoColorParameterValues.clear();
+        twoColorFirstParameterValues.clear();
+        twoColorFirstProtocolRefId.clear();
+        twoColorProtocolRefId.clear();
+        if (!twoColorHybDataRows.isEmpty()) 
+        {
+          twoColorHybDataRows.clear();
           twoColorHyb=false;
         } 
@@ -716 +807 @@
       }
       
-      //Protocol Section
+      /*
+        Tab2Mage Protocol Section
+       */
       out.write("Protocol section \n");
       out.write("accession\ttext\tname\ttype\tparameters\n");
@@ -745 +838 @@
       out.flush();
       
-      //Hybridization Section
+      /*
+        Tab2Mage Hybridization Section
+       */
       out.write("Hybridization section \n");  
+        //header
       for (String header:hybSectionHeader)
       {
@@ -753 +849 @@
       
       out.write("\n");
-      //values
+        //values
       for (String hybRow: hybridizationDataRows)
       {
@@ -765 +861 @@
         }
       }
-      //for (String twoColor :twoColorHybDataRowsFirstSection )
-      //{
-      //  if (twoColor!="-done-")
-      //  {
-      //    out.write(twoColor+"\t");
-      //  }
-      //  else if("-done-".equals(twoColor))
-      //  {
-      //    out.write("\n");
-      //  }
-      //}
       out.write("\n");
     
@@ -792 +877 @@
     }       
   }
-  //   get all the experimental factors for this experiments,
+  /**
+     get all the experimental factors for an experiments
+     @param DcControl dc, the database control
+     @param Experiment experiment, the experiment
+     @param RawBioassay, the rawbioassay that the experimental factors are obtained from
+     @return List, list of annotations
+   */ 
   private static List<Annotation> getExperimentalFactorValues(DbControl dc, Experiment experiment, RawBioAssay rba)
   {
@@ -799 +890 @@
     experimentalFactorsQuery.include(Include.MINE,Include.IN_PROJECT, Include.SHARED, Include.OTHERS);
     ItemResultList<AnnotationType> experimentalFactors = experimentalFactorsQuery.list(dc);
-    for (AnnotationType exprFactor :experimentalFactors) //create the factor value for this experiment obtaining annotations from rawbioassay
+    for (AnnotationType exprFactor :experimentalFactors) //create the expr factor value for this experiment, obtaining annotations from rawbioassay
     {
       factorValuesHybSectionHeader.add("FactorValue["+exprFactor.getName()+"]");
@@ -811 +902 @@
     return values;
   }
-  // get the base format id for the protocol if protocol is null and empty string is returned , this helps to  mentain the tab delim format
+  /**
+    Gets the base format id for the protocol, if protocol is null and tab string is returned
+    this is required to have consistent tab delimeted format
+    @param protocol, the protocol used in the experiment
+    @return protocol id, this is a tab when the protocol is null 
+   */ 
   private static String getFormattedProtocolId (Protocol protocol)
   {
-    String empty="";
+    String tab="\t";
     String protocolId;
     if (protocol!=null)
@@ -822 +918 @@
     else
     {
-      protocolId= empty;
+      protocolId= tab;
     }
     return  protocolId ;