From 1e05a1e901f5ac87b4d142091f97cbdb0229770e Mon Sep 17 00:00:00 2001
From: Matthias Blum <mat.blum@gmail.com>
Date: Sun, 5 Jan 2025 19:15:02 +0000
Subject: [PATCH] Use PrimaryIndex

---
 .../server/service/impl/BerkeleyMatchDBService.java    | 10 ++++------
 .../server/service/impl/BerkeleySiteDBService.java     | 10 ++++------
 2 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/core/precalcmatches/server/src/main/java/uk/ac/ebi/interpro/scan/precalc/server/service/impl/BerkeleyMatchDBService.java b/core/precalcmatches/server/src/main/java/uk/ac/ebi/interpro/scan/precalc/server/service/impl/BerkeleyMatchDBService.java
index 3d2c7d7556..fd91b0f0dd 100644
--- a/core/precalcmatches/server/src/main/java/uk/ac/ebi/interpro/scan/precalc/server/service/impl/BerkeleyMatchDBService.java
+++ b/core/precalcmatches/server/src/main/java/uk/ac/ebi/interpro/scan/precalc/server/service/impl/BerkeleyMatchDBService.java
@@ -29,7 +29,7 @@ public class BerkeleyMatchDBService extends AbstractDBService {
 
     private String databasePath;
 
-    private SecondaryIndex<String, Long, KVSequenceEntry> secIDX = null;
+    private PrimaryIndex<String, KVSequenceEntry> index = null;
 
     private int cacheSizeInBytes;
 
@@ -65,8 +65,8 @@ protected void finalize() throws Throwable {
         shutdown();
     }
 
-    SecondaryIndex<String, Long, KVSequenceEntry> getMD5Index() {
-        return secIDX;
+    PrimaryIndex<String, KVSequenceEntry> getMD5Index() {
+        return index;
     }
 
     private void initializeMD5Index() {
@@ -89,9 +89,7 @@ private void initializeMD5Index() {
         myEnv = new Environment(file, myEnvConfig);
         store = new EntityStore(myEnv, "EntityStore", storeConfig);
 
-
-        PrimaryIndex<Long, KVSequenceEntry> primIDX = store.getPrimaryIndex(Long.class, KVSequenceEntry.class);
-        secIDX = store.getSecondaryIndex(primIDX, String.class, "proteinMD5");
+        index = store.getPrimaryIndex(String.class, KVSequenceEntry.class);
     }
 
     public void displayServerStats(){
diff --git a/core/precalcmatches/server/src/main/java/uk/ac/ebi/interpro/scan/precalc/server/service/impl/BerkeleySiteDBService.java b/core/precalcmatches/server/src/main/java/uk/ac/ebi/interpro/scan/precalc/server/service/impl/BerkeleySiteDBService.java
index 8a296a2aa0..76fdd1de76 100644
--- a/core/precalcmatches/server/src/main/java/uk/ac/ebi/interpro/scan/precalc/server/service/impl/BerkeleySiteDBService.java
+++ b/core/precalcmatches/server/src/main/java/uk/ac/ebi/interpro/scan/precalc/server/service/impl/BerkeleySiteDBService.java
@@ -30,7 +30,7 @@ public class BerkeleySiteDBService extends AbstractDBService {
 
     private String databasePath;
 
-    private SecondaryIndex<String, Long, KVSequenceEntry> secIDX = null;
+    private PrimaryIndex<String, KVSequenceEntry> index = null;
 
     private int cacheSizeInBytes;
 
@@ -66,8 +66,8 @@ protected void finalize() throws Throwable {
         shutdown();
     }
 
-    SecondaryIndex<String, Long, KVSequenceEntry> getMD5Index() {
-        return secIDX;
+    PrimaryIndex<String, KVSequenceEntry> getMD5Index() {
+        return index;
     }
 
     private void initializeMD5Index() {
@@ -90,9 +90,7 @@ private void initializeMD5Index() {
         myEnv = new Environment(file, myEnvConfig);
         store = new EntityStore(myEnv, "EntityStore", storeConfig);
 
-
-        PrimaryIndex<Long, KVSequenceEntry> primIDX = store.getPrimaryIndex(Long.class, KVSequenceEntry.class);
-        secIDX = store.getSecondaryIndex(primIDX, String.class, "proteinMD5");
+        index = store.getPrimaryIndex(String.class, KVSequenceEntry.class);
     }
 
     public void displayServerStats(){