All Packages Class Hierarchy This Package Previous Next Index
Class iubio.readseq.BioseqDocImpl
java.lang.Object
|
+----iubio.readseq.BioseqDocImpl
- public abstract class BioseqDocImpl
- extends java.lang.Object
- implements iubio.readseq.BioseqDoc, java.lang.Cloneable
sequence format information (document,features)
common document fields among formats
- See Also:
- iubio.drawseq.DrawableBioseqDoc
-
bioseqprop
-
-
gbfeatname
-
-
kLinewidth
-
-
sExtractionFeature
-
-
sExtractRangeFeature
-
-
BioseqDocImpl()
-
-
BioseqDocImpl(BioseqDoc)
-
-
addBasicName(String)
-
-
addComment(String)
-
-
addDate(Date)
-
-
addDocField(DocItem)
-
-
addDocField(int, String)
-
-
addDocField(String, String, int, boolean)
-
-
addDocField(String, String, int, int, boolean)
-
-
addDocLine(OpenString)
-
-
addDocLine(String)
-
-
addDocText(String)
-
-
addFeature(FeatureItem)
-
-
addFeature(String, SeqRange)
-
-
addFeature(String, String, int, boolean)
-
-
addFeatureNote(FeatureItem, String)
-
-
addFeatureNote(FeatureItem, String, String)
-
-
addFeatureNote(String)
-
-
addFeatureNote(String, String)
-
-
addFeatures(FastVector)
-
-
addFeatureText(String)
-
-
addSequenceStats(Bioseq)
-
-
clone()
-
-
deleteDocItem(FastVector, int, int)
-
-
deleteDocItem(int)
-
-
deleteFeature(String, SeqRange)
-
-
documents()
-
-
features()
-
-
findDocItem(FastVector, int, int)
-
-
findDocItem(FastVector, String, int)
-
-
findDocItem(int, int)
-
-
findFeature(Object)
-
-
findFeature(String)
-
-
findFeature(String, SeqRange)
-
-
findFeatures(Hashtable, SeqRange, Vector)
-
-
findFeatures(SeqRange)
-
-
findFeatures(SeqRange, Vector)
-
-
findFeatures(String)
-
-
findFeatures(String, SeqRange)
-
-
findFeatures(String, SeqRange, Vector)
-
-
findFeatures(String, Vector)
-
-
getBiodocInteger(String)
-
-
getBiodockey(int)
-
-
getBiodockey(String)
-
-
getBiodocKind(String)
-
-
getBiodoclabel(int)
-
-
getContinueLabel(DocItem)
-
-
getCurFieldItem()
-
-
getDocField(FastVector, int, int)
-
-
getDocField(FastVector, String, int)
-
-
getDocField(int)
-
-
getDocField(String)
-
-
getDocField(String, int)
-
-
getDocumentText()
-
-
getFeature(String)
-
-
getFeatureRanges(Hashtable, int, int)
-
-
getFeatureRanges(int, int)
-
-
getFeaturesAt(SeqRange)
-
-
getFeatureText()
-
-
getFieldName(int)
-
-
getID()
-
-
getIndent()
-
-
getStandardFeatureList()
-
-
getStandardQualifiersList()
-
-
getTitle()
-
-
hasDocument()
-
-
hasFeatures()
-
-
insertRange(SeqRange)
-
-
isNotWantedFeature()
-
-
linesWritten()
-
-
removeRange(SeqRange)
-
-
replaceDocField(int, String)
-
-
replaceDocItem(int, DocItem)
-
-
setCurFieldItem(FeatureItem)
-
-
setKeepField(int)
-
-
setOutput(OutputStream)
-
-
setOutput(Writer)
-
-
setSkipDocs(boolean)
-
-
setSourceDoc(BioseqDoc)
-
-
setWantedFeatures(boolean, Hashtable, SeqRange)
-
-
setWantedFeatures(Hashtable)
-
-
setWantedFeatures(Hashtable, SeqRange)
-
-
updateRange(int, int, int, byte[])
- changeflags: SeqRange.kDelete = 1, kInsert = 2, kReorder = 4, kChange = 8;
-
wantedFeatures()
-
-
wantedRange()
-
-
writeAllText()
-
-
writeDocumentText()
-
-
writeFeatureText()
-
-
writeTo(Writer)
-
-
writeTo(Writer, boolean)
-
-
writeWrapText(String)
-
bioseqprop
public static java.lang.String bioseqprop
gbfeatname
public static java.lang.String gbfeatname
kLinewidth
public int kLinewidth
sExtractionFeature
public static final java.lang.String sExtractionFeature
sExtractRangeFeature
public static final java.lang.String sExtractRangeFeature
BioseqDocImpl
public BioseqDocImpl()
BioseqDocImpl
public BioseqDocImpl(iubio.readseq.BioseqDoc source)
getStandardQualifiersList
public static java.lang.String[] getStandardQualifiersList()
getStandardFeatureList
public static java.lang.String[] getStandardFeatureList()
getFieldName
public abstract java.lang.String getFieldName(int kind)
getBiodockey
public abstract java.lang.String getBiodockey(java.lang.String field)
addDocLine
public abstract void addDocLine(java.lang.String line)
addDocLine
public void addDocLine(flybase.OpenString line)
getBiodockey
public static java.lang.String getBiodockey(int kind)
getBiodoclabel
public static java.lang.String getBiodoclabel(int kind)
getBiodocInteger
public java.lang.Integer getBiodocInteger(java.lang.String field)
getBiodocKind
public int getBiodocKind(java.lang.String field)
clone
public java.lang.Object clone()
- Overrides:
- clone in class java.lang.Object
getID
public java.lang.String getID()
getTitle
public java.lang.String getTitle()
hasFeatures
public boolean hasFeatures()
hasDocument
public boolean hasDocument()
documents
public flybase.FastVector documents()
features
public flybase.FastVector features()
setSourceDoc
public void setSourceDoc(iubio.readseq.BioseqDoc source)
getDocField
public final java.lang.String getDocField(int kind)
getDocField
public final java.lang.String getDocField(flybase.FastVector doc,
int kind,
int which)
deleteDocItem
public void deleteDocItem(int kind)
deleteDocItem
public void deleteDocItem(flybase.FastVector doc,
int kind,
int which)
replaceDocItem
public final void replaceDocItem(int kind,
iubio.readseq.DocItem newitem)
findDocItem
public final iubio.readseq.DocItem findDocItem(int kind,
int which)
findDocItem
public iubio.readseq.DocItem findDocItem(flybase.FastVector doc,
int kind,
int which)
getDocField
public final java.lang.String getDocField(java.lang.String field)
getFeature
public final java.lang.String getFeature(java.lang.String field)
getDocField
public final java.lang.String getDocField(java.lang.String field,
int which)
getDocField
public final java.lang.String getDocField(flybase.FastVector doc,
java.lang.String field,
int which)
findDocItem
public iubio.readseq.DocItem findDocItem(flybase.FastVector doc,
java.lang.String field,
int which)
getCurFieldItem
public iubio.readseq.FeatureItem getCurFieldItem()
setCurFieldItem
public void setCurFieldItem(iubio.readseq.FeatureItem fi)
setKeepField
public void setKeepField(int kind)
setSkipDocs
public void setSkipDocs(boolean turnon)
addBasicName
public void addBasicName(java.lang.String desc)
addComment
public void addComment(java.lang.String comment)
addDate
public void addDate(java.util.Date date)
addSequenceStats
public void addSequenceStats(iubio.bioseq.Bioseq seq)
addDocText
public void addDocText(java.lang.String text)
addFeatureText
public void addFeatureText(java.lang.String text)
addDocField
public void addDocField(iubio.readseq.DocItem di)
addDocField
public void addDocField(int fieldId,
java.lang.String value)
replaceDocField
public void replaceDocField(int fieldId,
java.lang.String value)
addDocField
public void addDocField(java.lang.String field,
java.lang.String value,
int level,
boolean append)
addDocField
public void addDocField(java.lang.String field,
java.lang.String value,
int kind,
int level,
boolean append)
addFeatureNote
public void addFeatureNote(iubio.readseq.FeatureItem featItem,
java.lang.String key,
java.lang.String value)
addFeatureNote
public void addFeatureNote(iubio.readseq.FeatureItem featItem,
java.lang.String value)
addFeatureNote
public void addFeatureNote(java.lang.String key,
java.lang.String value)
addFeatureNote
public void addFeatureNote(java.lang.String value)
addFeature
public void addFeature(iubio.readseq.FeatureItem fi)
addFeature
public iubio.readseq.FeatureItem addFeature(java.lang.String name,
iubio.bioseq.SeqRange sr)
addFeatures
public void addFeatures(flybase.FastVector addfeats)
addFeature
public void addFeature(java.lang.String field,
java.lang.String value,
int level,
boolean append)
deleteFeature
public void deleteFeature(java.lang.String name,
iubio.bioseq.SeqRange sr)
findFeature
public iubio.readseq.FeatureItem findFeature(java.lang.String name,
iubio.bioseq.SeqRange sr)
findFeature
public iubio.readseq.FeatureItem findFeature(java.lang.String name)
findFeature
public iubio.readseq.FeatureItem findFeature(java.lang.Object item)
findFeatures
public final iubio.readseq.FeatureItem[] findFeatures(iubio.bioseq.SeqRange sr)
findFeatures
public final iubio.readseq.FeatureItem[] findFeatures(java.lang.String name)
findFeatures
public iubio.readseq.FeatureItem[] findFeatures(java.lang.String name,
iubio.bioseq.SeqRange sr)
findFeatures
public final java.util.Vector findFeatures(iubio.bioseq.SeqRange sr,
java.util.Vector addto)
findFeatures
public final java.util.Vector findFeatures(java.lang.String name,
java.util.Vector addto)
findFeatures
public java.util.Vector findFeatures(java.lang.String name,
iubio.bioseq.SeqRange sr,
java.util.Vector addto)
findFeatures
public java.util.Vector findFeatures(java.util.Hashtable wantfeatures,
iubio.bioseq.SeqRange sr,
java.util.Vector addto)
getFeaturesAt
public java.lang.String[] getFeaturesAt(iubio.bioseq.SeqRange sr)
updateRange
public void updateRange(int changeflags,
int start,
int length,
byte changes[])
- changeflags: SeqRange.kDelete = 1, kInsert = 2, kReorder = 4, kChange = 8;
removeRange
public final void removeRange(iubio.bioseq.SeqRange sr)
insertRange
public final void insertRange(iubio.bioseq.SeqRange sr)
wantedFeatures
public java.util.Hashtable wantedFeatures()
wantedRange
public iubio.bioseq.SeqRange wantedRange()
isNotWantedFeature
public boolean isNotWantedFeature()
setWantedFeatures
public void setWantedFeatures(java.util.Hashtable wantfeatures)
setWantedFeatures
public void setWantedFeatures(java.util.Hashtable wantfeatures,
iubio.bioseq.SeqRange wantedrange)
setWantedFeatures
public void setWantedFeatures(boolean extract,
java.util.Hashtable wantfeatures,
iubio.bioseq.SeqRange wantedrange)
getFeatureRanges
public final iubio.bioseq.SeqRange getFeatureRanges(int offset,
int seqlen)
getFeatureRanges
public iubio.bioseq.SeqRange getFeatureRanges(java.util.Hashtable wantfeatures,
int offset,
int seqlen)
linesWritten
public int linesWritten()
getIndent
public int getIndent()
getContinueLabel
public java.lang.String getContinueLabel(iubio.readseq.DocItem di)
setOutput
public void setOutput(java.io.Writer outs)
setOutput
public void setOutput(java.io.OutputStream outs)
writeTo
public int writeTo(java.io.Writer outs)
writeTo
public int writeTo(java.io.Writer outs,
boolean doId)
writeAllText
public void writeAllText()
writeDocumentText
public void writeDocumentText()
writeFeatureText
public void writeFeatureText()
getDocumentText
public java.lang.String getDocumentText()
getFeatureText
public java.lang.String getFeatureText()
writeWrapText
public java.lang.String writeWrapText(java.lang.String val)
All Packages Class Hierarchy This Package Previous Next Index