Use american english for method names

cBioPortal · Jul 12, 2024 · 641450c · 641450c
1 parent e40fb26
commit 641450c
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Showing 4 changed files with 10 additions and 10 deletions.
diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java b/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java
@@ -93,12 +93,12 @@ private void ensureNumberOfValuesIsCorrect(int valuesNumber) {
     }
 
 
-    public void initialise() {
+    public void initialize() {
         try {
             storeOrderedSampleList();
         } catch (DaoException e) {
             throw new RuntimeException(e);
         }
     }
-    public void finalise() { }
+    public void finalize() { }
 }
diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java b/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java
@@ -43,7 +43,7 @@ public boolean store(int geneticEntityId, String[] values) throws DaoException {
     }
 
     @Override
-    public void initialise() {
+    public void initialize() {
         try {
             this.geneticAlterationMap = daoGeneticAlteration.getGeneticAlterationMapForEntityIds(geneticProfileId, null);
             ArrayList <Integer> savedOrderedSampleList = DaoGeneticProfileSamples.getOrderedSampleList(this.geneticProfileId);
@@ -66,13 +66,13 @@ public void initialise() {
         } catch (DaoException e) {
             throw new RuntimeException(e);
         }
-        super.initialise();
+        super.initialize();
     }
 
     @Override
-    public void finalise() {
+    public void finalize() {
         expandRemainingGeneticEntityTabDelimitedRowsWithBlankValue();
-        super.finalise();
+        super.finalize();
     }
 
     private String[] extendValues(int geneticEntityId, String[] values) {

diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java b/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java
@@ -153,7 +153,7 @@ private void doImportData() throws Exception {
         orderedSampleList = newArrayList(toImport.eventsTable.columnKeySet());
         this.geneticAlterationGeneImporter = isIncrementalUpdateMode ?  new GeneticAlterationIncrementalImporter(geneticProfileId, orderedSampleList)
                 : new GeneticAlterationImporter(geneticProfileId, orderedSampleList);
-        geneticAlterationGeneImporter.initialise();
+        geneticAlterationGeneImporter.initialize();
         DaoSampleProfile.upsertSampleToProfileMapping(orderedSampleList, geneticProfileId, genePanelId);
 
         for (Long entrezId : toImport.eventsTable.rowKeySet()) {
@@ -171,7 +171,7 @@ private void doImportData() throws Exception {
 
         ProgressMonitor.setCurrentMessage(" --> total number of samples skipped (normal samples): " + getSamplesSkipped());
         buf.close();
-        geneticAlterationGeneImporter.finalise();
+        geneticAlterationGeneImporter.finalize();
         MySQLbulkLoader.flushAll();
     }
 

diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java b/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java
@@ -305,7 +305,7 @@ private void doImportData() throws IOException, DaoException {
             this.geneticAlterationImporter = isIncrementalUpdateMode ? new GeneticAlterationIncrementalImporter(geneticProfileId, orderedSampleList)
                     : new GeneticAlterationImporter(geneticProfileId, orderedSampleList);
 
-            geneticAlterationImporter.initialise();
+            geneticAlterationImporter.initialize();
 
             //cache for data found in  cna_event' table:
             Set<CnaEvent.Event> existingCnaEvents = new HashSet<>();
@@ -389,7 +389,7 @@ private void doImportData() throws IOException, DaoException {
                 line = buf.readLine();
             }
             DaoSampleProfile.upsertSampleToProfileMapping(orderedSampleList, geneticProfileId, genePanelId);
-            geneticAlterationImporter.finalise();
+            geneticAlterationImporter.finalize();
             if (MySQLbulkLoader.isBulkLoad()) {
                 MySQLbulkLoader.flushAll();
             }