Changeset 4563

Timestamp:

Apr 10, 2015, 3:41:16 PM (8 years ago)

Author:

Fredrik Levander

Message:

Updated tab feature importer to support new feature format

File:

• trunk/plugin/src/org/proteios/plugins/TabFeatureImporter.java (modified) (10 diffs)

trunk/plugin/src/org/proteios/plugins/TabFeatureImporter.java

@@ -59 +59 @@
 
 /**
- * This plug-in reads a features.tsv file and imports it into the
- * features table. 
+ * This plug-in reads a features.tsv file and imports it into the features
+ * table.
  * 
  * @author fredrik
@@ -72 +72 @@
   private static final org.apache.log4j.Logger log = org.apache.log4j.LogManager
     .getLogger("org.proteios.io");
-  
+
 
   public TabFeatureImporter()
@@ -89 +89 @@
   {
     return new AboutImpl("Tab feature importer",
-      "Import of tab separated features to database", "0.1",
-      "2010, Fredrik Levander", null, null,
-      "http://www.proteios.org");
+      "Import of tab separated features to database", "0.2",
+      "2010-2015, Fredrik Levander", null, null, "http://www.proteios.org");
   }
 
@@ -121 +120 @@
       {
         ItemQuery<Feature> featureQuery = qf.select(Feature.class);
-        featureQuery.restrict(Restrictions.eq(Hql
-          .property("featureFile"), Hql.entity(featureFile)));
+        featureQuery.restrict(Restrictions.eq(
+          Hql.property("featureFile"), Hql.entity(featureFile)));
         if (featureQuery.count(dc) > 0)
         {
@@ -162 +161 @@
               index[6] = line.indexOf("intensity");
               index[7] = line.indexOf("intensity");
-              if (line.indexOf("IntegratedIntensity")>1)
+              if (line.indexOf("IntegratedIntensity") > 1)
               {
                 index[7] = line.indexOf("IntegratedIntensity");
               }
+              // For Dinosaur feature format:
+              if (index[0] < 1)
+                index[0] = line.indexOf("rtApex");
+              if (index[1] < 1)
+                index[1] = line.indexOf("monoisoMz");
+              if (index[2] < 1)
+                index[2] = line.indexOf("rtStart");
+              if (index[5] < 1)
+                index[5] = line.indexOf("rtEnd");
+              if (index[6] < 1)
+                index[6] = line.indexOf("intensityApex");
+              if (index[7] < 1)
+                index[7] = line.indexOf("intensitySum");
               featureStart = true;
             }
@@ -187 +199 @@
               feature.setApexIntensity(Float.valueOf(line
                 .get(index[6])));
-              feature.setStartRetentionTimeInMinutes(Float.valueOf(line.get(index[2])));
-              feature.setEndRetentionTimeInMinutes(Float.valueOf(line.get(index[5])));
+              feature.setStartRetentionTimeInMinutes(Float
+                .valueOf(line.get(index[2])));
+              feature.setEndRetentionTimeInMinutes(Float
+                .valueOf(line.get(index[5])));
               feature.setFeatureFile(featureFile);
               feature.setMsFile(mzXMLFile);
@@ -204 +218 @@
         {
           throw new BaseException(
-            "Not a valid tab-separated feature file. First line should start with '# algorithm=F' or '# algorithm=M'");
+            "Not a valid tab-separated feature file. First line should start with '# algorithm=F','# algorithm=M', 'monoisoMz' or 'mz'");
         }
       }
@@ -270 +284 @@
     else if (fileName.contains(".features"))
     {
-      searchString = fileName.substring(0, fileName
-        .lastIndexOf(".features")) + ".mzML";
+      searchString = fileName.substring(0,
+        fileName.lastIndexOf(".features")) + ".mzML";
     }
     if (searchString != null)
@@ -296 +310 @@
 
 
-  
   // ----------------------------------------------------------
   /*
@@ -317 +330 @@
       if ((line = inreader.readLine()) != null)
       {
-        ok = (line.startsWith("mz") || line.startsWith("# algorithm=M") || line.startsWith("# algorithm=F"));
+        ok = (line.startsWith("monoisoMz") || line.startsWith("mz") || line
+          .startsWith("# algorithm=M") || line
+          .startsWith("# algorithm=F"));
       }
       inreader.close();