protein modification uses string mapping for state

model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java

@@ -6,6 +6,8 @@ import java.text.DecimalFormat;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
 import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
@@ -65,6 +67,7 @@ public class ModificationResidue implements Serializable, ElementModification {
   /**
    * State in which this modification is.
    */
+  @Enumerated(EnumType.STRING)
   private ModificationState state = null;
 
   @Column(name = "position")

persist/src/db/12.1.0~alpha.0/fix_db_20180710.sql

+-- state of modification_residue is mapped via string
+
+alter table modification_residue_table add column state_string varchar(255);
+update modification_residue_table set state_string='PHOSPHORYLATED' where state=0;
+update modification_residue_table set state_string='ACETYLATED' where state=1;
+update modification_residue_table set state_string='UBIQUITINATED' where state=2;
+update modification_residue_table set state_string='METHYLATED' where state=3;
+update modification_residue_table set state_string='HYDROXYLATED' where state=4;
+update modification_residue_table set state_string='MYRISTOYLATED' where state=5;
+update modification_residue_table set state_string='SULFATED' where state=6;
+update modification_residue_table set state_string='PRENYLATED' where state=7;
+update modification_residue_table set state_string='GLYCOSYLATED' where state=8;
+update modification_residue_table set state_string='PALMYTOYLATED' where state=9;
+update modification_residue_table set state_string='UNKNOWN' where state=10;
+update modification_residue_table set state_string='EMPTY' where state=11;
+update modification_residue_table set state_string='PROTONATED' where state=12;
+update modification_residue_table set state_string='DONT_CARE' where state=13;
+alter table modification_residue_table drop column state;
+alter table modification_residue_table rename column state_string to state;

persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java

@@ -31,7 +31,7 @@ public class AliasDaoTest extends PersistTestFunctions {
   @Before
   public void setUp() throws Exception {
     project = projectDao.getProjectByProjectId(projectId);
-		if (project!=null) {
+    if (project != null) {
       projectDao.delete(project);
     }
     project = new Project();