All Packages  Class Hierarchy

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

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

U

uncertain(). Method in class iubio.bioseq.SeqRange
ungetline(). Method in class iubio.readseq.BioseqReader
unparsedEntityDecl(String, String, String, String). Method in class iubio.readseq.XmlSeqReader
updateRange(int, int, int). Method in class iubio.bioseq.SeqRange
updateRange(int, int, int, byte[]). Method in class iubio.readseq.BioseqDocImpl
changeflags: SeqRange.kDelete = 1, kInsert = 2, kReorder = 4, kChange = 8;
updateRange(int, int, int, byte[]). Method in class iubio.readseq.FeatureItem
updateRange(int, int, int, byte[]). Method in class iubio.bioseq.SeqRange
upperCase(). Method in class flybase.OpenString
usage(). Static method in class iubio.readseq.run
usage(PrintStream). Static method in class iubio.readseq.run
userchoice. Variable in class iubio.readseq.WriteseqOpts
userset(). Method in class iubio.readseq.WriteseqOpts
Utils(). Constructor for class flybase.Utils

V

val(). Static method in class flybase.Debug
value. Variable in class iubio.readseq.DocItem
value. Variable in class flybase.OpenString
The value is used for character storage.
valueOf(char[]). Static method in class flybase.OpenString
valueOf(char[], int, int). Static method in class flybase.OpenString
varkey. Static variable in class iubio.readseq.cgi
vector(). Method in class flybase.SortedEnumeration
verbose. Static variable in class iubio.readseq.BioseqReader
verbose. Variable in class iubio.readseq.Readseq
version. Static variable in class iubio.readseq.Readseq
VeryRawSeqReader(). Constructor for class iubio.readseq.VeryRawSeqReader

W

wantedFeatures(). Method in class iubio.readseq.BioseqDocImpl
wantedRange(). Method in class iubio.readseq.BioseqDocImpl
wantsDocument(). Method in class iubio.readseq.BioseqWriter
wantsDocument(). Method in interface iubio.readseq.BioseqWriterIface
true if reader should collect documentation/features for this writer.
wantsDocument(). Method in class iubio.readseq.XmlSeqWriter
warning(SAXParseException). Method in class iubio.readseq.XmlSeqReader
write(). Method in class iubio.readseq.Writeseq
writeAllText(). Method in class iubio.readseq.BioseqDocImpl
writeCharacters(byte[], int, int). Method in class iubio.readseq.XmlPrintWriter
writeCharacters(char[], int, int). Method in class iubio.readseq.XmlPrintWriter
writeCharacters(String, int, int). Method in class iubio.readseq.XmlPrintWriter
writeDoc(). Method in class iubio.readseq.BioseqWriter
writeDoc(). Method in interface iubio.readseq.BioseqWriterIface
write documentation for record, form where all doc is known from setSeq()
writeDoc(). Method in class iubio.readseq.XmlSeqWriter
write documentation for record, form where all doc is known from setSeq()
writeDocumentText(). Method in class iubio.readseq.BioseqDocImpl
writeEmptyElement(String, int). Method in class iubio.readseq.XmlPrintWriter
writeEndElement(String, boolean, int). Method in class iubio.readseq.XmlPrintWriter
writeEndElement(String, int). Method in class iubio.readseq.XmlPrintWriter
writeFeatureText(). Method in class iubio.readseq.BioseqDocImpl
writeHeader(). Method in class iubio.readseq.BioseqWriter
writeHeader(). Method in interface iubio.readseq.BioseqWriterIface
writeHeader(). Method in class iubio.readseq.InterleavedSeqWriter
writeHeader(). Method in class iubio.readseq.XmlSeqWriter
writeObject(OutputStream, Object, boolean). Static method in class flybase.Utils
writeRecordEnd(). Method in class iubio.readseq.BioseqWriter
writeRecordEnd(). Method in interface iubio.readseq.BioseqWriterIface
end of seq record
writeRecordEnd(). Method in class iubio.readseq.XmlSeqWriter
end of seq record
writeRecordStart(). Method in class iubio.readseq.BioseqWriter
writeRecordStart(). Method in interface iubio.readseq.BioseqWriterIface
start of sequence record, initialize per seq, subclasses customize as needed
writeRecordStart(). Method in class iubio.readseq.InterleavedSeqWriter
writeRecordStart(). Method in class iubio.readseq.XmlSeqWriter
start of sequence record, initialize per seq, subclasses customize as needed
writeSeq(). Method in class iubio.readseq.BioseqWriter
writeSeq(). Method in interface iubio.readseq.BioseqWriterIface
write sequence data, when all seq is known from setSeq()
Writeseq(). Constructor for class iubio.readseq.Writeseq
writeSeq(). Method in class iubio.readseq.XmlSeqWriter
write sequence data, when all seq is known from setSeq()
Writeseq(int). Constructor for class iubio.readseq.Writeseq
writeSeqEnd(). Method in class iubio.readseq.BioseqWriter
writeSeqEnd(). Method in interface iubio.readseq.BioseqWriterIface
end of seq before newline or end of record - called at end of writeSeq() generally
writeSeqEnd(). Method in class iubio.readseq.XmlSeqWriter
end of seq before newline or end of record
WriteseqOpts(). Constructor for class iubio.readseq.WriteseqOpts
writeSeqRecord(). Method in class iubio.readseq.BioseqWriter
writeSeqRecord(). Method in interface iubio.readseq.BioseqWriterIface
write a full seq record, given setSeq()

implementation does writeRecordStart(), writeDoc(), writeSeq(), writeRecordEnd()

writeSeqRecord(). Method in class iubio.readseq.XmlSeqWriter
writeSeqTo(SeqFileInfo, BioseqWriterIface, BioseqWriterIface). Method in class iubio.readseq.Readseq
writeStartElement(String, boolean, int). Method in class iubio.readseq.XmlPrintWriter
writeStartElement(String, int). Method in class iubio.readseq.XmlPrintWriter
writeTag(String, String, int). Method in class iubio.readseq.XmlPrintWriter
writeTagStart(String, String, int). Method in class iubio.readseq.XmlPrintWriter
writeTo(Writer). Method in class iubio.readseq.BioseqDocImpl
writeTo(Writer). Method in class iubio.readseq.XmlDoc
writeTo(Writer, boolean). Method in class iubio.readseq.BioseqDocImpl
writeTo(Writer, boolean). Method in class iubio.readseq.XmlDoc
writeTrailer(). Method in class iubio.readseq.BioseqWriter
writeTrailer(). Method in interface iubio.readseq.BioseqWriterIface
writeTrailer(). Method in class iubio.readseq.InterleavedSeqWriter
writeTrailer(). Method in class iubio.readseq.XmlSeqWriter
writeValue(String). Method in class iubio.readseq.XmlPrintWriter
writeWrapText(String). Method in class iubio.readseq.BioseqDocImpl
writeWrapText(String, int, int). Method in class iubio.readseq.XmlPrintWriter

X

XmlDoc(). Constructor for class iubio.readseq.XmlDoc
XmlDoc(BioseqDoc). Constructor for class iubio.readseq.XmlDoc
XmlDoc(String). Constructor for class iubio.readseq.XmlDoc
XmlPrintWriter(OutputStream). Constructor for class iubio.readseq.XmlPrintWriter
XmlPrintWriter(OutputStream, boolean). Constructor for class iubio.readseq.XmlPrintWriter
XmlPrintWriter(Writer). Constructor for class iubio.readseq.XmlPrintWriter
XmlPrintWriter(Writer, boolean). Constructor for class iubio.readseq.XmlPrintWriter
xmlprop. Static variable in class iubio.readseq.XmlDoc
XmlSeqFormat(). Constructor for class iubio.readseq.XmlSeqFormat
XmlSeqReader(). Constructor for class iubio.readseq.XmlSeqReader
XmlSeqWriter(). Constructor for class iubio.readseq.XmlSeqWriter
xprop. Static variable in class iubio.readseq.BasicBioseqDoc
xwin. Static variable in class flybase.Native

Z

ZF. Static variable in class Acme.Fmt
ZipChecksum(Bioseq, int, int, Checksum). Static method in class iubio.readseq.BioseqWriter
ZukerSeqFormat(). Constructor for class iubio.readseq.ZukerSeqFormat