From 9e006501f9e33467a8428199bd94b71dbff063ef Mon Sep 17 00:00:00 2001
From: Anbang Xu <anbangx@gmail.com>
Date: Fri, 26 Jul 2013 14:10:33 -0700
Subject: [PATCH] p2 pass all the tests except 9

---
 .../genomix/data/test/KmerBytesWritableTest.java   | 76 +++++++++++++++++++++-
 .../genomix/pregelix/io/VertexValueWritable.java   |  2 +-
 .../operator/pathmerge/BasicPathMergeVertex.java   | 35 +++++-----
 .../pathmerge/LogAlgorithmForPathMergeVertex.java  |  8 +--
 .../pregelix/JobRun/PathMergeSmallTestSuite.java   |  2 +-
 5 files changed, 98 insertions(+), 25 deletions(-)

diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
index bda73e5..fbfbeeb 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
@@ -229,14 +229,34 @@ public class KmerBytesWritableTest {
         merge.mergeWithRFKmer(i, kmer2);
         Assert.assertEquals("GGCACAACAACCC", merge.toString());
         
-        String test1 = "CTA";
-        String test2 = "AGA";
+        String test1;
+        String test2;
+        test1 = "CTA";
+        test2 = "AGA";
         KmerBytesWritable k1 = new KmerBytesWritable(3);
         KmerBytesWritable k2 = new KmerBytesWritable(3);
         k1.setByRead(test1.getBytes(), 0);
         k2.setByRead(test2.getBytes(), 0);
         k1.mergeWithRFKmer(3, k2);
         Assert.assertEquals("TCTA", k1.toString());
+        
+        test1 = "CTA";
+        test2 = "ATA"; //TAT
+        k1 = new KmerBytesWritable(3);
+        k2 = new KmerBytesWritable(3);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k1.mergeWithFRKmer(3, k2);
+        Assert.assertEquals("CTAT", k1.toString());
+        
+        test1 = "ATA";
+        test2 = "CTA"; //TAT
+        k1 = new KmerBytesWritable(3);
+        k2 = new KmerBytesWritable(3);
+        k1.setByRead(test1.getBytes(), 0);
+        k2.setByRead(test2.getBytes(), 0);
+        k1.mergeWithFRKmer(3, k2);
+        Assert.assertEquals("ATAG", k1.toString());
     }
     
     
@@ -281,5 +301,55 @@ public class KmerBytesWritableTest {
             }
         }
     }
-
+    
+    @Test
+    public void TestFinalMerge() {
+        String selfString;
+        String match;
+        String msgString;
+        int index;
+        KmerBytesWritable kmer = new KmerBytesWritable();
+        int kmerSize = 3;
+        
+        String F1 = "AATAG";
+        String F2 = "TAGAA";
+        String R1 = "CTATT";
+        String R2 = "TTCTA";
+        
+        //FF test
+        selfString = F1;
+        match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
+        msgString = F2;
+        index = msgString.indexOf(match);
+        kmer.reset(msgString.length() - index);
+        kmer.setByRead(msgString.substring(index).getBytes(), 0);
+        System.out.println(kmer.toString());
+        
+        //FR test
+        selfString = F1;
+        match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
+        msgString = GeneCode.reverseComplement(R2);
+        index = msgString.indexOf(match);
+        kmer.reset(msgString.length() - index);
+        kmer.setByRead(msgString.substring(index).getBytes(), 0);
+        System.out.println(kmer.toString());
+        
+        //RF test
+        selfString = R1;
+        match = selfString.substring(0,kmerSize - 1); 
+        msgString = GeneCode.reverseComplement(F2);
+        index = msgString.lastIndexOf(match) + kmerSize - 2;
+        kmer.reset(index + 1);
+        kmer.setByReadReverse(msgString.substring(0, index + 1).getBytes(), 0);
+        System.out.println(kmer.toString());
+        
+        //RR test
+        selfString = R1;
+        match = selfString.substring(0,kmerSize - 1); 
+        msgString = R2;
+        index = msgString.lastIndexOf(match) + kmerSize - 2;
+        kmer.reset(index + 1);
+        kmer.setByRead(msgString.substring(0, index + 1).getBytes(), 0);
+        System.out.println(kmer.toString());
+    }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
index 6d4f683..065bfd5 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -32,7 +32,7 @@ public class VertexValueWritable implements WritableComparable<VertexValueWritab
         public static final byte SHOULD_MERGEWITHNEXT = 0b01 << 3;
         public static final byte SHOULD_MERGEWITHPREV = 0b10 << 3;
         public static final byte SHOULD_MERGE_MASK = 0b11 << 3;
-        public static final byte SHOULD_MERGE_CLEAR = 0b1110011;
+        public static final byte SHOULD_MERGE_CLEAR = 0b1100111;
     }
     
     private PositionListWritable nodeIdList;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
index b7b0814..ec608c5 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
@@ -495,6 +495,7 @@ public class BasicPathMergeVertex extends
     
     public void setStateAsMergeWithNext(){
     	byte state = getVertexValue().getState();
+    	state &= State.SHOULD_MERGE_CLEAR;
         state |= State.SHOULD_MERGEWITHNEXT;
         getVertexValue().setState(state);
     }
@@ -512,6 +513,7 @@ public class BasicPathMergeVertex extends
     
     public void setStateAsMergeWithPrev(){
         byte state = getVertexValue().getState();
+        state &= State.SHOULD_MERGE_CLEAR;
         state |= State.SHOULD_MERGEWITHPREV;
         getVertexValue().setState(state);
     }
@@ -638,7 +640,7 @@ public class BasicPathMergeVertex extends
         String match;
         String msgString;
         int index;
-        switch(neighborToMergeDir){
+        switch(neighborToMeDir){
             case MessageFlag.DIR_FF:
                 selfString = getVertexValue().getKmer().toString();
                 match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
@@ -648,28 +650,29 @@ public class BasicPathMergeVertex extends
                 kmer.setByRead(msgString.substring(index).getBytes(), 0);
                 break;
             case MessageFlag.DIR_FR:
-                selfString = getVertexId().toString();
-                match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length());
+                selfString = getVertexValue().getKmer().toString();
+                match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length()); 
                 msgString = GeneCode.reverseComplement(msg.getKmer().toString());
                 index = msgString.indexOf(match);
                 kmer.reset(msgString.length() - index);
-                kmer.setByRead(msgString.substring(index).getBytes(), 0);
+                kmer.setByReadReverse(msgString.substring(index).getBytes(), 0);
                 break;
             case MessageFlag.DIR_RF:
-                selfString = GeneCode.reverseComplement(getVertexValue().getKmer().toString());
-                match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length());
-                msgString = msg.getKmer().toString();
-                index = msgString.indexOf(match);
-                kmer.reset(msgString.length() - index);
-                kmer.setByRead(msgString.substring(index).getBytes(), 0);
+                selfString = getVertexValue().getKmer().toString();
+                match = selfString.substring(0,kmerSize - 1); 
+                msgString = GeneCode.reverseComplement(msg.getKmer().toString());
+                index = msgString.lastIndexOf(match) + kmerSize - 2;
+                kmer.reset(index + 1);
+                kmer.setByReadReverse(msgString.substring(0, index + 1).getBytes(), 0);
                 break;
             case MessageFlag.DIR_RR:
-                selfString = GeneCode.reverseComplement(getVertexValue().getKmer().toString());
-                match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length());
-                msgString = GeneCode.reverseComplement(msg.getKmer().toString());
-                index = msgString.indexOf(match);
-                kmer.reset(msgString.length() - index);
-                kmer.setByRead(msgString.substring(index).getBytes(), 0);
+                selfString = getVertexValue().getKmer().toString();
+                match = selfString.substring(0,kmerSize - 1); 
+                msgString = msg.getKmer().toString();
+                index = msgString.lastIndexOf(match) + kmerSize - 2;
+                kmer.reset(index + 1);
+                kmer.setByRead(msgString.substring(0, index + 1).getBytes(), 0);
+                System.out.println(kmer.toString());
                 break;
         }
        
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
index a68b646..3b5a782 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
@@ -170,22 +170,22 @@ public class LogAlgorithmForPathMergeVertex extends
                 case MessageFromHead.BothMsgsFromHead:
                 case MessageFromHead.OneMsgFromOldHeadAndOneFromHead:
                     for(int i = 0; i < 2; i++)
-                        processMerge(receivedMsgList.get(i));
+                        processFinalMerge(receivedMsgList.get(i)); //processMerge()
                     getVertexValue().setState(State.IS_FINAL);
                     voteToHalt();
                     break;
                 case MessageFromHead.OneMsgFromHeadAndOneFromNonHead:
                     for(int i = 0; i < 2; i++)
-                        processMerge(receivedMsgList.get(i));
+                        processFinalMerge(receivedMsgList.get(i));
                     getVertexValue().setState(State .IS_HEAD);
                     break;
                 case MessageFromHead.BothMsgsFromNonHead:
                     for(int i = 0; i < 2; i++)
-                        processMerge(receivedMsgList.get(i));
+                        processFinalMerge(receivedMsgList.get(i));
                     break;
                 case MessageFromHead.NO_MSG:
                     //halt
-                    deleteVertex(getVertexId());
+                    voteToHalt(); //deleteVertex(getVertexId());
                     break;
             }
         }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
index 9f96b5a..1578dfc 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
@@ -52,7 +52,7 @@ public class PathMergeSmallTestSuite extends TestSuite {
 //    + "6", PreFix + File.separator
 //    + "7", PreFix + File.separator
 //    + "8", PreFix + File.separator
-    + "5"};
+    + "9"};
     private static final String ACTUAL_RESULT_DIR = "data/actual/pathmerge";
     private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
     private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";
-- 
1.7.11.1