JIRA: RW-2383 Fixed asn_cleanup -K u in huge mode

git-svn-id: https://anonsvn.ncbi.nlm.nih.gov/repos/v1/trunk/c++@103490 78c7ea69-d796-4a43-9a09-de51944f1b03

Author: foleyjp

include/objtools/cleanup/cleanup.hpp

@@ -342,6 +342,10 @@ class NCBI_CLEANUP_EXPORT CCleanup : public CObject
 /// @return Boolean return value indicates whether title was added
     static bool AddProteinTitle(CBioseq_Handle bsh);
 
+/// Removes NcbiCleanup User Objects in the Seq-descr
+/// @return Boolean return value indicates whether object was removed
+    static bool RemoveNcbiCleanupObject(CSeq_descr& descr);
+
 /// Removes NcbiCleanup User Objects in the Seq-entry
 /// @param seq_entry Seq-entry to edit
 /// @return Boolean return value indicates whether object was removed

src/app/asn_cleanup/asn_cleanup.cpp

@@ -367,6 +367,11 @@ void CCleanupApp::x_ProcessOneFile(const string& filename)
         options |= CCleanupHugeAsnReader::eEnableSmallGenomeSets;
     }
 
+    if (args["K"] && NStr::Find(args["K"].AsString(), "u") != NPOS) {
+        options |= CCleanupHugeAsnReader::eRemoveNcbiUserObjects;
+    }
+
+
     edit::CHugeFileProcess huge_process(new CCleanupHugeAsnReader(options));
     huge_process.OpenFile(filename);
 

src/app/asn_cleanup/huge_file_cleanup.cpp

@@ -217,6 +217,9 @@ void CCleanupHugeAsnReader::x_CleanupTopLevelDescriptors()
         m_Changes.SetChanged(CCleanupChange::eAddNcbiCleanupObject);
     }
 
+    if (m_CleanupOptions & eRemoveNcbiUserObjects) {
+        CCleanup::RemoveNcbiCleanupObject(m_top_entry->SetDescr());
+    }
 
     if (descriptors.empty()) {
         m_top_entry->SetSet().ResetDescr();

src/app/asn_cleanup/huge_file_cleanup.hpp

@@ -53,6 +53,7 @@ class CCleanupHugeAsnReader: public edit::CHugeAsnReader
         eExtendedCleanup       = 1,
         eNoNcbiUserObjects     = 1<<1,
         eEnableSmallGenomeSets = 1<<2,
+        eRemoveNcbiUserObjects = 1<<3,
     };
 
     using TOptions = int;

src/objtools/cleanup/cleanup.cpp

@@ -1895,50 +1895,75 @@ bool CCleanup::AddProteinTitle(CBioseq_Handle bsh)
 }
 
 
+
+static bool s_IsCleanupObject(const CSeqdesc& desc)
+{
+    return (desc.IsUser() && 
+            (desc.GetUser().GetObjectType() == CUser_object::eObjectType_Cleanup));
+}
+
+
+bool CCleanup::RemoveNcbiCleanupObject(CSeq_descr& descr)
+{
+    if (!descr.IsSet() || descr.Get().empty()) {
+        return false;
+    }
+
+    auto& elements = descr.Set();
+    auto it = elements.begin();
+
+    bool rval = false;
+    while (it != elements.end()) {
+        if (s_IsCleanupObject(**it)) {
+            it = elements.erase(it);
+            rval = true;
+        } 
+        else {
+            ++it;
+        }
+    }
+    return rval;
+}
+
+
 bool CCleanup::RemoveNcbiCleanupObject(CSeq_entry &seq_entry)
 {
     bool rval = false;
+
     if (seq_entry.IsSetDescr()) {
-        CBioseq::TDescr::Tdata::iterator it = seq_entry.SetDescr().Set().begin();
-        while (it != seq_entry.SetDescr().Set().end()) {
-            if ((*it)->IsUser() && (*it)->GetUser().GetObjectType() == CUser_object::eObjectType_Cleanup){
-                it = seq_entry.SetDescr().Set().erase(it);
-                rval = true;
-            }
-            else {
-                ++it;
-            }
-        }
-        if (seq_entry.SetDescr().Set().empty()) {
-            if (seq_entry.IsSeq()) {
+        rval = RemoveNcbiCleanupObject(seq_entry.SetDescr());
+        if (rval && seq_entry.GetDescr().Get().empty()) {
+            if (seq_entry.IsSet()) {
                 seq_entry.SetSeq().ResetDescr();
             }
             else if (seq_entry.IsSet()) {
                 seq_entry.SetSet().ResetDescr();
             }
         }
     }
+
     if (seq_entry.IsSet() && seq_entry.GetSet().IsSetSeq_set()) {
-        NON_CONST_ITERATE(CBioseq_set::TSeq_set, it, seq_entry.SetSet().SetSeq_set()) {
-            rval |= RemoveNcbiCleanupObject(**it);
+        for (auto pEntry : seq_entry.SetSet().SetSeq_set()) {
+            rval |= RemoveNcbiCleanupObject(*pEntry);
         }
     }
     return rval;
 }
 
+
 void CCleanup::AddNcbiCleanupObject(int ncbi_cleanup_version, CSeq_descr& descr)
 {
     // update existing
     if (descr.IsSet()) {
         for (auto pDesc : descr.Set()) {
-            if (pDesc->IsUser() && pDesc->GetUser().GetObjectType() == CUser_object::eObjectType_Cleanup) {
+            if (s_IsCleanupObject(*pDesc)) {
                 pDesc->SetUser().UpdateNcbiCleanup(ncbi_cleanup_version);
                 return;
             }
         }
     }
 
-    // create new
+    // create new cleanup object
     auto pCleanupObject = Ref(new CSeqdesc());
     auto& user = pCleanupObject->SetUser();
     user.UpdateNcbiCleanup(ncbi_cleanup_version);