X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FBSMLFileTest.java;fp=test%2Fjalview%2Fio%2FBSMLFileTest.java;h=30526581d9f27fb2a9d4d35f54ed69ad76fb75e4;hb=586ade46bdcd05ff028a1cff82c3c527326d28ec;hp=0000000000000000000000000000000000000000;hpb=adcef27f5747b4e70e89a56c3735bc3afb8ce9bf;p=jalview.git
diff --git a/test/jalview/io/BSMLFileTest.java b/test/jalview/io/BSMLFileTest.java
new file mode 100644
index 0000000..3052658
--- /dev/null
+++ b/test/jalview/io/BSMLFileTest.java
@@ -0,0 +1,68 @@
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
+
+import java.io.IOException;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class BSMLFileTest
+{
+ @Test(groups="Functional")
+ public void testParse_BSML() throws IOException
+ {
+ //@formatter:off
+ String data = "\r\n" +
+ "\r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " --AATTTT-ATTTAGTGTCT-----------\r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ " \r\n" +
+ "\r\n" +
+ "";
+ BSMLFile cf = new BSMLFile(data, DataSourceType.PASTE);
+// why twice? cf.parse();
+ SequenceI[] seqs = cf.getSeqsAsArray();
+ assertEquals(seqs.length, 1);
+ SequenceI seq = seqs[0];
+ assertEquals(seq.getName(), "EP1");
+ assertEquals(seq.getStart(), 1);
+ assertEquals(seq.getEnd(), 31);
+ assertTrue(seq.getSequenceAsString().equals("--AATTTT-ATTTAGTGTCT-----------"));
+ SequenceFeaturesI features = seq.getFeatures();
+ List genes = features.getAllFeatures("GENE");
+ assertEquals(genes.size(), 1);
+ SequenceFeature sf = genes.get(0);
+ assertEquals(sf.getDescription(), "TEST-001");
+ assertEquals(sf.begin + "," + sf.end, "10,20");
+
+ }
+
+}