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JAL-3253 code tidies and tweaks to Desktop
[jalview.git] / test / jalview / io / FeaturesFileTest.java
diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index ab07289..04ddeb0 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;
@@ -62,6 +61,7 @@ import org.testng.annotations.Test;
 
 public class FeaturesFileTest
 {
+  private static final String LINE_SEPARATOR = System.getProperty("line.separator");
   private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
 
   @AfterClass(alwaysRun = true)
@@ -70,9 +70,7 @@ public class FeaturesFileTest
     /*
      * remove any sequence mappings created so they don't pollute other tests
      */
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
-    ssm.resetAll();
+    Desktop.getStructureSelectionManager().resetAll();
   }
 
   @BeforeClass(alwaysRun = true)
@@ -481,15 +479,19 @@ public class FeaturesFileTest
     assertEquals(expected, exported);
 
     /*
-     * include non-positional features
+     * include non-positional features, but still no positional features
      */
     fr.setGroupVisibility("uniprot", true);
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
             true);
-    expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
-            + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
+    expected = "\nSTARTGROUP\tuniprot\n"
+            + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
+            + "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", LINE_SEPARATOR),
+            exported);
 
     /*
      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
@@ -504,7 +506,7 @@ 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
@@ -513,7 +515,7 @@ public class FeaturesFileTest
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
             false);
     /*
-     * features are output within group, ordered by sequence and by type
+     * features are output within group, ordered by sequence and type
      */
     expected = "METAL\tcc9900\n"
             + "Pfam\tff0000\n"
@@ -523,11 +525,38 @@ public class FeaturesFileTest
             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
             + "ENDGROUP\tuniprot\n"
-            // null / empty group features output after features in named
-            // groups:
+            // 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(fixLineEnd(expected), exported);
+
+    /*
+     * hide uniprot group
+     */
+    fr.setGroupVisibility("uniprot", false);
+    expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
+            + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+            + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
+            + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
+    exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+            false);
+    assertEquals(fixLineEnd(expected), exported);
+
+    /*
+     * include non-positional (overrides group not shown)
+     */
+    exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+            true);
+    expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
+            + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+            + "\nSTARTGROUP\tuniprot\n"
+            + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
+            + "ENDGROUP\tuniprot\n"
+            + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
             + "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" })
@@ -546,10 +575,14 @@ 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
@@ -586,7 +619,9 @@ public class FeaturesFileTest
      */
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
             false);
-    assertEquals(gffHeader, exported);
+    assertEquals(
+            fixLineEnd(gffHeader),
+            exported);
 
     /*
      * include non-positional features
@@ -597,7 +632,9 @@ 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
@@ -609,7 +646,9 @@ 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", LINE_SEPARATOR),
+            exported);
 
     /*
      * set s3dm group visible
@@ -620,7 +659,9 @@ 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", LINE_SEPARATOR),
+            exported);
 
     /*
      * now set Pfam visible
@@ -633,7 +674,12 @@ 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(fixLineEnd(expected), exported);
+  }
+
+  private String fixLineEnd(String s)
+  {
+    return s.replace("\n", LINE_SEPARATOR);
   }
 
   /**
@@ -708,7 +754,7 @@ 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());
   }
 
   /**
@@ -745,12 +791,13 @@ 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
      */
-    FeatureColourI fc = new FeatureColour(Color.white, Color.BLACK,
+    FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
             Color.white, 0f, 2f);
     fc.setAboveThreshold(true);
     fc.setThreshold(1.1f);
@@ -758,7 +805,7 @@ 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
@@ -768,7 +815,7 @@ 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
@@ -780,7 +827,7 @@ 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);
   }
 
   /**
@@ -820,13 +867,15 @@ 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
      * (and there should be no empty STARTGROUP/ENDGROUP output)
      */
-    FeatureColourI fc = new FeatureColour(Color.white, Color.BLACK,
+    FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
             Color.white, 0f, 2f);
     fc.setAboveThreshold(true);
     fc.setThreshold(1.1f);
@@ -837,7 +886,9 @@ 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", LINE_SEPARATOR),
+            exported);
   
     /*
      * remove threshold and check sf2 is exported
@@ -851,7 +902,7 @@ 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
@@ -868,6 +919,6 @@ 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);
   }
 }