public class RNAStructReader
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
(package private) static class |
RNAStructReader.AlifoldLine |
static class |
RNAStructReader.AlifoldResult |
(package private) static class |
RNAStructReader.RNAOut |
Modifier and Type | Field and Description |
---|---|
(package private) static java.lang.String |
alignmentP |
(package private) static java.lang.String |
bracket |
(package private) static java.lang.String |
centStructP |
(package private) static java.lang.String |
energyP |
(package private) static java.lang.String |
ensembleFreqP |
(package private) static java.lang.String |
floatP |
(package private) static java.lang.String |
freeEnergyP |
(package private) static java.lang.String |
freqP |
(package private) static java.lang.String |
justStructP |
(package private) static java.lang.String |
MEAStructP |
(package private) static java.lang.String |
mfeStructP |
(package private) static java.lang.String |
notData |
(package private) static java.lang.String |
ps |
(package private) static java.lang.String |
PStructP |
(package private) static java.lang.String |
s |
(package private) static java.lang.String |
seqP |
(package private) static java.lang.String |
stochBTStructP |
(package private) static java.lang.String |
structP |
Constructor and Description |
---|
RNAStructReader() |
Modifier and Type | Method and Description |
---|---|
private static RNAStructReader.RNAOut |
identify(java.lang.String token) |
private static RNAStructReader.AlifoldLine |
identifyLine(java.lang.String line) |
static void |
main(java.lang.String[] args) |
static java.util.TreeSet<Score> |
newEmptyScore(java.lang.Enum<?> res) |
private static java.util.TreeSet<Score> |
newSetScore(java.lang.Enum<?> res,
java.util.List<java.lang.Float> scores) |
static RNAStructScoreManager |
readRNAStructStream(java.io.InputStream stdout) |
static RNAStructScoreManager |
readRNAStructStream(java.io.InputStream stdout,
java.io.InputStream alifold) |
static java.lang.String s
static java.lang.String bracket
static java.lang.String notData
static java.lang.String seqP
static java.lang.String structP
static java.lang.String floatP
static java.lang.String energyP
static java.lang.String freqP
static java.lang.String ps
static java.lang.String alignmentP
static java.lang.String mfeStructP
static java.lang.String justStructP
static java.lang.String stochBTStructP
static java.lang.String PStructP
static java.lang.String centStructP
static java.lang.String MEAStructP
static java.lang.String freeEnergyP
static java.lang.String ensembleFreqP
public static RNAStructScoreManager readRNAStructStream(java.io.InputStream stdout) throws java.io.IOException
java.io.IOException
private static java.util.TreeSet<Score> newSetScore(java.lang.Enum<?> res, java.util.List<java.lang.Float> scores)
public static java.util.TreeSet<Score> newEmptyScore(java.lang.Enum<?> res)
public static RNAStructScoreManager readRNAStructStream(java.io.InputStream stdout, java.io.InputStream alifold) throws java.io.IOException
java.io.IOException
private static RNAStructReader.RNAOut identify(java.lang.String token)
private static RNAStructReader.AlifoldLine identifyLine(java.lang.String line)
public static void main(java.lang.String[] args)