commit 0e690456227f9ab600d34ed17ab5f658406eb19b
author Jianfeng Jia <jianfeng.jia@gmail.com> Tue Jun 04 16:31:23 2013 -0700
committer Jianfeng Jia <jianfeng.jia@gmail.com> Tue Jun 04 16:31:23 2013 -0700
tree 4e6f04932745ef2ba29008bd464c60b76fbab6a1
parent c49f7b965d666614de3dcb9d8b997e1e44cf885a

change iterator to for loop to save time.

genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java

diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
index cf9d566..80834f7 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
@@ -203,7 +203,8 @@
 
         private void setReverseOutgoingList(NodeReference node, int offset) {
             setCachList(offset);
-            for (PositionWritable pos : cachePositionList) {
+            for(int i = 0; i < cachePositionList.getCountOfPosition(); i++){
+                PositionWritable pos = cachePositionList.getPosition(i);
                 if (pos.getPosInRead() > 0) {
                     node.getRFList().append(pos);
                 } else {
@@ -214,7 +215,8 @@
 
         private void setReverseIncomingList(NodeReference node, int offset) {
             setCachList(offset);
-            for (PositionWritable pos : cachePositionList) {
+            for(int i = 0; i < cachePositionList.getCountOfPosition(); i++){
+                PositionWritable pos = cachePositionList.getPosition(i);
                 if (pos.getPosInRead() > 0) {
                     if (pos.getPosInRead() > 1) {
                         node.getFRList().append(pos.getReadID(), (byte) (pos.getPosInRead() - 1));
@@ -231,7 +233,8 @@
 
         private void setForwardOutgoingList(NodeReference node, int offset) {
             setCachList(offset);
-            for (PositionWritable pos : cachePositionList) {
+            for(int i = 0; i < cachePositionList.getCountOfPosition(); i++){
+                PositionWritable pos = cachePositionList.getPosition(i);
                 if (pos.getPosInRead() > 0) {
                     node.getFFList().append(pos);
                 } else {
@@ -242,7 +245,8 @@
 
         private void setForwardIncomingList(NodeReference node, int offset) {
             setCachList(offset);
-            for (PositionWritable pos : cachePositionList) {
+            for(int i = 0; i < cachePositionList.getCountOfPosition(); i++){
+                PositionWritable pos = cachePositionList.getPosition(i);
                 if (pos.getPosInRead() > 0) {
                     if (pos.getPosInRead() > 1) {
                         node.getRRList().append(pos.getReadID(), (byte) (pos.getPosInRead() - 1));