JAL-3438 spotless for 2.11.2.0

[jalview.git] / test / jalview / analysis / scoremodels / FeatureDistanceModelTest.java

diff --git a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
index 16ca70d..92f1542 100644 (file)
--- a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
@@ -75,8 +75,8 @@ public class FeatureDistanceModelTest
    */
   public AlignFrame getTestAlignmentFrame()
   {
-    AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
-            alntestFile, DataSourceType.PASTE);
+    AlignFrame alf = new FileLoader(false)
+            .LoadFileWaitTillLoaded(alntestFile, DataSourceType.PASTE);
     AlignmentI al = alf.getViewport().getAlignment();
     Assert.assertEquals(al.getHeight(), 4);
     Assert.assertEquals(al.getWidth(), 5);
@@ -104,8 +104,9 @@ public class FeatureDistanceModelTest
     alf.getFeatureRenderer().setVisible("sf2");
     alf.getFeatureRenderer().setVisible("sf3");
     alf.getFeatureRenderer().findAllFeatures(true);
-    Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
-            .size(), 3, "Number of feature types");
+    Assert.assertEquals(
+            alf.getFeatureRenderer().getDisplayedFeatureTypes().size(), 3,
+            "Number of feature types");
     assertTrue(alf.getCurrentView().areFeaturesDisplayed());
     return alf;
   }
@@ -119,8 +120,7 @@ public class FeatureDistanceModelTest
             alf.getCurrentView().getAlignPanel());
     alf.selectAllSequenceMenuItem_actionPerformed(null);
 
-    MatrixI dm = sm.findDistances(
-            alf.getViewport().getAlignmentView(true),
+    MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
             SimilarityParams.Jalview);
     assertEquals(dm.getValue(0, 2), 0d,
             "FER1_MESCR (0) should be identical with RAPSA (2)");
@@ -138,8 +138,7 @@ public class FeatureDistanceModelTest
     sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
             alf.getCurrentView().getAlignPanel());
     alf.selectAllSequenceMenuItem_actionPerformed(null);
-    MatrixI dm = sm.findDistances(
-            alf.getViewport().getAlignmentView(true),
+    MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
             SimilarityParams.Jalview);
     assertEquals(dm.getValue(0, 2), 0d,
             "FER1_MESCR (0) should be identical with RAPSA (2)");
@@ -159,22 +158,20 @@ public class FeatureDistanceModelTest
     sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
             alf.getCurrentView().getAlignPanel());
     alf.selectAllSequenceMenuItem_actionPerformed(null);
-    MatrixI dm = sm.findDistances(
-            alf.getViewport().getAlignmentView(true),
+    MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
             SimilarityParams.Jalview);
-    assertEquals(
-            dm.getValue(0, 2),
-            0d,
+    assertEquals(dm.getValue(0, 2), 0d,
             "After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
-    assertEquals(
-            dm.getValue(0, 1),
-            0d,
+    assertEquals(dm.getValue(0, 1), 0d,
             "After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)");
     for (int s = 0; s < 3; s++)
     {
-      assertTrue(dm.getValue(s, 3) > 0d, "After hiding last two columns "
-              + alf.getViewport().getAlignment().getSequenceAt(s).getName()
-              + "(" + s + ") should still be distinct from FER1_MAIZE (3)");
+      assertTrue(dm.getValue(s, 3) > 0d,
+              "After hiding last two columns "
+                      + alf.getViewport().getAlignment().getSequenceAt(s)
+                              .getName()
+                      + "(" + s
+                      + ") should still be distinct from FER1_MAIZE (3)");
     }
   }
 
@@ -196,26 +193,33 @@ public class FeatureDistanceModelTest
     assertTrue(sf.isContactFeature());
     af.refreshFeatureUI(true);
     af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond"));
-    Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
-            .size(), 1, "Should be just one feature type displayed");
+    Assert.assertEquals(
+            af.getFeatureRenderer().getDisplayedFeatureTypes().size(), 1,
+            "Should be just one feature type displayed");
     // step through and check for pointwise feature presence/absence
-    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 1)
-            .size(), 0);
+    Assert.assertEquals(
+            af.getFeatureRenderer().findFeaturesAtColumn(aseq, 1).size(),
+            0);
     // step through and check for pointwise feature presence/absence
-    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2)
-            .size(), 1);
+    Assert.assertEquals(
+            af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2).size(),
+            1);
     // step through and check for pointwise feature presence/absence
-    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3)
-            .size(), 0);
+    Assert.assertEquals(
+            af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3).size(),
+            0);
     // step through and check for pointwise feature presence/absence
-    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4)
-            .size(), 0);
+    Assert.assertEquals(
+            af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4).size(),
+            0);
     // step through and check for pointwise feature presence/absence
-    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5)
-            .size(), 1);
+    Assert.assertEquals(
+            af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5).size(),
+            1);
     // step through and check for pointwise feature presence/absence
-    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6)
-            .size(), 0);
+    Assert.assertEquals(
+            af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6).size(),
+            0);
   }
 
   @Test(groups = { "Functional" })
@@ -239,18 +243,18 @@ public class FeatureDistanceModelTest
      *     20120 (two features of the same type doesn't affect score)
      *  giving an average (pairwise distance) of 5/5 or 1.0 
      */
-    s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 3, 0f,
-            null));
-    s1.addSequenceFeature(new SequenceFeature("variant", null, 2, 4, 0f,
-            null));
-    s1.addSequenceFeature(new SequenceFeature("variant", null, 3, 5, 0f,
-            null));
-    s2.addSequenceFeature(new SequenceFeature("domain", null, 2, 4, 0f,
-            null));
-    s2.addSequenceFeature(new SequenceFeature("variant", null, 1, 2, 0f,
-            null));
-    s2.addSequenceFeature(new SequenceFeature("variant", null, 5, 5, 0f,
-            null));
+    s1.addSequenceFeature(
+            new SequenceFeature("domain", null, 1, 3, 0f, null));
+    s1.addSequenceFeature(
+            new SequenceFeature("variant", null, 2, 4, 0f, null));
+    s1.addSequenceFeature(
+            new SequenceFeature("variant", null, 3, 5, 0f, null));
+    s2.addSequenceFeature(
+            new SequenceFeature("domain", null, 2, 4, 0f, null));
+    s2.addSequenceFeature(
+            new SequenceFeature("variant", null, 1, 2, 0f, null));
+    s2.addSequenceFeature(
+            new SequenceFeature("variant", null, 5, 5, 0f, null));
     alf.setShowSeqFeatures(true);
     alf.getFeatureRenderer().findAllFeatures(true);
 
@@ -259,8 +263,7 @@ public class FeatureDistanceModelTest
             alf.getCurrentView().getAlignPanel());
     alf.selectAllSequenceMenuItem_actionPerformed(null);
 
-    AlignmentView alignmentView = alf.getViewport()
-            .getAlignmentView(true);
+    AlignmentView alignmentView = alf.getViewport().getAlignmentView(true);
     MatrixI distances = sm.findDistances(alignmentView,
             SimilarityParams.Jalview);
     assertEquals(distances.width(), 2);
@@ -303,7 +306,7 @@ public class FeatureDistanceModelTest
     assertEquals(distances.getValue(1, 1), 0d);
     assertEquals(distances.getValue(0, 1), 13d / 6); // should be 13d/6
     assertEquals(distances.getValue(1, 0), 13d / 6);
-  
+
     /*
      * exclude gaps
      * score = 3 + 3 + 0 + 0 + 0 + 0 = 6/6
@@ -339,12 +342,16 @@ public class FeatureDistanceModelTest
     SequenceI s1 = new Sequence("s1", "FR K S");
     SequenceI s2 = new Sequence("s2", "FS  L");
 
-    s1.addSequenceFeature(new SequenceFeature("chain", null, 1, 4, 0f, null));
-    s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 4, 0f,
-            null));
-    s2.addSequenceFeature(new SequenceFeature("chain", null, 1, 3, 0f, null));
-    s2.addSequenceFeature(new SequenceFeature("metal", null, 1, 3, 0f, null));
-    s2.addSequenceFeature(new SequenceFeature("Pfam", null, 1, 3, 0f, null));
+    s1.addSequenceFeature(
+            new SequenceFeature("chain", null, 1, 4, 0f, null));
+    s1.addSequenceFeature(
+            new SequenceFeature("domain", null, 1, 4, 0f, null));
+    s2.addSequenceFeature(
+            new SequenceFeature("chain", null, 1, 3, 0f, null));
+    s2.addSequenceFeature(
+            new SequenceFeature("metal", null, 1, 3, 0f, null));
+    s2.addSequenceFeature(
+            new SequenceFeature("Pfam", null, 1, 3, 0f, null));
     AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
     AlignFrame af = new AlignFrame(al, 300, 300);
     af.setShowSeqFeatures(true);