221       final Range real_range = new Range (real_start, real_end);  in complementRange()  local
223       return real_range;  in complementRange()
306     final Range real_range;  in getMatchingCodons()  local
309       real_range = range;  in getMatchingCodons()
311       real_range = complementRange(range);  in getMatchingCodons()
335     final int range_start_index = real_range.getStart () - 1;  in getMatchingCodons()
336     final int range_end_index = real_range.getEnd () - 1;  in getMatchingCodons()
510     final Range real_range;  in getStopCodons()  local
513       real_range = range;  in getStopCodons()
515       real_range = complementRange (range);  in getStopCodons()
534     int range_start_index = real_range.getStart();  in getStopCodons()
535     int range_end_index   = real_range.getEnd();  in getStopCodons()
668     final Range real_range;  in getStopOrStartCodons()  local
671       real_range = range;  in getStopOrStartCodons()
673       real_range = complementRange(range);  in getStopOrStartCodons()
695     int range_start_index = real_range.getStart();  in getStopOrStartCodons()
696     int range_end_index   = real_range.getEnd();  in getStopOrStartCodons()
885     final Range real_range;  in getSubSequence()  local
888       real_range = range;  in getSubSequence()
890       real_range = complementRange (range);  in getSubSequence()
897     if(real_range.getStart () < 1)  in getSubSequence()
900       sub_seq_start_index = real_range.getStart ();  in getSubSequence()
902     if(real_range.getEnd () > getLength ())   in getSubSequence()
905       sub_seq_end_index = real_range.getEnd ();  in getSubSequence()
912     if (real_range.getStart () < 1) {  in getSubSequence()
913       final int dummy_base_count = 1 - real_range.getStart ();  in getSubSequence()
923     if (real_range.getEnd () > getLength ()) {  in getSubSequence()
924       final int dummy_base_count = real_range.getEnd () - getLength ();  in getSubSequence()
943     final Range real_range;  in getSubSequenceC()  local
946       real_range = range;  in getSubSequenceC()
948       real_range = complementRange (range);  in getSubSequenceC()
955     if(real_range.getStart () < 1)   in getSubSequenceC()
958       sub_seq_start_index = real_range.getStart ();  in getSubSequenceC()
960     if(real_range.getEnd () > getLength ())   in getSubSequenceC()
963       sub_seq_end_index = real_range.getEnd ();  in getSubSequenceC()
968     if(real_range.getStart() < 1)   in getSubSequenceC()
970       final int dummy_base_count = 1 - real_range.getStart();  in getSubSequenceC()
980     if(real_range.getEnd() > getLength())   in getSubSequenceC()
982       final int dummy_base_count = real_range.getEnd() - getLength();  in getSubSequenceC()