6.3.4 - disable to output ClinVar Pathogenic data

nickzren · Mar 2, 2016 · 3b9979a · 3b9979a
1 parent 4eed72e
commit 3b9979a
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Showing 3 changed files with 40 additions and 40 deletions.
diff --git a/src/main/java/function/external/knownvar/KnownVarManager.java b/src/main/java/function/external/knownvar/KnownVarManager.java
@@ -16,7 +16,7 @@
 public class KnownVarManager {
 
     public static final String clinVarTable = "knownvar.clinvar_2015_10_12";
-    public static final String clinVarPathoratioTable = "knownvar.clinvar_pathoratio_2015_10_12";
+//    public static final String clinVarPathoratioTable = "knownvar.clinvar_pathoratio_2015_10_12";
     public static final String hgmdTable = "knownvar.hgmd_2015_4";
     public static final String omimTable = "knownvar.omim_2016_02_12";
     public static final String acmgTable = "knownvar.ACMG_2015_12_09";
@@ -41,11 +41,11 @@ public static String getTitle() {
                     + "ClinVar Other Ids,"
                     + "ClinVar Disease Name,"
                     + "ClinVar Flanking Count,"
-                    + "ClinVar Pathogenic Indel Count,"
-                    + "ClinVar Pathogenic Copy Count,"
-                    + "ClinVar Pathogenic SNV Splice Count,"
-                    + "ClinVar Pathogenic SNV Nonsense Count,"
-                    + "ClinVar Pathogenic SNV Missense Count,"
+//                    + "ClinVar Pathogenic Indel Count,"
+//                    + "ClinVar Pathogenic Copy Count,"
+//                    + "ClinVar Pathogenic SNV Splice Count,"
+//                    + "ClinVar Pathogenic SNV Nonsense Count,"
+//                    + "ClinVar Pathogenic SNV Missense Count,"
                     + "HGMD Variant Class,"
                     + "HGMD Pmid,"
                     + "HGMD Disease Name,"
@@ -66,7 +66,7 @@ public static void init() {
         if (KnownVarCommand.isIncludeKnownVar) {
             initClinvarMap();
 
-            initClinVarPathoratioMap();
+//            initClinVarPathoratioMap();
 
             initHGMDMap();
 
@@ -111,35 +111,35 @@ private static void initClinvarMap() {
         }
     }
 
-    private static void initClinVarPathoratioMap() {
-        try {
-            String sql = "SELECT * From " + clinVarPathoratioTable;
-
-            ResultSet rs = DBManager.executeQuery(sql);
-
-            while (rs.next()) {
-                String geneName = rs.getString("geneName").toUpperCase();
-                int indelCount = rs.getInt("indelCount");
-                int copyCount = rs.getInt("copyCount");
-                int snvSpliceCount = rs.getInt("snvSpliceCount");
-                int snvNonsenseCount = rs.getInt("snvNonsenseCount");
-                int snvMissenseCount = rs.getInt("snvMissenseCount");
-
-                ClinVarPathoratio clinVarPathoratio = new ClinVarPathoratio(
-                        indelCount,
-                        copyCount,
-                        snvSpliceCount,
-                        snvNonsenseCount,
-                        snvMissenseCount);
-
-                clinVarPathoratioMap.put(geneName, clinVarPathoratio);
-            }
-
-            rs.close();
-        } catch (Exception e) {
-            ErrorManager.send(e);
-        }
-    }
+//    private static void initClinVarPathoratioMap() {
+//        try {
+//            String sql = "SELECT * From " + clinVarPathoratioTable;
+//
+//            ResultSet rs = DBManager.executeQuery(sql);
+//
+//            while (rs.next()) {
+//                String geneName = rs.getString("geneName").toUpperCase();
+//                int indelCount = rs.getInt("indelCount");
+//                int copyCount = rs.getInt("copyCount");
+//                int snvSpliceCount = rs.getInt("snvSpliceCount");
+//                int snvNonsenseCount = rs.getInt("snvNonsenseCount");
+//                int snvMissenseCount = rs.getInt("snvMissenseCount");
+//
+//                ClinVarPathoratio clinVarPathoratio = new ClinVarPathoratio(
+//                        indelCount,
+//                        copyCount,
+//                        snvSpliceCount,
+//                        snvNonsenseCount,
+//                        snvMissenseCount);
+//
+//                clinVarPathoratioMap.put(geneName, clinVarPathoratio);
+//            }
+//
+//            rs.close();
+//        } catch (Exception e) {
+//            ErrorManager.send(e);
+//        }
+//    }
 
     private static void initHGMDMap() {
         try {

diff --git a/src/main/java/function/external/knownvar/KnownVarOutput.java b/src/main/java/function/external/knownvar/KnownVarOutput.java
@@ -9,7 +9,7 @@
 public class KnownVarOutput {
 
     ClinVar clinVar;
-    ClinVarPathoratio clinVarPathoratio;
+//    ClinVarPathoratio clinVarPathoratio;
     HGMD hgmd;
     String omimDiseaseName;
     String acmg;
@@ -26,7 +26,7 @@ public class KnownVarOutput {
     public KnownVarOutput(AnnotatedVariant annotatedVar) {
         String geneName = annotatedVar.getGeneName().toUpperCase();
         clinVar = KnownVarManager.getClinVar(annotatedVar);
-        clinVarPathoratio = KnownVarManager.getClinPathoratio(geneName);
+//        clinVarPathoratio = KnownVarManager.getClinPathoratio(geneName);
         hgmd = KnownVarManager.getHGMD(annotatedVar);
         omimDiseaseName = KnownVarManager.getOMIM(geneName);
         acmg = KnownVarManager.getACMG(geneName);
@@ -41,7 +41,7 @@ public String toString() {
         StringBuilder sb = new StringBuilder();
 
         sb.append(clinVar.toString());
-        sb.append(clinVarPathoratio.toString());
+//        sb.append(clinVarPathoratio.toString());
         sb.append(hgmd.toString());
         sb.append(omimDiseaseName).append(",");
         sb.append(acmg).append(",");

diff --git a/src/main/java/function/external/knownvar/ListKnownVar.java b/src/main/java/function/external/knownvar/ListKnownVar.java
@@ -71,7 +71,7 @@ public String toString() {
         return "It is running a list KnownVar function... \n\n"
                 + "KnownVar database tables: \n\n"
                 + KnownVarManager.clinVarTable + "\n\n"
-                + KnownVarManager.clinVarPathoratioTable + "\n\n"
+//                + KnownVarManager.clinVarPathoratioTable + "\n\n"
                 + KnownVarManager.hgmdTable + "\n\n"
                 + KnownVarManager.omimTable + "\n\n"
                 + KnownVarManager.acmgTable + "\n\n"