small adjustments to new node and position classes
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
index 8eb2cbd..60e733d 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
@@ -30,7 +30,7 @@
}
public NodeWritable() {
- this(21);
+ this(0);
}
public NodeWritable(int kmerSize) {
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
index 49f1b11..5f72906 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
@@ -30,6 +30,7 @@
public PositionListWritable(List<PositionWritable> posns) {
this();
+ setSize(posns.size()); // reserve space for all elements
for (PositionWritable p : posns) {
append(p);
}
@@ -48,12 +49,7 @@
}
public void append(PositionWritable pos) {
- if(pos != null){
- setSize((1 + valueCount) * PositionWritable.LENGTH);
- System.arraycopy(pos.getByteArray(), pos.getStartOffset(), storage, offset + valueCount
- * PositionWritable.LENGTH, pos.getLength());
- valueCount += 1;
- }
+ append(pos.getUUID());
}
/*
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java
index 74ef9d5..7cf9bfc 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java
@@ -14,8 +14,7 @@
private static final long serialVersionUID = 1L;
protected byte[] storage;
protected int offset;
- public static final int LENGTH = 5;
- public static final int LONGBYTES = 8;
+ public static final int LENGTH = 8;
public PositionWritable() {
storage = new byte[LENGTH];