Changeset 1007

Timestamp:

Mar 27, 2009, 10:59:20 PM (14 years ago)

Author:

Jari Häkkinen

Message:

metadata is split into reporter and assay metadata. Added flags to assay meta data if ref assay.

File:

• plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/qQuantileNormalization.java (modified) (9 diffs)

plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/qQuantileNormalization.java

@@ -54 +54 @@
 import java.io.PrintWriter; // Jari, remove this?
 import java.sql.SQLException;
+import java.util.ArrayList; // Jari, remove this?
 import java.util.EnumSet;
 import java.util.List; // Jari, remove this?
@@ -111 +112 @@
   // http://base.thep.lu.se/ticket/1256, and
   // http://baseplugins.thep.lu.se/ticket/183.
+  @SuppressWarnings("unchecked")
   private void exportData()
     throws IOException
@@ -128 +130 @@
     }
 
-    // creating a meta-data file to track the information in the plain
-    // matrix file created above. This will be removed when BASE
-    // BioAssaySetExporter is refactored. Of course, the current
-    // meta-data file is highly specific for the needs here, but this
-    // use case should be covered hete. Or, way not fall back on a
-    // BASEfile?
+    // creating a reporter meta data file to track the information in
+    // the plain matrix file created above. This will be removed when
+    // BASE BioAssaySetExporter is refactored. Of course, the current
+    // reporter meta data file is highly specific for the needs here,
+    // but this use case should be covered hete. Or, way not fall back
+    // on a BASEfile?
 
     // The query must be the same as the one done in BASE core plug-in
@@ -155 +157 @@
         column_channel[i]=spotData.getIndex(VirtualColumn.channel(i+1).getName());
 
-      PrintWriter output = new PrintWriter(getExecDirectory() +
-                                           java.io.File.separator + metadata);
-
-      // first line in meta data is assay column numbers in BASE data cube
+      ArrayList<Short> referenceSelection=new ArrayList<Short>();
+      List<BioAssay> assays = (List<BioAssay>)job.getValues(selectBASid);
+      for (BioAssay assay : assays)
+      {
+        assay = BioAssay.getById(dc, assay.getId());
+        referenceSelection.add(assay.getDataCubeColumnNo());
+      }
+
+      PrintWriter assayWriter = new PrintWriter(getExecDirectory() +
+                                                java.io.File.separator +
+                                                assaydata);
       List<BioAssay> sourceAssays = sourceBAS.getBioAssays().list(dc);
       int nofAssays=sourceAssays.size();
       for (int i=0; i<nofAssays; ++i)
       {
-        if (i>0) output.print('\t');
-        output.print(sourceAssays.get(i).getDataCubeColumnNo());
-      }
-      output.println();
-
+        Short colno=sourceAssays.get(i).getDataCubeColumnNo();
+        String ref=(referenceSelection.contains(colno) ? "yes" : "no");
+        assayWriter.println(colno + "\t" + ref);
+      }
+      assayWriter.close();
+
+      PrintWriter reporterWriter = new PrintWriter(getExecDirectory() +
+                                                   java.io.File.separator +
+                                                   reporterdata);
       // write positions needed for storing result in BASE.
       int position=0;
@@ -175 +188 @@
         SqlResult item = spotData.next();
         position=item.getInt(column_position);
-        if (position!=prev_position) output.println(position);
-      }
-      output.close();
+        if (position!=prev_position) reporterWriter.println(position);
+      }
+      reporterWriter.close();
     }
     catch (SQLException e)
@@ -198 +211 @@
     subprocess_stdin="in.data";
     subprocess_stdout="out.data";
-    metadata="meta.data";
+    reporterdata="reporter.data";
+    assaydata="assay.data";
     exportData();
     String[] cmd = { "qQN" };
@@ -211 +225 @@
     try
     {
-      BufferedReader metainput =
+      BufferedReader assayinput =
         new BufferedReader(new FileReader(getExecDirectory() +
-                                          java.io.File.separator + metadata));
+                                          java.io.File.separator + assaydata));
+      // first column on each row in assay meta data is assay column
+      // numbers in BASE data cube
+      String inputline=null;
+      ArrayList<Short> column=new ArrayList<Short>();
+      while ((inputline = assayinput.readLine()) != null)
+      {
+        String[] lineSplit = inputline.split("\\s");
+        column.add(Short.parseShort(lineSplit[0]));
+      }
+      assayinput.close();
+
+      BufferedReader reporterinput =
+        new BufferedReader(new FileReader(getExecDirectory() +
+                                          java.io.File.separator +
+                                          reporterdata));
       BufferedReader input =
         new BufferedReader(new FileReader(getExecDirectory() +
@@ -219 +248 @@
                                           subprocess_stdout));
 
-      // first line in meta data is assay column numbers in BASE data cube
-      String inputline=metainput.readLine();
-      String[] lineSplit = inputline.split("\\s");
-      Short[] column=new Short[lineSplit.length];
-      for (int i=0; i<lineSplit.length; ++i)
-        column[i]=Short.parseShort(lineSplit[i]);
       while ((inputline = input.readLine()) != null)
       {
-        lineSplit = inputline.split("\\s");
-        if (lineSplit.length != column.length)
+        String[] lineSplit = inputline.split("\\s");
+        if (lineSplit.length != column.size())
           throw new BaseException("File/bioassay set size mismatch");
-        if ((inputline = metainput.readLine()) == null)
+        if ((inputline = reporterinput.readLine()) == null)
           throw new BaseException("Data and result file size mismatch");
         int position = Integer.parseInt(inputline);
-        for (int i=0; i<column.length; ++i)
+        for (int i=0; i<column.size(); ++i)
         {
           // C/C++ style string nan's (Java expects NaN) will cause a
@@ -240 +263 @@
           // resulting matrix. Postponing exception catching until
           // they start occuring.
-          batcher.insert(column[i], position, Float.parseFloat(lineSplit[i]));
+          batcher.insert(column.get(i), position,
+                         Float.parseFloat(lineSplit[i]));
         }
       }
       input.close();
+      reporterinput.close();
     }
     catch (Exception e)