Changeset 2956

Timestamp:

Nov 26, 2006, 11:33:11 PM (16 years ago)

Author:

Jari Häkkinen

Message:

Addresses #430. Most things fixed for export but experimental factors wont come out. Also fixed other minor issues.

File:

• branches/2.1/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (12 diffs)

branches/2.1/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -197 +197 @@
       for (String key : parameters.keySet())
       {
-        out.println(key+"/t"+parameters.get(key));
+        out.println(key+"\t"+parameters.get(key));
       }
       out.println("%");
@@ -204 +204 @@
     
     // assay section    
-    out.println("section/tassays");
+    out.println("section\tassays");
     
     out.println("%");
@@ -214 +214 @@
         out.print("\t");
         Set<Object> values = BioAssaySetUtil.getAnnotationValues(dc, ba, at);
-        for (Object v : values) out.print("/t"+v);
+        for (Object v : values) out.print("\t"+v);
       }
     }
@@ -220 +220 @@
     
     // spot section(s)
-    out.println("section/tspots");
+    out.println("section\tspots");
     out.println("%");
     out.println();
@@ -226 +226 @@
   
 
-  private void exportMeV(BioAssaySet bioassayset, File file)
+  private void exportMeV(BioAssaySet bioassayset, File file,
+                         ProgressReporter progress)
     throws IOException, SQLException
   {
@@ -241 +242 @@
     */
 
-    // data header
-    out.write("UID\tID");
+    List<ExtendedProperty> reporterProperties =
+      ExtendedProperties.getProperties("ReporterData");
+
+    // Data header
+    // Reporter headers
+    out.write("reporterInternalId\treporterID\tlastUpdate\tgeneSymbol");
+    for (ExtendedProperty ep : reporterProperties)
+      out.write("\t"+ep.getName());
+    // Number 3 in below statement comes from using three reporter
+    // entries from ReporterData. Below there is dependencies on this
+    // '3' such as the selectReporter("") in below query.select()
+    // statements (and more).
+    int nof_reporter_columns=3+reporterProperties.size();
+    // Bioassay headers
+    out.write("\texperimentalFactor");
     short nof_bioassays=0;
     for (BioAssay bioassay : bioassayset.getBioAssays().list(dc))
@@ -250 +264 @@
     }
 
-    // data
+    // Experimental factors
+    for (AnnotationType at : getExperimentalFactors(dc, bioassayset))
+    {
+      out.write("\n");
+      for (int i=0; i<nof_reporter_columns; ++i) out.write("\t");
+      out.write("\t"+at.getName());
+      for (BioAssay bioassay : bioassayset.getBioAssays().list(dc))
+      {
+        Set<Object> values = BioAssaySetUtil.getAnnotationValues(dc,bioassay,at);
+        for (Object v : values) out.write("\t"+v);
+      }
+    }
+
+    progress.display(0, "Exporting ... performing database query");
+    // Reporter annotations and expression levels
     int nofchannels=bioassayset.getRawDataType().getChannels();
     DynamicSpotQuery query=bioassayset.getSpotData();
@@ -257 +285 @@
     query.select(Dynamic.select(VirtualColumn.COLUMN));
     query.select(Dynamic.selectReporter("externalId"));
+    query.select(Dynamic.selectReporter("lastUpdate"));
+    query.select(Dynamic.selectReporter("symbol"));
+    for (ExtendedProperty ep : reporterProperties)
+    {
+      query.select(Dynamic.selectReporter(ep.getName()));
+    }
     for (int i=1; i<=nofchannels; ++i)
     {
@@ -266 +300 @@
     int column_position=spotData.getIndex(VirtualColumn.POSITION.getName());
     int column_column=spotData.getIndex(VirtualColumn.COLUMN.getName());
-    int column_reporter=spotData.getIndex("externalId");
+    int[] column_reporter= new int[nof_reporter_columns];
+    column_reporter[0]=spotData.getIndex("externalId");
+    column_reporter[1]=spotData.getIndex("lastUpdate");
+    column_reporter[2]=spotData.getIndex("symbol");
+    int idx=3;
+    for (ExtendedProperty ep : reporterProperties)
+    {
+      column_reporter[idx++]=spotData.getIndex(ep.getName());
+    }
     int[] column_channel = new int[nofchannels];
     for (int i=1; i<=nofchannels; ++i)
@@ -275 +317 @@
     short column=nof_bioassays;
     double log2=Math.log(2.0);
+    int nof_reporters=bioassayset.getNumReporters();
+    int progress_report_interval=nof_reporters/10;
+    int nof_processed_reporters=0;
     while (spotData.hasNext())
     {
+      if (nof_processed_reporters%progress_report_interval == 0)
+      {
+        progress.display(100 * nof_processed_reporters / nof_reporters,
+                         "Exporting ... " + nof_processed_reporters + " of " +
+                         nof_reporters + " done.");
+      }
+
       SqlResult item = spotData.next();
       int thisposition=item.getInt(column_position);
@@ -283 +335 @@
       if (position!=thisposition) // new reporter
       {
+        ++nof_processed_reporters;
         // fill missing values before next spot
         while (nof_bioassays>column++) out.write("\t");
         column=0;
         position=thisposition;
-        out.write("\npos:" + position + "\t" + item.getString(column_reporter));
+        out.write("\n" + position);
+        for (int i=0; i<nof_reporter_columns; ++i)
+        {
+          String str=item.getString(column_reporter[i]);
+          out.write("\t" + (str!=null ? str : ""));
+        }
+        out.write("\t"); // experimentalFactor is always empty for reporters
       }
       // fill missing values up to next available column (bioassay)
@@ -602 +661 @@
       bioassayset = BioAssaySet.getById(dc, bioassayset.getId());
 
-      progress.display(1, "Exporting ...");
+      progress.display(0, "Exporting ...");
 
       // Add other export formats here
       String format = (String) job.getValue("fileformat");
-      if (format.equals(FORMAT_MEV)) exportMeV(bioassayset,file);
+      if (format.equals(FORMAT_MEV)) exportMeV(bioassayset,file,progress);
       else if (format.equals(FORMAT_BASEFILE)) 
       {