From 7596cd64543481df859a9bd2e73a3b3bb6b2e42c Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 20 Jul 2016 14:30:29 +0100 Subject: [PATCH] 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