JAL-966 JAL-1738 JAL-345 interfaces for SearchResults and SearchResults.Match

[jalview.git] / test / jalview / util / MappingUtilsTest.java

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index d131ed2..6d04661 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -33,8 +33,8 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -81,9 +81,9 @@ public class MappingUtilsTest
     /*
      * Check protein residue 12 maps to codon 5-7, 13 to codon 8-10
      */
-    SearchResults sr = MappingUtils.buildSearchResults(aseq1, 12, acfList);
+    SearchResultsI sr = MappingUtils.buildSearchResults(aseq1, 12, acfList);
     assertEquals(1, sr.getResults().size());
-    Match m = sr.getResults().get(0);
+    SearchResultMatchI m = sr.getResults().get(0);
     assertEquals(seq1.getDatasetSequence(), m.getSequence());
     assertEquals(5, m.getStart());
     assertEquals(7, m.getEnd());
@@ -134,9 +134,9 @@ public class MappingUtilsTest
     /*
      * Check protein residue 8 maps to [6, 8, 9]
      */
-    SearchResults sr = MappingUtils.buildSearchResults(aseq1, 8, acfList);
+    SearchResultsI sr = MappingUtils.buildSearchResults(aseq1, 8, acfList);
     assertEquals(2, sr.getResults().size());
-    Match m = sr.getResults().get(0);
+    SearchResultMatchI m = sr.getResults().get(0);
     assertEquals(seq1.getDatasetSequence(), m.getSequence());
     assertEquals(6, m.getStart());
     assertEquals(6, m.getEnd());
@@ -867,7 +867,7 @@ public class MappingUtilsTest
   public void testMapColumnSelection_hiddenColumns() throws IOException
   {
     setupMappedAlignments();
-  
+
     ColumnSelection proteinSelection = new ColumnSelection();
 
     /*
@@ -875,8 +875,8 @@ public class MappingUtilsTest
      * in dna respectively, overall 0-4
      */
     proteinSelection.hideColumns(0);
-    ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
-            proteinView, dnaView);
+    ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(
+            proteinSelection, proteinView, dnaView);
     assertEquals("[]", dnaSelection.getSelected().toString());
     List<int[]> hidden = dnaSelection.getHiddenColumns();
     assertEquals(1, hidden.size());
@@ -891,7 +891,8 @@ public class MappingUtilsTest
     // deselect these or hideColumns will be expanded to include 0
     proteinSelection.clear();
     proteinSelection.hideColumns(1);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
+    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
+            proteinView, dnaView);
     hidden = dnaSelection.getHiddenColumns();
     assertEquals(1, hidden.size());
     assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
@@ -902,7 +903,8 @@ public class MappingUtilsTest
     proteinSelection.revealAllHiddenColumns();
     proteinSelection.clear();
     proteinSelection.hideColumns(2);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
+    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
+            proteinView, dnaView);
     assertTrue(dnaSelection.getHiddenColumns().isEmpty());
 
     /*
@@ -913,7 +915,8 @@ public class MappingUtilsTest
     proteinSelection.clear();
     proteinSelection.hideColumns(3); // 5-10 hidden in dna
     proteinSelection.addElement(1); // 0-3 selected in dna
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
+    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
+            proteinView, dnaView);
     assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
     hidden = dnaSelection.getHiddenColumns();
     assertEquals(1, hidden.size());
@@ -926,7 +929,8 @@ public class MappingUtilsTest
     proteinSelection.clear();
     proteinSelection.hideColumns(1);
     proteinSelection.hideColumns(3);
-    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
+    dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
+            proteinView, dnaView);
     hidden = dnaSelection.getHiddenColumns();
     assertEquals(2, hidden.size());
     assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
@@ -1060,42 +1064,42 @@ public class MappingUtilsTest
     int[] adjusted = MappingUtils.removeStartPositions(0, ranges);
     assertEquals("[10, 1]", Arrays.toString(adjusted));
     assertEquals("[10, 1]", Arrays.toString(ranges));
-  
+
     ranges = adjusted;
     adjusted = MappingUtils.removeStartPositions(1, ranges);
     assertEquals("[9, 1]", Arrays.toString(adjusted));
     assertEquals("[10, 1]", Arrays.toString(ranges));
-  
+
     ranges = adjusted;
     adjusted = MappingUtils.removeStartPositions(1, ranges);
     assertEquals("[8, 1]", Arrays.toString(adjusted));
     assertEquals("[9, 1]", Arrays.toString(ranges));
-  
+
     ranges = new int[] { 12, 11, 9, 6 };
     adjusted = MappingUtils.removeStartPositions(1, ranges);
     assertEquals("[11, 11, 9, 6]", Arrays.toString(adjusted));
     assertEquals("[12, 11, 9, 6]", Arrays.toString(ranges));
-  
+
     ranges = new int[] { 12, 12, 8, 4 };
     adjusted = MappingUtils.removeStartPositions(1, ranges);
     assertEquals("[8, 4]", Arrays.toString(adjusted));
     assertEquals("[12, 12, 8, 4]", Arrays.toString(ranges));
-  
+
     ranges = new int[] { 12, 12, 8, 4 };
     adjusted = MappingUtils.removeStartPositions(2, ranges);
     assertEquals("[7, 4]", Arrays.toString(adjusted));
     assertEquals("[12, 12, 8, 4]", Arrays.toString(ranges));
-  
+
     ranges = new int[] { 12, 12, 10, 10, 8, 4 };
     adjusted = MappingUtils.removeStartPositions(1, ranges);
     assertEquals("[10, 10, 8, 4]", Arrays.toString(adjusted));
     assertEquals("[12, 12, 10, 10, 8, 4]", Arrays.toString(ranges));
-  
+
     ranges = new int[] { 12, 12, 10, 10, 8, 4 };
     adjusted = MappingUtils.removeStartPositions(2, ranges);
     assertEquals("[8, 4]", Arrays.toString(adjusted));
     assertEquals("[12, 12, 10, 10, 8, 4]", Arrays.toString(ranges));
-  
+
     ranges = new int[] { 12, 11, 8, 4 };
     adjusted = MappingUtils.removeStartPositions(3, ranges);
     assertEquals("[7, 4]", Arrays.toString(adjusted));