All Packages  Class Hierarchy

Index of all Fields and Methods

A

AcedbSeqFormat(). Constructor for class iubio.readseq.AcedbSeqFormat

add(byte[], int, int). Method in class iubio.bioseq.SeqInfo

add(char[], int, int). Method in class iubio.bioseq.SeqInfo

add(int). Method in class iubio.bioseq.SeqInfo

add(SeqRange). Method in class iubio.bioseq.SeqRange

add(String, int, int). Method in class iubio.bioseq.SeqInfo

addBasicName(String). Method in interface iubio.readseq.BioseqDoc

addBasicName(String). Method in class iubio.readseq.BioseqDocImpl

addComment(String). Method in class iubio.readseq.BioseqDocImpl

addDate(Date). Method in class iubio.readseq.BioseqDocImpl

addDocField(DocItem). Method in class iubio.readseq.BioseqDocImpl

addDocField(int, String). Method in class iubio.readseq.BioseqDocImpl

addDocField(String, String, int, boolean). Method in interface iubio.readseq.BioseqDoc

addDocField(String, String, int, boolean). Method in class iubio.readseq.BioseqDocImpl

addDocField(String, String, int, boolean). Method in class iubio.readseq.EmblDoc

addDocField(String, String, int, boolean). Method in class iubio.readseq.GenbankDoc

addDocField(String, String, int, int, boolean). Method in class iubio.readseq.BioseqDocImpl

addDocLine(OpenString). Method in interface iubio.readseq.BioseqDoc

addDocLine(OpenString). Method in class iubio.readseq.BioseqDocImpl

addDocLine(String). Method in class iubio.readseq.BasicBioseqDoc

addDocLine(String). Method in interface iubio.readseq.BioseqDoc

addDocLine(String). Method in class iubio.readseq.BioseqDocImpl

addDocLine(String). Method in class iubio.readseq.EmblDoc

addDocLine(String). Method in class iubio.readseq.GenbankDoc

addDocLine(String). Method in class iubio.readseq.XmlDoc

addDocText(String). Method in class iubio.readseq.BioseqDocImpl

addElement(Object). Method in class flybase.FastVector

Adds the specified object as the last element of the vector.

addFeature(FeatureItem). Method in class iubio.readseq.BioseqDocImpl

addFeature(String, SeqRange). Method in class iubio.readseq.BioseqDocImpl

addFeature(String, String, int, boolean). Method in class iubio.readseq.BioseqDocImpl

addFeature(String, String, int, boolean). Method in class iubio.readseq.SwissDoc

addFeature(String, String, int, boolean). Method in class iubio.readseq.XmlDoc

addFeatureNote(FeatureItem, String). Method in class iubio.readseq.BioseqDocImpl

addFeatureNote(FeatureItem, String, String). Method in class iubio.readseq.BioseqDocImpl

addFeatureNote(String). Method in class iubio.readseq.BioseqDocImpl

addFeatureNote(String, String). Method in class iubio.readseq.BioseqDocImpl

addFeatures(FastVector). Method in class iubio.readseq.BioseqDocImpl

addFeatureText(String). Method in class iubio.readseq.BioseqDocImpl

addInputObject(Object). Method in class iubio.readseq.run

addItem(Object). Method in class flybase.FastVector

addSeq(Object, String, int, int, Object, boolean). Method in class iubio.readseq.Writeseq

addSeq(SeqFileInfo). Method in class iubio.readseq.Writeseq

addSequenceStats(Bioseq). Method in class iubio.readseq.BioseqDocImpl

allprintflag. Static variable in class iubio.bioseq.BaseKind

allresults(). Method in class iubio.readseq.Readseq

allresults(). Method in class iubio.readseq.Writeseq

allSeqs(). Method in class iubio.readseq.Readseq

alnumseqflag. Static variable in class iubio.bioseq.BaseKind

alphaseqflag. Static variable in class iubio.bioseq.BaseKind

Amino123(char). Static method in class iubio.bioseq.BaseKind

Amino321(String). Static method in class iubio.bioseq.BaseKind

aminoConsensus(byte, byte). Static method in class iubio.bioseq.BaseKind

aminoflag. Static variable in class iubio.bioseq.BaseKind

app(). Constructor for class app

app(String[]). Constructor for class iubio.readseq.app

append(String, String). Method in class flybase.Environ

appendNote(String). Method in class iubio.readseq.FeatureItem

appendValue(String). Method in class iubio.readseq.DocItem

appendValue(String). Method in class iubio.readseq.FeatureItem

appendValue(String, String). Method in class iubio.readseq.DocItem

AppResources(). Constructor for class flybase.AppResources

appusage(). Static method in class iubio.readseq.app

appusage(PrintStream). Static method in class iubio.readseq.app

arg(). Method in class flybase.Args

argFlag. Static variable in class flybase.Args

argKey(). Method in class flybase.Args

Args(String[]). Constructor for class flybase.Args

Args(String[], boolean). Constructor for class flybase.Args

argType(). Method in class flybase.Args

argValue(). Method in class flybase.Args

Asn1SeqFormat(). Constructor for class iubio.readseq.Asn1SeqFormat

atColumn(). Method in class iubio.readseq.XmlPrintWriter

atNewline(). Method in class iubio.readseq.XmlPrintWriter

atresult(). Method in class iubio.readseq.Readseq

atresult(). Method in class iubio.readseq.Writeseq

atseq. Variable in class iubio.readseq.SeqFileInfo

atseq. Variable in class iubio.readseq.WriteseqOpts

B

base(int, int). Method in class iubio.bioseq.Bioseq

basebyte(int). Method in class iubio.bioseq.Bioseq

basebyte(int). Method in class iubio.bioseq.BioseqFiled

basechar(int). Method in class iubio.bioseq.Bioseq

BaseKind(). Constructor for class iubio.bioseq.BaseKind

baseOnly. Static variable in class iubio.bioseq.Bioseq

baseonlynum. Variable in class iubio.readseq.WriteseqOpts

bases(). Method in class iubio.bioseq.Bioseq

BasicBioseqDoc(). Constructor for class iubio.readseq.BasicBioseqDoc

BasicBioseqDoc(BioseqDoc). Constructor for class iubio.readseq.BasicBioseqDoc

BasicBioseqDoc(String). Constructor for class iubio.readseq.BasicBioseqDoc

Bioseq(). Constructor for class iubio.bioseq.Bioseq

Bioseq(byte[]). Constructor for class iubio.bioseq.Bioseq

Bioseq(byte[], int, int). Constructor for class iubio.bioseq.Bioseq

Bioseq(char[]). Constructor for class iubio.bioseq.Bioseq

Bioseq(char[], int, int). Constructor for class iubio.bioseq.Bioseq

Bioseq(int). Constructor for class iubio.bioseq.Bioseq

Bioseq(Object). Constructor for class iubio.bioseq.Bioseq

Bioseq(String). Constructor for class iubio.bioseq.Bioseq

BioseqDocImpl(). Constructor for class iubio.readseq.BioseqDocImpl

BioseqDocImpl(BioseqDoc). Constructor for class iubio.readseq.BioseqDocImpl

BioseqFiled(). Constructor for class iubio.bioseq.BioseqFiled

BioseqFiled(byte[]). Constructor for class iubio.bioseq.BioseqFiled

BioseqFiled(byte[], int, int). Constructor for class iubio.bioseq.BioseqFiled

BioseqFiled(char[]). Constructor for class iubio.bioseq.BioseqFiled

BioseqFiled(char[], int, int). Constructor for class iubio.bioseq.BioseqFiled

BioseqFiled(File, boolean). Constructor for class iubio.bioseq.BioseqFiled

BioseqFiled(int). Constructor for class iubio.bioseq.BioseqFiled

BioseqFiled(String). Constructor for class iubio.bioseq.BioseqFiled

BioseqFormat(). Constructor for class iubio.readseq.BioseqFormat

bioseqFormat(int). Static method in class iubio.readseq.BioseqFormats

BioseqFormats(). Constructor for class iubio.readseq.BioseqFormats

bioseqprop. Static variable in class iubio.readseq.BioseqDocImpl

BioseqReader(). Constructor for class iubio.readseq.BioseqReader

BioseqReader(Reader). Constructor for class iubio.readseq.BioseqReader

BioseqRecord(). Constructor for class iubio.readseq.BioseqRecord

BioseqRecord(Bioseq, BioseqDocImpl). Constructor for class iubio.readseq.BioseqRecord

BioseqRecord(Bioseq, BioseqDocImpl, String). Constructor for class iubio.readseq.BioseqRecord

BioseqRecord(SeqFileInfo). Constructor for class iubio.readseq.BioseqRecord

BioseqWriter(). Constructor for class iubio.readseq.BioseqWriter

bitset(String). Static method in class flybase.Utils

blankpad. Variable in class iubio.readseq.WriteseqOpts

blastKey. Static variable in class iubio.readseq.BlastOutputFormat

BlastOutputFormat(). Constructor for class iubio.readseq.BlastOutputFormat

booleanValue(). Method in class flybase.Args

C

calculateChecksum(Bioseq, int, int, Checksum). Static method in class iubio.readseq.BioseqWriter

canread(). Method in class iubio.readseq.AcedbSeqFormat

canread(). Method in class iubio.readseq.Asn1SeqFormat

canread(). Method in class iubio.readseq.BioseqFormat

canread(). Method in class iubio.readseq.BlastOutputFormat

canread(). Method in class iubio.readseq.ClustalSeqFormat

canread(). Method in class iubio.readseq.EmblSeqFormat

canread(). Method in class iubio.readseq.FitchSeqFormat

canread(). Method in class iubio.readseq.FlatFeatFormat

canread(). Method in class iubio.readseq.GcgSeqFormat

canread(). Method in class iubio.readseq.GenbankSeqFormat

canread(). Method in class iubio.readseq.GFFSeqFormat

canread(). Method in class iubio.readseq.IgSeqFormat

canread(). Method in class iubio.readseq.MsfSeqFormat

canread(). Method in class iubio.readseq.NbrfSeqFormat

canread(). Method in class iubio.readseq.OlsenSeqFormat

canread(). Method in class iubio.readseq.PaupSeqFormat

canread(). Method in class iubio.readseq.PearsonSeqFormat

canread(). Method in class iubio.readseq.PhylipSeqFormat

canread(). Method in class iubio.readseq.PirSeqFormat

canread(). Method in class iubio.readseq.PlainSeqFormat

canread(). Method in class iubio.readseq.PrettySeqFormat

canread(). Method in class iubio.readseq.Readseq

canread(). Method in class iubio.readseq.ScfTraceFormat

canread(). Method in class iubio.readseq.StriderSeqFormat

canread(). Method in class iubio.readseq.XmlSeqFormat

canread(). Method in class iubio.readseq.ZukerSeqFormat

canread(int). Static method in class iubio.readseq.BioseqFormats

canReadMore(). Method in class iubio.readseq.Readseq

canwrite(). Method in class iubio.readseq.AcedbSeqFormat

canwrite(). Method in class iubio.readseq.Asn1SeqFormat

canwrite(). Method in class iubio.readseq.BioseqFormat

canwrite(). Method in class iubio.readseq.BlastOutputFormat

canwrite(). Method in class iubio.readseq.ClustalSeqFormat

canwrite(). Method in class iubio.readseq.EmblSeqFormat

canwrite(). Method in class iubio.readseq.FitchSeqFormat

canwrite(). Method in class iubio.readseq.FlatFeatFormat

canwrite(). Method in class iubio.readseq.GcgSeqFormat

canwrite(). Method in class iubio.readseq.GenbankSeqFormat

canwrite(). Method in class iubio.readseq.GFFSeqFormat

canwrite(). Method in class iubio.readseq.IgSeqFormat

canwrite(). Method in class iubio.readseq.MsfSeqFormat

canwrite(). Method in class iubio.readseq.NbrfSeqFormat

canwrite(). Method in class iubio.readseq.OlsenSeqFormat

canwrite(). Method in class iubio.readseq.PaupSeqFormat

canwrite(). Method in class iubio.readseq.PearsonSeqFormat

canwrite(). Method in class iubio.readseq.PhylipSeqFormat

canwrite(). Method in class iubio.readseq.PirSeqFormat

canwrite(). Method in class iubio.readseq.PlainSeqFormat

canwrite(). Method in class iubio.readseq.PrettySeqFormat

canwrite(). Method in class iubio.readseq.ScfTraceFormat

canwrite(). Method in class iubio.readseq.StriderSeqFormat

canwrite(). Method in class iubio.readseq.Writeseq

canwrite(). Method in class iubio.readseq.XmlSeqFormat

canwrite(). Method in class iubio.readseq.ZukerSeqFormat

canwrite(int). Static method in class iubio.readseq.BioseqFormats

capacity(). Method in class flybase.FastVector

Returns the current capacity of the vector.

cgi(). Constructor for class cgi

cgi(String[]). Constructor for class iubio.readseq.cgi

cgiusage(). Static method in class iubio.readseq.cgi

cgiusage(PrintStream). Static method in class iubio.readseq.cgi

characters(char[], int, int). Method in class iubio.readseq.XmlSeqReader

charAt(int). Method in class flybase.OpenString

checkFlag. Static variable in class flybase.Args

checkInList(FastVector, String). Method in class iubio.readseq.Readseq

checkInString(String). Method in class iubio.readseq.Readseq

checkInString(String, String). Method in class iubio.readseq.Readseq

checkSeqID(). Method in class iubio.readseq.SeqFileInfo

checksumTime. Static variable in class iubio.readseq.BioseqWriter

checksumTotal. Static variable in class iubio.readseq.BioseqWriter

cleanSeqID(String). Static method in class iubio.readseq.SeqFileInfo

clear(). Method in class flybase.FastHashtable

Clears this hashtable so that it contains no keys.

clone(). Method in class iubio.bioseq.Bioseq

clone(). Method in class iubio.readseq.BioseqDocImpl

clone(). Method in class iubio.bioseq.BioseqFiled

clone(). Method in class iubio.readseq.BioseqRecord

clone(). Method in class iubio.readseq.DocItem

clone(). Method in class flybase.FastHashtable

Creates a shallow copy of this hashtable.

clone(). Method in class flybase.FastVector

Clones this vector.

clone(). Method in class iubio.readseq.FeatureItem

clone(). Method in class iubio.readseq.SeqFileInfo

clone(). Method in class iubio.bioseq.SeqRange

close(). Method in class iubio.readseq.BioseqWriter

close(). Method in interface iubio.readseq.BioseqWriterIface

close(). Method in class iubio.readseq.Readseq

close(). Method in class iubio.readseq.Writeseq

close(). Method in class iubio.readseq.XmlSeqWriter

ClustalSeqFormat(). Constructor for class iubio.readseq.ClustalSeqFormat

cmp(Bioseq, int). Method in class iubio.bioseq.Bioseq

cmp(byte[], byte[], int). Static method in class iubio.bioseq.Bioseq

commentEnd(). Method in class iubio.readseq.XmlPrintWriter

commentStart(). Method in class iubio.readseq.XmlPrintWriter

compare(int, int). Method in interface flybase.Comparator

compareAt(int, int). Method in interface flybase.ComparableVector

compareAt(int, int). Method in class flybase.CompareStrings

compareObjects(Object, Object). Method in interface flybase.ObjectComparator

compareObjects(Object, Object). Method in class flybase.StringComparator

CompareStrings(FastVector). Constructor for class flybase.CompareStrings

compareTo(Object). Method in interface flybase.CompareTo

compareTo(OpenString). Method in class flybase.OpenString

compareTo(OpenString, boolean). Method in class flybase.OpenString

compareTo(SeqRange). Method in class iubio.bioseq.SeqRange

compatableXmlChars. Static variable in class iubio.readseq.XmlPrintWriter

compress(byte). Method in class iubio.bioseq.Bioseq

compress(byte[], int, int, byte). Static method in class iubio.bioseq.Bioseq

compress(int, int, byte). Method in class iubio.bioseq.Bioseq

concat(OpenString). Method in class flybase.OpenString

contains(Object). Method in class flybase.FastHashtable

Tests if some key maps into the specified value in this hashtable.

contains(Object). Method in class flybase.FastVector

Returns true if the specified object is a value of the collection.

contains(SeqRange). Method in class iubio.bioseq.SeqRange

containsKey(Object). Method in class flybase.FastHashtable

Tests if the specified object is a key in this hashtable.

contentType(). Method in class iubio.readseq.AcedbSeqFormat

contentType(). Method in class iubio.readseq.Asn1SeqFormat

contentType(). Method in class iubio.readseq.BioseqFormat

contentType(). Method in class iubio.readseq.BlastOutputFormat

contentType(). Method in class iubio.readseq.ClustalSeqFormat

contentType(). Method in class flybase.DocFormat

contentType(). Method in class iubio.readseq.EmblSeqFormat

contentType(). Method in class iubio.readseq.FitchSeqFormat

contentType(). Method in class iubio.readseq.FlatFeatFormat

contentType(). Method in class iubio.readseq.GcgSeqFormat

contentType(). Method in class iubio.readseq.GenbankSeqFormat

contentType(). Method in class iubio.readseq.GFFSeqFormat

contentType(). Method in class iubio.readseq.IgSeqFormat

contentType(). Method in class iubio.readseq.MsfSeqFormat

contentType(). Method in class iubio.readseq.NbrfSeqFormat

contentType(). Method in class iubio.readseq.OlsenSeqFormat

contentType(). Method in class iubio.readseq.PaupSeqFormat

contentType(). Method in class iubio.readseq.PearsonSeqFormat

contentType(). Method in class iubio.readseq.Phylip2SeqFormat

contentType(). Method in class iubio.readseq.PhylipSeqFormat

contentType(). Method in class iubio.readseq.PirSeqFormat

contentType(). Method in class iubio.readseq.PlainSeqFormat

contentType(). Method in class iubio.readseq.PrettySeqFormat

contentType(). Method in class iubio.readseq.ScfTraceFormat

contentType(). Method in class iubio.readseq.StriderSeqFormat

contentType(). Method in class iubio.readseq.XmlSeqFormat

contentType(). Method in class iubio.readseq.ZukerSeqFormat

contentType(int). Static method in class iubio.readseq.BioseqFormats

contentType(int). Static method in class flybase.DocFormat

contentTypeFromIndex(int). Static method in class iubio.readseq.BioseqFormats

convertHtmlCode(String). Static method in class flybase.Utils

convertIsoCode(String). Static method in class flybase.Utils

copy(byte[], int, byte[], int, int). Static method in class iubio.bioseq.Bioseq

copy(byte[], int, int). Method in class iubio.bioseq.Bioseq

copy(SeqRange). Method in class iubio.bioseq.SeqRange

copyFrom(byte[]). Method in class iubio.bioseq.Bioseq

copyFrom(byte[], int, int). Method in class iubio.bioseq.Bioseq

copyFrom(char[]). Method in class iubio.bioseq.Bioseq

copyFrom(char[], int, int). Method in class iubio.bioseq.Bioseq

copyFrom(File). Method in class iubio.bioseq.BioseqFiled

copyFrom(Object). Method in class iubio.bioseq.Bioseq

copyFrom(Object). Method in class iubio.bioseq.BioseqFiled

copyFrom(String). Method in class iubio.bioseq.Bioseq

copyInto(Object[]). Method in class flybase.FastVector

Copies the elements of this vector into the specified array.

copyto(SeqFileInfo). Method in class iubio.readseq.BioseqReader

copyto(SeqFileInfo). Method in interface iubio.readseq.BioseqReaderIface

copy last read sequence to storage record

copyTo(SeqFileInfo). Method in class iubio.readseq.BioseqRecord

copyto(SeqFileInfo). Method in class iubio.readseq.SeqFileInfo

copyto(SeqFileInfo). Method in class iubio.readseq.VeryRawSeqReader

copyto(SeqFileInfo). Method in class iubio.readseq.XmlSeqReader

copyValueOf(char[]). Static method in class flybase.OpenString

copyValueOf(char[], int, int). Static method in class flybase.OpenString

count. Variable in class flybase.OpenString

The count is the number of characters in the OpenString.

countChar(String, char). Static method in class flybase.Utils

countChars(String, String). Static method in class flybase.Utils

CRC32checksum(Bioseq, int, int). Static method in class iubio.readseq.BioseqWriter

crctab. Static variable in class iubio.bioseq.BaseKind

D

DATA. Static variable in class flybase.DocFormat

dbKey. Static variable in class iubio.readseq.BlastOutputFormat

Debug(). Constructor for class flybase.Debug

decode(String). Static method in class flybase.Utils

decrypt(String). Static method in class flybase.Utils

decrypt(String, long). Static method in class flybase.Utils

defaultRezpath. Static variable in class flybase.AppResources

defaultRezpath. Static variable in class flybase.FastProperties

degap. Variable in class iubio.readseq.WriteseqOpts

deleteDocItem(FastVector, int, int). Method in class iubio.readseq.BioseqDocImpl

deleteDocItem(int). Method in class iubio.readseq.BioseqDocImpl

deleteFeature(String, SeqRange). Method in class iubio.readseq.BioseqDocImpl

dictionaryCompareTo(OpenString, boolean). Method in class flybase.OpenString

digitflag. Static variable in class iubio.bioseq.BaseKind

docbaseUrlKey. Static variable in class iubio.readseq.cgi

DocFormat(). Constructor for class flybase.DocFormat

DocFormat(File). Constructor for class flybase.DocFormat

DocFormat(InputStream). Constructor for class flybase.DocFormat

DocFormat(int). Constructor for class flybase.DocFormat

DocFormat(String). Constructor for class flybase.DocFormat

DocItem(). Constructor for class iubio.readseq.DocItem

DocItem(DocItem). Constructor for class iubio.readseq.DocItem

DocItem(String, String, int, int). Constructor for class iubio.readseq.DocItem

documents(). Method in interface iubio.readseq.BioseqDoc

documents(). Method in class iubio.readseq.BioseqDocImpl

domatch. Variable in class iubio.readseq.WriteseqOpts

doRead(). Method in class iubio.readseq.BioseqReader

doRead(). Method in interface iubio.readseq.BioseqReaderIface

read next sequence to internal data

doRead(). Method in class iubio.readseq.XmlSeqReader

doubleToString(double). Static method in class Acme.Fmt

doubleValue(). Method in class flybase.Args

dtdUrl. Static variable in class iubio.readseq.XmlSeqWriter

dup(). Method in class iubio.bioseq.Bioseq

dup(byte[]). Static method in class iubio.bioseq.Bioseq

E

elementAt(int). Method in class flybase.FastVector

Returns the element at the specified index.

elements(). Method in class flybase.FastHashtable

Returns an enumeration of the values in this hashtable.

elements(). Method in class flybase.FastVector

Returns an enumeration of the elements.

elements(). Method in class flybase.SortedEnumeration

EmblDoc(). Constructor for class iubio.readseq.EmblDoc

EmblDoc(BioseqDoc). Constructor for class iubio.readseq.EmblDoc

EmblDoc(String). Constructor for class iubio.readseq.EmblDoc

emblprop. Static variable in class iubio.readseq.EmblDoc

EmblSeqFormat(). Constructor for class iubio.readseq.EmblSeqFormat

empty(). Method in class flybase.FastStack

Returns true if the stack is empty.

encrypt(String). Static method in class flybase.Utils

encrypt(String, long). Static method in class flybase.Utils

endDocument(). Method in class iubio.readseq.XmlSeqReader

endElement(String). Method in class iubio.readseq.XmlSeqReader

endFeature(int, String, String). Method in class iubio.readseq.XmlDoc

called thru SAX parser endElement()

endOfFile(). Method in class iubio.readseq.BioseqReader

endOfFile(). Method in interface iubio.readseq.BioseqReaderIface

end of sequence input stream was reached

endOfFile(). Method in class iubio.readseq.InterleavedSeqReader

endOfFile(). Method in class iubio.readseq.XmlSeqReader

endOfSequence(). Method in class iubio.readseq.BioseqReader

endOfSequence(). Method in class iubio.readseq.PlainSeqReader

endsWith(OpenString). Method in class flybase.OpenString

ensureCapacity(int). Method in class flybase.FastVector

Ensures that the vector has at least the specified capacity.

Environ(). Constructor for class flybase.Environ

Environ(String). Constructor for class flybase.Environ

envPropertiesName. Static variable in class flybase.Environ

eof(). Method in class iubio.readseq.Readseq

equals(Bioseq). Method in class iubio.bioseq.Bioseq

equals(byte[], byte[]). Static method in class iubio.bioseq.Bioseq

equals(Object). Method in class iubio.readseq.DocItem

equals(Object). Method in class iubio.readseq.FeatureItem

equals(Object). Method in class flybase.OpenString

equals(Object). Method in class iubio.bioseq.SeqRange

equals(SeqInfo). Method in class iubio.bioseq.SeqInfo

equalsIgnoreCase(Bioseq). Method in class iubio.bioseq.Bioseq

equalsIgnoreCase(byte[], byte[]). Static method in class iubio.bioseq.Bioseq

equalsIgnoreCase(OpenString). Method in class flybase.OpenString

equalsIgnoreCase(String). Method in class flybase.OpenString

err. Variable in class iubio.readseq.SeqFileInfo

errmessage(String). Method in interface iubio.readseq.MessageApp

error(SAXParseException). Method in class iubio.readseq.XmlSeqReader

expand(byte[], int). Static method in class iubio.bioseq.Bioseq

expand(int). Method in class iubio.bioseq.Bioseq

extractBases(SeqRange). Method in class iubio.readseq.BioseqRecord

extractFeatureBases(FeatureItem). Method in class iubio.readseq.BioseqRecord

extractFeatureBases(Hashtable). Method in class iubio.readseq.BioseqRecord

extractFeatureBases(Hashtable, SeqRange). Method in class iubio.readseq.BioseqRecord

extractRemoveFeatureBases(boolean, Hashtable, SeqRange). Method in class iubio.readseq.BioseqRecord

extradata. Variable in class iubio.readseq.SeqFileInfo

extraHelp(). Method in class iubio.readseq.help

extraHelp(PrintStream). Method in class iubio.readseq.help

F

FastHashtable(). Constructor for class flybase.FastHashtable

Constructs a new, empty hashtable with a default capacity and load factor.

FastHashtable(Hashtable). Constructor for class flybase.FastHashtable

FastHashtable(int). Constructor for class flybase.FastHashtable

Constructs a new, empty hashtable with the specified initial capacity and default load factor.

FastHashtable(int, float). Constructor for class flybase.FastHashtable

Constructs a new, empty hashtable with the specified initial capacity and the specified load factor.

FastProperties(). Constructor for class flybase.FastProperties

FastProperties(FastProperties). Constructor for class flybase.FastProperties

FastStack(). Constructor for class flybase.FastStack

FastVector(). Constructor for class flybase.FastVector

Constructs an empty vector.

FastVector(int). Constructor for class flybase.FastVector

Constructs an empty vector with the specified storage capacity.

FastVector(int, int). Constructor for class flybase.FastVector

Constructs an empty vector with the specified storage capacity and the specified capacityIncrement.

FastVector(Vector). Constructor for class flybase.FastVector

fatalError(SAXParseException). Method in class iubio.readseq.XmlSeqReader

FeatureItem(). Constructor for class iubio.readseq.FeatureItem

FeatureItem(String, SeqRange). Constructor for class iubio.readseq.FeatureItem

FeatureItem(String, SeqRange, int). Constructor for class iubio.readseq.FeatureItem

FeatureItem(String, String, int). Constructor for class iubio.readseq.FeatureItem

FeatureNote(). Constructor for class iubio.readseq.FeatureNote

FeatureNote(DocItem). Constructor for class iubio.readseq.FeatureNote

FeatureNote(String, String). Constructor for class iubio.readseq.FeatureNote

FeatureNote(String, String, int, int). Constructor for class iubio.readseq.FeatureNote

features(). Method in interface iubio.readseq.BioseqDoc

features(). Method in class iubio.readseq.BioseqDocImpl

filePath(String). Static method in class flybase.Native

fileSizeLabel(long, boolean). Static method in class flybase.Utils

finalize(). Method in class iubio.bioseq.BioseqFiled

finalize(). Method in class iubio.readseq.InterleavedSeqWriter

findDocItem(FastVector, int, int). Method in class iubio.readseq.BioseqDocImpl

findDocItem(FastVector, String, int). Method in class iubio.readseq.BioseqDocImpl

findDocItem(int, int). Method in class iubio.readseq.BioseqDocImpl

findFeature(Object). Method in class iubio.readseq.BioseqDocImpl

findFeature(String). Method in class iubio.readseq.BioseqDocImpl

findFeature(String, SeqRange). Method in class iubio.readseq.BioseqDocImpl

findFeatures(Hashtable). Method in class iubio.readseq.BioseqRecord

findFeatures(Hashtable, SeqRange). Method in class iubio.readseq.BioseqRecord

findFeatures(Hashtable, SeqRange, Vector). Method in class iubio.readseq.BioseqDocImpl

findFeatures(SeqRange). Method in class iubio.readseq.BioseqDocImpl

findFeatures(SeqRange). Method in class iubio.readseq.BioseqRecord

findFeatures(SeqRange, Vector). Method in class iubio.readseq.BioseqDocImpl

findFeatures(String). Method in class iubio.readseq.BioseqDocImpl

findFeatures(String). Method in class iubio.readseq.BioseqRecord

findFeatures(String, SeqRange). Method in class iubio.readseq.BioseqDocImpl

findFeatures(String, SeqRange, Vector). Method in class iubio.readseq.BioseqDocImpl

findFeatures(String, Vector). Method in class iubio.readseq.BioseqDocImpl

findFeatures(String[]). Method in class iubio.readseq.BioseqRecord

findPath(String). Method in class flybase.AppResources

findString(String[], String, boolean). Static method in class flybase.Utils

firstElement(). Method in class flybase.FastVector

Returns the first element of the sequence.

FitchSeqFormat(). Constructor for class iubio.readseq.FitchSeqFormat

FlatFeatFormat(). Constructor for class iubio.readseq.FlatFeatFormat

Fmt(). Constructor for class Acme.Fmt

fmt(byte). Static method in class Acme.Fmt

fmt(byte, int). Static method in class Acme.Fmt

fmt(byte, int, int). Static method in class Acme.Fmt

fmt(char). Static method in class Acme.Fmt

fmt(char, int). Static method in class Acme.Fmt

fmt(char, int, int). Static method in class Acme.Fmt

fmt(double). Static method in class Acme.Fmt

fmt(double, int). Static method in class Acme.Fmt

fmt(double, int, int). Static method in class Acme.Fmt

fmt(double, int, int, int). Static method in class Acme.Fmt

fmt(float). Static method in class Acme.Fmt

fmt(float, int). Static method in class Acme.Fmt

fmt(float, int, int). Static method in class Acme.Fmt

fmt(float, int, int, int). Static method in class Acme.Fmt

fmt(int). Static method in class Acme.Fmt

fmt(int, int). Static method in class Acme.Fmt

fmt(int, int, int). Static method in class Acme.Fmt

fmt(long). Static method in class Acme.Fmt

fmt(long, int). Static method in class Acme.Fmt

fmt(long, int, int). Static method in class Acme.Fmt

fmt(Object). Static method in class Acme.Fmt

fmt(Object, int). Static method in class Acme.Fmt

fmt(Object, int, int). Static method in class Acme.Fmt

fmt(short). Static method in class Acme.Fmt

fmt(short, int). Static method in class Acme.Fmt

fmt(short, int, int). Static method in class Acme.Fmt

fmt(String). Static method in class Acme.Fmt

fmt(String, int). Static method in class Acme.Fmt

fmt(String, int, int). Static method in class Acme.Fmt

format. Variable in class iubio.readseq.SeqFileInfo

format(). Method in class flybase.DocFormat

formatDocName(). Method in class iubio.readseq.BioseqFormat

formatDouble(double, int, int). Static method in class flybase.Utils

formatFloat(float, int, int). Static method in class flybase.Utils

formatFromContentType(String). Static method in class iubio.readseq.BioseqFormats

formatFromContentType(String). Static method in class flybase.DocFormat

formatFromIndex(int). Static method in class iubio.readseq.BioseqFormats

formatFromName(String). Static method in class iubio.readseq.BioseqFormats

formatFromSuffix(String). Static method in class flybase.DocFormat

formatID(). Method in class iubio.readseq.BioseqFormat

formatID(). Method in interface iubio.readseq.BioseqIoIface

formatID(). Method in class iubio.readseq.BioseqReader

formatID(). Method in class iubio.readseq.BioseqWriter

formatID(). Method in class iubio.readseq.XmlSeqReader

formatID(). Method in class iubio.readseq.XmlSeqWriter

formatName(). Method in class iubio.readseq.AcedbSeqFormat

formatName(). Method in class iubio.readseq.Asn1SeqFormat

formatName(). Method in class iubio.readseq.BioseqFormat

formatName(). Method in class iubio.readseq.BlastOutputFormat

formatName(). Method in class iubio.readseq.ClustalSeqFormat

formatName(). Method in class iubio.readseq.EmblSeqFormat

formatName(). Method in class iubio.readseq.FitchSeqFormat

formatName(). Method in class iubio.readseq.FlatFeatFormat

formatName(). Method in class iubio.readseq.GcgSeqFormat

formatName(). Method in class iubio.readseq.GenbankSeqFormat

formatName(). Method in class iubio.readseq.GFFSeqFormat

formatName(). Method in class iubio.readseq.IgSeqFormat

formatName(). Method in class iubio.readseq.MsfSeqFormat

formatName(). Method in class iubio.readseq.NbrfSeqFormat

formatName(). Method in class iubio.readseq.OlsenSeqFormat

formatName(). Method in class iubio.readseq.PaupSeqFormat

formatName(). Method in class iubio.readseq.PearsonSeqFormat

formatName(). Method in class iubio.readseq.Phylip2SeqFormat

formatName(). Method in class iubio.readseq.PhylipSeqFormat

formatName(). Method in class iubio.readseq.PirSeqFormat

formatName(). Method in class iubio.readseq.PlainSeqFormat

formatName(). Method in class iubio.readseq.PrettySeqFormat

formatName(). Method in class iubio.readseq.ScfTraceFormat

formatName(). Method in class iubio.readseq.StriderSeqFormat

formatName(). Method in class iubio.readseq.XmlSeqFormat

formatName(). Method in class iubio.readseq.ZukerSeqFormat

formatName(int). Static method in class iubio.readseq.BioseqFormats

formatNameFromIndex(int). Static method in class iubio.readseq.BioseqFormats

formatNum(int, int). Static method in class flybase.Utils

formatReal(String, int, int). Static method in class flybase.Utils

formatString(String, int). Static method in class flybase.Utils

formatSuffix(). Method in class iubio.readseq.AcedbSeqFormat

formatSuffix(). Method in class iubio.readseq.Asn1SeqFormat

formatSuffix(). Method in class iubio.readseq.BioseqFormat

formatSuffix(). Method in class iubio.readseq.BlastOutputFormat

formatSuffix(). Method in class iubio.readseq.ClustalSeqFormat

formatSuffix(). Method in class iubio.readseq.EmblSeqFormat

formatSuffix(). Method in class iubio.readseq.FitchSeqFormat

formatSuffix(). Method in class iubio.readseq.FlatFeatFormat

formatSuffix(). Method in class iubio.readseq.GcgSeqFormat

formatSuffix(). Method in class iubio.readseq.GenbankSeqFormat

formatSuffix(). Method in class iubio.readseq.GFFSeqFormat

formatSuffix(). Method in class iubio.readseq.IgSeqFormat

formatSuffix(). Method in class iubio.readseq.MsfSeqFormat

formatSuffix(). Method in class iubio.readseq.NbrfSeqFormat

formatSuffix(). Method in class iubio.readseq.OlsenSeqFormat

formatSuffix(). Method in class iubio.readseq.PaupSeqFormat

formatSuffix(). Method in class iubio.readseq.PearsonSeqFormat

formatSuffix(). Method in class iubio.readseq.Phylip2SeqFormat

formatSuffix(). Method in class iubio.readseq.PhylipSeqFormat

formatSuffix(). Method in class iubio.readseq.PirSeqFormat

formatSuffix(). Method in class iubio.readseq.PlainSeqFormat

formatSuffix(). Method in class iubio.readseq.PrettySeqFormat

formatSuffix(). Method in class iubio.readseq.ScfTraceFormat

formatSuffix(). Method in class iubio.readseq.StriderSeqFormat

formatSuffix(). Method in class iubio.readseq.XmlSeqFormat

formatSuffix(). Method in class iubio.readseq.ZukerSeqFormat

formatSuffix(int). Static method in class iubio.readseq.BioseqFormats

formatSuffixFromIndex(int). Static method in class iubio.readseq.BioseqFormats

formatTestInit(). Method in class iubio.readseq.BioseqFormat

formatTestInit(). Static method in class iubio.readseq.BioseqFormats

formatTestInit(). Method in class iubio.readseq.BlastOutputFormat

formatTestInit(). Method in class iubio.readseq.PhylipSeqFormat

formatTestInit(). Method in class iubio.readseq.PlainSeqFormat

formatTestLikelihood(). Method in class iubio.readseq.BioseqFormat

formatTestLikelihood(). Method in class iubio.readseq.PlainSeqFormat

formatTestLikelihood(int). Static method in class iubio.readseq.BioseqFormats

formatTestLine(int, OpenString, int, int). Static method in class iubio.readseq.BioseqFormats

formatTestLine(int, String, int, int). Static method in class iubio.readseq.BioseqFormats

formatTestLine(OpenString, int, int). Method in class iubio.readseq.AcedbSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.Asn1SeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.BioseqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.BlastOutputFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.ClustalSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.EmblSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.FitchSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.FlatFeatFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.GcgSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.GenbankSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.GFFSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.IgSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.MsfSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.NbrfSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.OlsenSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.PaupSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.PearsonSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.PhylipSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.PirSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.PlainSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.ScfTraceFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.StriderSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.XmlSeqFormat

formatTestLine(OpenString, int, int). Method in class iubio.readseq.ZukerSeqFormat

formdataMimeType. Static variable in class flybase.Args

formfieldStart. Static variable in class flybase.Args

formpath. Static variable in class iubio.readseq.cgi

G

gapchar. Variable in class iubio.readseq.WriteseqOpts

gBaseType. Variable in class iubio.bioseq.Bioseq

gbfeatname. Static variable in class iubio.readseq.BioseqDocImpl

gBlanknum. Static variable in class iubio.readseq.SeqFileInfo

gBlankSeqid. Static variable in class iubio.readseq.SeqFileInfo

gbprop. Static variable in class iubio.readseq.GenbankDoc

GCGchecksum(Bioseq, int, int). Static method in class iubio.readseq.BioseqWriter

GcgSeqFormat(). Constructor for class iubio.readseq.GcgSeqFormat

GenbankDoc(). Constructor for class iubio.readseq.GenbankDoc

GenbankDoc(BioseqDoc). Constructor for class iubio.readseq.GenbankDoc

GenbankDoc(String). Constructor for class iubio.readseq.GenbankDoc

GenbankSeqFormat(). Constructor for class iubio.readseq.GenbankSeqFormat

gEnv. Static variable in class flybase.Environ

get(Object). Method in class flybase.FastHashtable

Returns the value to which the specified key is mapped in this hashtable.

get(String). Method in class flybase.Environ

get(String, String). Method in class flybase.Environ

getACGTcounts(). Method in class iubio.bioseq.SeqInfo

getargs(). Method in class iubio.readseq.run

getargs(String[]). Method in class iubio.readseq.cgi

getargs(String[]). Method in class iubio.readseq.run

getBaseCount(). Method in class iubio.bioseq.SeqInfo

getBiodocInteger(String). Method in class iubio.readseq.BioseqDocImpl

getBiodockey(int). Static method in class iubio.readseq.BioseqDocImpl

getBiodockey(String). Method in class iubio.readseq.BasicBioseqDoc

getBiodockey(String). Method in interface iubio.readseq.BioseqDoc

getBiodockey(String). Method in class iubio.readseq.BioseqDocImpl

getBiodockey(String). Method in class iubio.readseq.EmblDoc

getBiodockey(String). Method in class iubio.readseq.GenbankDoc

getBiodockey(String). Method in class iubio.readseq.XmlDoc

getBiodocKind(String). Method in class iubio.readseq.BioseqDocImpl

getBiodoclabel(int). Static method in class iubio.readseq.BioseqDocImpl

getBioseqFormat(). Method in class iubio.readseq.Readseq

getBioseqFormat(). Method in class iubio.readseq.Writeseq

getBoolean(String). Method in class flybase.Environ

getBytes(). Method in class flybase.OpenString

getBytes(int, int, byte[], int). Method in class flybase.OpenString

getBytes(String). Method in class flybase.AppResources

getBytes(String). Method in class flybase.OpenString

getBytes(String, String). Method in class flybase.AppResources

getChars(int, int, char[], int). Method in class flybase.OpenString

getChecksum(). Method in class iubio.readseq.BioseqWriter

getChecksum(). Method in class iubio.bioseq.SeqInfo

getChecksum(). Method in class iubio.readseq.XmlSeqWriter

getContinueLabel(DocItem). Method in class iubio.readseq.BioseqDocImpl

getCurFieldItem(). Method in class iubio.readseq.BioseqDocImpl

getData(String). Method in class flybase.AppResources

getData(String, String). Method in class flybase.AppResources

getdoc(). Method in class iubio.readseq.BioseqRecord

getDocField(FastVector, int, int). Method in class iubio.readseq.BioseqDocImpl

getDocField(FastVector, String, int). Method in class iubio.readseq.BioseqDocImpl

getDocField(int). Method in interface iubio.readseq.BioseqDoc

getDocField(int). Method in class iubio.readseq.BioseqDocImpl

getDocField(String). Method in class iubio.readseq.BioseqDocImpl

getDocField(String, int). Method in class iubio.readseq.BioseqDocImpl

getdocObject(). Method in class iubio.readseq.SeqFileInfo

getDocument(). Method in class iubio.readseq.BioseqFormat

getDocumentText(). Method in class iubio.readseq.BioseqDocImpl

getDTD(String). Method in class iubio.readseq.XmlSeqWriter

getError(). Method in class iubio.readseq.BioseqWriter

getError(). Method in interface iubio.readseq.BioseqWriterIface

getError(). Method in class iubio.readseq.XmlSeqWriter

getextraObject(). Method in class iubio.readseq.SeqFileInfo

getFeature(String). Method in class iubio.readseq.BioseqDocImpl

getFeatureRanges(Hashtable, int, int). Method in class iubio.readseq.BioseqDocImpl

getFeatureRanges(int, int). Method in class iubio.readseq.BioseqDocImpl

getFeaturesAt(SeqRange). Method in class iubio.readseq.BioseqDocImpl

getFeatureText(). Method in class iubio.readseq.BioseqDocImpl

getFieldName(int). Method in class iubio.readseq.BasicBioseqDoc

getFieldName(int). Method in interface iubio.readseq.BioseqDoc

getFieldName(int). Method in class iubio.readseq.BioseqDocImpl

getFieldName(int). Method in class iubio.readseq.EmblDoc

getFieldName(int). Method in class iubio.readseq.GenbankDoc

getFieldName(int). Method in class iubio.readseq.XmlDoc

getFilterReader(). Method in class iubio.readseq.Testseq

getFormat(). Method in class iubio.readseq.Readseq

getFormat(). Method in class iubio.readseq.Testseq

getFormat(). Method in class iubio.readseq.Writeseq

getFormatId(String). Static method in class iubio.readseq.BioseqFormats

getFormatName(). Method in class iubio.readseq.Readseq

gethash(). Method in class flybase.Environ

getHttpServerUrl(). Method in class iubio.readseq.cgi

getID(). Method in interface iubio.readseq.BioseqDoc

getID(). Method in class iubio.readseq.BioseqDocImpl

getID(). Method in class iubio.readseq.SeqFileInfo

getIndent(). Method in class iubio.readseq.BioseqDocImpl

getInfo(). Method in class iubio.readseq.Readseq

getInfo(int, String). Static method in class iubio.readseq.BioseqFormats

getInput(). Method in class iubio.readseq.BioseqReader

getInput(). Method in class iubio.readseq.Readseq

getInt(String). Method in class flybase.Environ

getInt(String, int). Method in class flybase.Environ

getKind(). Method in class iubio.readseq.DocItem

getKind(). Method in class iubio.bioseq.SeqInfo

getKindLabel(). Method in class iubio.bioseq.SeqInfo

getKindLabel(int). Static method in class iubio.bioseq.SeqInfo

getLevel(). Method in class iubio.readseq.DocItem

getline(). Method in class iubio.readseq.BioseqReader

getlineBuf(). Method in class iubio.readseq.BioseqReader

getList(String). Method in class flybase.Environ

getList(String, String, String). Method in class flybase.Environ

getLocation(). Method in class iubio.readseq.FeatureItem

getLocationString(). Method in class iubio.readseq.FeatureItem

getName(). Method in class iubio.readseq.DocItem

getNextBlankID(). Static method in class iubio.readseq.SeqFileInfo

getNextBlankID(String). Static method in class iubio.readseq.SeqFileInfo

getNote(String). Method in class iubio.readseq.FeatureItem

getNotes(). Method in class iubio.readseq.FeatureItem

getNotesText(). Method in class iubio.readseq.FeatureItem

getNoteValue(String). Method in class iubio.readseq.FeatureItem

getNseq(). Method in class iubio.readseq.BioseqReader

getNseq(). Method in interface iubio.readseq.BioseqReaderIface

get total number of sequences read

may not be valid till all data read, or return number of current sequence after doRead()

getNseq(). Method in class iubio.readseq.XmlSeqReader

getNseq(). Method in class iubio.readseq.XmlSeqWriter

getOffset(). Method in class flybase.OpenString

getOpts(). Method in class iubio.readseq.BioseqWriter

getOutput(). Method in class iubio.readseq.BioseqWriter

getOutputTranslation(). Method in class iubio.readseq.BioseqWriter

getOutputTranslation(). Method in interface iubio.readseq.BioseqWriterIface

get output translation/conversion of sequence chars

getOutputTranslation(). Method in class iubio.readseq.XmlSeqWriter

getPossibleNewInputReader(). Method in class iubio.readseq.Testseq

getProperty(String). Method in class flybase.FastProperties

getProperty(String, String). Method in class flybase.FastProperties

getReadChunkSize(). Method in class iubio.readseq.BioseqReader

getReader(). Method in class iubio.readseq.Readseq

getResource(String). Method in class flybase.Environ

getReverseComplement(). Method in class iubio.readseq.BioseqWriter

getReverseComplement(). Method in class iubio.readseq.XmlSeqWriter

getseq(). Method in class iubio.readseq.BioseqRecord

getSeqFileInfo(). Method in class iubio.readseq.BioseqRecord

getSeqInfo(int, boolean, boolean). Static method in class iubio.bioseq.SeqInfo

getseqObject(). Method in class iubio.readseq.SeqFileInfo

getSeqStats(). Method in class iubio.bioseq.Bioseq

getSeqStats(int, int). Method in class iubio.bioseq.Bioseq

getSeqStats(int, int). Method in class iubio.bioseq.BioseqFiled

getSeqtype(). Method in class iubio.bioseq.Bioseq

getSeqtype(). Method in class iubio.bioseq.BioseqFiled

getSeqtype(byte[], int, int). Static method in class iubio.bioseq.Bioseq

getSeqtype(String, int, int). Static method in class iubio.bioseq.Bioseq

getStandardFeatureList(). Static method in class iubio.readseq.BioseqDocImpl

getStandardQualifiersList(). Static method in class iubio.readseq.BioseqDocImpl

getStartLine(). Method in class iubio.readseq.Testseq

getStream(String). Method in class flybase.AppResources

getStream(String, String). Method in class flybase.AppResources

getsym(String). Method in class flybase.Environ

getTitle(). Method in interface iubio.readseq.BioseqDoc

getTitle(). Method in class iubio.readseq.BioseqDocImpl

getUrl(String). Method in class flybase.AppResources

getUrl(String, String). Method in class flybase.AppResources

getValue(). Method in class iubio.readseq.DocItem

getValue(). Method in class iubio.readseq.FeatureItem

getValue(). Method in class flybase.OpenString

getWriter(). Method in class iubio.readseq.Writeseq

getXMLFieldName(int). Static method in class iubio.readseq.XmlDoc

getXMLFieldName(Integer). Static method in class iubio.readseq.XmlDoc

GFFSeqFormat(). Constructor for class iubio.readseq.GFFSeqFormat

GIF. Static variable in class flybase.DocFormat

gJavaChecksum. Static variable in class iubio.readseq.BioseqWriter

global. Static variable in class flybase.AppResources

gMaskName. Static variable in class iubio.readseq.SeqFileInfo

gShortChecksum. Static variable in class iubio.readseq.BioseqWriter

guessContentType(File). Static method in class flybase.DocFormat

guessContentType(InputStream). Static method in class flybase.DocFormat

gUseByteArray. Static variable in class iubio.bioseq.Bioseq

gVarkey. Static variable in class flybase.Environ

gWriteMask. Static variable in class iubio.readseq.SeqFileInfo

H

hasdoc(). Method in class iubio.readseq.BioseqFormat

hasdoc(). Method in class iubio.readseq.EmblSeqFormat

hasdoc(). Method in class iubio.readseq.FlatFeatFormat

hasdoc(). Method in class iubio.readseq.GenbankSeqFormat

hasdoc(). Method in class iubio.readseq.GFFSeqFormat

hasdoc(). Method in class iubio.readseq.SeqFileInfo

hasdoc(). Method in class iubio.readseq.XmlSeqFormat

hasDocument(). Method in class iubio.readseq.BioseqDocImpl

hasFeatures(). Method in class iubio.readseq.BioseqDocImpl

hashCode(). Method in class flybase.OpenString

hashCode11(). Method in class flybase.OpenString

hashCode12(). Method in class flybase.OpenString

hasid(). Method in class iubio.readseq.SeqFileInfo

hasmask. Variable in class iubio.readseq.SeqFileInfo

hasmask(). Method in class iubio.readseq.SeqFileInfo

hasMoreArgs(). Method in class flybase.Args

hasMoreElements(). Method in class flybase.Args

hasMoreElements(). Method in class iubio.readseq.Readseq

hasMoreElements(). Method in class iubio.readseq.Writeseq

hasResource(String). Method in class flybase.AppResources

hasResource(String, String). Method in class flybase.AppResources

hasseq(). Method in class iubio.readseq.BioseqFormat

hasseq(). Method in class iubio.readseq.FlatFeatFormat

hasseq(). Method in class iubio.readseq.GFFSeqFormat

hasseq(). Method in class iubio.readseq.SeqFileInfo

hasValue(). Method in class flybase.Args

hasValue(). Method in class iubio.readseq.DocItem

haveInputData(). Method in class iubio.readseq.run

header(). Method in class iubio.readseq.XmlPrintWriter

help(). Constructor for class help

help(). Constructor for class iubio.readseq.help

help(PrintStream). Constructor for class iubio.readseq.help

help(PrintStream). Method in class iubio.readseq.help

help(String[]). Constructor for class iubio.readseq.help

hexLongValue(String). Static method in class flybase.Utils

hexValue(String). Static method in class flybase.Utils

HTML. Static variable in class flybase.DocFormat

htmlToText(String). Static method in class flybase.Utils

HX. Static variable in class Acme.Fmt

I

ignorableWhitespace(char[], int, int). Method in class iubio.readseq.XmlSeqReader

IgSeqFormat(). Constructor for class iubio.readseq.IgSeqFormat

includeDTD. Static variable in class iubio.readseq.XmlSeqWriter

indelEdge. Static variable in class iubio.bioseq.BaseKind

indelHard. Static variable in class iubio.bioseq.BaseKind

indelSoft. Static variable in class iubio.bioseq.BaseKind

indexFromFormat(int). Static method in class iubio.readseq.BioseqFormats

indexOf(byte, int). Method in class iubio.bioseq.Bioseq

indexOf(byte[], byte, int). Static method in class iubio.bioseq.Bioseq

indexOf(int). Method in class flybase.OpenString

indexOf(int, int). Method in class flybase.OpenString

indexOf(Object). Method in class flybase.FastVector

Searches for the specified object, starting from the first position and returns an index to it.

indexOf(Object, int). Method in class flybase.FastVector

Searches for the specified object, starting at the specified position and returns an index to it.

indexOf(OpenString). Method in class flybase.OpenString

indexOf(OpenString, int). Method in class flybase.OpenString

indexOf(String). Method in class flybase.OpenString

indexOf(String, int). Method in class flybase.OpenString

infomessage(String). Method in interface iubio.readseq.MessageApp

init(int). Method in class iubio.bioseq.SeqInfo

initIfNeeded(String). Method in class iubio.readseq.Readseq

insertElementAt(Object, int). Method in class flybase.FastVector

Inserts the specified object as an element at the specified index.

insertRange(SeqRange). Method in class iubio.readseq.BioseqDocImpl

interleaved(). Method in class iubio.readseq.BioseqFormat

interleaved(). Method in class iubio.readseq.BlastOutputFormat

interleaved(). Method in class iubio.readseq.ClustalSeqFormat

interleaved(). Method in class iubio.readseq.InterleavedSeqWriter

interleaved(). Method in class iubio.readseq.MsfSeqFormat

interleaved(). Method in class iubio.readseq.OlsenSeqFormat

interleaved(). Method in class iubio.readseq.PaupSeqFormat

interleaved(). Method in class iubio.readseq.PhylipSeqFormat

interleaved(). Method in class iubio.readseq.PrettySeqFormat

interleaved(). Method in class iubio.readseq.ScfTraceFormat

InterleavedSeqReader(). Constructor for class iubio.readseq.InterleavedSeqReader

InterleavedSeqWriter(). Constructor for class iubio.readseq.InterleavedSeqWriter

interline. Variable in class iubio.readseq.WriteseqOpts

intersection(SeqRange). Method in class iubio.bioseq.SeqRange

intersection0(SeqRange). Method in class iubio.bioseq.SeqRange

intersects(SeqRange). Method in class iubio.bioseq.SeqRange

intersectsMax(SeqRange). Method in class iubio.bioseq.SeqRange

intValue(). Method in class flybase.Args

invert(int). Method in class iubio.bioseq.SeqRange

isactive. Variable in class iubio.readseq.WriteseqOpts

isAlnumseq(int). Static method in class iubio.bioseq.BaseKind

isAlphaseq(int). Static method in class iubio.bioseq.BaseKind

isAmino(int). Static method in class iubio.bioseq.BaseKind

isAnyChar(int). Static method in class iubio.bioseq.BaseKind

isBasekind(int, int). Static method in class iubio.bioseq.BaseKind

isBoolean(). Method in class flybase.Args

isBytes(). Method in class iubio.bioseq.Bioseq

isBytes(). Method in class iubio.bioseq.BioseqFiled

isComplement(). Method in class iubio.bioseq.SeqRange

isComplex(). Method in class iubio.bioseq.SeqRange

isdefined(String). Method in class flybase.Environ

isDnanuc(int). Static method in class iubio.bioseq.BaseKind

isEmpty(). Method in class flybase.FastHashtable

Tests if this hashtable maps no keys to values.

isEmpty(). Method in class flybase.FastVector

Returns true if the collection contains no values.

isEmpty(). Method in class iubio.bioseq.SeqRange

isGCGSeqChar(int). Static method in class iubio.bioseq.BaseKind

isIndel(int). Static method in class iubio.bioseq.BaseKind

isIUBsym(int). Static method in class iubio.bioseq.BaseKind

isKnownFormat(). Method in class iubio.readseq.Readseq

ismask. Variable in class iubio.readseq.SeqFileInfo

isMydata(). Method in class iubio.readseq.Readseq

isNotWantedFeature(). Method in class iubio.readseq.BioseqDocImpl

isNucleicMatch(int, int). Static method in class iubio.bioseq.BaseKind

isoCodesToText(String). Static method in class flybase.Utils

isOn. Static variable in class flybase.Debug

isPrimenuc(int). Static method in class iubio.bioseq.BaseKind

isPrint(int). Static method in class iubio.bioseq.BaseKind

isProtonly(int). Static method in class iubio.bioseq.BaseKind

isRemote(). Method in class iubio.bioseq.SeqRange

isRnanuc(int). Static method in class iubio.bioseq.BaseKind

isSeqChar(int). Static method in class iubio.bioseq.BaseKind

isSeqNumChar(int). Static method in class iubio.bioseq.BaseKind

isSeqsym(int). Static method in class iubio.bioseq.BaseKind

isTrue(String). Method in class flybase.Environ

isTrue(String, boolean). Method in class flybase.Environ

isUrl(String). Static method in class flybase.Utils

itemAt(int). Method in class flybase.FastVector

iubextraflag. Static variable in class iubio.bioseq.BaseKind

iubnucflag. Static variable in class iubio.bioseq.BaseKind

iubsymflag. Static variable in class iubio.bioseq.BaseKind

J

joinRange(SeqRange). Method in class iubio.bioseq.SeqRange

joinStrings(OpenString[], String). Static method in class flybase.Utils

joinStrings(String[], String). Static method in class flybase.Utils

JPEG. Static variable in class flybase.DocFormat

K

kAccession. Static variable in interface iubio.readseq.BioseqDocVals

kAfterFeatures. Static variable in interface iubio.readseq.BioseqDocVals

kAmino. Static variable in class iubio.bioseq.Bioseq

kAmino. Static variable in class iubio.bioseq.SeqInfo

kAtFeatureHeader. Static variable in interface iubio.readseq.BioseqDocVals

kAuthor. Static variable in interface iubio.readseq.BioseqDocVals

kBeforeFeatures. Static variable in interface iubio.readseq.BioseqDocVals

kBetween. Static variable in class iubio.bioseq.SeqRange

kBioseq. Static variable in interface iubio.readseq.BioseqDocVals

kBioseqDoc. Static variable in interface iubio.readseq.BioseqDocVals

kBioseqSet. Static variable in interface iubio.readseq.BioseqDocVals

kBit5. Static variable in class iubio.bioseq.BaseKind

kBit6. Static variable in class iubio.bioseq.BaseKind

kBit7. Static variable in class iubio.bioseq.BaseKind

kBitA. Static variable in class iubio.bioseq.BaseKind

kBitC. Static variable in class iubio.bioseq.BaseKind

kBitExtra. Static variable in class iubio.bioseq.BaseKind

kBitG. Static variable in class iubio.bioseq.BaseKind

kBitT. Static variable in class iubio.bioseq.BaseKind

kBlank. Static variable in interface iubio.readseq.BioseqDocVals

kBufferSize. Static variable in class iubio.readseq.Testseq

kCgiForm. Static variable in class iubio.readseq.cgi

kChange. Static variable in class iubio.bioseq.SeqRange

kChecksum. Static variable in interface iubio.readseq.BioseqDocVals

kComment. Static variable in interface iubio.readseq.BioseqDocVals

kContinue. Static variable in interface iubio.readseq.BioseqDocVals

kCrossRef. Static variable in interface iubio.readseq.BioseqDocVals

kDataclass. Static variable in interface iubio.readseq.BioseqDocVals

kDate. Static variable in interface iubio.readseq.BioseqDocVals

kDelete. Static variable in class iubio.bioseq.SeqRange

kDescription. Static variable in interface iubio.readseq.BioseqDocVals

kDivision. Static variable in interface iubio.readseq.BioseqDocVals

kDNA. Static variable in class iubio.bioseq.Bioseq

kDNA. Static variable in class iubio.bioseq.SeqInfo

kEndless. Static variable in class iubio.bioseq.SeqRange

kEndMatchend. Static variable in class iubio.bioseq.SeqRange

kEndmore. Static variable in class iubio.bioseq.SeqRange

keys(). Method in class flybase.FastHashtable

Returns an enumeration of the keys in this hashtable.

kFeatCont. Static variable in interface iubio.readseq.BioseqDocVals

kFeatField. Static variable in interface iubio.readseq.BioseqDocVals

kFeatureItem. Static variable in interface iubio.readseq.BioseqDocVals

kFeatureKey. Static variable in interface iubio.readseq.BioseqDocVals

kFeatureLocation. Static variable in interface iubio.readseq.BioseqDocVals

kFeatureNote. Static variable in interface iubio.readseq.BioseqDocVals

kFeatureTable. Static variable in interface iubio.readseq.BioseqDocVals

kFeatureValue. Static variable in interface iubio.readseq.BioseqDocVals

kFeatWrap. Static variable in interface iubio.readseq.BioseqDocVals

kField. Static variable in interface iubio.readseq.BioseqDocVals

kind. Variable in class iubio.readseq.DocItem

kInFeatures. Static variable in interface iubio.readseq.BioseqDocVals

kInputStringKey. Static variable in class iubio.readseq.Readseq

special flag for readlist()

kInsert. Static variable in class iubio.bioseq.SeqRange

kJournal. Static variable in interface iubio.readseq.BioseqDocVals

kKeywords. Static variable in interface iubio.readseq.BioseqDocVals

kLinewidth. Variable in class iubio.readseq.BioseqDocImpl

kLinewidth. Static variable in class iubio.readseq.XmlPrintWriter

kListSequences. Static variable in interface iubio.readseq.BioseqReaderIface

flag for setChoice() to return only list of sequence IDs

kMask5. Static variable in class iubio.bioseq.BaseKind

kMask6. Static variable in class iubio.bioseq.BaseKind

kMask7. Static variable in class iubio.bioseq.BaseKind

kMaskA. Static variable in class iubio.bioseq.BaseKind

kMaskB. Static variable in class iubio.bioseq.BaseKind

kMaskC. Static variable in class iubio.bioseq.BaseKind

kMaskD. Static variable in class iubio.bioseq.BaseKind

kMaskExtra. Static variable in class iubio.bioseq.BaseKind

kMaskG. Static variable in class iubio.bioseq.BaseKind

kMaskH. Static variable in class iubio.bioseq.BaseKind

kMaskIndel. Static variable in class iubio.bioseq.BaseKind

kMaskK. Static variable in class iubio.bioseq.BaseKind

kMaskM. Static variable in class iubio.bioseq.BaseKind

kMaskN. Static variable in class iubio.bioseq.BaseKind

kMaskNucs. Static variable in class iubio.bioseq.BaseKind

kMaskR. Static variable in class iubio.bioseq.BaseKind

kMaskRna. Static variable in class iubio.bioseq.BaseKind

kMaskS. Static variable in class iubio.bioseq.BaseKind

kMaskT. Static variable in class iubio.bioseq.BaseKind

kMaskU. Static variable in class iubio.bioseq.BaseKind

kMaskV. Static variable in class iubio.bioseq.BaseKind

kMaskW. Static variable in class iubio.bioseq.BaseKind

kMaskY. Static variable in class iubio.bioseq.BaseKind

kMaxFormat. Static variable in class iubio.readseq.BioseqFormats

kName. Static variable in interface iubio.readseq.BioseqDocVals

kNamed. Static variable in class flybase.Args

kNid. Static variable in interface iubio.readseq.BioseqDocVals

kNocountsymbols. Static variable in class iubio.readseq.BioseqWriter

kNoformat. Static variable in class iubio.readseq.BioseqFormats

kNoValue. Static variable in class iubio.bioseq.SeqRange

kNucleic. Static variable in class iubio.bioseq.Bioseq

kNucleic. Static variable in class iubio.bioseq.SeqInfo

kNumA. Static variable in interface iubio.readseq.BioseqDocVals

kNumC. Static variable in interface iubio.readseq.BioseqDocVals

kNumG. Static variable in interface iubio.readseq.BioseqDocVals

kNumN. Static variable in interface iubio.readseq.BioseqDocVals

kNumT. Static variable in interface iubio.readseq.BioseqDocVals

kOtherSeq. Static variable in class iubio.bioseq.Bioseq

kOtherSeq. Static variable in class iubio.bioseq.SeqInfo

kReadseq2Help. Static variable in class iubio.readseq.help

kReadseqcHelp. Static variable in class iubio.readseq.run

kRefCrossref. Static variable in interface iubio.readseq.BioseqDocVals

kReference. Static variable in interface iubio.readseq.BioseqDocVals

kRefSeqindex. Static variable in interface iubio.readseq.BioseqDocVals

kReorder. Static variable in class iubio.bioseq.SeqRange

kRNA. Static variable in class iubio.bioseq.Bioseq

kRNA. Static variable in class iubio.bioseq.SeqInfo

kSeqcircle. Static variable in interface iubio.readseq.BioseqDocVals

kSeqdata. Static variable in interface iubio.readseq.BioseqDocVals

kSeqkind. Static variable in interface iubio.readseq.BioseqDocVals

kSeqlen. Static variable in interface iubio.readseq.BioseqDocVals

kSeqstats. Static variable in interface iubio.readseq.BioseqDocVals

kSource. Static variable in interface iubio.readseq.BioseqDocVals

kStartless. Static variable in class iubio.bioseq.SeqRange

kStartMatchend. Static variable in class iubio.bioseq.SeqRange

kStartmore. Static variable in class iubio.bioseq.SeqRange

kStrand. Static variable in interface iubio.readseq.BioseqDocVals

kSubfield. Static variable in interface iubio.readseq.BioseqDocVals

kSysMac. Static variable in class flybase.Native

kSysMSWin. Static variable in class flybase.Native

kSysOS2. Static variable in class flybase.Native

kSysUnknown. Static variable in class flybase.Native

kSysUntested. Static variable in class flybase.Native

kSysXWin. Static variable in class flybase.Native

kTaxonomy. Static variable in interface iubio.readseq.BioseqDocVals

kTitle. Static variable in interface iubio.readseq.BioseqDocVals

kUnknown. Static variable in interface iubio.readseq.BioseqDocVals

kUnknown. Static variable in class iubio.readseq.BioseqFormats

kUnnamed. Static variable in class flybase.Args

kVersion. Static variable in interface iubio.readseq.BioseqDocVals

kZero. Static variable in class iubio.bioseq.SeqRange

L

lastElement(). Method in class flybase.FastVector

Returns the last element of the sequence.

lastIndexOf(int). Method in class flybase.OpenString

lastIndexOf(int, int). Method in class flybase.OpenString

lastIndexOf(Object). Method in class flybase.FastVector

Searches backwards for the specified object, starting from the last position and returns an index to it.

lastIndexOf(Object, int). Method in class flybase.FastVector

Searches backwards for the specified object, starting from the specified position and returns an index to it.

lastIndexOf(OpenString). Method in class flybase.OpenString

lastIndexOf(OpenString, int). Method in class flybase.OpenString

lastIndexOf(String). Method in class flybase.OpenString

lastIndexOf(String, int). Method in class flybase.OpenString

length(). Method in class iubio.bioseq.Bioseq

length(). Method in class iubio.bioseq.BioseqFiled

length(). Method in class flybase.OpenString

length(). Method in class iubio.readseq.SeqFileInfo

level. Variable in class iubio.readseq.DocItem

lineEnd. Static variable in class iubio.readseq.BioseqReader

LineEnd(). Static method in class flybase.Native

LineEnd(int). Static method in class flybase.Native

linesWritten(). Method in class iubio.readseq.BioseqDocImpl

linesWritten(). Method in class iubio.readseq.XmlPrintWriter

list(PrintStream). Method in class flybase.FastProperties

list(PrintWriter). Method in class flybase.FastProperties

list(Writer). Method in class iubio.readseq.Readseq

LJ. Static variable in class Acme.Fmt

load(InputStream). Method in class flybase.FastProperties

loadProperties(String). Method in class flybase.FastProperties

locateXmlParser(). Static method in class iubio.readseq.XmlSeqFormat

lowerCase(). Method in class flybase.OpenString

M

mac. Static variable in class flybase.Native

macSire(). Method in class flybase.DocFormat

macSire(int). Static method in class flybase.DocFormat

macType(). Method in class flybase.DocFormat

macType(int). Static method in class flybase.DocFormat

main(String[]). Static method in class app

main(String[]). Static method in class iubio.readseq.app

main(String[]). Static method in class flybase.AppResources

main(String[]). Static method in class cgi

main(String[]). Static method in class iubio.readseq.cgi

main(String[]). Static method in class help

main(String[]). Static method in class iubio.readseq.help

main(String[]). Static method in class run

main(String[]). Static method in class iubio.readseq.run

maskOnly. Static variable in class iubio.bioseq.Bioseq

maskOnlyAsText. Static variable in class iubio.bioseq.Bioseq

matchchar. Variable in class iubio.readseq.WriteseqOpts

max(). Method in class iubio.bioseq.SeqRange

maxlines2check. Static variable in class iubio.readseq.Testseq

message(String). Static method in class iubio.readseq.BioseqReader

messageapp. Static variable in class iubio.readseq.BioseqReader

modtime. Variable in class iubio.readseq.SeqFileInfo

moreresults(). Method in class iubio.readseq.Readseq

moreresults(). Method in class iubio.readseq.Writeseq

MsfSeqFormat(). Constructor for class iubio.readseq.MsfSeqFormat

mswin. Static variable in class flybase.Native

mycontentType(int). Method in class flybase.DocFormat

myformatFromContentType(String). Method in class flybase.DocFormat

myguessContentType(File). Method in class flybase.DocFormat

myguessContentType(InputStream). Method in class flybase.DocFormat

mymacSire(int). Method in class flybase.DocFormat

mymacType(int). Method in class flybase.DocFormat

mysuffix(int). Method in class flybase.DocFormat

N

name. Variable in class iubio.readseq.DocItem

nameflags. Variable in class iubio.readseq.WriteseqOpts

nameleft. Variable in class iubio.readseq.WriteseqOpts

nameright. Variable in class iubio.readseq.WriteseqOpts

nametop. Variable in class iubio.readseq.WriteseqOpts

namewidth. Variable in class iubio.readseq.WriteseqOpts

Native(). Constructor for class flybase.Native

nbases(). Method in class iubio.bioseq.SeqRange

NbrfSeqFormat(). Constructor for class iubio.readseq.NbrfSeqFormat

needsamelength(). Method in class iubio.readseq.BioseqFormat

needsamelength(). Method in class iubio.readseq.BlastOutputFormat

needsamelength(). Method in class iubio.readseq.PaupSeqFormat

needsamelength(). Method in class iubio.readseq.PhylipSeqFormat

needsamelength(). Method in class iubio.readseq.ScfTraceFormat

newRange(). Method in class iubio.bioseq.SeqRange

newRange(int, int). Method in class iubio.bioseq.SeqRange

newReader(). Method in class iubio.readseq.AcedbSeqFormat

newReader(). Method in class iubio.readseq.Asn1SeqFormat

newReader(). Method in class iubio.readseq.BioseqFormat

newReader(). Method in class iubio.readseq.BlastOutputFormat

newReader(). Method in class iubio.readseq.ClustalSeqFormat

newReader(). Method in class iubio.readseq.EmblSeqFormat

newReader(). Method in class iubio.readseq.FitchSeqFormat

newReader(). Method in class iubio.readseq.FlatFeatFormat

newReader(). Method in class iubio.readseq.GcgSeqFormat

newReader(). Method in class iubio.readseq.GenbankSeqFormat

newReader(). Method in class iubio.readseq.GFFSeqFormat

newReader(). Method in class iubio.readseq.IgSeqFormat

newReader(). Method in class iubio.readseq.MsfSeqFormat

newReader(). Method in class iubio.readseq.NbrfSeqFormat

newReader(). Method in class iubio.readseq.OlsenSeqFormat

newReader(). Method in class iubio.readseq.PaupSeqFormat

newReader(). Method in class iubio.readseq.PearsonSeqFormat

newReader(). Method in class iubio.readseq.PhylipSeqFormat

newReader(). Method in class iubio.readseq.PirSeqFormat

newReader(). Method in class iubio.readseq.PlainSeqFormat

newReader(). Method in class iubio.readseq.ScfTraceFormat

newReader(). Method in class iubio.readseq.StriderSeqFormat

newReader(). Method in class iubio.readseq.XmlSeqFormat

newReader(). Method in class iubio.readseq.ZukerSeqFormat

newReader(int). Static method in class iubio.readseq.BioseqFormats

newWriter(). Method in class iubio.readseq.AcedbSeqFormat

newWriter(). Method in class iubio.readseq.Asn1SeqFormat

newWriter(). Method in class iubio.readseq.BioseqFormat

newWriter(). Method in class iubio.readseq.ClustalSeqFormat

newWriter(). Method in class iubio.readseq.EmblSeqFormat

newWriter(). Method in class iubio.readseq.FlatFeatFormat

newWriter(). Method in class iubio.readseq.GcgSeqFormat

newWriter(). Method in class iubio.readseq.GenbankSeqFormat

newWriter(). Method in class iubio.readseq.GFFSeqFormat

newWriter(). Method in class iubio.readseq.IgSeqFormat

newWriter(). Method in class iubio.readseq.MsfSeqFormat

newWriter(). Method in class iubio.readseq.NbrfSeqFormat

newWriter(). Method in class iubio.readseq.OlsenSeqFormat

newWriter(). Method in class iubio.readseq.PaupSeqFormat

newWriter(). Method in class iubio.readseq.PearsonSeqFormat

newWriter(). Method in class iubio.readseq.Phylip2SeqFormat

newWriter(). Method in class iubio.readseq.PhylipSeqFormat

newWriter(). Method in class iubio.readseq.PirSeqFormat

newWriter(). Method in class iubio.readseq.PlainSeqFormat

newWriter(). Method in class iubio.readseq.PrettySeqFormat

newWriter(). Method in class iubio.readseq.StriderSeqFormat

newWriter(). Method in class iubio.readseq.XmlSeqFormat

newWriter(int). Static method in class iubio.readseq.BioseqFormats

newWriter(int). Method in class iubio.readseq.GcgSeqFormat

newWriter(int, int). Static method in class iubio.readseq.BioseqFormats

next(). Method in class iubio.bioseq.SeqRange

nextArg(). Method in class flybase.Args

nextElement(). Method in class flybase.Args

nextElement(). Method in class iubio.readseq.Readseq

nextElement(). Method in class iubio.readseq.Writeseq

nextSeq(). Method in class iubio.readseq.Readseq

nextSeq(). Method in class iubio.readseq.Writeseq

nFormats(). Static method in class iubio.readseq.BioseqFormats

noleaves. Variable in class iubio.readseq.WriteseqOpts

notationDecl(String, String, String). Method in class iubio.readseq.XmlSeqReader

nresults(). Method in class iubio.readseq.Readseq

nresults(). Method in class iubio.readseq.Writeseq

nseq. Variable in class iubio.readseq.SeqFileInfo

nucAndMask. Static variable in class iubio.bioseq.Bioseq

nucleicBits(byte). Static method in class iubio.bioseq.BaseKind

nucleicBits(char). Static method in class iubio.bioseq.BaseKind

nucleicComplement(byte, boolean). Static method in class iubio.bioseq.BaseKind

nucleicConsensus(int, int). Static method in class iubio.bioseq.BaseKind

numbot. Variable in class iubio.readseq.WriteseqOpts

numflags. Variable in class iubio.readseq.WriteseqOpts

numleft. Variable in class iubio.readseq.WriteseqOpts

numline. Variable in class iubio.readseq.WriteseqOpts

numright. Variable in class iubio.readseq.WriteseqOpts

numtop. Variable in class iubio.readseq.WriteseqOpts

numwidth. Variable in class iubio.readseq.WriteseqOpts

O

OC. Static variable in class Acme.Fmt

offset. Variable in class flybase.OpenString

The offset is the first index of the storage that is used.

offset. Variable in class iubio.readseq.SeqFileInfo

offset(). Method in class iubio.readseq.SeqFileInfo

OlsenSeqFormat(). Constructor for class iubio.readseq.OlsenSeqFormat

opComplement. Static variable in class iubio.bioseq.SeqRange

open(File, int, int). Method in class iubio.readseq.Writeseq

open(Writer, int, int). Method in class iubio.readseq.Writeseq

OpenString(). Constructor for class flybase.OpenString

OpenString(byte[]). Constructor for class flybase.OpenString

OpenString(byte[], int). Constructor for class flybase.OpenString

OpenString(byte[], int, int). Constructor for class flybase.OpenString

OpenString(byte[], int, int, int). Constructor for class flybase.OpenString

OpenString(byte[], int, int, String). Constructor for class flybase.OpenString

OpenString(byte[], String). Constructor for class flybase.OpenString

OpenString(char[]). Constructor for class flybase.OpenString

OpenString(char[], int, int). Constructor for class flybase.OpenString

OpenString(int, int, char[]). Constructor for class flybase.OpenString

OpenString(OpenString). Constructor for class flybase.OpenString

OpenString(String). Constructor for class flybase.OpenString

operation(). Method in class iubio.bioseq.SeqRange

opGroup. Static variable in class iubio.bioseq.SeqRange

opint(). Method in class iubio.bioseq.SeqRange

opJoin. Static variable in class iubio.bioseq.SeqRange

opMax. Static variable in class iubio.bioseq.SeqRange

opNull. Static variable in class iubio.bioseq.SeqRange

opOneof. Static variable in class iubio.bioseq.SeqRange

opOrder. Static variable in class iubio.bioseq.SeqRange

origin. Variable in class iubio.readseq.WriteseqOpts

origin(). Method in class iubio.bioseq.SeqRange

os2. Static variable in class flybase.Native

otherprintflag. Static variable in class iubio.bioseq.BaseKind

outSeqChar(int). Method in interface iubio.readseq.OutBiobaseIntf

P

parse(String). Static method in class iubio.bioseq.SeqRange

parse1(String). Method in class iubio.bioseq.SeqRange

PaupSeqFormat(). Constructor for class iubio.readseq.PaupSeqFormat

PDF. Static variable in class flybase.DocFormat

PearsonSeqFormat(). Constructor for class iubio.readseq.PearsonSeqFormat

peek(). Method in class flybase.FastStack

Peeks at the top of the stack.

Phylip2SeqFormat(). Constructor for class iubio.readseq.Phylip2SeqFormat

PhylipSeqFormat(). Constructor for class iubio.readseq.PhylipSeqFormat

PICT. Static variable in class flybase.DocFormat

pipeStream(InputStream, OutputStream). Static method in class flybase.Utils

pipeTextStream(InputStream, OutputStream). Static method in class flybase.Utils

PirSeqFormat(). Constructor for class iubio.readseq.PirSeqFormat

plainInit(). Method in class iubio.readseq.WriteseqOpts

PlainSeqFormat(). Constructor for class iubio.readseq.PlainSeqFormat

PlainSeqReader(). Constructor for class iubio.readseq.PlainSeqReader

pop(). Method in class flybase.FastStack

Pops an item off the stack.

postMimeType. Static variable in class flybase.Args

POSTSCRIPT. Static variable in class flybase.DocFormat

prettyInit(). Method in class iubio.readseq.WriteseqOpts

PrettySeqFormat(). Constructor for class iubio.readseq.PrettySeqFormat

primenucflag. Static variable in class iubio.bioseq.BaseKind

print(char). Static method in class flybase.Debug

print(PrintStream). Method in class flybase.Environ

print(PrintWriter, BioseqDocImpl, String, String). Method in interface iubio.readseq.PrintableDocItem

print(String). Static method in class flybase.Debug

printAttributes(Object). Method in class iubio.readseq.XmlPrintWriter

printEncoded(char). Method in class iubio.readseq.XmlPrintWriter

PRINTJOB. Static variable in class flybase.DocFormat

println(). Static method in class flybase.Debug

println(). Method in class iubio.readseq.XmlPrintWriter

dang java.io.PrintWriter for not making newline() accessible!

println(boolean). Method in class iubio.readseq.XmlPrintWriter

println(char). Method in class iubio.readseq.XmlPrintWriter

println(char[]). Method in class iubio.readseq.XmlPrintWriter

println(double). Method in class iubio.readseq.XmlPrintWriter

println(float). Method in class iubio.readseq.XmlPrintWriter

println(int). Method in class iubio.readseq.XmlPrintWriter

println(long). Method in class iubio.readseq.XmlPrintWriter

println(Object). Method in class iubio.readseq.XmlPrintWriter

println(String). Static method in class flybase.Debug

println(String). Method in class iubio.readseq.XmlPrintWriter

printReadseqCgiUsage(). Method in class iubio.readseq.cgi

printWithEnvVars(PrintStream, String). Method in class iubio.readseq.cgi

printWithEnvVars(PrintStream, String, String). Method in class iubio.readseq.cgi

processingInstruction(String, String). Method in class iubio.readseq.XmlSeqReader

properties(). Method in class flybase.Args

propertyNames(). Method in class flybase.FastProperties

propname. Static variable in class iubio.readseq.BioseqFormats

protonlyflag. Static variable in class iubio.bioseq.BaseKind

push(Object). Method in class flybase.FastStack

Pushes an item onto the stack.

put(Object, Object). Method in class flybase.FastHashtable

Maps the specified key to the specified value in this hashtable.

putNote(DocItem). Method in class iubio.readseq.FeatureItem

Q

QSortVector(FastVector, ComparableVector). Constructor for class flybase.QSortVector

QSortVector(FastVector, ComparableVector, Comparator). Constructor for class flybase.QSortVector

QSortVector(Vector, ComparableVector). Constructor for class flybase.QSortVector

queryKey. Static variable in class iubio.readseq.BlastOutputFormat

quote(String). Static method in class flybase.Utils

R

readAt(int). Method in class iubio.readseq.Readseq

readChunkSize. Static variable in class iubio.readseq.XmlSeqReader

readInit(). Method in class iubio.readseq.Readseq

readInit(String). Method in class iubio.readseq.Readseq

readlist(Enumeration). Method in class iubio.readseq.Readseq

readlist(Enumeration, String). Method in class iubio.readseq.Readseq

readlist(FastVector). Method in class iubio.readseq.Readseq

Read a FastVector list of inputs: File, URL, InputStream, String of (File,URL,Data) -- moved here from readseqapp for handy usage

readlist(FastVector, String). Method in class iubio.readseq.Readseq

readNext(). Method in class iubio.readseq.Readseq

readObject(InputStream, boolean). Static method in class flybase.Utils

readOne(int). Method in class iubio.readseq.BioseqReader

readOne(int). Method in interface iubio.readseq.BioseqReaderIface

read one sequence to SeqFileInfo structure

readOne(int). Method in class iubio.readseq.InterleavedSeqReader

readOne(int). Method in class iubio.readseq.XmlSeqReader

readProperties(String). Method in class flybase.Environ

Readseq(). Constructor for class iubio.readseq.Readseq

Readseq(int). Constructor for class iubio.readseq.Readseq

ReadseqException(). Constructor for class iubio.readseq.ReadseqException

ReadseqException(String). Constructor for class iubio.readseq.ReadseqException

readSpeciesLength(OpenString). Static method in class iubio.readseq.PhylipSeqFormat

readTo(BioseqWriterIface). Method in class iubio.readseq.Readseq

readTo(BioseqWriterIface, boolean). Method in class iubio.readseq.Readseq

readTo(BioseqWriterIface, int). Method in class iubio.readseq.BioseqReader

readTo(BioseqWriterIface, int). Method in interface iubio.readseq.BioseqReaderIface

reads all of sequence entries in stream, writing to writer

for piping from one format to another

readTo(BioseqWriterIface, int). Method in class iubio.readseq.InterleavedSeqReader

readTo(BioseqWriterIface, int). Method in class iubio.readseq.XmlSeqReader

readToOld(BioseqWriterIface, boolean). Method in class iubio.readseq.Readseq

readToPair(BioseqWriterIface, BioseqWriterIface, boolean). Method in class iubio.readseq.Readseq

recordStartLine(). Method in class iubio.readseq.BioseqFormat

recordStartLine(int). Static method in class iubio.readseq.BioseqFormats

regionMatches(boolean, int, OpenString, int, int). Method in class flybase.OpenString

regionMatches(boolean, int, String, int, int). Method in class flybase.OpenString

regionMatches(int, OpenString, int, int). Method in class flybase.OpenString

regionMatches(int, String, int, int). Method in class flybase.OpenString

register(BioseqFormat). Static method in class iubio.readseq.BioseqFormats

remoteSeq(). Method in class iubio.bioseq.SeqRange

remove(Object). Method in class flybase.FastHashtable

Removes the key (and its corresponding value) from this hashtable.

removeAllElements(). Method in class flybase.FastVector

Removes all elements of the vector.

removeChars(String, String). Static method in class flybase.Utils

removeElement(Object). Method in class flybase.FastVector

Removes the element from the vector.

removeElementAt(int). Method in class flybase.FastVector

Deletes the element at the specified index.

removeFeatureBases(Hashtable). Method in class iubio.readseq.BioseqRecord

removeFeatureBases(Hashtable, SeqRange). Method in class iubio.readseq.BioseqRecord

removeRange(SeqRange). Method in class iubio.readseq.BioseqDocImpl

removeresults(). Method in class iubio.readseq.Readseq

removeresults(). Method in class iubio.readseq.Writeseq

replace(Bioseq, int, char, char). Static method in class iubio.bioseq.Bioseq

replace(Bioseq, int, String, String). Static method in class iubio.bioseq.Bioseq

replace(char, char). Method in class flybase.OpenString

replace(int, char, char). Method in class iubio.bioseq.Bioseq

replace(int, String, String). Method in class iubio.bioseq.Bioseq

replaceDocField(int, String). Method in class iubio.readseq.BioseqDocImpl

replaceDocItem(int, DocItem). Method in class iubio.readseq.BioseqDocImpl

reset(). Method in class flybase.Args

reset(). Method in class iubio.readseq.BioseqReader

reset(). Method in interface iubio.readseq.BioseqReaderIface

reset input stream for re-read (interleaved formats)

reset(). Method in class iubio.readseq.XmlSeqReader

resetSeq(). Method in class iubio.readseq.BioseqReader

resetSeq(). Method in interface iubio.readseq.BioseqReaderIface

reset sequence storage for new sequence

resetSeq(). Method in class iubio.readseq.XmlSeqReader

resolveEntity(String, String). Method in class iubio.readseq.XmlSeqReader

resort(ObjectComparator). Method in class flybase.SortedEnumeration

restartresults(). Method in class iubio.readseq.Readseq

restartresults(). Method in class iubio.readseq.Writeseq

result(). Method in class iubio.readseq.Readseq

result(). Method in class iubio.readseq.Writeseq

reverse(). Method in class iubio.bioseq.SeqRange

reverseComplement(). Method in class iubio.bioseq.Bioseq

reverseComplement(int, int). Method in class iubio.bioseq.Bioseq

rezPath(String, String). Method in class flybase.AppResources

run(). Constructor for class run

run(). Constructor for class iubio.readseq.run

run(). Method in class iubio.readseq.run

run(String[]). Constructor for class iubio.readseq.run

S

sameKind(DocItem). Method in class iubio.readseq.DocItem

sameKind(int). Method in class iubio.readseq.DocItem

sameLevel(DocItem). Method in class iubio.readseq.DocItem

sameName(DocItem). Method in class iubio.readseq.DocItem

sameName(String). Method in class iubio.readseq.DocItem

sameNameOrKind(Object). Method in class iubio.readseq.DocItem

sameValue(String). Method in class iubio.readseq.DocItem

sAppendBreak. Static variable in class iubio.readseq.DocItem

save(OutputStream, String). Method in class flybase.Environ

save(OutputStream, String). Method in class flybase.FastProperties

save(PrintWriter, String, boolean). Method in class flybase.FastProperties

save(Writer, String). Method in class flybase.FastProperties

saxParserClass. Static variable in class iubio.readseq.XmlSeqFormat

ScfTraceFormat(). Constructor for class iubio.readseq.ScfTraceFormat

search(Object). Method in class flybase.FastStack

Sees if an object is on the stack.

seq. Variable in class iubio.readseq.SeqFileInfo

seqdoc. Variable in class iubio.readseq.SeqFileInfo

SeqFileInfo(). Constructor for class iubio.readseq.SeqFileInfo

SeqFileInfo(Object, int, int). Constructor for class iubio.readseq.SeqFileInfo

seqid. Variable in class iubio.readseq.SeqFileInfo

SeqInfo(). Constructor for class iubio.bioseq.SeqInfo

seqlen. Variable in class iubio.readseq.SeqFileInfo

seqLen(). Method in class iubio.readseq.XmlSeqReader

seqLen(). Method in class iubio.readseq.XmlSeqWriter

SeqRange(). Constructor for class iubio.bioseq.SeqRange

SeqRange(int, int). Constructor for class iubio.bioseq.SeqRange

SeqRange(int, int, int). Constructor for class iubio.bioseq.SeqRange

SeqRange(int, int, int, String). Constructor for class iubio.bioseq.SeqRange

SeqRange(int, int, int, String, String, SeqRange). Constructor for class iubio.bioseq.SeqRange

SeqRange(String). Constructor for class iubio.bioseq.SeqRange

SeqRangeException(). Constructor for class iubio.bioseq.SeqRangeException

SeqRangeException(String). Constructor for class iubio.bioseq.SeqRangeException

seqsymflag. Static variable in class iubio.bioseq.BaseKind

sequenceLength(). Method in class iubio.readseq.PhylipSeqFormat

seqwidth. Variable in class iubio.readseq.WriteseqOpts

set(int, int). Method in class iubio.bioseq.SeqRange

set(Object, Object, String). Method in class iubio.readseq.BioseqRecord

set(String, boolean). Method in class flybase.Environ

set(String, double). Method in class flybase.Environ

set(String, int). Method in class flybase.Environ

set(String, Object). Method in class flybase.Environ

set(String, SeqRange). Method in class iubio.readseq.FeatureItem

set(String, String). Method in class flybase.Environ

setAmino(boolean). Method in class iubio.readseq.EmblDoc

setAmino(boolean). Method in class iubio.readseq.GenbankDoc

setArgPattern(String, boolean). Method in class flybase.Args

for unix style "ab:C:def"

setbase(int, byte). Method in class iubio.bioseq.Bioseq

setbase(int, byte). Method in class iubio.bioseq.BioseqFiled

setbase(int, char). Method in class iubio.bioseq.Bioseq

setBaseCount(int). Method in class iubio.bioseq.SeqInfo

setbases(byte[]). Method in class iubio.bioseq.Bioseq

setbases(byte[]). Method in class iubio.bioseq.BioseqFiled

setCharAt(int, char). Method in class flybase.OpenString

setChecksum(boolean). Method in class iubio.readseq.BioseqWriter

setChecksum(boolean). Method in class iubio.readseq.XmlSeqWriter

setChecksum(long). Method in class iubio.bioseq.SeqInfo

setChoice(int). Method in class iubio.readseq.BioseqReader

setChoice(int). Method in interface iubio.readseq.BioseqReaderIface

select which sequence to read

setChoice(int). Method in class iubio.readseq.XmlSeqReader

setCurFieldItem(FeatureItem). Method in class iubio.readseq.BioseqDocImpl

setDisplayOrigin(int). Method in class iubio.bioseq.SeqRange

setdoc(Object). Method in class iubio.readseq.SeqFileInfo

setDocumentLocator(Locator). Method in class iubio.readseq.XmlSeqReader

setElementAt(Object, int). Method in class flybase.FastVector

Sets the element at the specified index to be the specified object.

setextra(Object). Method in class iubio.readseq.SeqFileInfo

setExtractRange(SeqRange). Method in class iubio.readseq.Readseq

setFeatureExtraction(Hashtable). Method in class iubio.readseq.BioseqWriter

setFeatureExtraction(Hashtable). Method in interface iubio.readseq.BioseqWriterIface

set list of features to extract sequence of (good only if hasdoc)

setFeatureExtraction(Hashtable). Method in class iubio.readseq.XmlSeqWriter

setFeatureExtraction(Hashtable, SeqRange). Method in class iubio.readseq.Readseq

setFeatureSubrange(SeqRange). Method in class iubio.readseq.BioseqWriter

setFormat(int). Method in class iubio.readseq.Readseq

setFormat(int). Method in class iubio.readseq.Writeseq

setFormatID(int). Method in class iubio.readseq.BioseqFormat

setFormatID(int). Method in interface iubio.readseq.BioseqIoIface

setFormatID(int). Method in class iubio.readseq.BioseqReader

setFormatID(int). Method in class iubio.readseq.BioseqWriter

setFormatID(int). Method in class iubio.readseq.XmlSeqReader

setFormatID(int). Method in class iubio.readseq.XmlSeqWriter

setFormatTestor(Testseq). Method in class iubio.readseq.Readseq

setHttpcall(boolean). Method in class flybase.Args

setIndent(int). Method in class iubio.readseq.XmlDoc

setInput(byte[]). Method in class iubio.readseq.Readseq

setInput(char[]). Method in class iubio.readseq.Readseq

setInput(File). Method in class iubio.readseq.Readseq

input setters -

setInput(InputStream). Method in class iubio.readseq.BioseqReader

setInput(InputStream). Method in class iubio.readseq.Readseq

setInput(OpenString). Method in class iubio.readseq.Readseq

setInput(Reader). Method in class iubio.readseq.BioseqReader

setInput(Reader). Method in interface iubio.readseq.BioseqReaderIface

set input stream

setInput(Reader). Method in class iubio.readseq.InterleavedSeqReader

setInput(Reader). Method in class iubio.readseq.Readseq

setInput(Reader). Method in class iubio.readseq.XmlSeqReader

setInput(String). Method in class iubio.readseq.Readseq

setInput(URL). Method in class iubio.readseq.Readseq

setInputFile(File). Method in class iubio.readseq.PlainSeqReader

setInputFiles(File[]). Method in class iubio.readseq.run

setInputFormat(int). Method in class iubio.readseq.Readseq

setInputNames(String[]). Method in class iubio.readseq.run

setInputObject(Object). Method in class iubio.readseq.Readseq

setInputObjectChecked(Object). Method in class iubio.readseq.Readseq

setInputObjects(FastVector). Method in class iubio.readseq.run

setinterleaved(boolean). Method in class iubio.readseq.InterleavedSeqWriter

setKeepField(int). Method in class iubio.readseq.BioseqDocImpl

setKind(int). Method in class iubio.bioseq.SeqInfo

setLength(int). Method in class flybase.OpenString

setlength(int). Method in class iubio.readseq.SeqFileInfo

setLevel(int). Method in class iubio.readseq.DocItem

setMask(SeqFileInfo, String). Method in class iubio.readseq.BioseqWriter

setMask(SeqFileInfo, String). Method in interface iubio.readseq.BioseqWriterIface

setMask(SeqFileInfo, String). Method in class iubio.readseq.XmlSeqWriter

setNbases(int). Method in class iubio.bioseq.SeqRange

setNotesText(String, boolean). Method in class iubio.readseq.FeatureItem

setNseq(int). Method in class iubio.readseq.BioseqWriter

setNseq(int). Method in interface iubio.readseq.BioseqWriterIface

per output stream

setNseq(int). Method in class iubio.readseq.XmlSeqWriter

setOffset(int). Method in class flybase.OpenString

setoffset(int). Method in class iubio.readseq.SeqFileInfo

setOpts(WriteseqOpts). Method in class iubio.readseq.BioseqWriter

setOutput(OutputStream). Method in class iubio.readseq.BioseqDocImpl

setOutput(OutputStream). Method in class iubio.readseq.BioseqWriter

setOutput(OutputStream). Method in interface iubio.readseq.BioseqWriterIface

setOutput(OutputStream). Method in class iubio.readseq.XmlDoc

setOutput(OutputStream). Method in class iubio.readseq.XmlSeqWriter

setOutput(Writer). Method in class iubio.readseq.BioseqDocImpl

setOutput(Writer). Method in class iubio.readseq.BioseqWriter

setOutput(Writer). Method in interface iubio.readseq.BioseqWriterIface

setOutput(Writer). Method in class iubio.readseq.XmlDoc

setOutput(Writer). Method in class iubio.readseq.XmlSeqWriter

setOutputTranslation(OutBiobaseIntf). Method in class iubio.readseq.BioseqWriter

setOutputTranslation(OutBiobaseIntf). Method in interface iubio.readseq.BioseqWriterIface

set output translation/conversion of sequence chars

setOutputTranslation(OutBiobaseIntf). Method in class iubio.readseq.XmlSeqWriter

setReadChunkSize(int). Method in class iubio.readseq.BioseqReader

setReverseComplement(boolean). Method in class iubio.readseq.BioseqWriter

setReverseComplement(boolean). Method in class iubio.readseq.XmlSeqWriter

setseq(Object). Method in class iubio.readseq.SeqFileInfo

setSeq(Object, int, int, String, Object, int, int). Method in class iubio.readseq.BioseqWriter

setSeq(Object, int, int, String, Object, int, int). Method in interface iubio.readseq.BioseqWriterIface

setSeq(Object, int, int, String, Object, int, int). Method in class iubio.readseq.XmlSeqWriter

setSeq(SeqFileInfo). Method in class iubio.readseq.BioseqWriter

setSeq(SeqFileInfo). Method in interface iubio.readseq.BioseqWriterIface

per sequence

setSeq(SeqFileInfo). Method in class iubio.readseq.XmlSeqWriter

per sequence

setSeqID(String). Method in class iubio.readseq.SeqFileInfo

setSeqInfoTester(SeqInfo). Method in class iubio.readseq.PlainSeqFormat

setSeqName(String). Method in class iubio.readseq.BioseqWriter

setSeqName(String). Method in interface iubio.readseq.BioseqWriterIface

setSeqName(String). Method in class iubio.readseq.XmlSeqReader

setSeqName(String). Method in class iubio.readseq.XmlSeqWriter

setSeqPart(int). Method in class iubio.readseq.BioseqWriter

setSeqPart(int). Method in class iubio.readseq.XmlSeqWriter

setSize(int). Method in class flybase.FastVector

Sets the size of the vector.

setSkipDocs(boolean). Method in class iubio.readseq.BioseqDocImpl

setSkipDocs(boolean). Method in class iubio.readseq.BioseqReader

setSourceDoc(BioseqDoc). Method in class iubio.readseq.BioseqDocImpl

setSourceDoc(BioseqDoc). Method in class iubio.readseq.EmblDoc

setSourceDoc(BioseqDoc). Method in class iubio.readseq.GenbankDoc

setSourceDoc(BioseqDoc). Method in class iubio.readseq.XmlDoc

setStart(int). Method in class iubio.bioseq.SeqRange

setState(boolean). Static method in class flybase.Debug

setTranslation(String, boolean). Method in class iubio.readseq.run

setTrimValue(boolean). Method in class iubio.readseq.XmlPrintWriter

setVal(int). Static method in class flybase.Debug

setValue(char[]). Method in class flybase.OpenString

setValue(String). Method in class iubio.readseq.DocItem

setValue(String). Method in class iubio.readseq.FeatureItem

setVector(FastVector, ComparableVector). Method in class flybase.SortVector

setVector(Vector, ComparableVector). Method in class flybase.SortVector

setWantedFeatures(boolean, Hashtable, SeqRange). Method in class iubio.readseq.BioseqDocImpl

setWantedFeatures(Hashtable). Method in class iubio.readseq.BioseqDocImpl

setWantedFeatures(Hashtable, SeqRange). Method in class iubio.readseq.BioseqDocImpl

setWriteMask(boolean). Method in class iubio.readseq.Readseq

setWriteMask(boolean). Method in class iubio.readseq.Writeseq

sExtractionFeature. Static variable in class iubio.readseq.BioseqDocImpl

sExtractRangeFeature. Static variable in class iubio.readseq.BioseqDocImpl

showErrors. Variable in class iubio.readseq.XmlSeqReader

showErrors. Variable in class iubio.readseq.XmlSeqWriter

size(). Method in class flybase.FastHashtable

Returns the number of keys in this hashtable.

size(). Method in class flybase.FastVector

Returns the number of elements in the vector.

skiplines. Variable in class iubio.readseq.SeqFileInfo

skipNextEndElementNewline(). Method in class iubio.readseq.XmlPrintWriter

skipPastHeader(int). Method in class iubio.readseq.BioseqReader

skipPastHeader(int). Method in interface iubio.readseq.BioseqReaderIface

skip past non-sequence info at top of stream

skipPastHeader(int). Method in class iubio.readseq.XmlSeqReader

sOperators. Static variable in class iubio.bioseq.SeqRange

sort(). Method in class flybase.QSortVector

sort(). Method in class flybase.SortVector

SortedEnumeration(Enumeration). Constructor for class flybase.SortedEnumeration

SortedEnumeration(Enumeration, ObjectComparator). Constructor for class flybase.SortedEnumeration

SortVector(FastVector, ComparableVector). Constructor for class flybase.SortVector

SortVector(Vector, ComparableVector). Constructor for class flybase.SortVector

spacer. Variable in class iubio.readseq.WriteseqOpts

speciesCount(). Method in class iubio.readseq.PhylipSeqFormat

splitString(OpenString). Static method in class flybase.Utils

splitString(OpenString, String). Static method in class flybase.Utils

splitString(OpenString, String, int). Static method in class flybase.Utils

splitString(String). Static method in class flybase.Utils

splitString(String, String). Static method in class flybase.Utils

splitString(String, String, int). Static method in class flybase.Utils

standardLineEnd. Static variable in class flybase.Native

start(). Method in class iubio.bioseq.SeqRange

startDocument(). Method in class iubio.readseq.XmlSeqReader

startElement(String, AttributeList). Method in class iubio.readseq.XmlSeqReader

startFeature(int, String, String). Method in class iubio.readseq.XmlDoc

called thru SAX parser startElement() for kFeatureItem at appearance of 1st note?

startIsEnd(). Method in class iubio.bioseq.SeqRange

startsWith(OpenString). Method in class flybase.OpenString

startsWith(OpenString, int). Method in class flybase.OpenString

startsWith(String). Method in class flybase.OpenString

startsWith(String, int). Method in class flybase.OpenString

stop(). Method in class iubio.bioseq.SeqRange

stopIsEnd(). Method in class iubio.bioseq.SeqRange

StriderSeqFormat(). Constructor for class iubio.readseq.StriderSeqFormat

StringComparator(). Constructor for class flybase.StringComparator

stringHashCode(String). Static method in class flybase.Utils

stripHtmlCodes(String). Static method in class flybase.Utils

stuffLink(String, String). Static method in class flybase.Utils

stuffLink(String, String, boolean). Static method in class flybase.Utils

subrange(SeqRange). Method in class iubio.bioseq.SeqRange

substring(int). Method in class flybase.OpenString

substring(int, int). Method in class flybase.OpenString

suffix(). Method in class flybase.DocFormat

suffix(int). Static method in class flybase.DocFormat

summer. Static variable in class iubio.readseq.BioseqWriter

SwissDoc(). Constructor for class iubio.readseq.SwissDoc

public static String swissprop= "EmblDoc"; private static FastHashtable slabel2keys = new FastHashtable(); // format label => biodockey private static FastProperties keys2slabel= new FastProperties(); // biodockey => format label static { String pname= System.getProperty( swissprop, swissprop); getDocProperties(pname,keys2slabel,slabel2keys); } // this isnt helping - still missing doc data (no AA length for swiss -> embl public String getBiodockey(String field) { return (String) slabel2keys.get(field); } public String getFieldName(int kind) { indent= fFieldIndent; String lab= null; String biodockey= getBiodockey(kind); if (biodockey!=null) lab= (String) keys2slabel.get( biodockey); switch (kind) { case kFeatureTable: case kFeatureItem: case kFeatureNote: indent= fFeatIndent; break; } return lab; }

SwissDoc(BioseqDoc). Constructor for class iubio.readseq.SwissDoc

SwissDoc(String). Constructor for class iubio.readseq.SwissDoc

SystemFlavor(). Static method in class flybase.Native

SystemFlavors(). Static method in class flybase.Native

T

tab. Variable in class iubio.readseq.WriteseqOpts

tab(int). Method in class iubio.readseq.XmlPrintWriter

tablestr. Static variable in class iubio.readseq.BioseqFormats

tag1. Static variable in class iubio.readseq.XmlSeqFormat

tempFile. Static variable in class iubio.readseq.BioseqReader

tempFile(). Static method in class flybase.Native

tempFile(String). Static method in class flybase.Native

tempFilename(String). Static method in class flybase.Native

tempFilename(String, String). Static method in class flybase.Native

tempFolder(). Static method in class flybase.Native

testFormat(Reader, SeqFileInfo). Method in class iubio.readseq.Testseq

Testseq(). Constructor for class iubio.readseq.Testseq

TEXT. Static variable in class flybase.DocFormat

theArgs(). Method in class flybase.Args

titleToSentenceCase(OpenString). Static method in class flybase.Utils

titleToSentenceCase(String). Static method in class flybase.Utils

toBytes(). Method in class iubio.bioseq.Bioseq

toBytes(int). Method in class iubio.bioseq.Bioseq

toBytes(int). Method in class iubio.bioseq.BioseqFiled

toBytes(int, int, int). Method in class iubio.bioseq.Bioseq

toBytes(int, int, int). Method in class iubio.bioseq.BioseqFiled

toCharArray(). Method in class flybase.OpenString

toChars(). Method in class iubio.bioseq.Bioseq

toChars(int). Method in class iubio.bioseq.Bioseq

toChars(int, int, int). Method in class iubio.bioseq.Bioseq

toChars(int, int, int). Method in class iubio.bioseq.BioseqFiled

toHashtable(). Method in class flybase.FastHashtable

dgg additions

toLowerCase(). Method in class flybase.OpenString

toString(). Method in class iubio.bioseq.Bioseq

toString(). Method in class iubio.readseq.BioseqRecord

toString(). Method in class iubio.readseq.DocItem

toString(). Method in class flybase.FastHashtable

Returns a rather long string representation of this hashtable.

toString(). Method in class flybase.FastVector

Converts the vector to a string.

toString(). Method in class iubio.readseq.FeatureItem

toString(). Method in class flybase.OpenString

toString(). Method in class iubio.readseq.SeqFileInfo

toString(). Method in class iubio.bioseq.SeqRange

toUpperCase(). Method in class flybase.OpenString

toVector(). Method in class flybase.FastVector

dgg additions & synonyms

TR. Static variable in class Acme.Fmt

trim(). Method in class flybase.OpenString

trimSentenceEnd(OpenString, int). Static method in class flybase.Utils

trimSentenceEnd(String, int). Static method in class flybase.Utils

trimToSize(). Method in class flybase.FastVector

Trims the vector's capacity down to size.

trimValue(String). Method in class iubio.readseq.XmlPrintWriter