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sblivensbliven
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Adding sortBlocks method
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2 files changed

+171
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‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java‎

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@@ -2,6 +2,8 @@
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.List;
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import java.util.SortedSet;
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import java.util.TreeSet;
@@ -670,4 +672,36 @@ public static List<Integer> getCorePositions(Block block){
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}
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return corePositions;
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}
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/**
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* Sort blocks so that the specified row is in sequential order.
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* The sort happens in place.
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* @param blocks List of blocks
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* @param sortedIndex Index of the row to be sorted
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*/
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public static void sortBlocks(List<Block> blocks,final int sortedIndex) {
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Collections.sort(blocks, new Comparator<Block>() {
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@Override
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public int compare(Block o1, Block o2) {
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// Compare the first non-null residue of each block
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List<Integer> alignres1 = o1.getAlignRes().get(sortedIndex);
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List<Integer> alignres2 = o2.getAlignRes().get(sortedIndex);
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Integer res1 = null;
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Integer res2 = null;
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for(Integer r : alignres1) {
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if( r != null) {
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res1 = r;
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break;
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}
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}
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for(Integer r : alignres2) {
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if( r != null) {
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res2 = r;
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break;
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}
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}
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return res1.compareTo(res2);
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}
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});
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}
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}

‎biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentToolsTest.java‎

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package org.biojava.nbio.structure.align.multiple.util;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.fail;
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import java.util.Arrays;
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import java.util.List;
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import org.biojava.nbio.structure.align.multiple.Block;
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import org.biojava.nbio.structure.align.multiple.BlockImpl;
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import org.biojava.nbio.structure.align.multiple.BlockSet;
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import org.biojava.nbio.structure.align.multiple.BlockSetImpl;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl;
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import org.junit.Test;
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/**
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*
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* @author Spencer Bliven
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*
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*/
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public class MultipleAlignmentToolsTest {
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/**
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* Override the toString method to give shorter output for errors
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* @author blivens
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*
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*/
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public static class NamedBlock extends BlockImpl {
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private static final long serialVersionUID = 5060618718423340848L;
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private String name;
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public NamedBlock(String name, BlockSet bs) {
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super(bs);
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this.name = name;
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}
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@Override
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public String toString() {
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return String.format("Block[%s]", name);
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}
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}
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@SuppressWarnings("unchecked")
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@Test
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public void testSortBlocks() {
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// Sample alignment with blocks out of order
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// Row0: Already sorted
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// Row1: Unsorted
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// Row2: Test nulls at start
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// Row3: Test all nulls
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// Row4: Test overlapping ranges
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// Row5: Test only fist element used
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MultipleAlignment align = new MultipleAlignmentImpl();
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BlockSet bs = new BlockSetImpl(align);
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Block one = new NamedBlock("1",bs);
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one.setAlignRes(Arrays.asList(
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Arrays.asList( 10, 11, 12),
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Arrays.asList( 20, 21, 22),
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Arrays.asList( null, 21, 22),
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Arrays.asList( 20, 21, 22),
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Arrays.asList( 20, 21, 22),
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Arrays.asList( 20, 21, 22)
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));
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Block two = new NamedBlock("2",bs);
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two.setAlignRes(Arrays.asList(
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Arrays.asList( 20, 21, 22),
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Arrays.asList( 10, 11, 12),
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Arrays.asList( 10, null, 12),
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Arrays.asList( (Integer)null,null,null),
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Arrays.asList( 10, 11, 12),
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Arrays.asList( 10, 11, 12)
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));
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Block three = new NamedBlock("3",bs);
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three.setAlignRes(Arrays.asList(
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Arrays.asList( 30, 31, 32),
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Arrays.asList( 40, 41, 42),
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Arrays.asList( 40, 41, null),
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Arrays.asList( 40, 41, 42),
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Arrays.asList( 40, 41, 42),
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Arrays.asList( 20, 41, 42)
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));
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Block four = new NamedBlock("4",bs);
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four.setAlignRes(Arrays.asList(
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Arrays.asList( 40, 41, 42),
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Arrays.asList( 30, 31, 32),
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Arrays.asList( null, 31, 32),
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Arrays.asList( (Integer)null,null,null),
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Arrays.asList( 30, 51, 52),
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Arrays.asList( 30, 31, 32)
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));
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List<Block> blocks;
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int index;
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List<Block> expected;
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index = 0;
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blocks = align.getBlocks();
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MultipleAlignmentTools.sortBlocks(blocks, index);
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expected = Arrays.asList(one,two,three,four);
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assertEquals("Bad comparison of row "+index, expected,blocks);
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index = 1;
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blocks = align.getBlocks();
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MultipleAlignmentTools.sortBlocks(blocks, index);
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expected = Arrays.asList(two,one,four,three);
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assertEquals("Bad comparison of row "+index, expected,blocks);
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index = 2;
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blocks = align.getBlocks();
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MultipleAlignmentTools.sortBlocks(blocks, index);
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expected = Arrays.asList(two,one,four,three);
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assertEquals("Bad comparison of row "+index, expected,blocks);
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index = 3;
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blocks = align.getBlocks();
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try {
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MultipleAlignmentTools.sortBlocks(blocks, index);
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fail("Row "+index+" should throw NPE");
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} catch(NullPointerException e) {}
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index = 4;
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blocks = align.getBlocks();
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MultipleAlignmentTools.sortBlocks(blocks, index);
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expected = Arrays.asList(two,one,four,three);
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assertEquals("Bad comparison of row "+index, expected,blocks);
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index = 5;
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blocks = align.getBlocks();
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MultipleAlignmentTools.sortBlocks(blocks, index);
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expected = Arrays.asList(two,one,three,four);
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assertEquals("Bad comparison of row "+index, expected,blocks);
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}
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}

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