Changeset 3648

Timestamp:

Aug 9, 2007, 4:28:43 PM (16 years ago)

Author:

Peter Johansson

Message:

refs #639 removing the exportPlainMatrix method.

File:

• trunk/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (6 diffs)

trunk/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -102 +102 @@
      use in MeV (available from http://www.tm4.org).
    - BASEfile.
-   - Plain Matrix
-
-   @author enell, jari, peter
+
+   @author enell, jari
    @version 2.1
    @base.modified $Date$
@@ -746 +745 @@
 
 
-  public void exportPlainMatrix(BioAssaySet bioassayset, OutputStream os,
-                                ProgressReporter progress)
-    throws IOException, SQLException
-  {
-    DbControl dc=bioassayset.getDbControl();
-    PrintWriter out = new PrintWriter(os);
-    List<ExtendedProperty> reporterProperties =
-      ExtendedProperties.getProperties("ReporterData");
-
-    int nof_bioassays=0;
-    nof_bioassays=bioassayset.getBioAssays().list(dc).size();
-
-    if (progress != null)
-      progress.display(0, "Exporting ... performing database query");
-
-    DynamicSpotQuery query=bioassayset.getSpotData();
-    query.select(Dynamic.select(VirtualColumn.POSITION));
-    query.select(Dynamic.select(VirtualColumn.COLUMN));
-    query.select(Dynamic.select(VirtualColumn.channel(1)));
-    
-    query.order(Orders.asc(Dynamic.column(VirtualColumn.POSITION)));
-    query.order(Orders.asc(Dynamic.column(VirtualColumn.COLUMN)));
-
-    DynamicResultIterator spotData = query.iterate(dc);
-    int column_position=spotData.getIndex(VirtualColumn.POSITION.getName());
-    int column_column=spotData.getIndex(VirtualColumn.COLUMN.getName());
-    int column_channel=spotData.getIndex(VirtualColumn.channel(1).getName());
-    
-    int position=-1;
-    int column=nof_bioassays;
-    //double log2=Math.log(2.0);
-    int nof_spots=bioassayset.getNumSpots();
-    int progress_spot_interval=nof_spots/10;
-    int nof_processed_spots=0;
-    while (spotData.hasNext())
-    {
-      SqlResult item = spotData.next();
-      int thisposition=item.getInt(column_position);
-      short thiscolumn=item.getShort(column_column);
-
-      if (progress != null && 
-          (nof_processed_spots%progress_spot_interval == 0))
-        {
-          progress.display(100 * nof_processed_spots / nof_spots,
-                           "Exporting ..." + nof_processed_spots + " of " +
-                           nof_spots + " done.");
-        }
-        ++nof_processed_spots;
-  
-      if (position!=thisposition) // new position
-      {
-        // fill missing values before next spot
-        while (column < nof_bioassays) {
-          out.write("\t");
-          ++column;
-        }
-        column=1;
-        if (position != -1) // no leading newline in output 
-        {
-          out.write("\n");
-        }
-        position=thisposition;
-      }
-
-      // fill missing values up to next available column (bioassay)
-      while (column < thiscolumn) 
-      {
-        ++column;
-        out.write("\t");
-      }
-
-      // Calculate expression value
-      String ch1=item.getString(column_channel);
-      out.write(ch1);
-    }
-    out.flush();
-  }
-
-
   public About getAbout()
   {
@@ -1064 +984 @@
       formats.add(FORMAT_MEV, "MultiExperiment Viewer (MeV)");
       formats.add(FORMAT_BASEFILE, "BASEfile");
-      formats.add(FORMAT_PLAIN_MATRIX, "Plain Matrix");
       formatParameter = new PluginParameter<String>
         ( "fileformat",
@@ -1219 +1138 @@
         }
       }
-      else if (format.equals(FORMAT_PLAIN_MATRIX))
-      {
-        exportPlainMatrix(bas, out, progress);
-      }
       else
       {
@@ -1260 +1175 @@
       "- Tab Delimited, Multiple Sample Files (TDMS Format) for " +
       "use in MeV (available from http://www.tm4.org).\n"+
-      "- BASEfile, and Plain Matrix",
+      "- BASEfile",
       "2.0",
       "2006, Base 2 development team",
@@ -1288 +1203 @@
   private static final String FORMAT_BASEFILE = "BASEfile";
   private static final String FORMAT_MEV = "MeV";
-  private static final String FORMAT_PLAIN_MATRIX = "Plain Matrix";
-  
+
 
   public class QueryItem