git-svn-id: http://www.xerial.org/svn/project/XerialJ/trunk/xerial-core@3429 ae02f08e...

diff --git a/src/test/java/org/xerial/silk/FastaTest.java b/src/test/java/org/xerial/silk/FastaTest.java
new file mode 100644 (file)
index 0000000..7436460
--- /dev/null
+++ b/src/test/java/org/xerial/silk/FastaTest.java
@@ -0,0 +1,157 @@
+/*--------------------------------------------------------------------------\r
+ *  Copyright 2009 Taro L. Saito\r
+ *\r
+ *  Licensed under the Apache License, Version 2.0 (the "License");\r
+ *  you may not use this file except in compliance with the License.\r
+ *  You may obtain a copy of the License at\r
+ *\r
+ *     http://www.apache.org/licenses/LICENSE-2.0\r
+ *\r
+ *  Unless required by applicable law or agreed to in writing, software\r
+ *  distributed under the License is distributed on an "AS IS" BASIS,\r
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\r
+ *  See the License for the specific language governing permissions and\r
+ *  limitations under the License.\r
+ *--------------------------------------------------------------------------*/\r
+//--------------------------------------\r
+// XerialJ\r
+//\r
+// FastaTest.java\r
+// Since: Jul 3, 2009 7:11:49 PM\r
+//\r
+// $URL$\r
+// $Author$\r
+//--------------------------------------\r
+package org.xerial.silk;\r
+\r
+import java.lang.annotation.ElementType;\r
+import java.lang.annotation.Retention;\r
+import java.lang.annotation.RetentionPolicy;\r
+import java.lang.annotation.Target;\r
+import java.util.List;\r
+\r
+import org.junit.After;\r
+import org.junit.Before;\r
+import org.junit.Test;\r
+import org.xerial.lens.Lens;\r
+import org.xerial.lens.ObjectLens;\r
+import org.xerial.util.FileResource;\r
+import org.xerial.util.log.Logger;\r
+\r
+@Retention(RetentionPolicy.RUNTIME)\r
+@Target( { ElementType.TYPE, ElementType.METHOD })\r
+@interface EqJoin {\r
+\r
+    public String[] left();\r
+\r
+    public String[] right();\r
+\r
+    public Class< ? > leftClass();\r
+\r
+}\r
+\r
+public class FastaTest\r
+{\r
+    private static Logger _logger = Logger.getLogger(FastaTest.class);\r
+\r
+    @Before\r
+    public void setUp() throws Exception\r
+    {}\r
+\r
+    @After\r
+    public void tearDown() throws Exception\r
+    {}\r
+\r
+    public static class FastaQuery\r
+    {\r
+        FastaItem prev = null;\r
+\r
+        public void addGroup_Name(String group, FastaItem f)\r
+        {\r
+            _logger.info(String.format("group: %s, fasta: %s", group, ObjectLens.toJSON(f)));\r
+        }\r
+\r
+        public void addName(FastaItem f)\r
+        {\r
+            _logger.debug(ObjectLens.toJSON(f));\r
+\r
+            if (prev != null && prev.getSequence().contains("TTAGGG"))\r
+            {\r
+                // output both records\r
+            }\r
+\r
+            if (f.getSequence().contains("TTAGGG"))\r
+            {\r
+\r
+            }\r
+\r
+            prev = f;\r
+\r
+        }\r
+\r
+        public void flush()\r
+        {\r
+\r
+        }\r
+\r
+    }\r
+\r
+    public static class S1\r
+    {\r
+        public int id;\r
+        public String name;\r
+\r
+        public int getRid()\r
+        {\r
+            return id - 1;\r
+        }\r
+\r
+    }\r
+\r
+    public static class S2\r
+    {\r
+        public int rid;\r
+        public String info;\r
+    }\r
+\r
+    @EqJoin(left = "rid", leftClass = S1.class, right = "rid")\r
+    public static class S3\r
+    {\r
+        public S1 s1;\r
+\r
+        public List<S2> s2;\r
+\r
+    }\r
+\r
+    public static class FastaItem\r
+    {\r
+        public String value;\r
+        public String link;\r
+\r
+        private StringBuilder sequence = new StringBuilder();\r
+\r
+        public void appendSequence(String s)\r
+        {\r
+            sequence.append(s);\r
+        }\r
+\r
+        public String getSequence()\r
+        {\r
+            return sequence.toString();\r
+        }\r
+\r
+    }\r
+\r
+    @Test\r
+    public void testname() throws Exception\r
+    {\r
+        FastaQuery result = Lens.loadSilk(FastaQuery.class, FileResource.open(FastaTest.class, "fasta.silk"));\r
+        result.flush();\r
+\r
+        //ObjectStream<S3> sin = Lens.joinSilk(S3.class, "input1", "input2");\r
+\r
+        //ObjectStream<S4> out = Lens.joinSilk(S4.class, sin, "input3");\r
+\r
+    }\r
+\r
+}\r

diff --git a/src/test/java/org/xerial/silk/fasta.silk b/src/test/java/org/xerial/silk/fasta.silk
new file mode 100644 (file)
index 0000000..d0d756b
--- /dev/null
+++ b/src/test/java/org/xerial/silk/fasta.silk
@@ -0,0 +1,28 @@
+\r
+-group:A \r
+\r
+ -name:s1.b1\r
+  -sequence>\r
+ACCTTTTCTTAGGG\r
+ACCGGg\r
+\r
+\r
+ -name:s1.g1\r
+  -info\r
+   -link: http://werwwerw/\r
+   -sequence>\r
+AACCCCCCCCCTTTTTTTTT\r
+\r
+-group: B\r
+ -name:s2.b1\r
+  -info\r
+   -link: http://werwwerw/\r
+   -sequence>\r
+AACCCCCCCCCTTTTTTTTT\r
+\r
+\r
+\r
+\r
+\r
+\r
+\r