X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentAnnotationTests.java;h=f9e99d0733e22fb2f53ae54c0d733deb7cc76230;hb=c0501eaa85c0594f9275766f64de8ea44a59c368;hp=ade91504cfaffda66239d46082c9a53648f63157;hpb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index ade9150..f9e99d0 100644
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -74,8 +74,8 @@ public class AlignmentAnnotationTests
       al[i] = new Annotation(new Annotation("" + sq.getCharAt(i), "",
               (char) 0, sq.findPosition(i)));
     }
-    AlignmentAnnotation alan = new AlignmentAnnotation("For "
-            + sq.getName(), "Fake alignment annot", al);
+    AlignmentAnnotation alan = new AlignmentAnnotation(
+            "For " + sq.getName(), "Fake alignment annot", al);
     // create a sequence mapping for the annotation vector in its current state
     alan.createSequenceMapping(sq, sq.getStart(), false);
     alan.setProperty("CreatedBy", "createAnnotation");
@@ -98,9 +98,11 @@ public class AlignmentAnnotationTests
     {
       if (ala.annotations[p] != null)
       {
-        assertEquals("Mismatch at position " + p
-                + " between annotation position value and sequence"
-                + ala.annotations[p], (int) ala.annotations[p].value,
+        assertEquals(
+                "Mismatch at position " + p
+                        + " between annotation position value and sequence"
+                        + ala.annotations[p],
+                (int) ala.annotations[p].value,
                 ala.sequenceRef.findPosition(p));
       }
     }
@@ -135,10 +137,9 @@ public class AlignmentAnnotationTests
     alSeq2.setStart(sqTo.getStart() + align.getSeq2Start() - 1);
     alSeq2.setEnd(sqTo.getStart() + align.getSeq2End() - 1);
     alSeq2.setDatasetSequence(sqTo);
-    System.out.println(new AppletFormatAdapter()
-.formatSequences(
-            FileFormat.Stockholm, new Alignment(new SequenceI[] { sqFrom,
-                alSeq1, sqTo, alSeq2 }), true));
+    System.out.println(new AppletFormatAdapter().formatSequences(
+            FileFormat.Stockholm, new Alignment(new SequenceI[]
+            { sqFrom, alSeq1, sqTo, alSeq2 }), true));
 
     Mapping mp = align.getMappingFromS1(false);
 
@@ -161,9 +162,8 @@ public class AlignmentAnnotationTests
     AlignmentI all = new Alignment(new SequenceI[] { alSeq1, alSeq2 });
     all.addAnnotation(almap1);
     all.addAnnotation(almap2);
-    System.out.println(new AppletFormatAdapter().formatSequences(
-            FileFormat.Stockholm,
-            all, true));
+    System.out.println(new AppletFormatAdapter()
+            .formatSequences(FileFormat.Stockholm, all, true));
 
     for (int p = 0; p < alSeq1.getLength(); p++)
     {
@@ -186,12 +186,12 @@ public class AlignmentAnnotationTests
               "Mismatch on Original To and transferred annotation on 1",
               (orig1 != null) ? orig1.toString() : null,
               (trans1 != null) ? trans1.toString() : null);
-      String alm1 = ""
-              + (almap1.annotations.length > p ? almap1.annotations[p].displayCharacter
-                      : "Out of range");
-      String alm2 = ""
-              + (almap2.annotations.length > p ? almap2.annotations[p].displayCharacter
-                      : "Out of range");
+      String alm1 = "" + (almap1.annotations.length > p
+              ? almap1.annotations[p].displayCharacter
+              : "Out of range");
+      String alm2 = "" + (almap2.annotations.length > p
+              ? almap2.annotations[p].displayCharacter
+              : "Out of range");
       assertEquals("Position " + p + " " + alm1 + " " + alm2, alm1, alm2);
     }
   }
@@ -322,21 +322,24 @@ public class AlignmentAnnotationTests
     Assert.assertFalse(ann.isQuantitative(),
             "Empty annotation set should not be quantitative.");
 
-    ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
-        newAnnotation("4"), newAnnotation("1"), newAnnotation("1"),
-        newAnnotation("0.1"), newAnnotation("0.3") });
+    ann = new AlignmentAnnotation("an", "some an",
+            new Annotation[]
+            { newAnnotation("4"), newAnnotation("1"), newAnnotation("1"),
+                newAnnotation("0.1"), newAnnotation("0.3") });
     Assert.assertTrue(ann.isQuantitative(),
             "All numbers annotation set should be quantitative.");
 
-    ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
-        newAnnotation("E"), newAnnotation("E"), newAnnotation("E"),
-        newAnnotation("E"), newAnnotation("E") });
+    ann = new AlignmentAnnotation("an", "some an",
+            new Annotation[]
+            { newAnnotation("E"), newAnnotation("E"), newAnnotation("E"),
+                newAnnotation("E"), newAnnotation("E") });
     Assert.assertFalse(ann.isQuantitative(),
             "All 'E' annotation set should not be quantitative.");
 
-    ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
-        newAnnotation("E"), newAnnotation("1"), newAnnotation("2"),
-        newAnnotation("3"), newAnnotation("E") });
+    ann = new AlignmentAnnotation("an", "some an",
+            new Annotation[]
+            { newAnnotation("E"), newAnnotation("1"), newAnnotation("2"),
+                newAnnotation("3"), newAnnotation("E") });
     Assert.assertTrue(ann.isQuantitative(),
             "Mixed 'E' annotation set should be quantitative.");
   }