Changeset 1085

Timestamp:

May 19, 2009, 9:46:17 AM (14 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #215: BGX reporter importer hangs if the [Controls] section has less than 6 columns

File:

• plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BgxMergeControlsInputStream.java (modified) (2 diffs)

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

@@ -33 +33 @@
 import java.util.Map;
 import java.util.Set;
+
+import net.sf.basedb.core.signal.SignalException;
 
 /**
@@ -225 +227 @@
     while (line != null && !line.startsWith("["))
     {
+      if (Thread.interrupted()) throw new SignalException("Aborted by user");
       String[] cols = line.split("\\t");
-      if (cols.length < 6) continue; // 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
-        
-      Control control = controls.get(probeId);
-      if (control == null)
-      {
-        control = new Control(probeId, arrayAdressId, sequence);
-        controls.put(probeId, control);
-      }
-      control.merge(reporterGroupName, reporterGroupId, reporterCompositeMap);
+      if (cols.length >= 6)
+      {
+        // 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
+          
+        Control control = controls.get(probeId);
+        if (control == null)
+        {
+          control = new Control(probeId, arrayAdressId, sequence);
+          controls.put(probeId, control);
+        }
+        control.merge(reporterGroupName, reporterGroupId, reporterCompositeMap);
+      }
       line = in.readLine();
     }