X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FSequenceAnnotationReportTest.java;h=0b5dfdda390449a21a9d72de37336426db090fa9;hb=e51f922b88b1f316e27cf4c19eef437ff592d74d;hp=87e35c75fa3f02570f56205bad09724f1e3a2240;hpb=81c8008cff0d9a265e0fbe979b17b173e9e4fc0a;p=jalview.git

diff --git a/test/jalview/io/SequenceAnnotationReportTest.java b/test/jalview/io/SequenceAnnotationReportTest.java
index 87e35c7..0b5dfdd 100644
--- a/test/jalview/io/SequenceAnnotationReportTest.java
+++ b/test/jalview/io/SequenceAnnotationReportTest.java
@@ -37,11 +37,11 @@ import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import java.awt.Color;
 import java.util.Map;
 
-import junit.extensions.PA;
-
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class SequenceAnnotationReportTest
 {
 
@@ -62,17 +62,17 @@ public class SequenceAnnotationReportTest
             3, 1.2f, "group");
 
     // residuePos == 2 does not match start or end of feature, nothing done:
-    sar.appendFeature(sb, 2, null, sf);
+    sar.appendFeature(sb, 2, null, sf, null);
     assertEquals("123456", sb.toString());
 
     // residuePos == 1 matches start of feature, text appended (but no <br>)
     // feature score is not included
-    sar.appendFeature(sb, 1, null, sf);
+    sar.appendFeature(sb, 1, null, sf, null);
     assertEquals("123456disulfide bond 1:3", sb.toString());
 
     // residuePos == 3 matches end of feature, text appended
     // <br> is prefixed once sb.length() > 6
-    sar.appendFeature(sb, 3, null, sf);
+    sar.appendFeature(sb, 3, null, sf, null);
     assertEquals("123456disulfide bond 1:3<br>disulfide bond 1:3",
             sb.toString());
   }
@@ -86,7 +86,7 @@ public class SequenceAnnotationReportTest
             Float.NaN, "group");
     sf.setStatus("Confirmed");
 
-    sar.appendFeature(sb, 1, null, sf);
+    sar.appendFeature(sb, 1, null, sf, null);
     assertEquals("METAL 1 3; Fe2-S; (Confirmed)", sb.toString());
   }
 
@@ -100,7 +100,7 @@ public class SequenceAnnotationReportTest
 
     FeatureRendererModel fr = new FeatureRenderer(null);
     Map<String, float[][]> minmax = fr.getMinMax();
-    sar.appendFeature(sb, 1, fr, sf);
+    sar.appendFeature(sb, 1, fr, sf, null);
     /*
      * map has no entry for this feature type - score is not shown:
      */
@@ -110,7 +110,7 @@ public class SequenceAnnotationReportTest
      * map has entry for this feature type - score is shown:
      */
     minmax.put("METAL", new float[][] { { 0f, 1f }, null });
-    sar.appendFeature(sb, 1, fr, sf);
+    sar.appendFeature(sb, 1, fr, sf, null);
     // <br> is appended to a buffer > 6 in length
     assertEquals("METAL 1 3; Fe2-S<br>METAL 1 3; Fe2-S Score=1.3",
             sb.toString());
@@ -120,7 +120,7 @@ public class SequenceAnnotationReportTest
      */
     minmax.put("METAL", new float[][] { { 2f, 2f }, null });
     sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf);
+    sar.appendFeature(sb, 1, fr, sf, null);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
   }
 
@@ -132,7 +132,7 @@ public class SequenceAnnotationReportTest
     SequenceFeature sf = new SequenceFeature("METAL", "Fe2-S", 1, 3,
             Float.NaN, "group");
 
-    sar.appendFeature(sb, 1, null, sf);
+    sar.appendFeature(sb, 1, null, sf, null);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
   }
 
@@ -152,17 +152,18 @@ public class SequenceAnnotationReportTest
      * first with no colour by attribute
      */
     FeatureRendererModel fr = new FeatureRenderer(null);
-    sar.appendFeature(sb, 1, fr, sf);
+    sar.appendFeature(sb, 1, fr, sf, null);
     assertEquals("METAL 1 3; Fe2-S", sb.toString());
 
     /*
      * then with colour by an attribute the feature lacks
      */
-    FeatureColourI fc = new FeatureColour(Color.white, Color.black, 5, 10);
+    FeatureColourI fc = new FeatureColour(null, Color.white, Color.black,
+            null, 5, 10);
     fc.setAttributeName("Pfam");
     fr.setColour("METAL", fc);
     sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf);
+    sar.appendFeature(sb, 1, fr, sf, null);
     assertEquals("METAL 1 3; Fe2-S", sb.toString()); // no change
 
     /*
@@ -170,7 +171,7 @@ public class SequenceAnnotationReportTest
      */
     fc.setAttributeName("clinical_significance");
     sb.setLength(0);
-    sar.appendFeature(sb, 1, fr, sf);
+    sar.appendFeature(sb, 1, fr, sf, null);
     assertEquals("METAL 1 3; Fe2-S; clinical_significance=Benign",
             sb.toString());
   }
@@ -187,11 +188,12 @@ public class SequenceAnnotationReportTest
 
     FeatureRendererModel fr = new FeatureRenderer(null);
     Map<String, float[][]> minmax = fr.getMinMax();
-    FeatureColourI fc = new FeatureColour(Color.white, Color.blue, 12, 22);
+    FeatureColourI fc = new FeatureColour(null, Color.white, Color.blue,
+            null, 12, 22);
     fc.setAttributeName("clinical_significance");
     fr.setColour("METAL", fc);
     minmax.put("METAL", new float[][] { { 0f, 1f }, null });
-    sar.appendFeature(sb, 1, fr, sf);
+    sar.appendFeature(sb, 1, fr, sf, null);
 
     assertEquals(
             "METAL 1 3; Fe2-S Score=1.3; (Confirmed); clinical_significance=Benign",
@@ -207,13 +209,13 @@ public class SequenceAnnotationReportTest
             Float.NaN, "group");
 
     // description is not included if it duplicates type:
-    sar.appendFeature(sb, 1, null, sf);
+    sar.appendFeature(sb, 1, null, sf, null);
     assertEquals("METAL 1 3", sb.toString());
 
     sb.setLength(0);
     sf.setDescription("Metal");
     // test is case-sensitive:
-    sar.appendFeature(sb, 1, null, sf);
+    sar.appendFeature(sb, 1, null, sf, null);
     assertEquals("METAL 1 3; Metal", sb.toString());
   }
 
@@ -226,13 +228,13 @@ public class SequenceAnnotationReportTest
             "<html><body>hello<em>world</em></body></html>", 1, 3,
             Float.NaN, "group");
 
-    sar.appendFeature(sb, 1, null, sf);
+    sar.appendFeature(sb, 1, null, sf, null);
     // !! strips off </body> but not <body> ??
     assertEquals("METAL 1 3; <body>hello<em>world</em>", sb.toString());
 
     sb.setLength(0);
     sf.setDescription("<br>&kHD>6");
-    sar.appendFeature(sb, 1, null, sf);
+    sar.appendFeature(sb, 1, null, sf, null);
     // if no <html> tag, html-encodes > and < (only):
     assertEquals("METAL 1 3; &lt;br&gt;&kHD&gt;6", sb.toString());
   }
@@ -328,7 +330,8 @@ public class SequenceAnnotationReportTest
 
     // with showDbRefs = true, colour Variant features by clinical_significance
     sb.setLength(0);
-    FeatureColourI fc = new FeatureColour(Color.green, Color.pink, 2, 3);
+    FeatureColourI fc = new FeatureColour(null, Color.green, Color.pink,
+            null, 2, 3);
     fc.setAttributeName("clinical_significance");
     fr.setColour("Variant", fc);
     sar.createSequenceAnnotationReport(sb, seq, true, true, fr);