Rename and move Tests for consistency

lafita · lafita · commit d8c5d2fe6025 · 2015-07-23T18:13:30.000+02:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
@@ -28,6 +28,7 @@
  * <li>Transform the aligned Atoms of a MultipleAlignment
  * <li>Get all the core alignment positions of the alignment
  * <li>Calculate the average residue distance of all aligned positions
+ * <li>Sort Blocks in a MultipleAlignment by a specified row
  * </ul>
  * 
  * @author Spencer Bliven
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentScorer.java
@@ -1,4 +1,4 @@
-package org.biojava.nbio.structure.align.multiple;
+package org.biojava.nbio.structure.align.multiple.util;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -14,6 +14,12 @@
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.ResidueNumber;
 import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.align.multiple.Block;
+import org.biojava.nbio.structure.align.multiple.BlockImpl;
+import org.biojava.nbio.structure.align.multiple.BlockSet;
+import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
 import org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer;
 import org.junit.Test;
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentTools.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentTools.java
@@ -19,7 +19,7 @@
  * @author Spencer Bliven
  *
  */
-public class MultipleAlignmentToolsTest {
+public class TestMultipleAlignmentTools {
 
 	/**
 	 * Override the toString method to give shorter output for errors
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java
@@ -1,10 +1,13 @@
-package org.biojava.nbio.structure.align.multiple;
+package org.biojava.nbio.structure.align.multiple.util;
 
 import java.io.BufferedReader;
 import java.io.FileReader;
 import java.io.IOException;
 
 import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
+import org.biojava.nbio.structure.align.multiple.TestSampleGenerator;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
 import org.junit.Test;
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentXMLParser.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentXMLParser.java
@@ -1,4 +1,4 @@
-package org.biojava.nbio.structure.align.multiple;
+package org.biojava.nbio.structure.align.multiple.util;
 
 import static org.junit.Assert.*;
 
@@ -9,6 +9,11 @@
 import javax.xml.parsers.ParserConfigurationException;
 
 import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.align.multiple.Block;
+import org.biojava.nbio.structure.align.multiple.BlockSet;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
+import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsemble;
+import org.biojava.nbio.structure.align.multiple.TestSampleGenerator;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
 import org.biojava.nbio.structure.align.xml.MultipleAlignmentXMLParser;
 import org.junit.Test;

Original file line number	Diff line number	Diff line change
`@@ -28,6 +28,7 @@`
`28`	`28`	`* <li>Transform the aligned Atoms of a MultipleAlignment`
`29`	`29`	`* <li>Get all the core alignment positions of the alignment`
`30`	`30`	`* <li>Calculate the average residue distance of all aligned positions`
	`31`	`+ * <li>Sort Blocks in a MultipleAlignment by a specified row`
`31`	`32`	`* </ul>`
`32`	`33`	`*`
`33`	`34`	`* @author Spencer Bliven`
Original file line number	Diff line number	Diff line change
`@@ -19,7 +19,7 @@`
`19`	`19`	`* @author Spencer Bliven`
`20`	`20`	`*`
`21`	`21`	`*/`
`22`		`-public class MultipleAlignmentToolsTest {`
	`22`	`+public class TestMultipleAlignmentTools {`
`23`	`23`
`24`	`24`	`/**`
`25`	`25`	`* Override the toString method to give shorter output for errors`