Changeset 1147

Timestamp:

Jul 31, 2009, 2:32:32 PM (14 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #237: Add support for MicroRNA BGX files to reporter importer

File:

• plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BgxMergeControlsInputStream.java (modified) (4 diffs)

plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BgxMergeControlsInputStream.java

@@ -28 +28 @@
 import java.io.InputStreamReader;
 import java.nio.charset.Charset;
+import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.LinkedHashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -229 +231 @@
       if (Thread.interrupted()) throw new SignalException("Aborted by user");
       String[] cols = line.split("\\t");
-      if (cols.length >= 6)
+      if (cols.length >= 3)
       {
         // Ignore lines that have too few column
         String probeId = cols[0];               // Column 1 = Probe_ID
         String arrayAdressId = cols[1];         // Column 2 = Array_Address_Id
-        String reporterGroupName = cols[2];     // Column 3 = Reporter_Group_Name
-        String reporterGroupId = cols[3];       // Column 4 = Reporter_Group_Id
-        String reporterCompositeMap = cols[4];  // Column 5 = Reporter_Composite_Map
-        String sequence = cols[5];              // Column 6 = Probe_Sequence
+        int numExtraColumns = cols.length - 2;
+        List<String> moreColumns = new ArrayList<String>(numExtraColumns);
+        for (int i = 2; i < cols.length; ++i)
+        {
+          moreColumns.add(cols[i]);
+        }
           
         Control control = controls.get(probeId);
         if (control == null)
         {
-          control = new Control(probeId, arrayAdressId, sequence);
+          control = new Control(probeId, arrayAdressId, numExtraColumns);
           controls.put(probeId, control);
         }
-        control.merge(reporterGroupName, reporterGroupId, reporterCompositeMap);
+        control.merge(moreColumns);
       }
       line = in.readLine();
@@ -255 +259 @@
   /**
     Represents a single control identified by Probe_Id. Merge 
-    annotations by calling {@link #merge(String, String, String)}.
+    annotations by calling {@link #merge(List)}.
   */
   private static class Control
   {
     private final String probeId;
-    private final String sequence;
     private final String arrayAddressId;
-    private Set<String> reporterGroupNames;
-    private Set<String> reporterGroupIds;
-    private Set<String> reporterCompositeMaps;
-
-    private Control(String probeId, String arrayAddressId, String sequence)
+    private final List<Set<String>> mergedColumns;
+
+    private Control(String probeId, String arrayAddressId, int numColumns)
     {
       this.probeId = probeId;
       this.arrayAddressId = arrayAddressId;
-      this.sequence = sequence;
-      reporterGroupIds = new HashSet<String>();
-      reporterGroupNames = new HashSet<String>();
-      reporterCompositeMaps = new HashSet<String>();
+      this.mergedColumns = new ArrayList<Set<String>>(numColumns);
     }
     
-    private void merge(String reporterGroupName, String reporterGroupId, String reporterCompositeMap)
-    {
-      reporterGroupIds.add(reporterGroupId);
-      reporterGroupNames.add(reporterGroupName);
-      reporterCompositeMaps.add(reporterCompositeMap);
+    private void merge(List<String> values)
+    {
+      while (mergedColumns.size() < values.size())
+      {
+        mergedColumns.add(new HashSet<String>());
+      }
+      for (int i = 0; i < values.size(); ++i)
+      {
+        mergedColumns.get(i).add(values.get(i));
+      }
     }
     
@@ -291 +294 @@
     {
       StringBuffer sb = new StringBuffer();
-      sb.append(probeId).append("\t").append("").append("\t");
-      boolean first = true;
-      for (String s : reporterGroupNames)
-      {
-        if (!first) sb.append(";");
-        sb.append(s);
-        first = false;
-      }
-      sb.append("\t");
-      first = true;
-      for (String s : reporterGroupIds)
-      {
-        if (!first) sb.append(";");
-        sb.append(s);
-        first = false;
-      }
-      sb.append("\t");
-      first = true;
-      for (String s : reporterCompositeMaps)
-      {
-        if (!first) sb.append(";");
-        sb.append(s);
-        first = false;
-      }
-      sb.append("\t").append(sequence);
+      sb.append(probeId).append("\t").append("");
+      for (int i = 0; i < mergedColumns.size(); ++i)
+      {
+        sb.append("\t");
+        boolean firstValue = true;
+        for (String s : mergedColumns.get(i))
+        {
+          if (!firstValue) sb.append(";");
+          sb.append(s);
+          firstValue = false;
+        }
+      }
       return sb.toString();
     }