JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/test/jalview/io/IdentifyFileTest.java b/test/jalview/io/IdentifyFileTest.java
index 85410d1..c00cf06 100644 (file)
--- a/test/jalview/io/IdentifyFileTest.java
+++ b/test/jalview/io/IdentifyFileTest.java
@@ -1,5 +1,29 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -8,15 +32,47 @@ public class IdentifyFileTest
 {
 
   @Test(groups = { "Functional" }, dataProvider = "identifyFiles")
-  public void Identify(String data, String expectedFileType)
+  public void testIdentify(String data, String expectedFileType)
   {
     String protocol = AppletFormatAdapter.FILE;
     IdentifyFile ider = new IdentifyFile();
-    String actualFiletype = ider.Identify(data, protocol);
+    String actualFiletype = ider.identify(data, protocol);
     Assert.assertEquals(actualFiletype, expectedFileType,
             "File identification Failed!");
   }
 
+  /**
+   * Additional tests for Jalview features file
+   */
+  @Test(groups = "Functional")
+  public void testIdentify_featureFile()
+  {
+    IdentifyFile ider = new IdentifyFile();
+
+    /*
+     * Jalview format with features only, no feature colours
+     */
+    String data = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+            + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
+    assertEquals(IdentifyFile.FeaturesFile,
+            ider.identify(data, AppletFormatAdapter.PASTE));
+
+    /*
+     * Jalview feature colour followed by GFF format feature data
+     */
+    data = "METAL\tcc9900\n" + "GFF\n"
+            + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n";
+    assertEquals(IdentifyFile.FeaturesFile,
+            ider.identify(data, AppletFormatAdapter.PASTE));
+
+    /*
+     * Feature with '<' in the name (JAL-2098)
+     */
+    data = "kD < 3\tred\n" + "Low kD\tFER_CAPAA\t-1\t39\t39\tkD < 3\n";
+    assertEquals(IdentifyFile.FeaturesFile,
+            ider.identify(data, AppletFormatAdapter.PASTE));
+  }
+
   @DataProvider(name = "identifyFiles")
   public Object[][] IdentifyFileDP()
   {
@@ -34,8 +90,10 @@ public class IdentifyFileTest
         { "examples/testdata/test.html", "HTML" },
         { "examples/testdata/test.pileup", "PileUp" },
         { "examples/testdata/test.blc", "BLC" },
-        { "examples/testdata/simplegff3.gff", "GFF v2 or v3" },
+        { "examples/exampleFeatures.txt", IdentifyFile.FeaturesFile },
+        { "examples/testdata/simpleGff3.gff", IdentifyFile.FeaturesFile },
         { "examples/testdata/test.jvp", "Jalview" },
+        { "examples/testdata/test.cif", "mmCIF" },
         {
             "examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
             "FASTA" },
@@ -45,4 +103,22 @@ public class IdentifyFileTest
     };
   }
 
+  @Test(groups = "Functional")
+  public void testLooksLikeFeatureData()
+  {
+    IdentifyFile id = new IdentifyFile();
+    assertFalse(id.looksLikeFeatureData(null));
+    assertFalse(id.looksLikeFeatureData(""));
+    // too few columns:
+    assertFalse(id.looksLikeFeatureData("1 \t 2 \t 3 \t 4 \t 5"));
+    // GFF format:
+    assertTrue(id
+            .looksLikeFeatureData("Seq1\tlocal\tHelix\t2456\t2462\tss"));
+    // Jalview format:
+    assertTrue(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t2462\tss"));
+    // non-numeric start column:
+    assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t.\t2462\tss"));
+    // non-numeric start column:
+    assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t.\tss"));
+  }
 }