Changeset 4280

Timestamp:

Feb 2, 2012, 1:41:23 PM (12 years ago)

Author:

marianne

Message:

Refs #774. Committing complementary files.

Location:

trunk

Files:

• api/core/conf/common-queries.xml (modified) (1 diff)
• api/core/src/org/proteios/core/Feature.java (modified) (3 diffs)
• plugin/src/org/proteios/plugins/FeatureSequencePropagator.java (modified) (3 diffs)

trunk/api/core/conf/common-queries.xml

@@ -254 +254 @@
   </query>
   
-  <query id="GET_UNIQUE_SEQUNCES_IN_FEATURE_FILE_FOR_PROJECT" type="HQL">
+  <query id="GET_UNIQUE_SEQUENCES_IN_MSFILE_FOR_PROJECT" type="HQL">
     <sql>
       SELECT DISTINCT f.peptideSequence
       FROM FeatureData f
-      WHERE f.project = :project 
-      AND f.featureFile =:featureFile
-    </sql>
-    <description>
-      Load all distinct (unique) sequences for a feature file in the Feature table for a project 
+      WHERE f.project = :project
+      AND f.msFile = :msFile
+      AND NOT f.peptideSequence IS NULL
+      AND f.chargeState IS 2
+      ORDER by f.apexRetentionTimeInMinutes
+    </sql>
+    <description>
+      Load all distinct (unique) sequences for a ms file in the Feature table for a project 
     </description>
   </query>

trunk/api/core/src/org/proteios/core/Feature.java

@@ -21 +21 @@
   public static final Item TYPE = Item.PROTEIOS_FEATURE;
 
-
+  
+  /*@SuppressWarnings("unchecked")
+  public static List<String> getAllClusterIDs(DbControl dc)
+  {
+    org.hibernate.Query query = HibernateUtil.getPredefinedQuery(dc
+      .getHibernateSession(),
+      "GET_ALL_FEATURES_WITH_SPECIFIC_CLUSTERID");
+    List<String> retval = query.list();
+    return retval;
+  }*/
+  
+  
   @SuppressWarnings("unchecked")
   public static List<File> getUniqueMsFiles(Project project, DbControl dc)
@@ -37 +48 @@
     return retval;
   }
+  
+  
+
+
+  @SuppressWarnings("unchecked")
+  public static List<String> getUniqueFeatureSequences(Project project, DbControl dc, File msFile)
+  {
+    org.hibernate.Query query = HibernateUtil.getPredefinedQuery(dc
+      .getHibernateSession(),
+      "GET_UNIQUE_SEQUENCES_IN_MSFILE_FOR_PROJECT");
+    query.setEntity("project", project.getData());
+    query.setEntity("msFile", msFile.getData());
+    List<String> retval = query.list();
+    return retval;
+  }
 
   @SuppressWarnings("unchecked")
@@ -49 +75 @@
     return retval;
   }
+
 
   /*

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

@@ -28 +28 @@
 package org.proteios.plugins;
 
-import org.apache.commons.collections.ListUtils;
-import org.apache.commons.lang.ArrayUtils;
+import java.io.OutputStream;
+import java.io.PrintWriter;
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Date;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Random;
+import java.util.TreeSet;
+
 import org.apache.commons.math.ArgumentOutsideDomainException;
 import org.apache.commons.math.MathException;
@@ -35 +46 @@
 import org.apache.commons.math.analysis.polynomials.PolynomialSplineFunction;
 import org.apache.commons.math.stat.correlation.PearsonsCorrelation;
-import org.apache.commons.math.stat.descriptive.moment.Mean;
 import org.proteios.core.Annotation;
 import org.proteios.core.AnnotationType;
@@ -62 +72 @@
 import org.proteios.core.query.Orders;
 import org.proteios.core.query.Restrictions;
-
-import java.io.OutputStream;
-import java.io.PrintWriter;
-import java.sql.Timestamp;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.Date;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Random;
-import java.util.TreeMap;
-import java.util.TreeSet;
 
 /**