JAL-1270 test suits import order refactor

diff --git a/.externalToolBuilders/Jalview Release indices [Builder].launch b/.externalToolBuilders/Jalview Release indices [Builder].launch
index 9d81cc8..7d2c125 100644 (file)
--- a/.externalToolBuilders/Jalview Release indices [Builder].launch
+++ b/.externalToolBuilders/Jalview Release indices [Builder].launch
@@ -5,10 +5,10 @@
 <booleanAttribute key="org.eclipse.ant.ui.ATTR_TARGETS_UPDATED" value="true"/>
 <booleanAttribute key="org.eclipse.ant.ui.DEFAULT_VM_INSTALL" value="false"/>
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/jalview/build.xml"/>
+<listEntry value="/jalview"/>
 </listAttribute>
 <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="1"/>
+<listEntry value="4"/>
 </listAttribute>
 <booleanAttribute key="org.eclipse.debug.ui.ATTR_LAUNCH_IN_BACKGROUND" value="false"/>
 <stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.ant.ui.AntClasspathProvider"/>

diff --git a/.settings/org.eclipse.jdt.ui.prefs b/.settings/org.eclipse.jdt.ui.prefs
index 1986e85..5b61305 100644 (file)
--- a/.settings/org.eclipse.jdt.ui.prefs
+++ b/.settings/org.eclipse.jdt.ui.prefs
@@ -2,6 +2,10 @@ eclipse.preferences.version=1
 editor_save_participant_org.eclipse.jdt.ui.postsavelistener.cleanup=true
 formatter_profile=_Jalview
 formatter_settings_version=12
+org.eclipse.jdt.ui.ignorelowercasenames=true
+org.eclipse.jdt.ui.importorder=jalview;java;javax;org;com;
+org.eclipse.jdt.ui.ondemandthreshold=99
+org.eclipse.jdt.ui.staticondemandthreshold=99
 sp_cleanup.add_default_serial_version_id=true
 sp_cleanup.add_generated_serial_version_id=false
 sp_cleanup.add_missing_annotations=true

diff --git a/test/MCview/AtomTest.java b/test/MCview/AtomTest.java
index f337535..186ac03 100644 (file)
--- a/test/MCview/AtomTest.java
+++ b/test/MCview/AtomTest.java
@@ -1,8 +1,9 @@
 package MCview;
 
 import static org.testng.AssertJUnit.assertEquals;
-import org.testng.annotations.Test;
+
 import org.testng.Assert;
+import org.testng.annotations.Test;
 
 public class AtomTest
 {

diff --git a/test/MCview/BondTest.java b/test/MCview/BondTest.java
index 0060e3f..6f701e2 100644 (file)
--- a/test/MCview/BondTest.java
+++ b/test/MCview/BondTest.java
@@ -1,6 +1,7 @@
 package MCview;
 
 import static org.testng.AssertJUnit.assertEquals;
+
 import org.testng.annotations.Test;
 
 public class BondTest

diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index 193d294..0df7851 100644 (file)
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.java
@@ -1,12 +1,9 @@
 package MCview;
 
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import java.awt.Color;
-import java.util.Vector;
 
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
@@ -16,9 +13,15 @@ import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.TaylorColourScheme;
 
+import java.awt.Color;
+import java.util.Vector;
+
+import org.testng.annotations.Test;
+
 public class PDBChainTest
 {
   PDBChain c = new PDBChain("1GAQ", "A");
+
   Atom a1 = new Atom(1f, 2f, 3f);
 
   Atom a2 = new Atom(5f, 6f, 4f);

diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java
index cce8634..a4fd286 100644 (file)
--- a/test/MCview/PDBfileTest.java
+++ b/test/MCview/PDBfileTest.java
@@ -6,10 +6,6 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import java.io.IOException;
-
-import org.testng.annotations.Test;
-
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -18,6 +14,10 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 
+import java.io.IOException;
+
+import org.testng.annotations.Test;
+
 public class PDBfileTest
 {
   @Test

diff --git a/test/MCview/ResidueTest.java b/test/MCview/ResidueTest.java
index 5cebe3c..b5ca0ed 100644 (file)
--- a/test/MCview/ResidueTest.java
+++ b/test/MCview/ResidueTest.java
@@ -1,10 +1,12 @@
 package MCview;
 
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+import static org.testng.AssertJUnit.assertSame;
+
 import java.util.Vector;
 
+import org.testng.annotations.Test;
+
 public class ResidueTest
 {
 

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index 04ab3bf..eb496bb 100644 (file)
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -2,12 +2,14 @@
 package jalview.analysis;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
 import java.util.Hashtable;
 
+import org.testng.annotations.Test;
+
 public class AAFrequencyTest
 {
   private static final String C = AAFrequency.MAXCOUNT;

diff --git a/test/jalview/analysis/AlignmentAnnotationUtilsTest.java b/test/jalview/analysis/AlignmentAnnotationUtilsTest.java
index 34d2f32..606a840 100644 (file)
--- a/test/jalview/analysis/AlignmentAnnotationUtilsTest.java
+++ b/test/jalview/analysis/AlignmentAnnotationUtilsTest.java
@@ -3,8 +3,13 @@ package jalview.analysis;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.BitSet;
@@ -13,11 +18,8 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 public class AlignmentAnnotationUtilsTest
 {

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index d32181f..a503460 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -20,22 +20,11 @@
  */
 package jalview.analysis;
 
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
@@ -53,7 +42,20 @@ import jalview.io.FormatAdapter;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
-public class AlignmentUtilsTests 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.testng.annotations.Test;
+
+public class AlignmentUtilsTests
 {
   // @formatter:off
   private static final String TEST_DATA = 

diff --git a/test/jalview/analysis/AnnotationSorterTest.java b/test/jalview/analysis/AnnotationSorterTest.java
index dfe5532..8c3489b 100644 (file)
--- a/test/jalview/analysis/AnnotationSorterTest.java
+++ b/test/jalview/analysis/AnnotationSorterTest.java
@@ -2,6 +2,12 @@ package jalview.analysis;
 
 import static org.testng.AssertJUnit.assertEquals;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Random;
@@ -9,12 +15,6 @@ import java.util.Random;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-
 public class AnnotationSorterTest
 {
   private static final int NUM_SEQS = 6;

diff --git a/test/jalview/analysis/CodingUtilsTest.java b/test/jalview/analysis/CodingUtilsTest.java
index a4b6c3f..e787ac3 100644 (file)
--- a/test/jalview/analysis/CodingUtilsTest.java
+++ b/test/jalview/analysis/CodingUtilsTest.java
@@ -2,9 +2,11 @@ package jalview.analysis;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
+
 import java.util.Arrays;
 
+import org.testng.annotations.Test;
+
 public class CodingUtilsTest
 {
 

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 77bd6b9..095fc05 100644 (file)
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -1,10 +1,12 @@
 package jalview.analysis;
 
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertEquals;
-import org.testng.annotations.Test;
+import static org.testng.AssertJUnit.assertSame;
+
 import jalview.datamodel.DBRefEntry;
 
+import org.testng.annotations.Test;
+
 public class CrossRefTest
 {
   @Test

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 693c912..6371315 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -3,7 +3,7 @@ package jalview.analysis;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
+
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.Alignment;
@@ -15,6 +15,8 @@ import jalview.io.FormatAdapter;
 
 import java.io.IOException;
 
+import org.testng.annotations.Test;
+
 public class DnaTest
 {
   // @formatter:off

diff --git a/test/jalview/analysis/GroupingTest.java b/test/jalview/analysis/GroupingTest.java
index e046c0c..df04243 100644 (file)
--- a/test/jalview/analysis/GroupingTest.java
+++ b/test/jalview/analysis/GroupingTest.java
@@ -1,7 +1,5 @@
 package jalview.analysis;
 
-import org.testng.annotations.Test;
-import org.testng.AssertJUnit;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
@@ -12,6 +10,9 @@ import jalview.datamodel.SequenceI;
 import java.util.ArrayList;
 import java.util.Arrays;
 
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
 public class GroupingTest
 {
   Sequence s1 = new Sequence("s1", "AAAADDDDEEEE");

diff --git a/test/jalview/analysis/ParsePropertiesTest.java b/test/jalview/analysis/ParsePropertiesTest.java
index acf295e..90faedc 100644 (file)
--- a/test/jalview/analysis/ParsePropertiesTest.java
+++ b/test/jalview/analysis/ParsePropertiesTest.java
@@ -2,15 +2,17 @@ package jalview.analysis;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
-import java.util.List;
 
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class ParsePropertiesTest
 {
 

diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java
index 2845d91..81bcf86 100644 (file)
--- a/test/jalview/analysis/TestAlignSeq.java
+++ b/test/jalview/analysis/TestAlignSeq.java
@@ -22,14 +22,16 @@ package jalview.analysis;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
-import java.io.PrintStream;
 
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
+import java.io.PrintStream;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 /**
  * Test the alignment -> Mapping routines
  * 

diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
index b40382d..5ab0bb0 100644 (file)
--- a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
@@ -1,7 +1,5 @@
 package jalview.analysis.scoremodels;
 
-import org.testng.annotations.Test;
-import org.testng.AssertJUnit;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -9,6 +7,9 @@ import jalview.gui.AlignFrame;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
 public class FeatureScoreModelTest
 {
   public static String alntestFile = "FER1_MESCR/72-76 DVYIL\nFER1_SPIOL/71-75 DVYIL\nFER3_RAPSA/21-25 DVYVL\nFER1_MAIZE/73-77 DVYIL\n";

diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java
index df5e796..6c570d5 100644 (file)
--- a/test/jalview/commands/EditCommandTest.java
+++ b/test/jalview/commands/EditCommandTest.java
@@ -3,11 +3,6 @@ package jalview.commands;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertSame;
 
-import java.util.Map;
-
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
 import jalview.datamodel.Alignment;
@@ -15,6 +10,11 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
+import java.util.Map;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 /**
  * Unit tests for EditCommand
  * 

diff --git a/test/jalview/datamodel/AlignedCodonFrameTest.java b/test/jalview/datamodel/AlignedCodonFrameTest.java
index c081ced..63f6772 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/test/jalview/datamodel/AlignedCodonFrameTest.java
@@ -2,11 +2,13 @@ package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+
 import jalview.util.MapList;
 
 import java.util.Arrays;
 
+import org.testng.annotations.Test;
+
 public class AlignedCodonFrameTest
 {
 

diff --git a/test/jalview/datamodel/AlignedCodonIteratorTest.java b/test/jalview/datamodel/AlignedCodonIteratorTest.java
index 3e3a46d..65fe4bf 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonIteratorTest.java
+++ b/test/jalview/datamodel/AlignedCodonIteratorTest.java
@@ -2,12 +2,14 @@ package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
-import org.testng.annotations.Test;
-import org.testng.Assert;
+
 import jalview.util.MapList;
 
 import java.util.Iterator;
 
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
 /**
  * Unit tests for Mapping$AlignedCodonIterator
  * 

diff --git a/test/jalview/datamodel/AlignedCodonTest.java b/test/jalview/datamodel/AlignedCodonTest.java
index 8391e97..afa6169 100644 (file)
--- a/test/jalview/datamodel/AlignedCodonTest.java
+++ b/test/jalview/datamodel/AlignedCodonTest.java
@@ -3,6 +3,7 @@ package jalview.datamodel;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
+
 import org.testng.annotations.Test;
 
 public class AlignedCodonTest

diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index 5d67cb7..4c9eabe 100644 (file)
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -2,10 +2,12 @@ package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+
 import jalview.analysis.AlignSeq;
 import jalview.io.AppletFormatAdapter;
 
+import org.testng.annotations.Test;
+
 public class AlignmentAnnotationTests
 {
   @Test

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index fc73307..1be9bea 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -3,8 +3,7 @@ package jalview.datamodel;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
+
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FormatAdapter;
 import jalview.util.MapList;
@@ -12,6 +11,9 @@ import jalview.util.MapList;
 import java.io.IOException;
 import java.util.Iterator;
 
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 /**
  * Unit tests for Alignment datamodel.
  * 

diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 5e10337..2ffebe0 100644 (file)
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -1,9 +1,11 @@
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
-import org.testng.annotations.Test;
+
 import java.util.List;
 
+import org.testng.annotations.Test;
+
 public class ColumnSelectionTest
 {
 

diff --git a/test/jalview/datamodel/DBRefEntryTest.java b/test/jalview/datamodel/DBRefEntryTest.java
index 7e1e9a6..b5549f0 100644 (file)
--- a/test/jalview/datamodel/DBRefEntryTest.java
+++ b/test/jalview/datamodel/DBRefEntryTest.java
@@ -2,9 +2,11 @@ package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
+
 import jalview.util.MapList;
 
+import org.testng.annotations.Test;
+
 public class DBRefEntryTest
 {
 

diff --git a/test/jalview/datamodel/MappingTest.java b/test/jalview/datamodel/MappingTest.java
index 8bf036a..378d708 100644 (file)
--- a/test/jalview/datamodel/MappingTest.java
+++ b/test/jalview/datamodel/MappingTest.java
@@ -1,11 +1,13 @@
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
-import org.testng.annotations.Test;
-import java.util.Arrays;
 
 import jalview.util.MapList;
 
+import java.util.Arrays;
+
+import org.testng.annotations.Test;
+
 /**
  * Test class refactored from main method
  */

diff --git a/test/jalview/datamodel/PDBEntryTest.java b/test/jalview/datamodel/PDBEntryTest.java
index 71f46ee..093702f 100644 (file)
--- a/test/jalview/datamodel/PDBEntryTest.java
+++ b/test/jalview/datamodel/PDBEntryTest.java
@@ -1,9 +1,10 @@
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertTrue;
+
 import org.testng.annotations.AfterMethod;
-import org.testng.annotations.Test;
 import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 public class PDBEntryTest
 {

diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index d0e58ea..7f099c8 100644 (file)
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -1,6 +1,7 @@
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
+
 import org.testng.annotations.Test;
 
 public class SearchResultsTest

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 37d39b6..b216b13 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1,14 +1,16 @@
 package jalview.datamodel;
 
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
 import java.util.Arrays;
 import java.util.List;
 
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class SequenceTest
 {
   SequenceI seq;

diff --git a/test/jalview/datamodel/xdb/embl/EmblFileTest.java b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
index 9919186..2d9b713 100644 (file)
--- a/test/jalview/datamodel/xdb/embl/EmblFileTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
@@ -2,13 +2,15 @@ package jalview.datamodel.xdb.embl;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.DBRefEntry;
+
 import java.io.StringReader;
 import java.util.Vector;
 
-import jalview.datamodel.DBRefEntry;
+import org.testng.annotations.Test;
 
 public class EmblFileTest
 {

diff --git a/test/jalview/ext/jmol/PDBFileWithJmolTest.java b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
index 87078a9..0627217 100644 (file)
--- a/test/jalview/ext/jmol/PDBFileWithJmolTest.java
+++ b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
@@ -22,11 +22,6 @@ package jalview.ext.jmol;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
-import java.util.Vector;
-
-import MCview.PDBfile;
 
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -36,6 +31,13 @@ import jalview.gui.AlignFrame;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FileLoader;
 
+import java.util.Vector;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import MCview.PDBfile;
+
 /**
  * @author jimp
  * 

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index d4f57d8..d8582af 100644 (file)
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -22,6 +22,11 @@ package jalview.ext.paradise;
 
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.FastaFile;
+import jalview.io.FormatAdapter;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.Reader;
@@ -35,11 +40,6 @@ import MCview.PDBfile;
 
 import compbio.util.FileUtil;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.io.FastaFile;
-import jalview.io.FormatAdapter;
-
 public class TestAnnotate3D
 {
 

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index fa3b3bc..e8b6b19 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -2,13 +2,15 @@ package jalview.ext.rbvi.chimera;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
+
 import java.awt.Color;
 import java.util.Arrays;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
+import org.testng.annotations.Test;
+
 public class ChimeraCommandsTest
 {
   @Test

diff --git a/test/jalview/ext/rbvi/chimera/ChimeraConnect.java b/test/jalview/ext/rbvi/chimera/ChimeraConnect.java
index b96f4e5..d40a43d 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/ChimeraConnect.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraConnect.java
@@ -2,7 +2,9 @@ package jalview.ext.rbvi.chimera;
 
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
+
 import org.testng.annotations.Test;
+
 import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
 

diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index 8786ca5..59a0fdb 100644 (file)
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -1,9 +1,7 @@
 package jalview.ext.rbvi.chimera;
 
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeClass;
+
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -11,6 +9,10 @@ import jalview.gui.StructureViewer;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.FormatAdapter;
 
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 public class JalviewChimeraView
 {
 

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 69ca3a2..a6e7ea0 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -1,9 +1,8 @@
 package jalview.gui;
 
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertEquals;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
+import static org.testng.AssertJUnit.assertSame;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
@@ -11,6 +10,9 @@ import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class AlignViewportTest
 {
 

diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java
index 6bee4ec..3f56985 100644 (file)
--- a/test/jalview/gui/AnnotationChooserTest.java
+++ b/test/jalview/gui/AnnotationChooserTest.java
@@ -3,8 +3,17 @@ package jalview.gui;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
+
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MessageManager;
+
 import java.awt.BorderLayout;
 import java.awt.Checkbox;
 import java.awt.Component;
@@ -17,15 +26,8 @@ import java.util.List;
 import javax.swing.JButton;
 import javax.swing.JPanel;
 
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.util.MessageManager;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 /**
  * Unit tests for AnnotationChooser

diff --git a/test/jalview/gui/FontChooserTest.java b/test/jalview/gui/FontChooserTest.java
index 0d2d2e8..646016c 100644 (file)
--- a/test/jalview/gui/FontChooserTest.java
+++ b/test/jalview/gui/FontChooserTest.java
@@ -1,10 +1,11 @@
 package jalview.gui;
 
-import org.testng.annotations.Test;
 import java.awt.Canvas;
 import java.awt.Font;
 import java.awt.FontMetrics;
 
+import org.testng.annotations.Test;
+
 public class FontChooserTest
 {
 

diff --git a/test/jalview/gui/HelpTest.java b/test/jalview/gui/HelpTest.java
index 745cb2e..f280797 100644 (file)
--- a/test/jalview/gui/HelpTest.java
+++ b/test/jalview/gui/HelpTest.java
@@ -1,7 +1,7 @@
 package jalview.gui;
 
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
+
 import jalview.gui.Help.HelpId;
 
 import java.net.URL;
@@ -10,6 +10,8 @@ import javax.help.HelpSet;
 import javax.help.HelpSetException;
 import javax.help.Map;
 
+import org.testng.annotations.Test;
+
 public class HelpTest
 {
   @Test

diff --git a/test/jalview/gui/JAL1353bugdemo.java b/test/jalview/gui/JAL1353bugdemo.java
index 3cad6b2..4a17622 100644 (file)
--- a/test/jalview/gui/JAL1353bugdemo.java
+++ b/test/jalview/gui/JAL1353bugdemo.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
+
 import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -37,8 +39,6 @@ import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-import jalview.bin.Cache;
-
 public class JAL1353bugdemo
 {
 

diff --git a/test/jalview/gui/JvSwingUtilsTest.java b/test/jalview/gui/JvSwingUtilsTest.java
index 868fe38..1a16053 100644 (file)
--- a/test/jalview/gui/JvSwingUtilsTest.java
+++ b/test/jalview/gui/JvSwingUtilsTest.java
@@ -1,9 +1,11 @@
 package jalview.gui;
 
 import static org.testng.AssertJUnit.assertEquals;
-import org.testng.annotations.Test;
+
 import javax.swing.JScrollBar;
 
+import org.testng.annotations.Test;
+
 public class JvSwingUtilsTest
 {
 

diff --git a/test/jalview/gui/PDBSearchPanelTest.java b/test/jalview/gui/PDBSearchPanelTest.java
index e06a870..3a1c554 100644 (file)
--- a/test/jalview/gui/PDBSearchPanelTest.java
+++ b/test/jalview/gui/PDBSearchPanelTest.java
@@ -2,12 +2,14 @@ package jalview.gui;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
+
 import javax.swing.JInternalFrame;
 import javax.swing.JTextField;
 
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class PDBSearchPanelTest
 {
 

diff --git a/test/jalview/gui/PaintRefresherTest.java b/test/jalview/gui/PaintRefresherTest.java
index aff4715..adbf385 100644 (file)
--- a/test/jalview/gui/PaintRefresherTest.java
+++ b/test/jalview/gui/PaintRefresherTest.java
@@ -1,11 +1,9 @@
 package jalview.gui;
 
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
@@ -17,6 +15,10 @@ import java.util.Map;
 
 import javax.swing.JPanel;
 
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class PaintRefresherTest
 {
   // TODO would prefer PaintRefresher to be a single rather than static

diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index 787171d..ba1b275 100644 (file)
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -4,6 +4,13 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FormatAdapter;
+
 import java.awt.Component;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -17,13 +24,6 @@ import javax.swing.JSeparator;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.FormatAdapter;
-
 public class PopupMenuTest
 {
   // 4 sequences x 13 positions

diff --git a/test/jalview/gui/ProgressBarTest.java b/test/jalview/gui/ProgressBarTest.java
index 192c941..281ed2d 100644 (file)
--- a/test/jalview/gui/ProgressBarTest.java
+++ b/test/jalview/gui/ProgressBarTest.java
@@ -2,8 +2,7 @@ package jalview.gui;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import org.testng.Assert;
+
 import java.awt.Component;
 import java.awt.FlowLayout;
 import java.awt.GridLayout;
@@ -11,6 +10,9 @@ import java.awt.GridLayout;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
 public class ProgressBarTest
 {
 

diff --git a/test/jalview/gui/SequenceRendererTest.java b/test/jalview/gui/SequenceRendererTest.java
index f01562e..64d15b8 100644 (file)
--- a/test/jalview/gui/SequenceRendererTest.java
+++ b/test/jalview/gui/SequenceRendererTest.java
@@ -1,7 +1,7 @@
 package jalview.gui;
 
 import static org.testng.AssertJUnit.assertEquals;
-import org.testng.annotations.Test;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
@@ -10,6 +10,8 @@ import jalview.schemes.ZappoColourScheme;
 
 import java.awt.Color;
 
+import org.testng.annotations.Test;
+
 public class SequenceRendererTest
 {
 

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 6d5af25..44b51f2 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -2,9 +2,7 @@ package jalview.gui;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
+
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
@@ -12,6 +10,10 @@ import jalview.datamodel.SequenceI;
 
 import java.util.Vector;
 
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class StructureChooserTest
 {
   Sequence seq;

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index 576201a..1c6a489 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -4,14 +4,6 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
-import java.io.File;
-
-import org.junit.Assert;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -23,6 +15,14 @@ import jalview.gui.Desktop;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 
+import java.io.File;
+
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class AnnotatedPDBFileInputTest
 {
 

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 3d911e0..d36a82b 100644 (file)
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -23,16 +23,16 @@ package jalview.io;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.io.AnnotationFile.ViewDef;
+
 import java.io.File;
 import java.util.Hashtable;
 
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.io.AnnotationFile.ViewDef;
-
 public class AnnotationFileIOTest
 {
 

diff --git a/test/jalview/io/BioJsHTMLOutputTest.java b/test/jalview/io/BioJsHTMLOutputTest.java
index 619a4e0..8440b6d 100644 (file)
--- a/test/jalview/io/BioJsHTMLOutputTest.java
+++ b/test/jalview/io/BioJsHTMLOutputTest.java
@@ -1,5 +1,8 @@
 package jalview.io;
 
+import jalview.json.binding.v1.BioJSReleasePojo;
+import jalview.json.binding.v1.BioJSRepositoryPojo;
+
 import java.io.File;
 import java.io.IOException;
 import java.net.MalformedURLException;
@@ -12,9 +15,6 @@ import org.testng.Assert;
 import org.testng.AssertJUnit;
 import org.testng.annotations.Test;
 
-import jalview.json.binding.v1.BioJSReleasePojo;
-import jalview.json.binding.v1.BioJSRepositoryPojo;
-
 
 public class BioJsHTMLOutputTest
 {

diff --git a/test/jalview/io/FileIOTester.java b/test/jalview/io/FileIOTester.java
index 1f3df1f..6b7de77 100644 (file)
--- a/test/jalview/io/FileIOTester.java
+++ b/test/jalview/io/FileIOTester.java
@@ -20,13 +20,14 @@
  */
 package jalview.io;
 
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeClass;
-import org.testng.AssertJUnit;
 import java.io.File;
 import java.io.IOException;
 
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 /**
  * @author jimp
  * 

diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index ec3f77b..33e67ce 100644 (file)
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -2,10 +2,7 @@ package jalview.io;
 
 
 import static org.testng.AssertJUnit.assertNotNull;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
-import org.testng.AssertJUnit;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -23,6 +20,11 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class JSONFileTest
 {
 

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index b3e37f4..7d24727 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -22,14 +22,6 @@ package jalview.io;
 
 import static org.testng.AssertJUnit.assertTrue;
 
-import java.io.File;
-
-import org.testng.Assert;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ViewStyleI;
 import jalview.bin.Cache;
@@ -41,6 +33,14 @@ import jalview.gui.Desktop;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
 
+import java.io.File;
+
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 public class Jalview2xmlTests
 {
 

diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java
index ee731e8..a016134 100644 (file)
--- a/test/jalview/io/NewickFileTests.java
+++ b/test/jalview/io/NewickFileTests.java
@@ -20,25 +20,24 @@
  */
 package jalview.io;
 
-import org.testng.annotations.Factory;
 import static org.testng.ConversionUtils.wrapDataProvider;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeClass;
-import org.testng.Assert;
-import org.testng.AssertJUnit;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.Vector;
 
 import jalview.analysis.NJTree;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 
-import org.jmol.util.ArrayUtil;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Vector;
+
 import org.junit.runners.Parameterized.Parameters;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Factory;
+import org.testng.annotations.Test;
 
 /**
  * @author jimp
@@ -129,7 +128,7 @@ public class NewickFileTests
       {
         olsqs[i] = (SequenceI) ((SequenceNode) oseqs.get(i)).element();
       }
-      nseqs = (Vector) new NJTree(new SequenceI[0], nf_regen).findLeaves(
+      nseqs = new NJTree(new SequenceI[0], nf_regen).findLeaves(
               nf_regen.getTree(), new Vector());
       AssertJUnit.assertTrue(stage + "No nodes in regerated tree.", nseqs.size() > 0);
       SequenceI[] nsqs = new SequenceI[nseqs.size()];

diff --git a/test/jalview/io/PhylipFileTests.java b/test/jalview/io/PhylipFileTests.java
index 2fd8e20..9db4763 100644 (file)
--- a/test/jalview/io/PhylipFileTests.java
+++ b/test/jalview/io/PhylipFileTests.java
@@ -3,15 +3,15 @@ package jalview.io;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.SequenceI;
+
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.Map;
 
 import org.testng.annotations.Test;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.SequenceI;
-
 /**
  * Test file for {@link PhylipFile}.
  *

diff --git a/test/jalview/io/RNAMLfileTest.java b/test/jalview/io/RNAMLfileTest.java
index a838cf7..1c4825f 100644 (file)
--- a/test/jalview/io/RNAMLfileTest.java
+++ b/test/jalview/io/RNAMLfileTest.java
@@ -20,10 +20,11 @@
  */
 package jalview.io;
 
+import java.io.File;
+
 import org.testng.annotations.AfterClass;
-import org.testng.annotations.Test;
 import org.testng.annotations.BeforeClass;
-import java.io.File;
+import org.testng.annotations.Test;
 
 public class RNAMLfileTest
 {

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 12a8e9c..1c46d1f 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -24,13 +24,6 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
-import java.io.File;
-import java.util.BitSet;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.testng.annotations.Test;
-
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -38,6 +31,13 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 
+import java.io.File;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.testng.annotations.Test;
+
 public class StockholmFileTest
 {
 

diff --git a/test/jalview/io/TCoffeeScoreFileTest.java b/test/jalview/io/TCoffeeScoreFileTest.java
index df4b660..b7da5e4 100644 (file)
--- a/test/jalview/io/TCoffeeScoreFileTest.java
+++ b/test/jalview/io/TCoffeeScoreFileTest.java
@@ -20,8 +20,6 @@
  */
 package jalview.io;
 
-import org.testng.annotations.Test;
-import org.testng.AssertJUnit;
 import jalview.io.TCoffeeScoreFile.Block;
 import jalview.io.TCoffeeScoreFile.Header;
 
@@ -30,14 +28,8 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.List;
 
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
 
 public class TCoffeeScoreFileTest
 {

diff --git a/test/jalview/schemes/DnaCodonTests.java b/test/jalview/schemes/DnaCodonTests.java
index d84f567..75877ee 100644 (file)
--- a/test/jalview/schemes/DnaCodonTests.java
+++ b/test/jalview/schemes/DnaCodonTests.java
@@ -21,9 +21,11 @@
 package jalview.schemes;
 
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
+
 import java.util.Map;
 
+import org.testng.annotations.Test;
+
 public class DnaCodonTests
 {
 

diff --git a/test/jalview/schemes/ResiduePropertiesTest.java b/test/jalview/schemes/ResiduePropertiesTest.java
index 429323b..d7e0e0b 100644 (file)
--- a/test/jalview/schemes/ResiduePropertiesTest.java
+++ b/test/jalview/schemes/ResiduePropertiesTest.java
@@ -2,10 +2,12 @@ package jalview.schemes;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+
 import java.util.Collections;
 import java.util.List;
 
+import org.testng.annotations.Test;
+
 public class ResiduePropertiesTest
 {
 

diff --git a/test/jalview/schemes/ScoreMatrixPrinter.java b/test/jalview/schemes/ScoreMatrixPrinter.java
index 5868210..0b15b60 100644 (file)
--- a/test/jalview/schemes/ScoreMatrixPrinter.java
+++ b/test/jalview/schemes/ScoreMatrixPrinter.java
@@ -20,11 +20,12 @@
  */
 package jalview.schemes;
 
-import org.testng.annotations.Test;
 import jalview.api.analysis.ScoreModelI;
 
 import java.util.Map;
 
+import org.testng.annotations.Test;
+
 public class ScoreMatrixPrinter
 {
   @Test

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index 74dddb4..db0ea49 100644 (file)
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -3,12 +3,6 @@ package jalview.structure;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
-import org.testng.Assert;
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import MCview.PDBfile;
-
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
@@ -17,6 +11,12 @@ import jalview.gui.AlignFrame;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import MCview.PDBfile;
+
 public class Mapping
 {
 

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index 62a9f43..589adde 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -2,13 +2,15 @@ package jalview.structure;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
+
 import jalview.datamodel.AlignedCodonFrame;
 
 import java.util.HashSet;
 import java.util.Set;
 
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class StructureSelectionManagerTest
 {
   private StructureSelectionManager ssm;

diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index 4209577..7871e77 100644 (file)
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -3,10 +3,6 @@ package jalview.structures.models;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
-import java.util.Arrays;
-import java.util.List;
 
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -19,6 +15,12 @@ import jalview.structure.AtomSpec;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel.SuperposeData;
 
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 /**
  * Unit tests for non-abstract methods of abstract base class
  * 

diff --git a/test/jalview/util/ColorUtilsTest.java b/test/jalview/util/ColorUtilsTest.java
index 4e2c92e..ad6e6d0 100644 (file)
--- a/test/jalview/util/ColorUtilsTest.java
+++ b/test/jalview/util/ColorUtilsTest.java
@@ -2,9 +2,11 @@ package jalview.util;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+
 import java.awt.Color;
 
+import org.testng.annotations.Test;
+
 public class ColorUtilsTest
 {
 

diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index 0a40784..837cbe6 100644 (file)
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -3,10 +3,12 @@ package jalview.util;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
+
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
+import org.testng.annotations.Test;
+
 public class ComparisonTest
 {
 

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index 925a375..036ad91 100644 (file)
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -1,11 +1,11 @@
 package jalview.util;
 
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
@@ -13,6 +13,8 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
+import org.testng.annotations.Test;
+
 public class DBRefUtilsTest
 {
 

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 1bbdc1e..0f2baf4 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -1,16 +1,8 @@
 package jalview.util;
 
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import java.awt.Color;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignedCodonFrame;
@@ -26,6 +18,16 @@ import jalview.gui.AlignViewport;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FormatAdapter;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.annotations.Test;
+
 public class MappingUtilsTest
 {
   private AlignViewportI dnaView;

diff --git a/test/jalview/util/ShiftListTest.java b/test/jalview/util/ShiftListTest.java
index fa240d5..ea9b2e4 100644 (file)
--- a/test/jalview/util/ShiftListTest.java
+++ b/test/jalview/util/ShiftListTest.java
@@ -2,10 +2,12 @@ package jalview.util;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+
 import java.util.Arrays;
 import java.util.List;
 
+import org.testng.annotations.Test;
+
 public class ShiftListTest
 {
 

diff --git a/test/jalview/util/StringUtilsTest.java b/test/jalview/util/StringUtilsTest.java
index 0a0fac0..7442530 100644 (file)
--- a/test/jalview/util/StringUtilsTest.java
+++ b/test/jalview/util/StringUtilsTest.java
@@ -1,11 +1,13 @@
 package jalview.util;
 
 import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
+import static org.testng.AssertJUnit.assertTrue;
+
 import java.util.Arrays;
 
+import org.testng.annotations.Test;
+
 public class StringUtilsTest
 {
 

diff --git a/test/jalview/viewmodel/styles/ViewStyleTest.java b/test/jalview/viewmodel/styles/ViewStyleTest.java
index 32003c2..64b15a6 100644 (file)
--- a/test/jalview/viewmodel/styles/ViewStyleTest.java
+++ b/test/jalview/viewmodel/styles/ViewStyleTest.java
@@ -3,12 +3,14 @@ package jalview.viewmodel.styles;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import org.testng.AssertJUnit;
+
 import java.awt.Color;
 import java.lang.reflect.Field;
 import java.util.Random;
 
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
 
 public class ViewStyleTest
 {

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index 9ecf524..ef03fd0 100644 (file)
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -22,16 +22,16 @@ package jalview.ws;
 
 import static org.testng.AssertJUnit.assertTrue;
 
-import java.util.List;
-
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class PDBSequenceFetcherTest
 {
 

diff --git a/test/jalview/ws/dbsources/PDBRestClientTest.java b/test/jalview/ws/dbsources/PDBRestClientTest.java
index f92a32e..3b3ef86 100644 (file)
--- a/test/jalview/ws/dbsources/PDBRestClientTest.java
+++ b/test/jalview/ws/dbsources/PDBRestClientTest.java
@@ -2,10 +2,7 @@ package jalview.ws.dbsources;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
-import org.testng.Assert;
+
 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
 import jalview.ws.uimodel.PDBRestRequest;
 import jalview.ws.uimodel.PDBRestResponse;
@@ -23,6 +20,11 @@ import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
+import org.testng.Assert;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import com.sun.jersey.api.client.Client;
 import com.sun.jersey.api.client.ClientResponse;
 import com.sun.jersey.api.client.WebResource;

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index 60a1111..9fba1cb 100644 (file)
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -2,15 +2,17 @@ package jalview.ws.dbsources;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
-import java.io.Reader;
-import java.io.StringReader;
-import java.util.Vector;
 
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.UniprotEntry;
 
+import java.io.Reader;
+import java.io.StringReader;
+import java.util.Vector;
+
+import org.testng.annotations.Test;
+
 public class UniprotTest
 {
   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml

diff --git a/test/jalview/ws/gui/Jws2ParamView.java b/test/jalview/ws/gui/Jws2ParamView.java
index 5ff4aed..a3ae56d 100644 (file)
--- a/test/jalview/ws/gui/Jws2ParamView.java
+++ b/test/jalview/ws/gui/Jws2ParamView.java
@@ -20,6 +20,14 @@
  */
 package jalview.ws.gui;
 
+import jalview.bin.Cache;
+import jalview.gui.WsJobParameters;
+import jalview.util.MessageManager;
+import jalview.ws.jabaws.JalviewJabawsTestUtils;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+
 import java.awt.BorderLayout;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
@@ -36,14 +44,6 @@ import org.testng.annotations.Test;
 import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 
-import jalview.bin.Cache;
-import jalview.gui.WsJobParameters;
-import jalview.util.MessageManager;
-import jalview.ws.jabaws.JalviewJabawsTestUtils;
-import jalview.ws.jws2.JabaPreset;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-
 public class Jws2ParamView
 {
   /**

diff --git a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index c184722..470c39b 100644 (file)
--- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@ -22,10 +22,7 @@ package jalview.ws.jabaws;
 
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeClass;
-import org.testng.Assert;
+
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.io.AnnotationFile;
@@ -38,6 +35,11 @@ import jalview.ws.jws2.jabaws2.Jws2Instance;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 public class DisorderAnnotExportImport
 {
   public static String testseqs = "examples/uniref50.fa";

diff --git a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
index 546ba90..ec901da 100644 (file)
--- a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
+++ b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java
@@ -23,14 +23,14 @@ package jalview.ws.jabaws;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
+import jalview.ws.jws2.Jws2Discoverer;
+
 import java.util.Vector;
 
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-import jalview.ws.jws2.Jws2Discoverer;
-
 public class JalviewJabawsTestUtils
 {
 

diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
index 0b17169..49a3064 100644 (file)
--- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@ -23,6 +23,18 @@ package jalview.ws.jabaws;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.AlignmentI;
+import jalview.gui.Jalview2XML;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.JPred301Client;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.SequenceAnnotationWSClient;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
 import java.awt.Component;
 import java.util.ArrayList;
 import java.util.List;
@@ -38,18 +50,6 @@ import org.testng.annotations.Test;
 import compbio.metadata.Argument;
 import compbio.metadata.WrongParameterException;
 
-import jalview.datamodel.AlignmentI;
-import jalview.gui.Jalview2XML;
-import jalview.io.AnnotationFile;
-import jalview.io.FormatAdapter;
-import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.JPred301Client;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.AutoCalcSetting;
-
 public class JpredJabaStructExportImport
 {
   public static String testseqs = "examples/uniref50.fa";

diff --git a/test/jalview/ws/jabaws/MinJabawsClientTests.java b/test/jalview/ws/jabaws/MinJabawsClientTests.java
index 244ee4f..0a50e47 100644 (file)
--- a/test/jalview/ws/jabaws/MinJabawsClientTests.java
+++ b/test/jalview/ws/jabaws/MinJabawsClientTests.java
@@ -1,11 +1,13 @@
 package jalview.ws.jabaws;
 
 import static org.testng.AssertJUnit.assertEquals;
-import org.testng.annotations.Test;
-import org.testng.Assert;
+
 import java.util.ArrayList;
 import java.util.List;
 
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
 import compbio.data.msa.MsaWS;
 import compbio.data.msa.RegistryWS;
 import compbio.data.sequence.FastaSequence;
@@ -13,7 +15,8 @@ import compbio.metadata.JobStatus;
 import compbio.ws.client.Jws2Client;
 import compbio.ws.client.Services;
 
-public class MinJabawsClientTests {
+public class MinJabawsClientTests
+{
 
        /**
         * simple test for the benefit of JAL-1338

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 6b92b85..5d9773a 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -23,6 +23,18 @@ package jalview.ws.jabaws;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.gui.Jalview2XML;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.RNAalifoldClient;
+import jalview.ws.jws2.SequenceAnnotationWSClient;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
 import java.awt.Component;
 import java.util.ArrayList;
 import java.util.List;
@@ -37,18 +49,6 @@ import org.testng.annotations.Test;
 
 import compbio.metadata.WrongParameterException;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.gui.Jalview2XML;
-import jalview.io.AnnotationFile;
-import jalview.io.FormatAdapter;
-import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.RNAalifoldClient;
-import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.AutoCalcSetting;
-
 public class RNAStructExportImport
 {
   public static String testseqs = "examples/RF00031_folded.stk";

diff --git a/test/jalview/ws/jws2/ParameterUtilsTest.java b/test/jalview/ws/jws2/ParameterUtilsTest.java
index d24a790..3403446 100644 (file)
--- a/test/jalview/ws/jws2/ParameterUtilsTest.java
+++ b/test/jalview/ws/jws2/ParameterUtilsTest.java
@@ -23,22 +23,24 @@ package jalview.ws.jws2;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeClass;
+
+import jalview.bin.Cache;
+import jalview.ws.jabaws.JalviewJabawsTestUtils;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import compbio.metadata.Option;
 import compbio.metadata.Parameter;
 import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.WrongParameterException;
 
-import jalview.bin.Cache;
-import jalview.ws.jabaws.JalviewJabawsTestUtils;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-
 public class ParameterUtilsTest
 {
   /*

diff --git a/test/jalview/ws/rest/RestClientTest.java b/test/jalview/ws/rest/RestClientTest.java
index 325febc..70071a5 100644 (file)
--- a/test/jalview/ws/rest/RestClientTest.java
+++ b/test/jalview/ws/rest/RestClientTest.java
@@ -1,11 +1,13 @@
 package jalview.ws.rest;
 
 import static org.testng.AssertJUnit.assertEquals;
-import org.testng.annotations.Test;
-import java.util.Vector;
 
 import jalview.bin.Cache;
 
+import java.util.Vector;
+
+import org.testng.annotations.Test;
+
 public class RestClientTest
 {
   /**

diff --git a/test/jalview/ws/rest/ShmmrRSBSService.java b/test/jalview/ws/rest/ShmmrRSBSService.java
index d562644..99135d9 100644 (file)
--- a/test/jalview/ws/rest/ShmmrRSBSService.java
+++ b/test/jalview/ws/rest/ShmmrRSBSService.java
@@ -23,12 +23,12 @@ package jalview.ws.rest;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.gui.AlignFrame;
+
 import java.util.Map;
 
 import org.testng.annotations.Test;
 
-import jalview.gui.AlignFrame;
-
 /**
  * @author jimp
  * 

diff --git a/test/jalview/ws/seqfetcher/DasSequenceFetcher.java b/test/jalview/ws/seqfetcher/DasSequenceFetcher.java
index bac0b5e..c830f23 100644 (file)
--- a/test/jalview/ws/seqfetcher/DasSequenceFetcher.java
+++ b/test/jalview/ws/seqfetcher/DasSequenceFetcher.java
@@ -1,7 +1,7 @@
 package jalview.ws.seqfetcher;
 
-import org.testng.annotations.Test;
 import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
 
 public class DasSequenceFetcher
 {

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index 302c0f7..d6bd4b0 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -23,11 +23,6 @@ package jalview.ws.seqfetcher;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeClass;
-import java.util.ArrayList;
-import java.util.List;
 
 import jalview.analysis.CrossRef;
 import jalview.datamodel.AlignmentI;
@@ -36,6 +31,13 @@ import jalview.datamodel.DBRefSource;
 import jalview.util.DBRefUtils;
 import jalview.ws.SequenceFetcher;
 
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 /**
  * @author jimp
  *