From 7596cd64543481df859a9bd2e73a3b3bb6b2e42c Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 20 Jul 2016 14:30:29 +0100
Subject: [PATCH 1/1] JAL-1926 JAL-2106 remove startRes/endRes fields - not
 used

---
 src/jalview/api/DBRefEntryI.java           |   26 --------------------------
 src/jalview/datamodel/DBRefEntry.java      |   26 --------------------------
 src/jalview/io/StructureFile.java          |    2 --
 test/jalview/ws/sifts/SiftsClientTest.java |    6 ------
 4 files changed, 60 deletions(-)

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index 2ce7e4a..32245b3 100644
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -48,32 +48,6 @@ public interface DBRefEntryI
   public void setVersion(String version);
 
   /**
-   * 
-   * @param startRes
-   *          index of start residue in the source DB
-   */
-  public void setStartRes(int startRes);
-
-  /**
-   * 
-   * @return index of start residue in the source DB
-   */
-  public int getStartRes();
-
-  /**
-   * 
-   * @param endRes
-   *          index of end residue in the source DB
-   */
-  public void setEndRes(int endRes);
-
-  /**
-   * 
-   * @return index of end residue in the source DB
-   */
-  public int getEndRes();
-
-  /**
    * access a mapping, if present that can be used to map positions from the
    * associated dataset sequence to the DBRef's sequence frame.
    * 
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index efdf0ac..a641b1b 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -25,8 +25,6 @@ import jalview.api.DBRefEntryI;
 public class DBRefEntry implements DBRefEntryI
 {
   String source = "", version = "", accessionId = "";
-
-  private int startRes, endRes;
   /**
    * maps from associated sequence to the database sequence's coordinate system
    */
@@ -282,28 +280,4 @@ public class DBRefEntry implements DBRefEntryI
   {
     return getSrcAccString();
   }
-
-  @Override
-  public int getStartRes()
-  {
-    return startRes;
-  }
-
-  @Override
-  public void setStartRes(int startRes)
-  {
-    this.startRes = startRes;
-  }
-
-  @Override
-  public int getEndRes()
-  {
-    return endRes;
-  }
-
-  @Override
-  public void setEndRes(int endRes)
-  {
-    this.endRes = endRes;
-  }
 }
diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 97e11eb..de4affa 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -116,8 +116,6 @@ public abstract class StructureFile extends AlignFile
     DBRefEntry sourceDBRef = new DBRefEntry();
     sourceDBRef.setAccessionId(getId());
     sourceDBRef.setSource(DBRefSource.PDB);
-    sourceDBRef.setStartRes(pdbSequence.getStart());
-    sourceDBRef.setEndRes(pdbSequence.getEnd());
     pdbSequence.setSourceDBRef(sourceDBRef);
     pdbSequence.addPDBId(entry);
     pdbSequence.addDBRef(sourceDBRef);
diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index 9141bad..6f9a864 100644
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -251,8 +251,6 @@ public class SiftsClientTest
 
     // TODO delete when auto-fetching of DBRefEntry is implemented
     DBRefEntry dbRef = new DBRefEntry("uniprot", "", "P00221");
-    dbRef.setStartRes(1);
-    dbRef.setEndRes(147);
     testSeq.addDBRef(dbRef);
     // testSeq.setSourceDBRef(dbRef);
 
@@ -327,8 +325,6 @@ public class SiftsClientTest
       DBRefEntryI expectedDBRef = new DBRefEntry();
       expectedDBRef.setSource(DBRefSource.UNIPROT);
       expectedDBRef.setAccessionId("P00221");
-      expectedDBRef.setStartRes(1);
-      expectedDBRef.setEndRes(147);
       expectedDBRef.setVersion("");
       Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
     } catch (Exception e)
@@ -376,8 +372,6 @@ public class SiftsClientTest
     DBRefEntryI validDBRef = new DBRefEntry();
     validDBRef.setSource(DBRefSource.UNIPROT);
     validDBRef.setAccessionId("P00221");
-    validDBRef.setStartRes(1);
-    validDBRef.setEndRes(147);
     validDBRef.setVersion("");
     Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef));
   }
-- 
1.7.10.2