Changeset 4506

Timestamp:

Aug 13, 2013, 2:20:17 PM (10 years ago)

Author:

Fredrik Levander

Message:

Fixes #812. Querying only for distinct score types with at least one not null value for combined fdr. Ignoring Proteios score type.

Location:

trunk

Files:

• api/core/conf/common-queries.xml (modified) (1 diff)
• api/core/src/org/proteios/core/Hit.java (modified) (1 diff)
• plugin/src/org/proteios/plugins/PrideExportPlugin.java (modified) (10 diffs)

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

@@ -158 +158 @@
     </description>
   </query>
+  
+    <query id="GET_UNIQUE_SCORE_TYPES_IN_HITS_FOR_PROJECT_WITH_FDR" type="HQL">
+    <sql>
+      SELECT DISTINCT h.scoreType
+      FROM HitData h
+      WHERE h.project = :project
+      AND h.combinedFDR IS NOT NULL 
+      ORDER by h.scoreType
+    </sql>
+    <description>
+      Load all distinct (unique) score types in the Hits table for a project 
+    </description>
+  </query>
 
   <query id="GET_UNIQUE_PLATEIDS_IN_HITS_FOR_PROJECT" type="HQL">

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

@@ -51 +51 @@
       .getHibernateSession(),
       "GET_UNIQUE_SCORE_TYPES_IN_HITS_FOR_PROJECT");
+    query.setEntity("project", project.getData());
+    return query.list();
+  }
+
+  @SuppressWarnings("unchecked")
+  // Retrieve unique score types with combined FDR not null.
+  public static List<String> getUniqueScoreTypesWithCombinedFDR(Project project, DbControl dc)
+  {
+    org.hibernate.Query query = HibernateUtil.getPredefinedQuery(dc
+      .getHibernateSession(),
+      "GET_UNIQUE_SCORE_TYPES_IN_HITS_FOR_PROJECT_WITH_FDR");
     query.setEntity("project", project.getData());
     return query.list();

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

@@ -502 +502 @@
         }
         project = (Project) job.getValue("project");
-        // Check if an alternative spectrum file in mzML format exists in directory
+        // Check if an alternative spectrum file in mzML format exists
+        // in directory
         File mzMLFile = fetchAlternativeSpectrumFile(factory,
           peakListFile, ".mzML");
@@ -508 +509 @@
         if (mzMLFile == null)
         {
-          // Check if an alternative spectrum file in mzML format exists in project
+          // Check if an alternative spectrum file in mzML format
+          // exists in project
           mzMLFile = fetchAlternativeSpectrumFileInProject(factory,
             peakListFile, ".mzML");
@@ -516 +518 @@
         if (mzMLFile != null)
         {
-          log.debug("mzMLFile path = " + mzMLFile.getPath().toString());
+          log.debug("mzMLFile path = " + mzMLFile.getPath()
+            .toString());
           retrieveInstrumentFromMZML(mzMLFile);
         }
@@ -606 +609 @@
    * @param factory ItemFactory The ItemFactory to use.
    * @param spectrumFile File The input spectrum file.
-   * @param alternativeFileExtension String File extension for alternative spectrum file.
+   * @param alternativeFileExtension String File extension for alternative
+   *        spectrum file.
    * @return File The alternative spectrum file, if found.
    */
@@ -650 +654 @@
 
   /**
-   * Fetches an alternative spectrum file in project. The alternative
-   * spectrum file is assumed to already exist, and have the same base name
-   * as the original spectrum file, but with specified file extension.
-   * If several files with the same name exist in the project, the
-   * first found is returned. Returns null if no file can be found.
+   * Fetches an alternative spectrum file in project. The alternative spectrum
+   * file is assumed to already exist, and have the same base name as the
+   * original spectrum file, but with specified file extension. If several
+   * files with the same name exist in the project, the first found is
+   * returned. Returns null if no file can be found.
    * 
    * @param factory ItemFactory The ItemFactory to use.
    * @param spectrumFile File The input spectrum file.
-   * @param alternativeFileExtension String File extension for alternative spectrum file.
+   * @param alternativeFileExtension String File extension for alternative
+   *        spectrum file.
    * @return File The alternative spectrum file, if found.
    */
@@ -678 +683 @@
     {
       // Remove part after and including last dot
-      spectrumFileBasename = spectrumFilename.substring(0,
-        lastDotIndex);
+      spectrumFileBasename = spectrumFilename.substring(0, lastDotIndex);
     }
     String alternativeSpectrumFilename = spectrumFileBasename + alternativeFileExtension;
@@ -690 +694 @@
     fileQuery.include(Include.IN_PROJECT);
     ItemResultList<File> alternativeSpectrumFileList = fileQuery.list(dc);
-    log.debug("alternativeSpectrumFileList.size() = " + alternativeSpectrumFileList.size());
+    log.debug("alternativeSpectrumFileList.size() = " + alternativeSpectrumFileList
+      .size());
     // Get first file in project
     File alternativeSpectrumFile = null;
@@ -1779 +1784 @@
         List<String> usedScoreTypeList = fetchUsedScoreTypeList(dc);
         log.debug("usedScoreTypeList = " + usedScoreTypeList);
-        if (usedScoreTypeList != null && usedScoreTypeList.size() > 0)
-        {
-          scoreType = new String(
-            "Proteios SE, combination of " + usedScoreTypeList
-              .get(0));
-          for (int i = 1; i < usedScoreTypeList.size(); i++)
+        if (usedScoreTypeList != null)
+        {
+          if (usedScoreTypeList.size() > 1)
           {
-            // Get separator for middle elements
-            String separator = new String(", ");
-            // Get separator for last element
-            if (i == (usedScoreTypeList.size() - 1))
+            scoreType = new String(
+              "Proteios SE, combination of " + usedScoreTypeList
+                .get(0));
+            for (int i = 1; i < usedScoreTypeList.size(); i++)
             {
-              separator = new String(" and ");
+              // Get separator for middle elements
+              String separator = new String(", ");
+              // Get separator for last element
+              if (i == (usedScoreTypeList.size() - 1))
+              {
+                separator = new String(" and ");
+              }
+              scoreType = scoreType + separator + usedScoreTypeList
+                .get(i);
             }
-            scoreType = scoreType + separator + usedScoreTypeList
-              .get(i);
+          }
+          else if (usedScoreTypeList.size() == 1)
+          {
+            scoreType = usedScoreTypeList.get(0);
           }
         }
@@ -1873 +1885 @@
   {
     // Get score types from Hit query
-    List<String> scoreTypeList = Hit.getUniqueScoreTypes(project, dc);
+    List<String> scoreTypeList = Hit.getUniqueScoreTypesWithCombinedFDR(project, dc);
     log.debug("scoreTypeList = " + scoreTypeList);
     List<String> usedScoreTypeList = new ArrayList<String>();
@@ -1889 +1901 @@
         // Skip "Proteios Protein" score types, as these hits are
         // already combined
-        if (scoreType.equals("Proteios Protein"))
+        if (scoreType.startsWith("Proteios"))
         {
           continue;