static void |
RNAUtils.addLastP(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to add a phosphate to the last polymer's nucleotide
|
static boolean |
RNAUtils.areAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation polymerOne,
org.helm.notation2.parser.notation.polymer.PolymerNotation polymerTwo) |
method to check if two given polymers are complement to each other
|
static org.helm.notation2.parser.notation.polymer.PolymerNotation |
RNAUtils.getAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the antiparallel polymer for a rna/dna polymer
|
static org.helm.notation2.parser.notation.polymer.PolymerNotation |
RNAUtils.getComplement(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the normal complement polymer for a given rna/dna polymer
|
static String[] |
HELM2NotationUtils.getFormatedSirnaSequences(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
generate formated siRNA sequence with default padding char " " and
base-pair char "|"
|
static String[] |
HELM2NotationUtils.getFormatedSirnaSequences(org.helm.notation2.parser.notation.HELM2Notation helm2notation,
String paddingChar,
String basePairChar) |
|
static org.helm.notation2.parser.notation.polymer.PolymerNotation |
RNAUtils.getInverse(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the polymer with the inverse sequence of the current
polymer
|
static String |
RNAUtils.getModifiedNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the modifiedNucleotideSequence of the given PolymerNotation
|
static String |
RNAUtils.getNaturalAnalogSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to generate the natural analogue sequence of a rna/dna of a given
polymer
|
static List<Nucleotide> |
RNAUtils.getNucleotideList(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get all nucleotides for one polymer
|
static String |
RNAUtils.getNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the nucleotide sequence for the polymer
|
static org.helm.notation2.parser.notation.polymer.PolymerNotation |
RNAUtils.getReverseComplement(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the polymer with the reverse complement sequence of the
current polymer
|
static String |
RNAUtils.getReverseSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to generate the reverse rna/dna sequence of a given polymer
|
static String |
RNAUtils.getSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation one) |
method to get the rna sequence of the given PolymerNotation
|
static org.helm.notation2.parser.notation.HELM2Notation |
SiRNANotation.getSirnaNotation(String senseSeq,
String antiSenseSeq,
String rnaDesignType) |
this method converts nucleotide sequences into HELM notation based on
design pattern
|
static org.helm.notation2.parser.notation.HELM2Notation |
SiRNANotation.getSiRNANotation(String senseSeq,
String antiSenseSeq) |
this method converts nucleotide sequences into HELM2Notation
|
static String |
RNAUtils.getTrimmedNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to get the trimmed nucleotide sequence
|
static void |
ChangeObjects.hybridize(org.helm.notation2.parser.notation.HELM2Notation helm2notation) |
this method will automatically add base pair info into notation only if
it contains two RNA polymer notations and there is no base pairing info
|
static List<org.helm.notation2.parser.notation.connection.ConnectionNotation> |
RNAUtils.hybridize(org.helm.notation2.parser.notation.polymer.PolymerNotation one,
org.helm.notation2.parser.notation.polymer.PolymerNotation two) |
method to hybridize two given PolymerNotations together
|
static List<org.helm.notation2.parser.notation.connection.ConnectionNotation> |
RNAUtils.hybridizeAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation one,
org.helm.notation2.parser.notation.polymer.PolymerNotation two) |
method to hybridize two PolymerNotations together if they are
antiparallel
|
static void |
RNAUtils.removeLastP(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) |
method to remove the phosphate of the last nucleotide
|