Merge branch 'feature/JAL-3121gffAttributeMap' into develop

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

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 090de6f..298ae6b 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -268,10 +268,12 @@ public class FeaturesFileTest
     AlignFrame af = new AlignFrame(al, 500, 500);
     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
             .getFeatureColours();
-    // GFF3 uses '=' separator for name/value pairs in colum 9
+    // GFF3 uses '=' separator for name/value pairs in column 9
+    // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in values
     String gffData = "##gff-version 3\n"
             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
-            + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
+            + "Note=Iron-sulfur (2Fe-2S);Note=another note,and another;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465;"
+            + "CSQ=AF=21,POLYPHEN=benign,possibly_damaging,clin_sig=Benign%3Dgood\n"
             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
     FeaturesFile featuresFile = new FeaturesFile(gffData,
             DataSourceType.PASTE);
@@ -284,14 +286,25 @@ public class FeaturesFileTest
     assertEquals(1, sfs.size());
     SequenceFeature sf = sfs.get(0);
     // description parsed from Note attribute
-    assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
+    assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
+            sf.description);
     assertEquals(39, sf.begin);
     assertEquals(39, sf.end);
     assertEquals("uniprot", sf.featureGroup);
     assertEquals("METAL", sf.type);
-    assertEquals(
-            "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
-            sf.getValue("ATTRIBUTES"));
+    assertEquals(5, sf.otherDetails.size());
+    assertEquals("ECO;0000255,PROSITE=ProRule:PRU00465", // url decoded
+            sf.getValue("evidence"));
+    assertEquals("Iron-sulfur (2Fe-2S),another note,and another",
+            sf.getValue("Note"));
+    assertEquals("21", sf.getValueAsString("CSQ", "AF"));
+    assertEquals("benign,possibly_damaging",
+            sf.getValueAsString("CSQ", "POLYPHEN"));
+    assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url decoded
+    // todo change STRAND and !Phase into fields of SequenceFeature instead
+    assertEquals(".", sf.otherDetails.get("STRAND"));
+    assertEquals(0, sf.getStrand());
+    assertEquals(".", sf.getPhase());
 
     // verify feature on FER1_SOLLC1
     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
@@ -593,9 +606,14 @@ public class FeaturesFileTest
                             "s3dm"));
     SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
             "Uniprot");
-    sf.setAttributes("x=y;black=white");
     sf.setStrand("+");
     sf.setPhase("2");
+    sf.setValue("x", "y");
+    sf.setValue("black", "white");
+    Map<String, String> csq = new HashMap<>();
+    csq.put("SIFT", "benign,mostly benign,cloudy, with meatballs");
+    csq.put("consequence", "missense_variant");
+    sf.setValue("CSQ", csq);
     al.getSequenceAt(1).addSequenceFeature(sf);
 
     /*
@@ -660,7 +678,11 @@ public class FeaturesFileTest
     // Pfam feature columns include strand(+), phase(2), attributes
     expected = gffHeader
             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
-            + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n"
+            // CSQ output as CSQ=att1=value1,att2=value2
+            // note all commas are encoded here which is wrong - it should be
+            // SIFT=benign,mostly benign,cloudy%2C with meatballs
+            + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white;"
+            + "CSQ=SIFT=benign%2Cmostly benign%2Ccloudy%2C with meatballs,consequence=missense_variant\n"
             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
     assertEquals(expected, exported);
   }
@@ -772,8 +794,8 @@ public class FeaturesFileTest
     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
             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";
+            + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
+            + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
     assertEquals(expected, exported);
 
     /*
@@ -786,7 +808,8 @@ public class FeaturesFileTest
     fr.setColour("METAL", fc);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
             false, false);
-    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.\tclin_sig=Likely Pathogenic;AF=24\n";
     assertEquals(expected, exported);
 
     /*
@@ -795,8 +818,9 @@ public class FeaturesFileTest
     fc.setAboveThreshold(false);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
             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";
+    expected = gffHeader
+            + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\tclin_sig=Likely Pathogenic;AF=24\n"
+            + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
     assertEquals(expected, exported);
 
     /*
@@ -808,7 +832,8 @@ public class FeaturesFileTest
     fr.setFeatureFilter("METAL", filter);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
             false, false);
-    expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+    expected = gffHeader
+            + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\tclin_sig=Benign;AF=46\n";
     assertEquals(expected, exported);
   }