Move long tests to the intergationtest package

lafita · lafita · commit 167750e9ccdc · 2016-09-01T16:14:12.000+02:00
Long tests for Subunit clustering, quaternary symmetry detection and
quaternary structure alignment with some real structure examples have
been moved to the integrationtest module, so that they can be easily
skipped with a configuration option.
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/qsalign/TestQsAlignExamples.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/qsalign/TestQsAlignExamples.java
@@ -1,4 +1,4 @@
-package org.biojava.nbio.structure.align.quaternary;
+package org.biojava.nbio.structure.test.align.qsalign;
 
 import static org.junit.Assert.*;
 
@@ -7,6 +7,10 @@
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.align.quaternary.QsAlign;
+import org.biojava.nbio.structure.align.quaternary.QsAlignParameters;
+import org.biojava.nbio.structure.align.quaternary.QsAlignResult;
+import org.biojava.nbio.structure.align.quaternary.QsRelation;
 import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
 import org.junit.Test;
 
@@ -18,7 +22,7 @@
  * @since 5.0.0
  *
  */
-public class TestQsAlign {
+public class TestQsAlignExamples {
 
 	/**
 	 * Identity: test hemoglobin (4HHB) against itself.
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/cluster/TestSubunitClustererExamples.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/cluster/TestSubunitClustererExamples.java
@@ -18,7 +18,7 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.cluster;
+package org.biojava.nbio.structure.test.cluster;
 
 import static org.junit.Assert.*;
 
@@ -28,6 +28,10 @@
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.cluster.SubunitCluster;
+import org.biojava.nbio.structure.cluster.SubunitClusterer;
+import org.biojava.nbio.structure.cluster.SubunitClustererMethod;
+import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
 import org.junit.Test;
 
 /**
@@ -37,7 +41,7 @@
  * @author Aleix Lafita
  *
  */
-public class TestSubunitClusterer {
+public class TestSubunitClustererExamples {
 
 	/**
 	 * Test modified residues: 1HIV
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java
@@ -18,7 +18,7 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.test.symmetry;
 
 import static org.junit.Assert.*;
 
@@ -37,14 +37,14 @@
 import org.junit.Test;
 
 /**
- * Test the algorithm for symmetry detection on a variety of structures with
- * different symmetries.
+ * Test the {@link QuatSymmetryDetector} algorithm for symmetry detection on a
+ * variety of structures with different symmetries.
  * 
  * @author Peter Rose
  * @author Aleix Lafita
  *
  */
-public class TestQuatSymmetryDetector {
+public class TestQuatSymmetryDetectorExamples {
 
 	/**
 	 * An NMR multi-model entry: 1B4C
@@ -56,12 +56,12 @@ public class TestQuatSymmetryDetector {
 	public void testNMR() throws IOException, StructureException {
 
 		Structure pdb = StructureIO.getStructure("BIO:1b4c:1");
-		
+
 		SubunitClustererParameters clusterParams = new SubunitClustererParameters();
 		QuatSymmetryParameters symmParams = new QuatSymmetryParameters();
 		QuatSymmetryResults symmetry = QuatSymmetryDetector.calcGlobalSymmetry(
 				pdb, symmParams, clusterParams);
-		
+
 		// C2 symmetry non pseudosymmetric
 		assertEquals("C2", symmetry.getSymmetry());
 		assertEquals("A2", symmetry.getStoichiometry());
