From 3158d6fc128da5a06e30446e8eabb4afa9c53cb6 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 17 Oct 2022 12:19:24 +0100
Subject: [PATCH] JAL-2349 JAL-3855 tests that probably should be part of
 Functional..

---
 test/jalview/analysis/AlignmentUtilsTests.java     |   33 ++++++++++----------
 .../structure/StructureSelectionManagerTest.java   |   26 +++++++--------
 2 files changed, 30 insertions(+), 29 deletions(-)

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index c1eb9fd..8b6f67d 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -27,21 +27,34 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.analysis.AlignmentUtils.DnaVariant;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLociI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SeqDistanceContactMatrix;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.JvOptionPane;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
@@ -51,18 +64,6 @@ import jalview.io.FormatAdapter;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
-import jalview.ws.params.InvalidArgumentException;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
 
 public class AlignmentUtilsTests
 {
@@ -2457,7 +2458,7 @@ public class AlignmentUtilsTests
    * the given protein. That is, given a transcript-to-peptide mapping, find the
    * cds-to-peptide mapping that relates to both, and return the CDS sequence.
    */
-  @Test
+  @Test(groups = "Functional")
   public void testFindCdsForProtein()
   {
     List<AlignedCodonFrame> mappings = new ArrayList<>();
@@ -2527,7 +2528,7 @@ public class AlignmentUtilsTests
    * cds-to-peptide mapping that relates to both, and return the CDS sequence.
    * This test is for the case where transcript and CDS are the same length.
    */
-  @Test
+  @Test(groups = "Functional")
   public void testFindCdsForProtein_noUTR()
   {
     List<AlignedCodonFrame> mappings = new ArrayList<>();
diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index 66514f9..aac7b84 100644
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -25,6 +25,18 @@ import static org.testng.Assert.assertNotNull;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import jalview.analysis.AlignmentUtils;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
@@ -50,18 +62,6 @@ import jalview.util.MapList;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.sifts.SiftsSettings;
 
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedMap;
-import java.util.TreeMap;
-
-import org.testng.Assert;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 @Test(singleThreaded = true)
 public class StructureSelectionManagerTest extends Jalview2xmlBase
 {
@@ -433,7 +433,7 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
       AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
               tipEntries, candidates, al);
       AlignmentUtils.addReferenceAnnotations(candidates, al, null);
-
+      // FAILS BECAUSE LABEL HAS PDB ID STRING
       if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator()
               .hasNext())
       {
-- 
1.7.10.2