From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 16 Nov 2016 14:38:42 +0000 (+0000)
Subject: Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
X-Git-Tag: Release_2_10_1~11^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8bb1df31c9d46763d2a3278d27d52ce69ba441b3;hp=c3c7f93c27f8bc65da1b5491204b6abbeb557ed3;p=jalview.git

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
---

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index c75d6f2..0baa78e 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -208,7 +208,9 @@ public class SequenceFeature
     }
 
     SequenceFeature sf = (SequenceFeature) o;
-    if (begin != sf.begin || end != sf.end || score != sf.score)
+    boolean sameScore = Float.isNaN(score) ? Float.isNaN(sf.score)
+            : score == sf.score;
+    if (begin != sf.begin || end != sf.end || !sameScore)
     {
       return false;
     }
diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index eb094da..27db604 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -511,13 +511,13 @@ public class SiftsClient implements SiftsClientI
     if (os != null)
     {
       MappingOutputPojo mop = new MappingOutputPojo();
-      mop.setSeqStart(pdbStart);
-      mop.setSeqEnd(pdbEnd);
+      mop.setSeqStart(seqStart);
+      mop.setSeqEnd(seqEnd);
       mop.setSeqName(seq.getName());
       mop.setSeqResidue(matchedSeq);
 
-      mop.setStrStart(seqStart);
-      mop.setStrEnd(seqEnd);
+      mop.setStrStart(pdbStart);
+      mop.setStrEnd(pdbEnd);
       mop.setStrName(structId);
       mop.setStrResidue(targetStrucSeqs.toString());
 
diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index 2ec824d..5150337 100644
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -112,56 +112,83 @@ public class SequenceFeatureTest
     assertEquals(sf1.hashCode(), sf2.hashCode());
 
     // changing type breaks equals:
+    String restores = sf2.getType();
     sf2.setType("Type");
     assertFalse(sf1.equals(sf2));
+    sf2.setType(restores);
 
     // changing description breaks equals:
-    sf2.setType("type");
+    restores = sf2.getDescription();
     sf2.setDescription("Desc");
     assertFalse(sf1.equals(sf2));
+    sf2.setDescription(restores);
+
+    // changing score breaks equals:
+    float restoref = sf2.getScore();
+    sf2.setScore(12.4f);
+    assertFalse(sf1.equals(sf2));
+    sf2.setScore(restoref);
+
+    // NaN doesn't match a number
+    restoref = sf2.getScore();
+    sf2.setScore(Float.NaN);
+    assertFalse(sf1.equals(sf2));
+
+    // NaN matches NaN
+    sf1.setScore(Float.NaN);
+    assertTrue(sf1.equals(sf2));
+    sf1.setScore(restoref);
+    sf2.setScore(restoref);
 
     // changing start position breaks equals:
-    sf2.setDescription("desc");
+    int restorei = sf2.getBegin();
     sf2.setBegin(21);
     assertFalse(sf1.equals(sf2));
+    sf2.setBegin(restorei);
 
     // changing end position breaks equals:
-    sf2.setBegin(22);
+    restorei = sf2.getEnd();
     sf2.setEnd(32);
     assertFalse(sf1.equals(sf2));
+    sf2.setEnd(restorei);
 
     // changing feature group breaks equals:
-    sf2.setEnd(33);
+    restores = sf2.getFeatureGroup();
     sf2.setFeatureGroup("Group");
     assertFalse(sf1.equals(sf2));
+    sf2.setFeatureGroup(restores);
 
     // changing ID breaks equals:
-    sf2.setFeatureGroup("group");
+    restores = (String) sf2.getValue("ID");
     sf2.setValue("ID", "id2");
     assertFalse(sf1.equals(sf2));
+    sf2.setValue("ID", restores);
 
     // changing Name breaks equals:
-    sf2.setValue("ID", "id");
+    restores = (String) sf2.getValue("Name");
     sf2.setValue("Name", "Name");
     assertFalse(sf1.equals(sf2));
+    sf2.setValue("Name", restores);
 
     // changing Parent breaks equals:
-    sf2.setValue("Name", "name");
+    restores = (String) sf1.getValue("Parent");
     sf1.setValue("Parent", "Parent");
     assertFalse(sf1.equals(sf2));
+    sf1.setValue("Parent", restores);
 
     // changing strand breaks equals:
-    sf1.setValue("Parent", "parent");
+    restorei = sf2.getStrand();
     sf2.setStrand("-");
     assertFalse(sf1.equals(sf2));
+    sf2.setStrand(restorei == 1 ? "+" : "-");
 
     // changing phase breaks equals:
-    sf2.setStrand("+");
+    restores = sf1.getPhase();
     sf1.setPhase("2");
     assertFalse(sf1.equals(sf2));
+    sf1.setPhase(restores);
 
     // restore equality as sanity check:
-    sf1.setPhase("1");
     assertTrue(sf1.equals(sf2));
     assertTrue(sf2.equals(sf1));
     assertEquals(sf1.hashCode(), sf2.hashCode());
diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index f22a3b7..3f67c4c 100644
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -387,8 +387,8 @@ public class SiftsClientTest
               testSeq, testPDBId, "A");
       String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
               + "Method: SIFTS\n\n"
-              + "P00221 :  1 - 97 Maps to \n"
-              + "1A70|A :  51 - 147\n\n"
+              + "P00221 :  51 - 147 Maps to \n"
+              + "1A70|A :  1 - 97\n\n"
               + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
               + "       |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
               + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n"