Allow subprojects to build their own precomputed indices

soedinglab · Dec 29, 2021 · a506d67 · a506d67
1 parent 75af0c8
commit a506d67
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Showing 4 changed files with 42 additions and 18 deletions.
diff --git a/src/MMseqsBase.cpp b/src/MMseqsBase.cpp
@@ -3,6 +3,8 @@
 #include "CommandDeclarations.h"
 #include "DownloadDatabase.h"
 
+const char* MMSEQS_CURRENT_INDEX_VERSION = "16";
+
 Parameters& par = Parameters::getInstance();
 std::vector<Command> baseCommands = {
         {"easy-search",          easysearch,           &par.easysearchworkflow,   COMMAND_EASY,

diff --git a/src/commons/IndexReader.h b/src/commons/IndexReader.h
@@ -8,12 +8,18 @@
 
 class IndexReader {
 public:
-    const static int PRELOAD_NO = 0;
-    const static int PRELOAD_DATA = 1;
-    const static int PRELOAD_INDEX = 2;
+    const static unsigned int PRELOAD_NO = 0;
+    const static unsigned int PRELOAD_DATA = 1;
+    const static unsigned int PRELOAD_INDEX = 2;
 
-    IndexReader(const std::string &dataName, int threads, int databaseType = SEQUENCES | HEADERS, int preloadMode = false, int dataMode=(DBReader<unsigned int>::USE_INDEX | DBReader<unsigned int>::USE_DATA))
-            : sequenceReader(NULL), index(NULL) {
+    IndexReader(
+            const std::string &dataName,
+            int threads,
+            unsigned int databaseType = SEQUENCES | HEADERS,
+            unsigned int preloadMode = false,
+            int dataMode = DBReader<unsigned int>::USE_INDEX | DBReader<unsigned int>::USE_DATA,
+            std::string failSuffix = ""
+    ) : sequenceReader(NULL), index(NULL) {
         int targetDbtype = FileUtil::parseDbType(dataName.c_str());
         if (Parameters::isEqualDbtype(targetDbtype, Parameters::DBTYPE_INDEX_DB)) {
             index = new DBReader<unsigned int>(dataName.c_str(), (dataName + ".index").c_str(), 1, DBReader<unsigned int>::USE_DATA|DBReader<unsigned int>::USE_INDEX);
@@ -24,13 +30,19 @@ class IndexReader {
                 seqType = data.seqType;
                 bool touchIndex = preloadMode & PRELOAD_INDEX;
                 bool touchData = preloadMode & PRELOAD_DATA;
-                if (databaseType & SRC_SEQUENCES) {
+                if (databaseType & USER_SELECT) {
+                    sequenceReader = PrefilteringIndexReader::openNewReader(
+                            index,
+                            (databaseType & ~USER_SELECT) + 1,
+                            databaseType & ~USER_SELECT,
+                            dataMode & DBReader<unsigned int>::USE_DATA, threads, touchIndex, touchData
+                    );
+                } else if (databaseType & SRC_SEQUENCES) {
                     sequenceReader = PrefilteringIndexReader::openNewReader(index,
-                            PrefilteringIndexReader::DBR2DATA, PrefilteringIndexReader::DBR2INDEX, dataMode & DBReader<unsigned int>::USE_DATA, threads, touchIndex, touchData);
-
+                                                                            PrefilteringIndexReader::DBR2DATA, PrefilteringIndexReader::DBR2INDEX, dataMode & DBReader<unsigned int>::USE_DATA, threads, touchIndex, touchData);
                 } else if (databaseType & SEQUENCES) {
                     sequenceReader = PrefilteringIndexReader::openNewReader(index,
-                            PrefilteringIndexReader::DBR1DATA, PrefilteringIndexReader::DBR1INDEX, dataMode & DBReader<unsigned int>::USE_DATA, threads, touchIndex, touchData);
+                                                                            PrefilteringIndexReader::DBR1DATA, PrefilteringIndexReader::DBR1INDEX, dataMode & DBReader<unsigned int>::USE_DATA, threads, touchIndex, touchData);
                 } else if (databaseType & SRC_HEADERS) {
 
                     sequenceReader = PrefilteringIndexReader::openNewHeaderReader(index,
@@ -63,10 +75,12 @@ class IndexReader {
 
         if (sequenceReader == NULL) {
             if (databaseType & (HEADERS | SRC_HEADERS)) {
-                sequenceReader = new DBReader<unsigned int>((dataName + "_h").c_str(), (dataName + "_h.index").c_str(), threads, dataMode);
-            } else {
-                sequenceReader = new DBReader<unsigned int>(dataName.c_str(), (dataName + ".index").c_str(), threads, dataMode);
+                failSuffix = "_h";
             }
+            sequenceReader = new DBReader<unsigned int>(
+                    (dataName + failSuffix).c_str(), (dataName + failSuffix + ".index").c_str(),
+                    threads, dataMode
+            );
             sequenceReader->open(DBReader<unsigned int>::NOSORT);
             bool touchData = preloadMode & PRELOAD_DATA;
             if (touchData) {
@@ -76,11 +90,16 @@ class IndexReader {
         }
     }
 
-    static const int SEQUENCES = 1;
-    static const int HEADERS   = 2;
-    static const int SRC_HEADERS = 4;
-    static const int SRC_SEQUENCES =  8;
-    static const int ALIGNMENTS = 16;
+    static const unsigned int SEQUENCES = 1;
+    static const unsigned int HEADERS   = 2;
+    static const unsigned int SRC_HEADERS = 4;
+    static const unsigned int SRC_SEQUENCES =  8;
+    static const unsigned int ALIGNMENTS = 16;
+    static const unsigned int USER_SELECT = 1 << 31;
+
+    static unsigned int makeUserDatabaseType(unsigned int baseKey) {
+        return baseKey | USER_SELECT;
+    }
 
     int getDbtype() const {
         return seqType;

diff --git a/src/mmseqs.cpp b/src/mmseqs.cpp
@@ -7,6 +7,8 @@ const char* tool_introduction = "MMseqs2 (Many against Many sequence searching)
 const char* main_author = "Martin Steinegger (martin.steinegger@snu.ac.kr)";
 const char* show_extended_help = "1";
 const char* show_bash_info = "1";
+extern const char* MMSEQS_CURRENT_INDEX_VERSION;
+const char* index_version_compatible = MMSEQS_CURRENT_INDEX_VERSION;
 bool hide_base_commands = false;
 void (*validatorUpdate)(void) = 0;
 std::vector<Command> commands = {};

diff --git a/src/prefiltering/PrefilteringIndexReader.cpp b/src/prefiltering/PrefilteringIndexReader.cpp
@@ -6,7 +6,8 @@
 #include "IndexBuilder.h"
 #include "Parameters.h"
 
-const char*  PrefilteringIndexReader::CURRENT_VERSION = "16";
+extern const char* index_version_compatible;
+const char*  PrefilteringIndexReader::CURRENT_VERSION = index_version_compatible;
 unsigned int PrefilteringIndexReader::VERSION = 0;
 unsigned int PrefilteringIndexReader::META = 1;
 unsigned int PrefilteringIndexReader::SCOREMATRIXNAME = 2;