made HashMap into a LinkedHashMap to preserve order on graphs with graph invarient collisions

Author: tylerperyea

.gitignore

@@ -8,3 +8,5 @@
 #*.jar
 *.war
 *.ear
+/binaries/
+/target/

pom.xml

@@ -7,7 +7,7 @@
   <groupId>gov.nih.ncats</groupId>
   <artifactId>lychi</artifactId>
   <packaging>jar</packaging>
-  <version>0.5.0</version>
+  <version>0.5.1</version>
   <name>Lychi</name>
 
   <repositories>
@@ -42,11 +42,6 @@
         <artifactId>jchem</artifactId>
         <version>3.0.0</version>
     </dependency>
-    <dependency>
-        <groupId>junit</groupId>
-        <artifactId>junit</artifactId>
-        <version>4.12</version>
-    </dependency>
 </dependencies>
 
   <build>
@@ -78,45 +73,21 @@
    <configuration>
                <archive>
                   <manifest>
-                     <mainClass>tripod.molvec.ui.Viewer</mainClass>
+                     <mainClass>lychi.LyChIStandardizer</mainClass>
                   </manifest>
                </archive>
                <descriptorRefs>
                   <descriptorRef>jar-with-dependencies</descriptorRef>
                </descriptorRefs>
             </configuration>
   </plugin>
-  <!-- 
-  <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-assembly-plugin</artifactId>
-        <executions>
-          <execution>
-            <id>create-distribution</id>
-            <phase>package</phase>
-            <goals>
-              <goal>single</goal>
-            </goals>
-            <configuration>
-              <finalName>GSRSPull-${project.version}</finalName>
-              <appendAssemblyId>false</appendAssemblyId>
-              <descriptors>
-                <descriptor>assembly/sample.xml</descriptor>
-              </descriptors>
-            </configuration>
-          </execution>
-        </executions>
-      </plugin>
-      -->
     </plugins>
     <resources>
         <resource>
             <directory>src/main/java</directory>
             <includes>
-                <include>**/*.html</include>
-				<include>**/*.js</include>
-				<include>**/*.css</include>
-				<include>**/*.png</include>
+                <include>**/*.smi</include>
+  	        <include>**/*.smirks</include>
             </includes>
         </resource>
     </resources>

src/main/java/lychi/LyChIStandardizer.java

@@ -1,24 +1,36 @@
 package lychi;
 
-import java.io.*;
-import java.util.*;
-import java.util.logging.Logger;
-import java.util.logging.Level;
-import java.util.concurrent.ConcurrentHashMap;
-import java.util.concurrent.locks.ReentrantLock;
+import java.io.BufferedReader;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.PrintStream;
 import java.security.MessageDigest;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Comparator;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 
 import chemaxon.formats.MolImporter;
-import chemaxon.formats.MolFormatException;
+import chemaxon.struc.DPoint3;
 import chemaxon.struc.MolAtom;
 import chemaxon.struc.MolBond;
 import chemaxon.struc.Molecule;
-import chemaxon.struc.MoleculeGraph;
 import chemaxon.struc.RgMolecule;
 import chemaxon.util.MolHandler;
-import chemaxon.struc.DPoint3;
-import lychi.tautomers.*;
-import lychi.util.*;
+import lychi.tautomers.SayleDelanyTautomerGenerator;
+import lychi.util.Base32;
+import lychi.util.ChemUtil;
 
 /**
  * A new version of CanonicalForm but without using Reactor class;
@@ -918,8 +930,8 @@ public static void preprocessing (final Molecule m) {
         int[] rank = new int[m.getAtomCount()];
         m.getGrinv(rank);
 
-        Map<MolAtom, Integer> chirality = new HashMap<MolAtom, Integer>();
-        Map<MolAtom, MolBond[]> saturated = new HashMap<MolAtom, MolBond[]>();
+        Map<MolAtom, Integer> chirality = new LinkedHashMap<MolAtom, Integer>();
+        Map<MolAtom, MolBond[]> saturated = new LinkedHashMap<MolAtom, MolBond[]>();
         for (int i = 0; i < m.getAtomCount(); ++i) {
             int chiral = m.getChirality(i);
             MolAtom a = m.getAtom(i);
@@ -2864,7 +2876,6 @@ else if (tag == null) {
 
                 int dim = mol.getDim();
                 msz.standardize(mol);
-                
                 String smi = ChemUtil.canonicalSMILES (mol, true);
                 if (!format.startsWith("smi")) {
                     mol.setProperty("LyChI_SMILES", smi);
@@ -2910,7 +2921,9 @@ else if (tag == null) {
     }
 
     public static void main(String[] argv) throws Exception {
+    
         String tag = null;
+        
         List<String> input = new ArrayList<String>();
         for (int i = 0; i < argv.length; ++i) {
             if (argv[i].startsWith("tag=")) {