From ed5766b09cf7eeb2d124b17685ba607c7daf3594 Mon Sep 17 00:00:00 2001
From: Nees Jan van Eck <36573334+neesjanvaneck@users.noreply.github.com>
Date: Mon, 21 Aug 2023 10:12:12 +0200
Subject: [PATCH] Bump networkanalysis from 1.2.0 to 1.3.0

---
 build.gradle                                  |  2 +-
 .../run/DatabaseIO.java                       | 24 +++++++++++--------
 .../publicationclassification/run/FileIO.java | 23 +++++++++---------
 3 files changed, 27 insertions(+), 22 deletions(-)

diff --git a/build.gradle b/build.gradle
index 2f35cca..ec4753c 100644
--- a/build.gradle
+++ b/build.gradle
@@ -14,8 +14,8 @@ repositories {
 }
 
 dependencies {
+	implementation group: 'nl.cwts', name: 'networkanalysis', version: '1.3.0'
 	implementation group: 'com.microsoft.sqlserver', name: 'mssql-jdbc', version: '12.2.0.jre8'
-    implementation group: 'nl.cwts', name: 'networkanalysis', version: '1.2.0'
 }
 
 java {
diff --git a/src/main/java/nl/cwts/publicationclassification/run/DatabaseIO.java b/src/main/java/nl/cwts/publicationclassification/run/DatabaseIO.java
index 0291cc2..9a8cbd1 100644
--- a/src/main/java/nl/cwts/publicationclassification/run/DatabaseIO.java
+++ b/src/main/java/nl/cwts/publicationclassification/run/DatabaseIO.java
@@ -8,6 +8,8 @@
 import java.sql.Statement;
 
 import nl.cwts.networkanalysis.Network;
+import nl.cwts.util.LargeDoubleArray;
+import nl.cwts.util.LargeIntArray;
 
 public class DatabaseIO
 {
@@ -25,8 +27,8 @@ public class DatabaseIO
     public static Network readNetwork(String server, String database, String pubTable, String citLinkTable)
     {
         double[] pubWeight = null;
-        int[][] citLink = null;
-        double[] citLinkWeight = null;
+        LargeIntArray[] citLink = null;
+        LargeDoubleArray citLinkWeight = null;
 
         Connection connection = null;
         try
@@ -57,23 +59,25 @@ public static Network readNetwork(String server, String database, String pubTabl
 
             // Read number of citation links.
             statement = connection.createStatement();
-            resultSet = statement.executeQuery("select count(*) from " + citLinkTable);
+            resultSet = statement.executeQuery("select count_big(*) from " + citLinkTable);
             resultSet.next();
-            int nCitLinks = resultSet.getInt(1);
+            long nCitLinks = resultSet.getLong(1);
             statement.close();
 
-            citLink = new int[2][nCitLinks];
-            citLinkWeight = new double[nCitLinks];
+            citLink = new LargeIntArray[2];
+            citLink[0] = new LargeIntArray(nCitLinks);
+            citLink[1] = new LargeIntArray(nCitLinks);
+            citLinkWeight = new LargeDoubleArray(nCitLinks);
 
             // Read citation links.
             statement = connection.createStatement();
             resultSet = statement.executeQuery("select pub_no1, pub_no2, cit_weight from " + citLinkTable + " order by pub_no1, pub_no2");
-            for (int i = 0; i < nCitLinks; i++)
+            for (long i = 0; i < nCitLinks; i++)
             {
                 resultSet.next();
-                citLink[0][i] = resultSet.getInt(1);
-                citLink[1][i] = resultSet.getInt(2);
-                citLinkWeight[i] = resultSet.getDouble(3);
+                citLink[0].set(i, resultSet.getInt(1));
+                citLink[1].set(i, resultSet.getInt(2));
+                citLinkWeight.set(i, resultSet.getDouble(3));
             }
             statement.close();
 
diff --git a/src/main/java/nl/cwts/publicationclassification/run/FileIO.java b/src/main/java/nl/cwts/publicationclassification/run/FileIO.java
index 28209a3..3c3c440 100644
--- a/src/main/java/nl/cwts/publicationclassification/run/FileIO.java
+++ b/src/main/java/nl/cwts/publicationclassification/run/FileIO.java
@@ -8,8 +8,8 @@
 import java.io.IOException;
 
 import nl.cwts.networkanalysis.Network;
-import nl.cwts.util.DynamicDoubleArray;
-import nl.cwts.util.DynamicIntArray;
+import nl.cwts.util.LargeDoubleArray;
+import nl.cwts.util.LargeIntArray;
 
 public class FileIO
 {
@@ -29,11 +29,15 @@ public class FileIO
      */
     public static Network readNetwork(String pubFile, String citLinkFile)
     {
-        DynamicDoubleArray pubWeight = new DynamicDoubleArray(100);
-        DynamicIntArray[] citLink = new DynamicIntArray[2];
-        citLink[0] = new DynamicIntArray(100);
-        citLink[1] = new DynamicIntArray(100);
-        DynamicDoubleArray citLinkWeight = new DynamicDoubleArray(100);
+        LargeDoubleArray pubWeight = new LargeDoubleArray(0);
+        pubWeight.ensureCapacity(100);
+        LargeIntArray[] citLink = new LargeIntArray[2];
+        citLink[0] = new LargeIntArray(0);
+        citLink[0].ensureCapacity(100);
+        citLink[1] = new LargeIntArray(0);
+        citLink[1].ensureCapacity(100);
+        LargeDoubleArray citLinkWeight = new LargeDoubleArray(0);
+        citLinkWeight.ensureCapacity(100);
 
         BufferedReader reader = null;
         // Read publications file.
@@ -153,12 +157,9 @@ public static Network readNetwork(String pubFile, String citLinkFile)
 
         // Create citation network.
         Network citNetwork = null;
-        int[][] citLink2 = new int[2][];
-        citLink2[0] = citLink[0].toArray();
-        citLink2[1] = citLink[1].toArray();
         try
         {
-            citNetwork = new Network(pubWeight.toArray(), citLink2, citLinkWeight.toArray(), true, true);
+            citNetwork = new Network(pubWeight.toArray(), citLink, citLinkWeight, true, true);
         }
         catch (IllegalArgumentException e)
         {