Change DAO and worked in this version

pdb-alignment-api/src/main/java/org/cbioportal/pdb_annotation/web/controllers/AlignmentController.java

@@ -5,8 +5,8 @@
 import java.util.List;
 
 import org.cbioportal.pdb_annotation.web.models.Alignment;
-import org.cbioportal.pdb_annotation.web.models.AlignmentDAO;
-import org.cbioportal.pdb_annotation.web.models.EnsemblDAO;
+import org.cbioportal.pdb_annotation.web.persistancy.AlignmentRepository;
+import org.cbioportal.pdb_annotation.web.persistancy.EnsemblRepository;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.RequestMapping;
@@ -62,7 +62,7 @@ public boolean isExistedEnsemblidinAlignment(String ensemblid) {
 	  // ------------------------
 
 	  @Autowired
-	  private AlignmentDAO alignmentDao;
+	  private AlignmentRepository alignmentDao;
 
 	  //@Autowired
 	  //private EnsemblDAO ensemblDao;

pdb-alignment-api/src/main/java/org/cbioportal/pdb_annotation/web/persistancy/AlignmentRepository.java

@@ -0,0 +1,13 @@
+package org.cbioportal.pdb_annotation.web.persistancy;
+
+import javax.transaction.Transactional;
+
+import org.cbioportal.pdb_annotation.web.models.Alignment;
+import org.springframework.data.repository.CrudRepository;
+
+@Transactional
+public interface AlignmentRepository extends CrudRepository<Alignment, Long>{
+
+	public Iterable<Alignment> findByEnsemblId(String ensemblid);	
+
+}

pdb-alignment-api/src/main/java/org/cbioportal/pdb_annotation/web/persistancy/EnsemblRepository.java

@@ -0,0 +1,13 @@
+package org.cbioportal.pdb_annotation.web.persistancy;
+
+import javax.transaction.Transactional;
+
+import org.cbioportal.pdb_annotation.web.models.Alignment;
+import org.cbioportal.pdb_annotation.web.models.Ensembl;
+import org.springframework.data.repository.CrudRepository;
+
+@Transactional
+public interface EnsemblRepository extends CrudRepository<Alignment, Long>{
+
+	public Iterable<Ensembl> findByEnsemblId(String ensemblid);
+}

pdb-alignment-api/src/main/java/org/cbioportal/pdb_annotation/web/persistancy/PdbRepository.java

@@ -0,0 +1,11 @@
+package org.cbioportal.pdb_annotation.web.persistancy;
+
+import javax.transaction.Transactional;
+
+import org.cbioportal.pdb_annotation.web.models.Alignment;
+import org.springframework.data.repository.CrudRepository;
+
+@Transactional
+public interface PdbRepository extends CrudRepository<Alignment, Long>{
+
+}