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JAL-2490 test coverage of empty and null feature group in Jalview format
[jalview.git] / test / jalview / io / FeaturesFileTest.java
diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 6429e16..b88c2ee 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -39,7 +39,10 @@ import jalview.gui.JvOptionPane;
 import java.awt.Color;
 import java.io.File;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 import org.testng.annotations.BeforeClass;
@@ -417,21 +420,42 @@ public class FeaturesFileTest
     featuresFile.parse(al.getDataset(), colours, false);
 
     /*
+     * add positional and non-positional features with null and
+     * empty feature group to check handled correctly
+     */
+    SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
+    seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
+            null));
+    seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
+            Float.NaN, null));
+    seq = al.getSequenceAt(2); // FER1_SOLLC
+    seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
+            Float.NaN, ""));
+    seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
+            -2.6f, ""));
+
+    /*
      * first with no features displayed, exclude non-positional features
      */
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
     Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
+    List<String> visibleGroups = new ArrayList<String>(
+            Arrays.asList(new String[] {}));
     String exported = featuresFile.printJalviewFormat(
-            al.getSequencesArray(), visible, false);
+            al.getSequencesArray(), visible, visibleGroups, false);
     String expected = "No Features Visible";
     assertEquals(expected, exported);
 
     /*
      * include non-positional features
      */
+    visibleGroups.add("uniprot");
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
-            visible, true);
-    expected = "\nSTARTGROUP\tuniprot\nCath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\nENDGROUP\tuniprot\n";
+            visible, visibleGroups, true);
+    expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
+            + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
+            + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" // NaN is not output
+            + "\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n";
     assertEquals(expected, exported);
 
     /*
@@ -441,7 +465,7 @@ public class FeaturesFileTest
     fr.setVisible("GAMMA-TURN");
     visible = fr.getDisplayedFeatureCols();
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
-            visible, false);
+            visible, visibleGroups, false);
     expected = "METAL\tcc9900\n"
             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
             + "\nSTARTGROUP\tuniprot\n"
@@ -456,7 +480,7 @@ public class FeaturesFileTest
     fr.setVisible("Pfam");
     visible = fr.getDisplayedFeatureCols();
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
-            visible, false);
+            visible, visibleGroups, false);
     /*
      * features are output within group, ordered by sequence and by type
      */
@@ -467,7 +491,11 @@ 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"
             + "<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";
+            + "ENDGROUP\tuniprot\n"
+            // null / empty group features output after features in named
+            // groups:
+            + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
+            + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
     assertEquals(expected, exported);
   }
 
@@ -484,12 +512,14 @@ public class FeaturesFileTest
     FeaturesFile featuresFile = new FeaturesFile();
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
     Map<String, FeatureColourI> visible = new HashMap<String, FeatureColourI>();
-    String exported = featuresFile.printGffFormat(
-            al.getSequencesArray(), visible, false);
+    List<String> visibleGroups = new ArrayList<String>(
+            Arrays.asList(new String[] {}));
+    String exported = featuresFile.printGffFormat(al.getSequencesArray(),
+            visible, visibleGroups, false);
     String gffHeader = "##gff-version 2\n";
     assertEquals(gffHeader, exported);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
-            true);
+            visibleGroups, true);
     assertEquals(gffHeader, exported);
 
     /*
@@ -503,7 +533,8 @@ public class FeaturesFileTest
             .addSequenceFeature(
                     new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
                             "s3dm"));
-    SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f, "Uniprot");
+    SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
+            "Uniprot");
     sf.setAttributes("x=y;black=white");
     sf.setStrand("+");
     sf.setPhase("2");
@@ -513,40 +544,53 @@ public class FeaturesFileTest
      * with no features displayed, exclude non-positional features
      */
     exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
-            false);
+            visibleGroups, false);
     assertEquals(gffHeader, exported);
-  
+
     /*
      * include non-positional features
      */
-    exported = featuresFile.printGffFormat(al.getSequencesArray(),
-            visible, true);
+    visibleGroups.add("Uniprot");
+    exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
+            visibleGroups, true);
     String expected = gffHeader
             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
     assertEquals(expected, exported);
-  
+
     /*
      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
+     * only Uniprot group visible here...
      */
     fr.setVisible("METAL");
     fr.setVisible("GAMMA-TURN");
     visible = fr.getDisplayedFeatureCols();
-    exported = featuresFile.printGffFormat(al.getSequencesArray(),
-            visible, false);
+    exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
+            visibleGroups, 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);
+
+    /*
+     * set s3dm group visible
+     */
+    visibleGroups.add("s3dm");
+    exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
+            visibleGroups, 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";
     assertEquals(expected, exported);
-  
+
     /*
      * now set Pfam visible
      */
     fr.setVisible("Pfam");
     visible = fr.getDisplayedFeatureCols();
-    exported = featuresFile.printGffFormat(al.getSequencesArray(),
-            visible, false);
+    exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
+            visibleGroups, false);
     // Pfam feature columns include strand(+), phase(2), attributes
-    expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+    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";
     assertEquals(expected, exported);