refactor v2 code

Author: karlnicholas

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

@@ -48,7 +48,8 @@ private void run() {
             // 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/karnicho/Downloads/ATL03_20250302235544_11742607_007_01.h5");
-            Path dirPath = Paths.get("c:/users/karnicho/Downloads/ATL03_20250302235544_11742607_006_01.h5");
+//            Path dirPath = Paths.get("c:/users/karnicho/Downloads/ATL03_20250302235544_11742607_006_01.h5");
+            Path dirPath = Paths.get("c:/users/karnicho/Downloads/SMAP_L1B_TB_57204_D_20251016T224815_R19240_001.h5");
             processFile(dirPath);
         } catch (Exception e) {
             throw new IllegalStateException(e);

src/main/java/org/hdf5javalib/hdffile/dataobjects/messages/LinkMessage.java

@@ -71,7 +71,7 @@ public LinkMessage(
         this.linkInformation = linkInformation;
     }
 
-    public static HdfMessage parseHeaderMessage(int messageFlags, byte[] data, HdfDataFile hdfDataFile) throws IOException, InvocationTargetException, InstantiationException, IllegalAccessException {
+    public static LinkMessage parseHeaderMessage(int messageFlags, byte[] data, HdfDataFile hdfDataFile) throws IOException, InvocationTargetException, InstantiationException, IllegalAccessException {
         ByteBuffer buffer = ByteBuffer.wrap(data).order(ByteOrder.LITTLE_ENDIAN);
 
         int version = Byte.toUnsignedInt(buffer.get());

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

@@ -281,20 +281,15 @@ private void processV2BTreeLinks(HdfGroup group, LinkInfoMessage linkInfoMessage
         long fractalHeapOffset = linkInfoMessage.getFractalHeapAddress().getInstance(Long.class);
         FractalHeap fractalHeap = FractalHeap.read(fileChannel, fractalHeapOffset, this); // Assuming params
 
-        for (BTreeV2Record bTreeV2Record : bTreeV2Reader.getAllRecords()) {
+        List<BTreeV2Record> allRecs = bTreeV2Reader.getAllRecords();
+        for (BTreeV2Record bTreeV2Record : allRecs) {
             byte[] heapId = ((Type5Record) bTreeV2Record).heapId;
             ParsedHeapId parsedHeapId = new ParsedHeapId(heapId, fractalHeap);
             byte[] objectData = fractalHeap.getObject(parsedHeapId);
-            ByteBuffer retrievedData = ByteBuffer.wrap(objectData).order(ByteOrder.LITTLE_ENDIAN);
 
-            retrievedData.position(10); // Skip rowHeader
-            int sLength = Byte.toUnsignedInt(retrievedData.get());
-            byte[] stringBuffer = new byte[sLength];
-            retrievedData.get(stringBuffer);
-            String linkName = new String(stringBuffer);
-            long objectHeaderOffset = retrievedData.getLong();
+            LinkMessage linkMessage = LinkMessage.parseHeaderMessage(0, objectData, this);
 
-            processLink(group, linkName, objectHeaderOffset);
+            processLink(group, linkMessage.getLinkName(), linkMessage.getLinkInformation().getInstance(Long.class));
         }
     }
 
@@ -1132,7 +1127,7 @@ static HdfObjectHeaderPrefixV2 readV2ObjectHeader(SeekableByteChannel fileChanne
 
         // --- 6. Handle Continuation Messages ---
         Function<ByteBuffer, HdfMessage.OBJECT_HEADER_PREFIX> prefixReader = (flags & 0b00000100) > 0 ? HdfMessage.V2OBJECT_HEADER_READ_PREFIX_WITHORDER : HdfMessage.V2_OBJECT_HEADER_READ_PREFIX;
-        ;
+
         parseContinuationMessages(fileChannel, prefixReader, dataObjectHeaderMessages, hdfDataFile);
         // --- 7. Create the V2 Header Prefix Instance ---
         return new HdfObjectHeaderPrefixV2(flags, sizeOfChunk0, checksum,