From 8f953883bf107cb62be93004a48457bbde99daa3 Mon Sep 17 00:00:00 2001
From: rjawor <rjawor@amu.edu.pl>
Date: Tue, 24 Jun 2014 18:23:46 +0200
Subject: [PATCH] anubis search continued

Former-commit-id: 95a08f242a03311d067303bfff07bf4890796da5
---
 TODO.txt                      |  7 ++++++
 concordia/anubis_searcher.cpp | 41 ++++++++++++++++++++++++++++++++++-
 concordia/common/utils.cpp    | 15 +++++++++++++
 concordia/common/utils.hpp    |  3 +++
 concordia/t/test_utils.cpp    | 25 +++++++++++++++++++++
 5 files changed, 90 insertions(+), 1 deletion(-)

diff --git a/TODO.txt b/TODO.txt
index 950893d..8bbb613 100644
--- a/TODO.txt
+++ b/TODO.txt
@@ -4,3 +4,10 @@ DONE 3. Dzielenie zdań (max 255 tokenów)
 
 - concordia-server
 - zastanowić się nad empty hash examples
+
+
+zastanowić się nad optymalizacją:
+- unordered_map tmMatchesMap
+- LCP array
+
+Anubis search się komplikuje! Przy tworzeniu obiektu tmMatches dla przykładu trzeba podać id przykładu, długość patternu i długość przykładu. Dwa pierwsze mamy, ale niestety nie ma skąd wziąć długości przykładu. Pamiętamy tylko offset sufiksu.
diff --git a/concordia/anubis_searcher.cpp b/concordia/anubis_searcher.cpp
index adca075..8f389c7 100644
--- a/concordia/anubis_searcher.cpp
+++ b/concordia/anubis_searcher.cpp
@@ -1,7 +1,13 @@
 #include "concordia/anubis_searcher.hpp"
+#include "concordia/tm_matches.hpp"
 
-#include<iostream>
+#include <boost/ptr_container/ptr_map.hpp>
+#include <boost/foreach.hpp>
+#include <iostream>
+#include <map>
 
+typedef boost::ptr_map<SUFFIX_MARKER_TYPE, TmMatches> TmMatchesMap;
+typedef TmMatchesMap::iterator TmMatchesMapIterator;
 
 AnubisSearcher::AnubisSearcher() {
 }
@@ -18,6 +24,39 @@ boost::ptr_vector<AnubisSearchResult> AnubisSearcher::anubisSearch(
                 boost::shared_ptr<std::vector<INDEX_CHARACTER_TYPE> > pattern)
                                                 throw(ConcordiaException) {
     boost::ptr_vector<AnubisSearchResult> result;
+    
+    boost::shared_ptr<std::vector<sauchar_t> > patternVector =
+        Utils::indexVectorToSaucharVector(pattern);
+    
+    if (patternVector->size() != pattern->size() * sizeof(INDEX_CHARACTER_TYPE)) {
+        throw ConcordiaException("Increasing pattern resolution went wrong.");
+    } 
+
+    
+    TmMatchesMap tmMatchesMap;
+    for (int offset = 0;offset < pattern->size(); offset++) {
+        int highResOffset = offset * sizeof(INDEX_CHARACTER_TYPE);
+        boost::shared_ptr<std::vector<sauchar_t> > currentPattern =
+            boost::shared_ptr<std::vector<sauchar_t> >(new std::vector<sauchar_t>(
+            patternVector->begin()+highResOffset,patternVector->end()));
+        SUFFIX_MARKER_TYPE longestPrefixesLength;
+        boost::ptr_vector<SubstringOccurence> longestPrefixes = lcpSearch(T, markers, SA,
+                                                 currentPattern, longestPrefixesLength);
+
+        BOOST_FOREACH(SubstringOccurence & occurence, longestPrefixes) {
+            TmMatchesMapIterator mapIterator = tmMatchesMap.find(occurence.getId());
+            if(mapIterator != tmMatchesMap.end()) {
+
+            } else {
+            
+            }   
+        }
+
+        
+        
+        
+    }    
+        
     return result;
 }
 
diff --git a/concordia/common/utils.cpp b/concordia/common/utils.cpp
index 00a8fa7..7ae58cc 100644
--- a/concordia/common/utils.cpp
+++ b/concordia/common/utils.cpp
@@ -42,6 +42,19 @@ sauchar_t * Utils::indexVectorToSaucharArray(
     return patternArray;
 }
 
+boost::shared_ptr<std::vector<sauchar_t> > Utils::indexVectorToSaucharVector(
+                     boost::shared_ptr<vector<INDEX_CHARACTER_TYPE> > input) {
+    
+    boost::shared_ptr<std::vector<sauchar_t> > result = boost::shared_ptr<std::vector<sauchar_t> >(
+                                                    new std::vector<sauchar_t>);
+                                                    
+    for (vector<INDEX_CHARACTER_TYPE>::iterator it = input->begin();
+                                          it != input->end(); ++it) {
+        appendCharToSaucharVector(result, *it);
+    }
+    return result;
+}
+
 void Utils::appendCharToSaucharVector(
                              boost::shared_ptr<std::vector<sauchar_t> > vector,
                              INDEX_CHARACTER_TYPE character) {
@@ -58,4 +71,6 @@ void Utils::_insertCharToSaucharArray(sauchar_t * array,
         array[i] = characterArray[i-pos];
     }
 }
+             
+
 
diff --git a/concordia/common/utils.hpp b/concordia/common/utils.hpp
index 2f2bff7..4fc3897 100644
--- a/concordia/common/utils.hpp
+++ b/concordia/common/utils.hpp
@@ -34,6 +34,9 @@ public:
     static sauchar_t * indexVectorToSaucharArray(
                        boost::shared_ptr<vector<INDEX_CHARACTER_TYPE> > input);
 
+    static boost::shared_ptr<std::vector<sauchar_t> > indexVectorToSaucharVector(
+                       boost::shared_ptr<vector<INDEX_CHARACTER_TYPE> > input);
+
     static void appendCharToSaucharVector(
                              boost::shared_ptr<std::vector<sauchar_t> > vector,
                              INDEX_CHARACTER_TYPE character);
diff --git a/concordia/t/test_utils.cpp b/concordia/t/test_utils.cpp
index 042f301..184c542 100644
--- a/concordia/t/test_utils.cpp
+++ b/concordia/t/test_utils.cpp
@@ -60,6 +60,31 @@ BOOST_AUTO_TEST_CASE( IndexVectorToSaucharArray )
     BOOST_CHECK_EQUAL_COLLECTIONS(result->begin(), result->end(), expected->begin(), expected->end());      
 }
 
+BOOST_AUTO_TEST_CASE( IndexVectorToSaucharVector )
+{
+    boost::shared_ptr<vector<INDEX_CHARACTER_TYPE> > hash(new vector<INDEX_CHARACTER_TYPE>());
+    hash->push_back(123456789);         // in hex: 75BCD15
+                                       // in memory:  15  cd  5b  07
+                                       // in memory DEC:  21 205  91   7 
+
+    hash->push_back(987654321);         // in hex: 3ADE68B1
+                                       // in memory:  b1  68  de  3a
+                                       // in memory DEC: 177 104 222  58         
+    boost::shared_ptr<vector<sauchar_t> > result = Utils::indexVectorToSaucharVector(hash);
+    
+    boost::shared_ptr<vector<sauchar_t> > expected(new vector<sauchar_t>());
+    expected->push_back(21);
+    expected->push_back(205);
+    expected->push_back(91);
+    expected->push_back(7);
+    expected->push_back(177);
+    expected->push_back(104);
+    expected->push_back(222);
+    expected->push_back(58);
+
+    BOOST_CHECK_EQUAL_COLLECTIONS(result->begin(), result->end(), expected->begin(), expected->end());      
+}
+
 
 
 BOOST_AUTO_TEST_SUITE_END()