refactor v2 code

Author: karlnicholas

src/main/java/org/hdf5javalib/examples/hdf5examples/HDF5Debug.java

@@ -47,7 +47,7 @@ private void run() {
             // List all .h5 files in HDF5Examples resources directory
             // ATL03_20250302235544_11742607_006_01
 //            Path dirPath = Paths.get(Objects.requireNonNull(HDF5Debug.class.getClassLoader().getResource("HDF5Examples/h5ex_g_compact2.h5")).toURI());
-            Path dirPath = Paths.get("c:/users/karln/Downloads/ATL03_20250302235544_11742607_006_01.h5");
+            Path dirPath = Paths.get("c:/users/karnicho/Downloads/ATL03_20250302235544_11742607_007_01.h5");
             processFile(dirPath);
         } catch (Exception e) {
             throw new IllegalStateException(e);
@@ -69,7 +69,7 @@ private static void processFile(Path filePath) {
 //            System.out.println("{} " + dataSet);
 ////                System.out.println("{} " + dataSet.getObjectPath());
 ////                log.info("{} ", dataSet);
-//                HdfDisplaySumUtils.displayData(channel, dataSet, reader);
+//                HdfDisplayUtils.displayData(channel, dataSet, reader, HdfDisplayUtils.DisplayMode.SUMMARY_STATS);
 ////                displayScalarData(channel, dataSet, HdfFloatPoint.class, reader);
 
         } catch (Exception e) {

src/main/java/org/hdf5javalib/hdfjava/HdfDataset.java

@@ -282,10 +282,10 @@ public synchronized ByteBuffer getDatasetData(SeekableByteChannel channel, long
                 }
                 chunkBuffer.flip();
 
-                    Optional<FilterPipelineMessage> fpm = objectHeader.findMessageByType(FilterPipelineMessage.class);
-                    if ( fpm.isPresent() ) {
-                        chunkBuffer = fpm.get().getDeflater().deflate(chunkBuffer);
-                    }
+                Optional<FilterPipelineMessage> fpm = objectHeader.findMessageByType(FilterPipelineMessage.class);
+                if ( fpm.isPresent() ) {
+                    chunkBuffer = fpm.get().getDeflater().deflate(chunkBuffer);
+                }
                 // Handle filters/decompression (stubbed)
                 if (entry.getFilterMask() != 0) {
                     throw new UnsupportedOperationException("Filters  not supported yet");

src/main/java/org/hdf5javalib/hdfjava/HdfFileReader.java

@@ -181,7 +181,7 @@ private void readV1GroupHierarchy(HdfGroup parentGroup, HdfLocalHeap localHeap,
         } else {
             // Leaf node: process symbol table entries
             for (HdfGroupForGroupBTreeEntry entry : groupBTree.getEntries()) {
-                HdfGroupSymbolTableNode groupSymbolTableNode = ((HdfGroupForGroupBTreeEntry) entry).getGroupSymbolTableNode();
+                HdfGroupSymbolTableNode groupSymbolTableNode = entry.getGroupSymbolTableNode();
                 if (groupSymbolTableNode != null) {
                     for (HdfSymbolTableEntry symbolTableEntry : groupSymbolTableNode.getSymbolTableEntries()) {
                         String objectName = localHeap.stringAtOffset(symbolTableEntry.getLinkNameOffset());
@@ -250,9 +250,7 @@ private void processV2GroupLinks(HdfGroup group) throws Exception {
         // 2. Process links stored directly as Link Messages in the header (for smaller, compact groups)
         for (HdfMessage hdfMessage : group.getObjectHeader().getHeaderMessages()) {
             if (hdfMessage instanceof LinkMessage linkMessage) {
-                long objectHeaderOffset = linkMessage.getLinkInformation().getInstance(Long.class);
-                String linkName = linkMessage.getLinkName();
-                processLink(group, linkName, objectHeaderOffset);
+                processLink(group, linkMessage.getLinkName(), linkMessage.getLinkInformation().getInstance(Long.class));
             }
         }
     }
@@ -643,9 +641,7 @@ private static HdfBTreeV1ForGroup readFromSeekableByteChannelRecursiveForGroups(
         for (int i = 0; i < entriesUsed; i++) {
             HdfFixedPoint childPointer = HdfReadUtils.readHdfFixedPointFromBuffer(hdfOffset, entriesBuffer);
             HdfFixedPoint key = HdfReadUtils.readHdfFixedPointFromBuffer(hdfLength, entriesBuffer);
-            long filePosAfterEntriesBlock = fileChannel.position();
             long childAddress = childPointer.getInstance(Long.class);
-            fileChannel.position(childAddress);
 
             HdfGroupForGroupBTreeEntry entry;
             if (nodeLevel == 1) {
@@ -657,7 +653,6 @@ private static HdfBTreeV1ForGroup readFromSeekableByteChannelRecursiveForGroups(
                 HdfGroupSymbolTableNode child = readSnodFromSeekableByteChannel(fileChannel, hdfDataFile);
                 entry = new HdfGroupForGroupBTreeEntry(key, childPointer, null, child); // Assuming entry constructor accepts Object for last param
             }
-            fileChannel.position(filePosAfterEntriesBlock);
             entries.add(entry);
         }
         return currentNode;