X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcontroller%2FAlignViewControllerTest.java;h=ca3b55c07cd33784147d173e2e41cd5705bdfa18;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=efee93b2bb47dbcd6ae590d05c8fe990ae2a8492;hpb=baa077bd19420018433d78927aad3ad139e47351;p=jalview.git

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index efee93b..ca3b55c 100644
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.analysis.Finder;
 import jalview.api.AlignViewControllerI;
 import jalview.api.FeatureColourI;
+import jalview.api.FinderI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
@@ -67,18 +68,17 @@ public class AlignViewControllerTest
     /*
      * features start/end are base 1
      */
-    seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
-            null));
-    seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
-            null));
-    seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10,
-            10f,
-            null));
-    seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
-            10f, null));
+    seq1.addSequenceFeature(
+            new SequenceFeature("Metal", "desc", 2, 4, 0f, null));
+    seq1.addSequenceFeature(
+            new SequenceFeature("Helix", "desc", 1, 15, 0f, null));
+    seq2.addSequenceFeature(
+            new SequenceFeature("Metal", "desc", 4, 10, 10f, null));
+    seq3.addSequenceFeature(
+            new SequenceFeature("Metal", "desc", 11, 15, 10f, null));
     // disulfide bond is a 'contact feature' - only select its 'start' and 'end'
-    seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc",
-            8, 12, 0f, null));
+    seq3.addSequenceFeature(
+            new SequenceFeature("disulfide bond", "desc", 8, 12, 0f, null));
 
     /*
      * select the first five columns --> Metal in seq1 cols 4-5
@@ -94,8 +94,9 @@ public class AlignViewControllerTest
     /*
      * set features visible on a viewport as only visible features are selected
      */
-    AlignFrame af = new AlignFrame(new Alignment(new SequenceI[] { seq1,
-        seq2, seq3, seq4 }), 100, 100);
+    AlignFrame af = new AlignFrame(
+            new Alignment(new SequenceI[]
+            { seq1, seq2, seq3, seq4 }), 100, 100);
     af.getFeatureRenderer().findAllFeatures(true);
 
     AlignViewController avc = new AlignViewController(af, af.getViewport(),
@@ -147,7 +148,8 @@ public class AlignViewControllerTest
      * seq1 feature in columns 4-6 is hidden
      * seq2 feature in columns 6-7 is shown
      */
-    FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
+    FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+            0f, 10f);
     fc.setAboveThreshold(true);
     fc.setThreshold(5f);
     af.getFeatureRenderer().setColour("Metal", fc);
@@ -203,7 +205,8 @@ public class AlignViewControllerTest
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
                     + "seq3 aaaaaaaaaaMMMMMaaaaa\n"
-                    + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE);
+                    + "seq4 aaaaaaaaaaaaaaaaaaaa\n",
+            DataSourceType.PASTE);
 
     SearchResultsI sr = new SearchResults();
     SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
@@ -222,10 +225,8 @@ public class AlignViewControllerTest
     /*
      *  test Match/Find works first
      */
-    Finder f = new Finder(af.getViewport().getAlignment(), null);
-    f.setFindAll(true);
-    f.setCaseSensitive(true);
-    f.find("M+");
+    FinderI f = new Finder(af.getViewport());
+    f.findAll("M+", true, false, false);
     assertEquals(
             "Finder found different set of results to manually created SearchResults",
             sr, f.getSearchResults());
@@ -237,8 +238,9 @@ public class AlignViewControllerTest
     AlignViewControllerI avc = af.avc;
 
     avc.markHighlightedColumns(false, false, false);
-    assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af
-            .getViewport().getColumnSelection().getSelectedRanges()
-            .toArray(), new int[][] { { 1, 14 } }));
+    assertTrue("Didn't select highlighted columns",
+            Arrays.deepEquals(af.getViewport().getColumnSelection()
+                    .getSelectedRanges().toArray(), new int[][]
+                    { { 1, 14 } }));
   }
 }