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JAL-3070 use object identity equivalence for lists of workers and Cache.log.debug...
[jalview.git] / test / jalview / io / FeaturesFileTest.java
diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index ab07289..090de6f 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -476,18 +476,20 @@ public class FeaturesFileTest
      */
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
     String exported = featuresFile
-            .printJalviewFormat(al.getSequencesArray(), fr, false);
+            .printJalviewFormat(al.getSequencesArray(), fr, false, false);
     String expected = "No Features Visible";
     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"
+            true, false);
+    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);
 
@@ -497,12 +499,12 @@ public class FeaturesFileTest
     fr.setVisible("METAL");
     fr.setVisible("GAMMA-TURN");
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = "METAL\tcc9900\n"
             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
             + "\nSTARTGROUP\tuniprot\n"
-            + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+            + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
             + "ENDGROUP\tuniprot\n";
     assertEquals(expected, exported);
 
@@ -511,21 +513,48 @@ public class FeaturesFileTest
      */
     fr.setVisible("Pfam");
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            false);
+            false, 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"
             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
             + "\nSTARTGROUP\tuniprot\n"
-            + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
             + "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"
+            + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+            + "ENDGROUP\tuniprot\n"
+            // 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);
+
+    /*
+     * 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, false);
+    assertEquals(expected, exported);
+
+    /*
+     * include non-positional (overrides group not shown)
+     */
+    exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+            true, false);
+    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"
-            // null / empty group features output after features in named
-            // groups:
+            + "\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);
   }
@@ -544,11 +573,11 @@ public class FeaturesFileTest
     FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
             .getFeatureRenderer();
     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
-            fr, false);
+            fr, false, false);
     String gffHeader = "##gff-version 2\n";
     assertEquals(gffHeader, exported);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            true);
+            true, false);
     assertEquals(gffHeader, exported);
 
     /*
@@ -585,7 +614,7 @@ public class FeaturesFileTest
      * with no features displayed, exclude non-positional features
      */
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     assertEquals(gffHeader, exported);
 
     /*
@@ -594,7 +623,7 @@ public class FeaturesFileTest
     fr.setGroupVisibility("Uniprot", true);
     fr.setGroupVisibility("s3dm", false);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            true);
+            true, false);
     String expected = gffHeader
             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
     assertEquals(expected, exported);
@@ -606,7 +635,7 @@ public class FeaturesFileTest
     fr.setVisible("METAL");
     fr.setVisible("GAMMA-TURN");
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, 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);
@@ -616,7 +645,7 @@ public class FeaturesFileTest
      */
     fr.setGroupVisibility("s3dm", true);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     // 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";
@@ -627,12 +656,12 @@ public class FeaturesFileTest
      */
     fr.setVisible("Pfam");
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     // Pfam feature columns include strand(+), phase(2), attributes
     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"
-            + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
+            + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n"
+            + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
     assertEquals(expected, exported);
   }
 
@@ -741,7 +770,7 @@ public class FeaturesFileTest
     fr.setVisible("METAL");
     fr.setColour("METAL", new FeatureColour(Color.PINK));
     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
-            fr, false);
+            fr, false, false);
     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";
@@ -750,13 +779,13 @@ public class FeaturesFileTest
     /*
      * 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);
     fr.setColour("METAL", fc);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
     assertEquals(expected, exported);
 
@@ -765,7 +794,7 @@ public class FeaturesFileTest
      */
     fc.setAboveThreshold(false);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, 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);
@@ -778,7 +807,7 @@ public class FeaturesFileTest
             "clin_sig"));
     fr.setFeatureFilter("METAL", filter);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
     assertEquals(expected, exported);
   }
@@ -814,7 +843,7 @@ public class FeaturesFileTest
     fr.setColour("METAL", new FeatureColour(Color.PINK));
     String exported = featuresFile.printJalviewFormat(
             al.getSequencesArray(),
-            fr, false);
+            fr, false, false);
     String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
@@ -826,13 +855,13 @@ public class FeaturesFileTest
      * 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);
     fr.setColour("METAL", fc);
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
             + "STARTGROUP\tgrp1\n"
             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
@@ -844,7 +873,7 @@ public class FeaturesFileTest
      */
     fc.setAboveThreshold(false);
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
             + "STARTGROUP\tgrp1\n"
             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
@@ -861,7 +890,7 @@ public class FeaturesFileTest
             "clin_sig"));
     fr.setFeatureFilter("METAL", filter);
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
             + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"