added an extremely important improvement to the concordia search algorithm - gapped overlays cut-off

concordia-console/concordia-console.cpp

@@ -60,7 +60,8 @@ void checkConcordiaResults(
 
 void performSearch(Concordia & concordia,
                    std::vector<std::string> & buffer,
-                   long lineCount) {
+                   long lineCount,
+                   int checkingScheme) {
     long baseLineCount = 0;
     if (lineCount % READ_BUFFER_LENGTH == 0) {
         baseLineCount = lineCount - READ_BUFFER_LENGTH;
@@ -93,9 +94,11 @@ void performSearch(Concordia & concordia,
           sentencesSearched << " sentences in "
           << timeElapsed << "ms. The speed: " <<
           speed << " sentences per second" << std::endl;
-    std::cout << "\tChecking this portion..." << std::endl;
+    if (checkingScheme == 1) {  // 100% correctness
-    checkConcordiaResults(results, baseLineCount);
+        std::cout << "\tChecking this portion..." << std::endl;
-    std::cout << "\tno errors." << std::endl;
+        checkConcordiaResults(results, baseLineCount);
+        std::cout << "\tno errors." << std::endl;
+    }
     std::cout << "\tTotal search progress: " <<
           lineCount << " sentences searched." << std::endl;
 }
@@ -115,6 +118,9 @@ int main(int argc, char** argv) {
                         "Pattern to be searched by anubis search in the index")
         ("concordia-search,x", boost::program_options::value<std::string>(),
                      "Pattern to be searched by concordia search in the index")
+        ("concordia-search-all,f",
+                                  boost::program_options::value<std::string>(),
+           "File with pattern to be searched by concordia search in the index")
         ("read-file,r", boost::program_options::value<std::string>(),
                                  "File to be read and added to index")
         ("test,t", boost::program_options::value<std::string>(),
@@ -241,6 +247,36 @@ int main(int argc, char** argv) {
                               << std::endl;
                 }
             }
+        } else if  (cli.count("concordia-search-all")) {
+            std::string filePath =
+                  cli["concordia-search-all"].as<std::string>();
+            std::cout << "\tConcordia searching from file: " << filePath <<
+                                                                  std::endl;
+
+            std::ifstream test_file(filePath.c_str());
+            std::string line;
+            if (test_file.is_open()) {
+                long lineCount = 0;
+                std::vector<std::string> buffer;
+                while (getline(test_file, line)) {
+                    lineCount++;
+                    buffer.push_back(line);
+                    if (lineCount % READ_BUFFER_LENGTH == 0) {
+                        performSearch(concordia, buffer, lineCount, 2);
+                    }
+                }
+                if (buffer.size() > 0) {
+                    performSearch(concordia, buffer, lineCount, 2);
+                }
+                test_file.close();
+                std::cout << "\tSearching finished. No errors reported."
+                  << std::endl;
+
+            } else {
+                   std::cerr << "Unable to open file: "<< filePath;
+                   return 1;
+            }
+
         } else if (cli.count("read-file")) {
             std::string filePath = cli["read-file"].as<std::string>();
             std::cout << "\tReading sentences from file: " << filePath <<
@@ -377,11 +413,11 @@ int main(int argc, char** argv) {
                     lineCount++;
                     buffer.push_back(line);
                     if (lineCount % READ_BUFFER_LENGTH == 0) {
-                        performSearch(concordia, buffer, lineCount);
+                        performSearch(concordia, buffer, lineCount, 1);
                     }
                 }
                 if (buffer.size() > 0) {
-                    performSearch(concordia, buffer, lineCount);
+                    performSearch(concordia, buffer, lineCount, 1);
                 }
                 test_file.close();
                 std::cout << "\tSearching finished. No errors reported."
@@ -394,7 +430,8 @@ int main(int argc, char** argv) {
 
         } else {
             std::cerr << "One of the options: simple-search, anubis-search, "
-                      << "concordia-search or read-file must be provided."
+                      << "concordia-search, concordia-search-file, test-file "
+                      << "or read-file must be provided."
                       << "See the options specification: "
                       << std::endl << desc << std::endl;
             return 1;

concordia/concordia_search_result.cpp

@@ -35,13 +35,40 @@ void ConcordiaSearchResult::_checkPossibleOverlays(
             SUFFIX_MARKER_TYPE lastAddedPos,
             SUFFIX_MARKER_TYPE patternSize) {
     bool allTerminal = true;
+
+    // startedFragments is a list of fragments which started the recurrent
+    // check in this _checkPossibleOverlays method invocation.
+    // If this list is non empty, there is no point in starting
+    // new invocations for fragments that do not intersect any in this list.
+    // In this case we would choose to add a fragment to the currentOverlay
+    // that could be preceded by a non intersecting fragment.
+
+    std::vector<MatchedPatternFragment> startedFragments;
     for (int i = lastAddedPos + 1; i < _matchedPatternFragments.size(); i++) {
         MatchedPatternFragment fragment = _matchedPatternFragments.at(i);
 
+        bool nonFilledGap = false;
+        if (startedFragments.size() > 0) {
+            BOOST_FOREACH(MatchedPatternFragment & startedFragment,
+                                                           startedFragments) {
+                if (!fragment.intersects(startedFragment)) {
+                    nonFilledGap = true;
+                }
+            }
+        }
+        if (nonFilledGap) {
+            // If the new fragment does not intersect with any of the
+            // started fragments, break out of the loop.
+            // There is no point in checking a currentOverlay with a gap
+            // that could have been filled.
+            break;
+        }
+
         // if fragment does not intersect currentOverlay
         if (currentOverlay.size() == 0 ||
             !currentOverlay.at(currentOverlay.size()-1).intersects(fragment)) {
             currentOverlay.push_back(fragment);
+            startedFragments.push_back(fragment);
             _checkPossibleOverlays(currentOverlay, i, patternSize);
             allTerminal = false;
         }