From 1fe5059a32d32ef7f47b015bc5b71d58bc02bfc9 Mon Sep 17 00:00:00 2001
From: Spencer Bliven <spencer.bliven@gmail.com>
Date: Mon, 7 Dec 2020 16:39:14 +0100
Subject: [PATCH] Ensure deterministic order in toConciseAlignmentString

Fixes #907
---
 .../structure/align/util/AlignmentTools.java  | 43 ++++++++++++++-----
 .../io/mmcif/ZipChemCompProvider.java         |  2 +-
 2 files changed, 33 insertions(+), 12 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
index f7660e2097..b35e80f941 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -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;
@@ -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>
@@ -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>>();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
index 9475a6d036..c6d14699d2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
@@ -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)) {
 			Files.createDirectories(pathWithinArchive);
 			for (File f : files) {
 				if (!f.isDirectory() && f.exists()) {