19 #ifndef OST_SEQ_SEQUENCE_HANDLE_HH
20 #define OST_SEQ_SEQUENCE_HANDLE_HH
39 namespace ost {
namespace seq {
42 class AlignmentHandle;
66 int GetResidueIndex(
int pos)
const;
70 int GetPos(
int residue_index)
const;
73 int GetFirstNonGap()
const;
76 int GetLastNonGap()
const;
81 const String& GetName()
const;
86 const String& GetString()
const;
89 String GetGaplessString()
const;
94 int GetOffset()
const;
97 int GetLength()
const;
100 int GetIndex(
const String& substr)
const;
103 char GetOneLetterCode(
int position)
const;
123 bool HasAttachedView()
const;
125 const String& GetRole()
const;
130 char operator[](
int index)
const;
136 bool IsValid()
const;
146 void CheckValidity()
const;
185 int GetResidueIndex(
int pos)
const;
189 int GetPos(
int residue_index)
const;
192 int GetFirstNonGap()
const;
195 int GetLastNonGap()
const;
200 const String& GetName()
const;
205 const String& GetString()
const;
208 String GetGaplessString()
const;
213 int GetOffset()
const;
216 int GetLength()
const;
219 char GetOneLetterCode(
int position)
const;
222 int GetIndex(
const String& substr)
const;
242 bool HasAttachedView()
const;
248 bool IsValid()
const;
256 void SetName(
const String& name);
259 void SetString(
const String& seq);
266 void SetOffset(
int offset);
273 void SetOneLetterCode(
int position,
char new_char);
275 char operator[](
size_t index)
const;
280 void Append(
char olc);
291 const String& GetRole()
const;
293 void SetRole(
const String& role)
const;
301 void CheckValidity()
const;
307 const String& role=
"UNKNOWN");
308 #if(OST_INFO_ENABLED)
319 const ConstSequenceHandle& sequence);
322 const ConstSequenceHandle& s2);