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Ensure deterministic order in toConciseAlignmentString #908

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Ensure deterministic order in toConciseAlignmentString #908

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43 changes: 32 additions & 11 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,37 @@
*/
package org.biojava.nbio.structure.align.util;

import org.biojava.nbio.structure.*;
import java.io.IOException;
import java.io.Writer;
import java.util.AbstractMap;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import javax.vecmath.Matrix4d;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.AtomImpl;
import org.biojava.nbio.structure.Calc;
import org.biojava.nbio.structure.Chain;
import org.biojava.nbio.structure.ChainImpl;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.ResidueNumber;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureImpl;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.AFPTwister;
import org.biojava.nbio.structure.align.ce.CECalculator;
import org.biojava.nbio.structure.align.fatcat.FatCatFlexible;
Expand All @@ -33,15 +63,6 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.IOException;
import java.io.Writer;
import java.util.*;
import java.util.Map.Entry;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import javax.vecmath.Matrix4d;

/**
* Methods for analyzing and manipulating AFPChains and for
* other pairwise alignment utilities. <p>
Expand Down Expand Up @@ -989,7 +1010,7 @@ public static Object resizeArray (Object oldArray, int newSize) {
*/
public static <S,T> String toConciseAlignmentString(Map<S,T> alignment, Map<T,S> identity) {
// Clone input to prevent changes
Map<S,T> alig = new HashMap<S,T>(alignment);
Map<S,T> alig = new TreeMap<S,T>(alignment);

// Generate inverse alignment
Map<S,List<S>> inverse = new HashMap<S,List<S>>();
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2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
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Original file line number Diff line number Diff line change
Expand Up @@ -293,7 +293,7 @@ private synchronized boolean addToZipFileSystem(Path zipFile, File[] files, Path
*/

// Copy in each file.
try (FileSystem zipfs = FileSystems.newFileSystem(zipFile, null)) {
try (FileSystem zipfs = FileSystems.newFileSystem(zipFile, (ClassLoader) null)) {
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This line fixes an error I was getting compiling with Java 1.8:

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.0:compile (default-compile) on project biojava-structure: Compilation failure
[ERROR] /Users/bliven_s/git/biojava_ws/biojava/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java:[296,52] reference to newFileSystem is ambiguous
[ERROR]   both method newFileSystem(java.nio.file.Path,java.lang.ClassLoader) in java.nio.file.FileSystems and method newFileSystem(java.nio.file.Path,java.util.Map<java.lang.String,?>) in java.nio.file.FileSystems match

The second form isn't documented, so it could be that this change will cause a warning with different JDKs.

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@sbliven
I did initially try to fix this error with the same change. However the TreeMap here, is not fixing this flaky error. The tool still marks it as flaky with error of the sort -

[ERROR] Failures: 
[ERROR]   AlignmentToolsTest.testToConciseAlignmentString:342 1. Cycles. expected:<[1>2>3>1] 7>7> but was:<[2>3>1>2] 7>7>
[INFO] 
[ERROR] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0

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@Vidishab18 Vidishab18 Dec 7, 2020 •
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@sbliven @josemduarte

Would like to link the Nondex tool here : https://github.com/TestingResearchIllinois/NonDex

The tool requires :

  • Adding the plugin as specified in the documentation which applies if you want to run NonDex mutliple times.

  • Run for the test -
    mvn -pl biojava-integrationtest nondex:nondex -Dtest=AlignmentToolsTest#testToConciseAlignmentString

  • Run for the whole module -
    mvn -pl biojava-integrationtest nondex:nondex.

  • Otherwise, one need not add the plugin to pom.xml file(s) and can run just run mvn edu.illinois:nondex-maven-plugin:1.1.2:nondex instead of mvn test. Please check that the command does work for you.

This could be added into travis.yml, so it can be run on new tests too.

It also has the debug feature that can be used to point to the file(s) that could require changes. The link to the tool has all the documentation.

Files.createDirectories(pathWithinArchive);
for (File f : files) {
if (!f.isDirectory() && f.exists()) {
Expand Down