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C
- Compound a Sequence holdspublic interface Sequence<C extends Compound>
Main interface for defining a collection of Compounds and accessing them using biological indexes
Method Summary | |
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int |
countCompounds(C... compounds)
Returns the number of times we found a compound in the Sequence |
List<C> |
getAsList()
Returns the Sequence as a List of compounds |
C |
getCompoundAt(int position)
Returns the Compound at the given biological index |
CompoundSet<C> |
getCompoundSet()
Gets the compound set used to back this Sequence |
int |
getIndexOf(C compound)
Scans through the Sequence looking for the first occurrence of the given compound |
SequenceView<C> |
getInverse()
Does the right thing to get the inverse of the current Sequence. |
int |
getLastIndexOf(C compound)
Scans through the Sequence looking for the last occurrence of the given compound |
int |
getLength()
Returns the length of the Sequence |
String |
getSequenceAsString()
Returns the String representation of the Sequence |
SequenceView<C> |
getSubSequence(Integer start,
Integer end)
Returns a portion of the sequence from the different positions. |
Methods inherited from interface java.lang.Iterable |
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iterator |
Methods inherited from interface org.biojava3.core.sequence.template.Accessioned |
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getAccession |
Method Detail |
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int getLength()
C getCompoundAt(int position)
position
- Biological index (1 to n)
int getIndexOf(C compound)
compound
- Compounds to look for
int getLastIndexOf(C compound)
compound
- Compounds to look for
String getSequenceAsString()
List<C> getAsList()
SequenceView<C> getSubSequence(Integer start, Integer end)
start
- Biological index start; must be greater than 0end
- Biological end; must be less than length + 1
CompoundSet<C> getCompoundSet()
int countCompounds(C... compounds)
compounds
- Vargs of the compounds to count
SequenceView<C> getInverse()
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