JAL-3253 ApplicationSingletonProvider replaces Instance

[jalview.git] / test / jalview / io / FeaturesFileTest.java

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index fdef53d..59d024c 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -43,7 +43,6 @@ import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.schemes.FeatureColour;
-import jalview.structure.StructureSelectionManager;
 import jalview.util.matcher.Condition;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
@@ -70,9 +69,7 @@ public class FeaturesFileTest
     /*
      * remove any sequence mappings created so they don't pollute other tests
      */
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.getInstance());
-    ssm.resetAll();
+    Desktop.getInstance().getStructureSelectionManager().resetAll();
   }
 
   @BeforeClass(alwaysRun = true)
@@ -491,7 +488,9 @@ public class FeaturesFileTest
             + "ENDGROUP\tuniprot\n\n"
             + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
             + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
-    assertEquals(expected, exported);
+    assertEquals(
+            expected.replace("\n", System.getProperty("line.separator")),
+            exported);
 
     /*
      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
@@ -506,7 +505,7 @@ public class FeaturesFileTest
             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
             + "ENDGROUP\tuniprot\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
 
     /*
      * now set Pfam visible
@@ -528,7 +527,7 @@ public class FeaturesFileTest
             // null / empty group features are output after named groups
             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
 
     /*
      * hide uniprot group
@@ -540,7 +539,7 @@ public class FeaturesFileTest
             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
             false);
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
 
     /*
      * include non-positional (overrides group not shown)
@@ -556,7 +555,7 @@ public class FeaturesFileTest
             + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
             + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
             + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
   }
 
   @Test(groups = { "Functional" })
@@ -575,10 +574,14 @@ public class FeaturesFileTest
     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
             fr, false);
     String gffHeader = "##gff-version 2\n";
-    assertEquals(gffHeader, exported);
+    assertEquals(
+            fixLineEnd(gffHeader),
+            exported);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
             true);
-    assertEquals(gffHeader, exported);
+    assertEquals(
+            fixLineEnd(gffHeader),
+            exported);
 
     /*
      * add some features
@@ -615,7 +618,9 @@ public class FeaturesFileTest
      */
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
             false);
-    assertEquals(gffHeader, exported);
+    assertEquals(
+            fixLineEnd(gffHeader),
+            exported);
 
     /*
      * include non-positional features
@@ -626,7 +631,9 @@ public class FeaturesFileTest
             true);
     String expected = gffHeader
             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            fixLineEnd(expected),
+            exported);
 
     /*
      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
@@ -638,7 +645,9 @@ public class FeaturesFileTest
             false);
     // METAL feature has null group: description used for column 2
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            expected.replace("\n", System.getProperty("line.separator")),
+            exported);
 
     /*
      * set s3dm group visible
@@ -649,7 +658,9 @@ public class FeaturesFileTest
     // METAL feature has null group: description used for column 2
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            expected.replace("\n", System.getProperty("line.separator")),
+            exported);
 
     /*
      * now set Pfam visible
@@ -662,7 +673,14 @@ public class FeaturesFileTest
             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
             + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            expected.replace("\n", System.getProperty("line.separator")),
+            exported);
+  }
+
+  private String fixLineEnd(String s)
+  {
+    return s.replace("\n", System.getProperty("line.separator"));
   }
 
   /**
@@ -737,7 +755,7 @@ public class FeaturesFileTest
     visible.put("foobar", new FeatureColour(Color.blue));
     ff.outputFeatureFilters(sb, visible, featureFilters);
     String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
-    assertEquals(expected, sb.toString());
+    assertEquals(fixLineEnd(expected), sb.toString());
   }
 
   /**
@@ -774,7 +792,8 @@ public class FeaturesFileTest
     String expected = gffHeader
             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            fixLineEnd(expected), exported);
 
     /*
      * now threshold to Score > 1.1 - should exclude sf2
@@ -787,7 +806,7 @@ public class FeaturesFileTest
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
             false);
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
 
     /*
      * remove threshold and check sf2 is exported
@@ -797,7 +816,7 @@ public class FeaturesFileTest
             false);
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
 
     /*
      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
@@ -809,7 +828,7 @@ public class FeaturesFileTest
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
             false);
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
   }
 
   /**
@@ -849,7 +868,9 @@ public class FeaturesFileTest
             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
             + "ENDGROUP\tgrp2\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            fixLineEnd(expected),
+            exported);
   
     /*
      * now threshold to Score > 1.1 - should exclude sf2
@@ -866,7 +887,9 @@ public class FeaturesFileTest
             + "STARTGROUP\tgrp1\n"
             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
             + "ENDGROUP\tgrp1\n";
-    assertEquals(expected, exported);
+    assertEquals(
+            expected.replace("\n", System.getProperty("line.separator")),
+            exported);
   
     /*
      * remove threshold and check sf2 is exported
@@ -880,7 +903,7 @@ public class FeaturesFileTest
             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
             + "ENDGROUP\tgrp2\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
   
     /*
      * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
@@ -897,6 +920,6 @@ public class FeaturesFileTest
             + "STARTGROUP\tgrp2\n"
             + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
             + "ENDGROUP\tgrp2\n";
-    assertEquals(expected, exported);
+    assertEquals(fixLineEnd(expected), exported);
   }
 }