From c05b2da460c1e6ba38e2c0a0d3e8399e0b847d60 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 23 May 2017 14:50:28 +0100
Subject: [PATCH] JAL-2490 test coverage for printGffFormat before refactoring

---
 test/jalview/io/FeaturesFileTest.java |   82 +++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 70a5f16..6429e16 100644
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -39,6 +39,7 @@ import jalview.gui.JvOptionPane;
 import java.awt.Color;
 import java.io.File;
 import java.io.IOException;
+import java.util.HashMap;
 import java.util.Map;
 
 import org.testng.annotations.BeforeClass;
@@ -469,4 +470,85 @@ public class FeaturesFileTest
             + "ENDGROUP\tuniprot\n";
     assertEquals(expected, exported);
   }
+
+  @Test(groups = { "Functional" })
+  public void testPrintGffFormat() throws Exception
+  {
+    File f = new File("examples/uniref50.fa");
+    AlignmentI al = readAlignmentFile(f);
+    AlignFrame af = new AlignFrame(al, 500, 500);
+
+    /*
+     * no features
+     */
+    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);
+    String gffHeader = "##gff-version 2\n";
+    assertEquals(gffHeader, exported);
+    exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
+            true);
+    assertEquals(gffHeader, exported);
+
+    /*
+     * add some features
+     */
+    al.getSequenceAt(0).addSequenceFeature(
+            new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
+    al.getSequenceAt(0).addSequenceFeature(
+            new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
+    al.getSequenceAt(1)
+            .addSequenceFeature(
+                    new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
+                            "s3dm"));
+    SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f, "Uniprot");
+    sf.setAttributes("x=y;black=white");
+    sf.setStrand("+");
+    sf.setPhase("2");
+    al.getSequenceAt(1).addSequenceFeature(sf);
+
+    /*
+     * with no features displayed, exclude non-positional features
+     */
+    exported = featuresFile.printGffFormat(al.getSequencesArray(), visible,
+            false);
+    assertEquals(gffHeader, exported);
+  
+    /*
+     * include non-positional features
+     */
+    exported = featuresFile.printGffFormat(al.getSequencesArray(),
+            visible, 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
+     */
+    fr.setVisible("METAL");
+    fr.setVisible("GAMMA-TURN");
+    visible = fr.getDisplayedFeatureCols();
+    exported = featuresFile.printGffFormat(al.getSequencesArray(),
+            visible, 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);
+    // 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";
+    assertEquals(expected, exported);
+  }
 }
-- 
1.7.10.2