把main函数中拆解read得到kmer的代码进行更改，拆解出的kmer需要使用0作为结尾

Author: ErianArcher

communicator.cpp

@@ -145,25 +145,28 @@ requestOtherRanksToStoreVertex(int currank, int world_size, VertexId vertexId, E
 }
 
 // 该方法负责char *指针的delete
+// TODO: 不负责read的delete
 int processRecvRead(const char *filename, size_t pos) {
     ifstream infile(filename);
-    string read;
+    string *read = new string;
     infile.seekg(pos);
-    getline(infile, read);
+    getline(infile, *read);
     infile.close();
-    delete filename;
-    if (requestWriteRead(read) == 0) return 0;
+    delete[] filename;
+    if (requestWriteRead(*read) == 0) return 0;
     return 1;
 }
 
 // 该方法负责char *指针的delete
 int processRecvEdge(EdgeList *edgeList, char *value, ReadId readId, KMERPOS_t kmerpos) {
-    string strValue(string(value, 0, getK()));
-
-    VertexId sourceVertex = getId(strValue.substr(0, strValue.size()-1));
-    VertexId sinkVertex = getId(strValue.substr(1, strValue.size()-1));
+    string *strValue = new string(value, 0, getK()-1);
+    VertexId sourceVertex = getId(*strValue);
+    delete strValue;
+    strValue = new string(value, 1, getK()-1);
+    VertexId sinkVertex = getId(*strValue);
+    delete strValue;
     int flag = addNewEdge(edgeList, value, sourceVertex, sinkVertex, readId, kmerpos);
-    delete value;
+    delete[] value;
     return flag;
 }
 
@@ -175,7 +178,7 @@ int processRecvVertex(VertexList *vertexList, SetOfID *tangleList, VertexId vert
         flag = addVertex(vertexList, vertexId, edgeId, 0, vertexMode);
 
     if (MULTI_OUT_DEGREE == (flag & MULTI_OUT_DEGREE)) {
-        tangleList->safe_insert(vertexId);
+        //tangleList->safe_insert(vertexId);
     }
     return flag;
 }
@@ -275,11 +278,12 @@ void *receiverRunner(void *args) {
                 char *kmer = nullptr;
                 ReadId readId;
                 MPI_Unpack(pack, packSize, &position, &strLen, 1, MPI_INT, MPI_COMM_WORLD);
-                kmer = new char[strLen];
+                kmer = new char[strLen+1];
                 if (strLen != getK()) {
                     cout << "Trasmission error: " << strLen << endl;
                 }
                 MPI_Unpack(pack, packSize, &position, kmer, strLen, MPI_CHAR, MPI_COMM_WORLD);
+                kmer[strLen] = '\0';
                 MPI_Unpack(pack, packSize, &position, &readId, 1, my_MPI_SIZE_T, MPI_COMM_WORLD);
                 KMERPOS_t kmerpos;
                 MPI_Unpack(pack, packSize, &position, &kmerpos, 1, MPI_UNSIGNED, MPI_COMM_WORLD);
@@ -394,14 +398,14 @@ item::item() {
 }
 
 // 不能与线程并行的共存
-void sendSuperContigToRankHead(int headrank, int currank, string superContig) {
+void sendSuperContigToRankHead(int headrank, int currank, string &superContig) {
     int msgsize = superContig.size();
     MPI_Send(&msgsize, 1, MPI_INT, headrank, TAG(currank, headrank), MPI_COMM_WORLD);
     MPI_Send(superContig.c_str(), superContig.size(), MPI_CHAR, headrank, TAG(currank, headrank), MPI_COMM_WORLD);
 }
 
 // 不能与线程并行的共存
-string reduceSuperContigFromOthers(int currank, int world_size, string superContig) {
+string reduceSuperContigFromOthers(int currank, int world_size, string &superContig) {
     stringstream sc;
     sc << superContig;
     //cout << superContig;

communicator.h

@@ -100,9 +100,9 @@ void *testReceiverRunner(void *arg);
 
 void *receiverRunner(void *recvArg);
 
-void sendSuperContigToRankHead(int headrank, int currank, string superContig);
+void sendSuperContigToRankHead(int headrank, int currank, string &superContig);
 
-string reduceSuperContigFromOthers(int currank, int world_size, string superContig);
+string reduceSuperContigFromOthers(int currank, int world_size, string &superContig);
 
 int queryEdgeById(string *pEdgeStr, int currank, int tarrank, EdgeId edgeId);
 

entity/idset.h

@@ -14,6 +14,10 @@ inline size_t getId(const std::string& value) {
     return std::hash<std::string>()(value);
 }
 
+inline size_t getId(const char *value) {
+    return std::hash<std::string>()(value);
+}
+
 //typedef std::unordered_set<size_t> SetOfID;
 typedef size_t ReadId;
 typedef size_t VertexId;

entity/k_mer.cpp

@@ -69,8 +69,7 @@ int addNewEdge(EdgeList *eList, char *value, VertexId sourceVId, VertexId sinkVI
 
 int
 addNewEdge(EdgeList *eList, char *value, EdgeId *fetchedEdgeId, VertexId sourceVId, VertexId sinkVId, ReadId rId, KMERPOS_t kmerpos) {
-    string idStr(value, 0, getK());
-    EdgeId eId = hash<string>()(idStr);
+    EdgeId eId = hash<string>()(value);
     Edge *e = nullptr;
     pthread_mutex_lock(&kmerMutex);
     if (eList->find(eId) == eList->end()) {
@@ -86,7 +85,9 @@ addNewEdge(EdgeList *eList, char *value, EdgeId *fetchedEdgeId, VertexId sourceV
             return 0;
         }
         // cout << string(value, 0, getK()).c_str() << endl;
-        strcpy(e->value, string(value, 0, getK()).c_str());
+        for (int i = 0; i < getK(); ++i) {
+            e->value[i] = value[i];
+        }
 
         e->sourceKMinusMerId = sourceVId;
         e->sinkKMinusMerId = sinkVId;

entity/k_mer.h

@@ -8,7 +8,7 @@
 
 #include "idset.h"
 #include "read.h"
-#include <unordered_map>
+#include <map>
 
 struct kMer {
     size_t id;
@@ -31,7 +31,7 @@ struct kMer {
 
 typedef struct kMer Edge;
 typedef struct kMer KMer;
-typedef std::unordered_map<EdgeId , Edge *> EdgeList;
+typedef std::map<EdgeId , Edge *> EdgeList;
 typedef EdgeList KMerList;
 
 void setK(int k);

entity/k_minus_mer.cpp

@@ -18,8 +18,7 @@ unsigned int addVertex(VertexList *vList, char *value, const EdgeId inKMerId, co
 
 unsigned int addVertex(VertexList *vList, char *value, VertexId *fetchedVertexId, const EdgeId inKMerId,
                        const EdgeId outKMerId, VertexMode_t mode) {
-    string idStr(string(value, 0, getK()-1));
-    VertexId vId = hash<string>()(idStr);
+    VertexId vId = hash<string>()(value);
     if (nullptr != fetchedVertexId) {
         *fetchedVertexId = vId;
     }

entity/k_minus_mer.h

@@ -6,7 +6,7 @@
 #define RANDOMSTRINGASSEMBLY_K_MINUS_MER_H
 
 #include "idset.h"
-#include <unordered_map>
+#include <map>
 
 // Constants for VertexMode_t
 #define HEAD_VERTEX 1u
@@ -34,7 +34,7 @@ struct kMinusMer {
 
 typedef struct kMinusMer Vertex;
 typedef struct kMinusMer KMinusMer;
-typedef std::unordered_map<VertexId, Vertex *> VertexList;
+typedef std::map<VertexId, Vertex *> VertexList;
 
 typedef unsigned int VertexMode_t;
 //typedef int VertexAddReturn_t;