X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStoreTest.java;fp=test%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStoreTest.java;h=b0a1ac8fe6bab3f9324701b1a528a177d188bd4b;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=c38cb1eabfa2de895aa7c2ea7e14ac7388f28c6d;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git

diff --git a/test/jalview/datamodel/features/FeatureStoreTest.java b/test/jalview/datamodel/features/FeatureStoreTest.java
index c38cb1e..b0a1ac8 100644
--- a/test/jalview/datamodel/features/FeatureStoreTest.java
+++ b/test/jalview/datamodel/features/FeatureStoreTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel.features;
 
 import static org.testng.Assert.assertEquals;
@@ -20,8 +40,7 @@ public class FeatureStoreTest
   public void testFindFeatures_nonNested()
   {
     FeatureStore fs = new FeatureStore();
-    fs.addFeature(new SequenceFeature("", "", 10, 20, Float.NaN,
-            null));
+    fs.addFeature(new SequenceFeature("", "", 10, 20, Float.NaN, null));
     // same range different description
     fs.addFeature(new SequenceFeature("", "desc", 10, 20, Float.NaN, null));
     fs.addFeature(new SequenceFeature("", "", 15, 25, Float.NaN, null));
@@ -213,8 +232,8 @@ public class FeatureStoreTest
             Float.NaN, null);
     store.addFeature(sf6);
     // contact feature
-    SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc",
-            18, 45, Float.NaN, null);
+    SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc", 18,
+            45, Float.NaN, null);
     store.addFeature(sf7);
 
     List<SequenceFeature> features = store.getPositionalFeatures();
@@ -257,8 +276,8 @@ public class FeatureStoreTest
     /*
      * contact feature deletion
      */
-    SequenceFeature sf3 = new SequenceFeature("", "Disulphide Bond", 11,
-            23, Float.NaN, null);
+    SequenceFeature sf3 = new SequenceFeature("", "Disulphide Bond", 11, 23,
+            Float.NaN, null);
     store.addFeature(sf3);
     assertEquals(store.getPositionalFeatures().size(), 1);
     assertTrue(store.getPositionalFeatures().contains(sf3));
@@ -309,10 +328,10 @@ public class FeatureStoreTest
   {
     FeatureStore fs = new FeatureStore();
 
-    SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
-            Float.NaN, null);
-    SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20,
-            Float.NaN, null);
+    SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+            null);
+    SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+            null);
 
     assertTrue(fs.addFeature(sf1));
     assertEquals(fs.getFeatureCount(true), 1); // positional
@@ -365,8 +384,8 @@ public class FeatureStoreTest
     /*
      * non-nested feature
      */
-    SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
-            Float.NaN, null);
+    SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+            null);
     fs.addFeature(sf1);
     assertFalse(fs.isEmpty());
     assertEquals(fs.getFeatureCount(true), 1);
@@ -389,7 +408,8 @@ public class FeatureStoreTest
     /*
      * contact feature
      */
-    sf1 = new SequenceFeature("Disulfide bond", "", 19, 49, Float.NaN, null);
+    sf1 = new SequenceFeature("Disulfide bond", "", 19, 49, Float.NaN,
+            null);
     fs.addFeature(sf1);
     assertFalse(fs.isEmpty());
     assertEquals(fs.getFeatureCount(true), 1);
@@ -401,10 +421,10 @@ public class FeatureStoreTest
      * sf2, sf3 added as nested features
      */
     sf1 = new SequenceFeature("Cath", "", 19, 49, Float.NaN, null);
-    SequenceFeature sf2 = new SequenceFeature("Cath", "", 20, 40,
-            Float.NaN, null);
-    SequenceFeature sf3 = new SequenceFeature("Cath", "", 25, 35,
-            Float.NaN, null);
+    SequenceFeature sf2 = new SequenceFeature("Cath", "", 20, 40, Float.NaN,
+            null);
+    SequenceFeature sf3 = new SequenceFeature("Cath", "", 25, 35, Float.NaN,
+            null);
     fs.addFeature(sf1);
     fs.addFeature(sf2);
     fs.addFeature(sf3);
@@ -428,7 +448,8 @@ public class FeatureStoreTest
     assertTrue(fs.getFeatureGroups(true).isEmpty());
     assertTrue(fs.getFeatureGroups(false).isEmpty());
 
-    SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f, "group1");
+    SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f,
+            "group1");
     fs.addFeature(sf1);
     Set<String> groups = fs.getFeatureGroups(true);
     assertEquals(groups.size(), 1);
@@ -437,7 +458,8 @@ public class FeatureStoreTest
     /*
      * add another feature of the same group, delete one, delete both
      */
-    SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "group1");
+    SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 20, 30, 1f,
+            "group1");
     fs.addFeature(sf2);
     groups = fs.getFeatureGroups(true);
     assertEquals(groups.size(), 1);
@@ -450,11 +472,14 @@ public class FeatureStoreTest
     groups = fs.getFeatureGroups(true);
     assertTrue(fs.getFeatureGroups(true).isEmpty());
 
-    SequenceFeature sf3 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "group2");
+    SequenceFeature sf3 = new SequenceFeature("Cath", "desc", 20, 30, 1f,
+            "group2");
     fs.addFeature(sf3);
-    SequenceFeature sf4 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "Group2");
+    SequenceFeature sf4 = new SequenceFeature("Cath", "desc", 20, 30, 1f,
+            "Group2");
     fs.addFeature(sf4);
-    SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 20, 30, 1f, null);
+    SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 20, 30, 1f,
+            null);
     fs.addFeature(sf5);
     groups = fs.getFeatureGroups(true);
     assertEquals(groups.size(), 3);
@@ -507,8 +532,8 @@ public class FeatureStoreTest
     assertEquals(fs.getTotalFeatureLength(), 93);
 
     // contact features count 1
-    SequenceFeature sf3 = new SequenceFeature("disulphide bond", "desc",
-            15, 35, 1f, "group1");
+    SequenceFeature sf3 = new SequenceFeature("disulphide bond", "desc", 15,
+            35, 1f, "group1");
     fs.addFeature(sf3);
     assertEquals(fs.getTotalFeatureLength(), 94);
 
@@ -528,9 +553,10 @@ public class FeatureStoreTest
     /*
      * positional feature
      */
-    SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f, "group1");
+    SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f,
+            "group1");
     assertEquals(FeatureStore.getFeatureLength(sf1), 11);
-  
+
     /*
      * non-positional feature
      */
@@ -541,8 +567,8 @@ public class FeatureStoreTest
     /*
      * contact feature counts 1
      */
-    SequenceFeature sf3 = new SequenceFeature("Disulphide Bond", "desc",
-            14, 28, 1f, "AGroup");
+    SequenceFeature sf3 = new SequenceFeature("Disulphide Bond", "desc", 14,
+            28, 1f, "AGroup");
     assertEquals(FeatureStore.getFeatureLength(sf3), 1);
   }
 
@@ -817,7 +843,7 @@ public class FeatureStoreTest
     assertTrue(features.contains(sf2));
     assertTrue(store.features.contains(sf1));
     assertTrue(store.features.contains(sf2));
-  
+
     /*
      * delete the first feature
      */
@@ -839,10 +865,10 @@ public class FeatureStoreTest
   public void testContains()
   {
     FeatureStore fs = new FeatureStore();
-    SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
-            Float.NaN, "group1");
-    SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20,
-            Float.NaN, "group2");
+    SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+            "group1");
+    SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+            "group2");
     SequenceFeature sf3 = new SequenceFeature("Cath", "", 0, 0, Float.NaN,
             "group1");
     SequenceFeature sf4 = new SequenceFeature("Cath", "", 0, 0, 0f,
@@ -868,8 +894,8 @@ public class FeatureStoreTest
     /*
      * add a nested feature
      */
-    SequenceFeature sf7 = new SequenceFeature("Cath", "", 12, 16,
-            Float.NaN, "group1");
+    SequenceFeature sf7 = new SequenceFeature("Cath", "", 12, 16, Float.NaN,
+            "group1");
     fs.addFeature(sf7);
     assertTrue(fs.contains(sf7));
     assertTrue(fs.contains(new SequenceFeature(sf7)));