Changeset 8281

Timestamp:

07/12/11 18:46:05 (6 months ago)

Author:

eissler

Message:

PTPan update to current version

Location:

branches/ptpan_back/ptpan

Files:

• changelog.txt (modified) (2 diffs)
• ptpan.cxx (modified) (1 diff)
• ptpan.h (modified) (1 diff)
• ptpan_tree.cxx (modified) (12 diffs)
• ptpan_tree.h (modified) (2 diffs)
• ptpan_tree_builder.cxx (modified) (1 diff)

branches/ptpan_back/ptpan/changelog.txt

@@ -1 +1 @@
 PTPan ARB integration
 
-v0.6.6 (?? ?? 2011)
+v0.6.7 (?? ?? 2011)
 
 - TODO
@@ -23 +23 @@
 - added method probeNongroupIncreaseArrayWidth()
 - added custom information field in index header
+- added convenience methods here and there
 
 - major refactoring to make interface easier to use

branches/ptpan_back/ptpan/ptpan.cxx

@@ -541 +541 @@
 
 /*!
+ * \brief Return pointer list of all Features
+ *
+ * \return const std::vector<PTPanFeature*>
+ */
+const std::vector<PTPanFeature*> PTPanFeatureContainer::getAllFeatures() const {
+    if (m_normal_mode) {
+        return *m_features;
+    }
+    return std::vector<PTPanFeature*>();
+}
+
+/*!
+ * \brief Return list of all Feature ids
+ *
+ * \return const std::vector<std::string>
+ */
+const std::vector<std::string> PTPanFeatureContainer::getAllFeatureIds() const {
+    if (m_normal_mode) {
+        std::vector<std::string> ret_values;
+        std::vector<PTPanFeature*>::const_iterator it;
+        for (it = m_features->begin(); it != m_features->end(); it++) {
+            ret_values.push_back((*it)->pf_name);
+        }
+        return ret_values;
+    }
+    return std::vector<std::string>();
+}
+
+/*!
  * \brief Returns the maximum byte size of this container for storing
  *

branches/ptpan_back/ptpan/ptpan.h

@@ -246 +246 @@
 
     const PTPanFeature * getFeatureByNumber(ULONG number) const;
+    const std::vector<PTPanFeature*> getAllFeatures() const;
+    const std::vector<std::string> getAllFeatureIds() const;
 
     ULONG byteSize() const;

branches/ptpan_back/ptpan/ptpan_tree.cxx

@@ -500 +500 @@
  * \brief Return PTPanReferenceEntry
  *
- * \warning Do not free! PtpanTree is still owner! This is no copy!
+ * \warning Do not free! PtpanTree is still owner! Does not return a copy!
  *
  * May return NULL if not available!
@@ -525 +525 @@
  * \brief Return pointer to first PTPanEntry in list
  *
- * \warning Do not free! PtpanTree is still owner! This is no copy!
+ * \warning Do not free! PtpanTree is still owner! Does not return a copy!
  *
  * \return struct PTPanEntry*
@@ -539 +539 @@
  * \brief Return PTPanEntry
  *
- * \warning Do not free! PtpanTree is still owner! This is no copy!
+ * \warning Do not free! PtpanTree is still owner! Does not return a copy!
  *
  * May return NULL if not available!
@@ -551 +551 @@
 
 /*!
+ * \brief Return PTPanEntry for given id
+ *
+ * \warning Do not free! PtpanTree is still owner! Does not return a copy!
+ *
+ * May return NULL if not available!
+ */
+const PTPanEntry* PtpanTree::getEntry(const std::string& id) const {
+
+    if (m_contains_features) {
+        // split id at '/' and try to find the parts!
+        // TODO FIXME better take '#' as delimiter, split and take first and second value of vector!
+        std::size_t pos = id.find('/');
+        if (pos != std::string::npos) {
+            std::string entry = id.substr(0, pos);
+            // NUMBER OF ENTRY: it->second - 1
+            PtpanEntryMap::const_iterator it = m_entry_map.find(entry.data());
+            if (it != m_entry_map.end()) {
+                PTPanEntry* ptpan_entry = m_EntriesMap[(it->second) - 1];
+                if (ptpan_entry) {
+                    return ptpan_entry;
+                }
+            }
+        } else {
+            // no feature(s), but maybe whole genomes!!
+            PtpanEntryMap::const_iterator it = m_entry_map.find(id.data());
+            if (it != m_entry_map.end()) {
+                PTPanEntry* ptpan_entry = m_EntriesMap[(it->second) - 1];
+                if (ptpan_entry) {
+                    return ptpan_entry;
+                }
+            }
+        }
+    } else {
+        PtpanEntryMap::const_iterator it = m_entry_map.find(id.data());
+        if (it != m_entry_map.end()) {
+            PTPanEntry* ptpan_entry = m_EntriesMap[(it->second) - 1];
+            if (ptpan_entry) {
+                return ptpan_entry;
+            }
+        }
+    }
+    return NULL;
+}
+
+/*!
  * \brief Return full name of entry
  *
- * \warning Do not free! PtpanTree is still owner! This is no copy!
+ * \warning Do not free! PtpanTree is still owner! Does not return a copy!
  *
  * May return NULL if not available!
@@ -567 +612 @@
  * \brief Return (string) id of entry
  *
- * \warning Do not free! PtpanTree is still owner! This is no copy!
+ * \warning Do not free! PtpanTree is still owner! Does not return a copy!
  *
  * May return NULL if not available!
@@ -588 +633 @@
     while (ps->pe_Node.ln_Succ) {
         ret_values.push_back(ps->pe_Name);
+        ps = (struct PTPanEntry *) ps->pe_Node.ln_Succ;
+    }
+    return ret_values;
+}
+
+/*!
+ * \brief Returns all entries
+ *
+ * \return const std::vector<PTPanEntry*>
+ */
+const std::vector<PTPanEntry*> PtpanTree::getAllEntries() const {
+    std::vector<PTPanEntry*> ret_values;
+    struct PTPanEntry* ps = (struct PTPanEntry *) m_entries->lh_Head;
+    while (ps->pe_Node.ln_Succ) {
+        ret_values.push_back(ps);
         ps = (struct PTPanEntry *) ps->pe_Node.ln_Succ;
     }
@@ -841 +901 @@
     UWORD seqcode = 0;
     ULONG length_corr =
-            (length < best_pp->pp_TreePruneLength) ?
-                    length : best_pp->pp_TreePruneLength;
+            (length < best_pp->pp_TreePruneLength) ? length :
+                    best_pp->pp_TreePruneLength;
 
     ULONG buffer_size;
@@ -2848 +2908 @@
         SearchQueryHandle& sqh) const {
     LONG query_len =
-            sq.sq_Query.size() > m_prune_length ?
-                    m_prune_length : (LONG) sq.sq_Query.size();
+            sq.sq_Query.size() > m_prune_length ? m_prune_length :
+                    (LONG) sq.sq_Query.size();
     LONG source_len =
-            sqh.sqh_MaxLength > m_prune_length ?
-                    m_prune_length : (LONG) sqh.sqh_MaxLength;
+            sqh.sqh_MaxLength > m_prune_length ? m_prune_length :
+                    (LONG) sqh.sqh_MaxLength;
 
     LONG max_check =
-            sq.sq_Query.size() < m_prune_length ?
-                    m_prune_length - sq.sq_Query.size() : 0;
+            sq.sq_Query.size() < m_prune_length ? m_prune_length
+                    - sq.sq_Query.size() :
+                    0;
     if (max_check > sq.sq_MaxErrors) {
         max_check = (LONG) sq.sq_MaxErrors;
@@ -3188 +3249 @@
                         // find the match with the lowest error count in range
                         // range = query length +- number of allowed indels
-                        for (ULONG l = 1; l <= levenshtein.m_max_check; l++) {
-                            if (levenshtein.m_distance_matrix[levenshtein.m_query_len
-                                    + l][levenshtein.m_query_len]
-                                    < sqh.sqh_State.sqs_ErrorCount && levenshtein.m_direction_matrix[levenshtein.m_query_len
-                                    + l][levenshtein.m_query_len]
-                                    == LEV_EQ) { // TODO FIXME why LEV_EQ??
-sqh                            .sqh_State.sqs_ErrorCount =
-                            levenshtein.m_distance_matrix[levenshtein.m_query_len
-                            + l][levenshtein.m_query_len];
-                            length = levenshtein.m_query_len + l;
+                        if (sq.sq_AllowInsert) {
+                            for (ULONG l = 1; l <= levenshtein.m_max_check;
+                                    l++) {
+                                if (levenshtein.m_distance_matrix[levenshtein.m_query_len
+                                        + l][levenshtein.m_query_len]
+                                        < sqh.sqh_State.sqs_ErrorCount && levenshtein.m_direction_matrix[levenshtein.m_query_len
+                                        + l][levenshtein.m_query_len]
+                                        == LEV_EQ) { // TODO FIXME why LEV_EQ??
+sqh                                .sqh_State.sqs_ErrorCount =
+                                levenshtein.m_distance_matrix[levenshtein.m_query_len
+                                + l][levenshtein.m_query_len];
+                                length = levenshtein.m_query_len + l;
+                            }
                         }
                     }
+
                         for (int l = 1; l <= (int) sq.sq_MaxErrors; l++) {
                             if (levenshtein.m_distance_matrix[levenshtein.m_query_len
@@ -3683 +3748 @@
                 qh->qh_sortKey =
                         (LLONG) (
-                                (qh->qh_Flags & QHF_REVERSED) ?
-                                        (1LL << 62) : 0LL)
-                                + ((qh->qh_InsertCount | qh->qh_DeleteCount) ?
-                                        (1LL << 61) : 0LL)
+                                (qh->qh_Flags & QHF_REVERSED) ? (1LL << 62) :
+                                        0LL)
+                                + ((qh->qh_InsertCount | qh->qh_DeleteCount) ? (1LL
+                                        << 61) :
+                                        0LL)
                                 + (((LLONG) (qh->qh_ReplaceCount
                                         + qh->qh_InsertCount
@@ -3714 +3780 @@
                 qh->qh_sortKey =
                         (LLONG) (
-                                (LLONG) (qh->qh_Flags & QHF_REVERSED) ?
-                                        (1LL << 62) : 0LL)
+                                (LLONG) (qh->qh_Flags & QHF_REVERSED) ? (1LL
+                                        << 62) :
+                                        0LL)
                                 + ((LLONG) (qh->qh_InsertCount
-                                        | qh->qh_DeleteCount) ?
-                                        (1LL << 61) : 0LL)
+                                        | qh->qh_DeleteCount) ? (1LL << 61) :
+                                        0LL)
                                 + (((LLONG) round(qh->qh_ErrorCount * 10.0))
                                         << 56)
@@ -3967 +4034 @@
     UWORD seqcode = m_as->wildcard_code + 1;
     ULONG length =
-            (dq.dq_ProbeLength < pp->pp_TreePruneLength) ?
-                    dq.dq_ProbeLength : pp->pp_TreePruneLength;
+            (dq.dq_ProbeLength < pp->pp_TreePruneLength) ? dq.dq_ProbeLength :
+                    pp->pp_TreePruneLength;
     double currtemp = 0.0;
     UWORD currgc = 0;

branches/ptpan_back/ptpan/ptpan_tree.h

@@ -318 +318 @@
      */
     static const std::string version() {
-        return "0.6.6_beta";
+        return "0.6.7_beta";
     }
 
@@ -333 +333 @@
     const PTPanEntry* getFirstEntry() const;
     const PTPanEntry* getEntry(ULONG id) const;
+    const PTPanEntry* getEntry(const std::string& id) const;
     CONST_STRPTR getEntryFullName(ULONG id) const;
     CONST_STRPTR getEntryId(ULONG id) const;
 
     const std::vector<std::string> getAllEntryIds() const;
+    const std::vector<PTPanEntry*> getAllEntries() const;
 
     ULONG getPruneLength() const;

branches/ptpan_back/ptpan/ptpan_tree_builder.cxx

@@ -1000 +1000 @@
                 mergeEntry();
                 m_threadpool->wait();
-                m_threadpool->clear();
             }