Merge pull request #4 from sa501428/removeIterators

Remove iterators

src/javastraw/StrawGlobals.java

@@ -25,7 +25,7 @@
 package javastraw;
 
 public class StrawGlobals {
-    public static final String versionNum = "2.09.02";
+    public static final String versionNum = "2.11.01";
     // min hic file version supported
     public static final int minVersion = 6;
     public static final int bufferSize = 2097152;

src/javastraw/reader/Dataset.java

@@ -74,6 +74,7 @@ public Dataset(DatasetReader reader) {
 
     public void clearCache(boolean onlyClearInter) {
         for (Matrix matrix : matrices.values()) {
+            if (matrix == null) continue;
             if (onlyClearInter && matrix.isIntra()) continue;
             try {
                 matrix.clearCache();

src/javastraw/reader/block/Block.java

@@ -24,13 +24,11 @@
 
 package javastraw.reader.block;
 
-//import java.awt.*;
-//import java.util.List;
-
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Objects;
 
-public class Block {
+public class Block implements Comparable<Block> {
 
     private final int number;
     private final String uniqueRegionID;
@@ -59,4 +57,32 @@ public String getUniqueRegionID() {
     public List<ContactRecord> getContactRecords() {
         return records;
     }
+
+    @Override
+    public int compareTo(Block o) {
+        if (this == o) return 0;
+        int[] comparisons = new int[]{Integer.compare(number, o.number),
+                uniqueRegionID.compareTo(o.uniqueRegionID),
+                Integer.compare(records.size(), o.records.size())
+        };
+        for (int val : comparisons) {
+            if (val != 0) {
+                return val;
+            }
+        }
+        return 0;
+    }
+
+    @Override
+    public boolean equals(Object obj) {
+        return obj instanceof Block
+                && ((Block) obj).number == number
+                && ((Block) obj).uniqueRegionID.equals(uniqueRegionID)
+                && ((Block) obj).records.size() == records.size();
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(number, uniqueRegionID, records.size());
+    }
 }

src/javastraw/reader/iterators/ContactRecordIterator.java

@@ -30,7 +30,7 @@
 import javastraw.reader.mzd.BlockCache;
 import javastraw.reader.mzd.BlockLoader;
 import javastraw.reader.type.HiCZoom;
-import javastraw.reader.type.NormalizationHandler;
+import javastraw.reader.type.NormalizationType;
 
 import java.io.IOException;
 import java.util.Iterator;
@@ -49,19 +49,21 @@ public class ContactRecordIterator implements Iterator<ContactRecord> {
     private final BlockCache blockCache;
     private final int chr1Idx, chr2Idx;
     private final HiCZoom zoom;
+    private final NormalizationType normType;
 
     /**
      * Initializes the iterator
      */
     public ContactRecordIterator(DatasetReader reader, String zdKey, BlockCache blockCache,
-                                 int chr1Idx, int chr2Idx, HiCZoom zoom) {
+                                 int chr1Idx, int chr2Idx, HiCZoom zoom, NormalizationType normType) {
         this.reader = reader;
         this.zdKey = zdKey;
         this.chr1Idx = chr1Idx;
         this.chr2Idx = chr2Idx;
         this.zoom = zoom;
         this.blockCache = blockCache;
         this.blockIdx = -1;
+        this.normType = normType;
         this.blockNumbers = reader.getBlockNumbers(zdKey);
     }
 
@@ -78,25 +80,29 @@ public boolean hasNext() {
             return true;
         } else {
             blockIdx++;
-            if (blockIdx < blockNumbers.size()) {
+            while (blockIdx < blockNumbers.size()) {
                 try {
                     int blockNumber = blockNumbers.get(blockIdx);
 
                     // Optionally check the cache
-                    String key = BlockLoader.getBlockKey(zdKey, blockNumber, NormalizationHandler.NONE);
+                    String key = BlockLoader.getBlockKey(zdKey, blockNumber, normType);
                     Block nextBlock;
                     if (blockCache.containsKey(key)) {
                         nextBlock = blockCache.get(key);
                     } else {
-                        nextBlock = reader.readNormalizedBlock(blockNumber, zdKey, NormalizationHandler.NONE,
+                        nextBlock = reader.readNormalizedBlock(blockNumber, zdKey, normType,
                                 chr1Idx, chr2Idx, zoom);
                     }
-                    currentBlockIterator = nextBlock.getContactRecords().iterator();
-                    return true;
+                    List<ContactRecord> contactRecords = nextBlock.getContactRecords();
+                    if (contactRecords != null && contactRecords.size() > 0) {
+                        currentBlockIterator = contactRecords.iterator();
+                        return true;
+                    }
                 } catch (IOException e) {
                     System.err.println("Error fetching block " + e.getMessage());
                     return false;
                 }
+                blockIdx++;
             }
         }
 

src/javastraw/reader/iterators/CoupledIteratorAndOffset.java

@@ -32,11 +32,18 @@ public class CoupledIteratorAndOffset implements Iterator<ContactRecord> {
 
     private final Iterator<ContactRecord> internalIterator;
     private final int xOffset, yOffset;
+    private final boolean isIntra;
 
-    public CoupledIteratorAndOffset(Iterator<ContactRecord> iterator, int xOffset, int yOffset) {
+    public CoupledIteratorAndOffset(Iterator<ContactRecord> iterator, int xOffset, int yOffset,
+                                    boolean isIntra) {
         internalIterator = iterator;
         this.xOffset = xOffset;
         this.yOffset = yOffset;
+        this.isIntra = isIntra;
+    }
+
+    public boolean getIsIntra() {
+        return isIntra;
     }
 
     @Override