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Commits on Source (2)
......@@ -6,17 +6,16 @@ Last-Update: 2019-07-20
Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp
===================================================================
--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 17:51:23.891331720 +0100
+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 17:51:23.879331619 +0100
--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 19:59:12.396009495 +0100
+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp 2019-07-20 19:59:12.388009427 +0100
@@ -18,10 +18,12 @@
ScoreMatrix* unserialized = ScoreMatrix::unserialize(serialized, subMat.alphabetSize, 3);
Debug(Debug::INFO) << unserialized->elementSize << " " << unserialized->rowSize << " "
- << unserialized->score[0] << " " << unserialized->index[0] << "\n";
-
- ScoreMatrix::cleanup(unserialized);
+ << unserialized->score[0] << "\n";
+
- ScoreMatrix::cleanup(unserialized);
free(serialized);
- ScoreMatrix::cleanup(extMattwo);
+ free(extMattwo);
......@@ -27,8 +26,8 @@ Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp
}
Index: mmseqs2/src/test/TestBestAlphabet.cpp
===================================================================
--- mmseqs2.orig/src/test/TestBestAlphabet.cpp 2019-07-20 08:12:45.250499276 +0100
+++ mmseqs2/src/test/TestBestAlphabet.cpp 2019-07-20 17:52:58.384128682 +0100
--- mmseqs2.orig/src/test/TestBestAlphabet.cpp 2019-07-20 19:59:12.396009495 +0100
+++ mmseqs2/src/test/TestBestAlphabet.cpp 2019-07-20 19:59:12.392009461 +0100
@@ -58,7 +58,7 @@
///////// | ////////////////
///////// Choose substitution matrix here V ! ////////////////
......@@ -49,3 +48,47 @@ Index: mmseqs2/src/test/TestBestAlphabet.cpp
DBReader<unsigned int> seqDb(dbPath.c_str(), dbIndexPath.c_str(), 1, DBReader<unsigned int>::USE_DATA|DBReader<unsigned int>::USE_INDEX);
seqDb.open(DBReader<unsigned int>::NOSORT);
Index: mmseqs2/src/test/TestAlignmentPerformance.cpp
===================================================================
--- mmseqs2.orig/src/test/TestAlignmentPerformance.cpp 2019-07-20 19:59:12.396009495 +0100
+++ mmseqs2/src/test/TestAlignmentPerformance.cpp 2019-07-20 19:59:12.392009461 +0100
@@ -83,7 +83,7 @@
int gap_extend = 1;
int mode = 0;
size_t cells = 0;
- std::vector<std::string> sequences = readData("/Users/mad/Documents/databases/rfam/Rfam.fasta");
+ std::vector<std::string> sequences = readData("../example-data/DB.fasta");
for(size_t seq_i = 0; seq_i < sequences.size(); seq_i++){
query->mapSequence(1,1,sequences[seq_i].c_str());
aligner.ssw_init(query, tinySubMat, &subMat, subMat.alphabetSize, 2);
Index: mmseqs2/src/test/TestDBReader.cpp
===================================================================
--- mmseqs2.orig/src/test/TestDBReader.cpp 2019-07-20 08:12:45.250499276 +0100
+++ mmseqs2/src/test/TestDBReader.cpp 2019-07-20 20:00:32.384684139 +0100
@@ -14,7 +14,7 @@
int main (int, const char**) {
// DBReader test
- DBReader<unsigned int> reader("dataLinear", "dataLinear.index", 1, 0);
+ DBReader<unsigned int> reader("dataLinear", "dataLinear.index", 1, 1);
reader.open(0);
reader.readMmapedDataInMemory();
reader.printMagicNumber();
@@ -24,7 +24,7 @@
std::cout << reader.getData(i, 0) << std::endl;
}
reader.close();
- DBReader<unsigned int> reader2("dataGap", "dataGap.index", 1, 0);
+ DBReader<unsigned int> reader2("dataGap", "dataGap.index", 1, 1);
reader2.open(0);
std::cout << reader2.getSize() << std::endl;
for(size_t i = 0; i < reader2.getSize(); i++){
@@ -45,7 +45,7 @@
std::cout << "Check length: " << (reader2.getSeqLens(reader2.getId(12)) == 10) << std::endl;
reader2.close();
// test sort mode
- DBReader<unsigned int> reader3("dataGap", "dataGap.index", 1, 0);
+ DBReader<unsigned int> reader3("dataGap", "dataGap.index", 1, 1);
reader3.open(DBReader<unsigned int>::SORT_BY_LENGTH);
for(size_t i = 0; i < reader3.getSize(); i++){
size_t id = reader3.getDbKey(i);
......@@ -67,3 +67,9 @@ echo "Invoking test_scorematrixserialization"
./test_scorematrixserialization
echo "Invoking test_bestalphabet"
./test_bestalphabet
echo "Invoking test_dbreader"
./test_dbreader
# Takes a very long time to complete
#echo "Invoke test_alignmentperformance"
#./test_alignmentperformance