fix up maf export to properly iterate over multiple sequences

ComparativeGenomicsToolkit · Oct 4, 2012 · f0f47e6 · f0f47e6
1 parent a01ef15
commit f0f47e6
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Showing 5 changed files with 29 additions and 75 deletions.
diff --git a/api/hdf5_impl/hdf5Genome.cpp b/api/hdf5_impl/hdf5Genome.cpp
@@ -548,7 +548,7 @@ ColumnIteratorConstPtr HDF5Genome::getColumnIterator(
       lastPosition >= (hal_index_t)(getSequenceLength()))
   {
     stringstream ss;
-    ss << "HDF5Genome::getColumnIteratorsetString: input indices "
+    ss << "HDF5Genome::getColumnIterator: input indices "
        << "(" << position << ", " << lastPosition << ") out of bounds";
     throw hal_exception(ss.str());
   }

diff --git a/api/hdf5_impl/hdf5Sequence.cpp b/api/hdf5_impl/hdf5Sequence.cpp
@@ -228,7 +228,7 @@ ColumnIteratorConstPtr HDF5Sequence::getColumnIterator(
       lastPosition >= (hal_index_t)(getStartPosition() + getSequenceLength()))
   {
     stringstream ss;
-    ss << "HDF5Sequence::getColumnIteratorsetString: input indices "
+    ss << "HDF5Sequence::getColumnIterators: input indices "
        << "(" << position << ", " << lastPosition << ") out of bounds";
     throw hal_exception(ss.str());
   }

diff --git a/maf/impl/hal2maf.cpp b/maf/impl/hal2maf.cpp
@@ -112,11 +112,13 @@ int main(int argc, char** argv)
     {
       refGenome = alignment->openGenome(alignment->getRootName());
     }
+    const SegmentedSequence* ref = refGenome;
 
     const Sequence* refSequence = NULL;
     if (refSequenceName != "\"\"")
     {
       refSequence = refGenome->getSequence(refSequenceName);
+      ref = refSequence;
       if (refSequence == NULL)
       {
         throw hal_exception(string("Reference sequence, ") + refSequenceName + 
@@ -134,17 +136,9 @@ int main(int argc, char** argv)
     MafExport mafExport;
     mafExport.setMaxRefGap(maxRefGap);
     mafExport.setNoDupes(noDupes);
-
-    if (refSequence == NULL)
-    {
-      mafExport.convertGenome(mafStream, alignment, refGenome, 
-                              start, length, rootGenome);
-    }
-    else
-    {
-      mafExport.convertSequence(mafStream, alignment, refSequence,
-                                start, length, rootGenome);
-    }
+
+    mafExport.convertSegmentedSequence(mafStream, alignment, ref, 
+                                       start, length, rootGenome);
 
   }
   catch(hal_exception& e)

diff --git a/maf/impl/halMafExport.cpp b/maf/impl/halMafExport.cpp
@@ -41,67 +41,34 @@ void MafExport::writeHeader()
   }
 }
 
-void MafExport::convertGenome(ostream& mafStream,
-                              AlignmentConstPtr alignment,
-                              const Genome* genome,
-                              hal_index_t startPosition,
-                              hal_size_t length,
-                              const Genome* root)
+void MafExport::convertSegmentedSequence(ostream& mafStream,
+                                         AlignmentConstPtr alignment,
+                                         const SegmentedSequence* seq,
+                                         hal_index_t startPosition,
+                                         hal_size_t length,
+                                         const Genome* root)
 {
-  if (length == 0)
-  {
-    length = genome->getSequenceLength() - startPosition;
-  }
-  if ((hal_size_t)startPosition + length > genome->getSequenceLength())
+  assert(seq != NULL);
+  if (startPosition >= (hal_index_t)seq->getSequenceLength() ||
+      (hal_size_t)startPosition + length > seq->getSequenceLength())
   {
     throw hal_exception("Invalid range specified for convertGenome");
   }
-  _mafStream = &mafStream;
-  _alignment = alignment;
-  writeHeader();
-  hal_index_t pos = startPosition;
-  hal_size_t doneLen = 0;
-
-  while (doneLen < length)
-  {
-    assert(pos < (hal_index_t)genome->getSequenceLength());
-    const Sequence* sequence = genome->getSequenceBySite(pos);
-    assert(sequence != NULL);
-    hal_index_t seqStart = pos - sequence->getStartPosition();
-    hal_size_t curLen = min(length - doneLen, 
-                            sequence->getSequenceLength() - seqStart);
-    assert(curLen > 0);
-    convertSequence(mafStream, alignment, sequence, seqStart, curLen, root);
-    pos += curLen;
-    doneLen += curLen;
-  }
-}
-
-void MafExport::convertSequence(ostream& mafStream,
-                                AlignmentConstPtr alignment,
-                                const Sequence* sequence,
-                                hal_index_t startPosition,
-                                hal_size_t length,
-                                const Genome* root)
-{
   if (length == 0)
   {
-    length = sequence->getSequenceLength();
-  }
-  if ((hal_size_t)startPosition + length > sequence->getSequenceLength())
-  {
-    throw hal_exception("Invalid range specified for convertSequence");
+    length = seq->getSequenceLength() - startPosition;
   }
   hal_index_t lastPosition = startPosition + (hal_index_t)(length - 1);
+
   _mafStream = &mafStream;
   _alignment = alignment;
   writeHeader();
 
-  ColumnIteratorConstPtr colIt = sequence->getColumnIterator(root,
-                                                             _maxRefGap, 
-                                                             startPosition,
-                                                             lastPosition,
-                                                             _noDupes);
+  ColumnIteratorConstPtr colIt = seq->getColumnIterator(root,
+                                                        _maxRefGap, 
+                                                        startPosition,
+                                                        lastPosition,
+                                                        _noDupes);
   _mafBlock.initBlock(colIt);
   assert(_mafBlock.canAppendColumn(colIt) == true);
 

diff --git a/maf/inc/halMafExport.h b/maf/inc/halMafExport.h
@@ -22,19 +22,12 @@ class MafExport
 
    virtual ~MafExport();
 
-   void convertGenome(std::ostream& mafStream,
-                      AlignmentConstPtr alignment,
-                      const Genome* genome,
-                      hal_index_t startPosition = 0,
-                      hal_size_t length = 0,
-                      const Genome* root = NULL);
-
-   void convertSequence(std::ostream& mafStream,
-                        AlignmentConstPtr alignment,
-                        const Sequence* sequence,
-                        hal_index_t startPosition = 0,
-                        hal_size_t length = 0,
-                        const Genome* root = NULL);
+   void convertSegmentedSequence(std::ostream& mafStream,
+                                 AlignmentConstPtr alignment,
+                                 const SegmentedSequence* seq,
+                                 hal_index_t startPosition,
+                                 hal_size_t length,
+                                 const Genome* root);
 
    void setMaxRefGap(hal_size_t maxRefGap);
    void setNoDupes(bool noDupes);