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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

Variable Index

 o bioseqprop
 o gbfeatname
 o kLinewidth
 o sExtractionFeature
 o sExtractRangeFeature

Constructor Index

 o BioseqDocImpl()
 o BioseqDocImpl(BioseqDoc)

Method Index

 o addBasicName(String)
 o addComment(String)
 o addDate(Date)
 o addDocField(DocItem)
 o addDocField(int, String)
 o addDocField(String, String, int, boolean)
 o addDocField(String, String, int, int, boolean)
 o addDocLine(OpenString)
 o addDocLine(String)
 o addDocText(String)
 o addFeature(FeatureItem)
 o addFeature(String, SeqRange)
 o addFeature(String, String, int, boolean)
 o addFeatureNote(FeatureItem, String)
 o addFeatureNote(FeatureItem, String, String)
 o addFeatureNote(String)
 o addFeatureNote(String, String)
 o addFeatures(FastVector)
 o addFeatureText(String)
 o addSequenceStats(Bioseq)
 o clone()
 o deleteDocItem(FastVector, int, int)
 o deleteDocItem(int)
 o deleteFeature(String, SeqRange)
 o documents()
 o features()
 o findDocItem(FastVector, int, int)
 o findDocItem(FastVector, String, int)
 o findDocItem(int, int)
 o findFeature(Object)
 o findFeature(String)
 o findFeature(String, SeqRange)
 o findFeatures(Hashtable, SeqRange, Vector)
 o findFeatures(SeqRange)
 o findFeatures(SeqRange, Vector)
 o findFeatures(String)
 o findFeatures(String, SeqRange)
 o findFeatures(String, SeqRange, Vector)
 o findFeatures(String, Vector)
 o getBiodocInteger(String)
 o getBiodockey(int)
 o getBiodockey(String)
 o getBiodocKind(String)
 o getBiodoclabel(int)
 o getContinueLabel(DocItem)
 o getCurFieldItem()
 o getDocField(FastVector, int, int)
 o getDocField(FastVector, String, int)
 o getDocField(int)
 o getDocField(String)
 o getDocField(String, int)
 o getDocumentText()
 o getFeature(String)
 o getFeatureRanges(Hashtable, int, int)
 o getFeatureRanges(int, int)
 o getFeaturesAt(SeqRange)
 o getFeatureText()
 o getFieldName(int)
 o getID()
 o getIndent()
 o getStandardFeatureList()
 o getStandardQualifiersList()
 o getTitle()
 o hasDocument()
 o hasFeatures()
 o insertRange(SeqRange)
 o isNotWantedFeature()
 o linesWritten()
 o removeRange(SeqRange)
 o replaceDocField(int, String)
 o replaceDocItem(int, DocItem)
 o setCurFieldItem(FeatureItem)
 o setKeepField(int)
 o setOutput(OutputStream)
 o setOutput(Writer)
 o setSkipDocs(boolean)
 o setSourceDoc(BioseqDoc)
 o setWantedFeatures(boolean, Hashtable, SeqRange)
 o setWantedFeatures(Hashtable)
 o setWantedFeatures(Hashtable, SeqRange)
 o updateRange(int, int, int, byte[])
changeflags: SeqRange.kDelete = 1, kInsert = 2, kReorder = 4, kChange = 8;
 o wantedFeatures()
 o wantedRange()
 o writeAllText()
 o writeDocumentText()
 o writeFeatureText()
 o writeTo(Writer)
 o writeTo(Writer, boolean)
 o writeWrapText(String)

Variables

 o bioseqprop
 public static java.lang.String bioseqprop
 o gbfeatname
 public static java.lang.String gbfeatname
 o kLinewidth
 public int kLinewidth
 o sExtractionFeature
 public static final java.lang.String sExtractionFeature
 o sExtractRangeFeature
 public static final java.lang.String sExtractRangeFeature

Constructors

 o BioseqDocImpl
 public BioseqDocImpl()
 o BioseqDocImpl
 public BioseqDocImpl(iubio.readseq.BioseqDoc source)

Methods

 o getStandardQualifiersList
 public static java.lang.String[] getStandardQualifiersList()
 o getStandardFeatureList
 public static java.lang.String[] getStandardFeatureList()
 o getFieldName
 public abstract java.lang.String getFieldName(int kind)
 o getBiodockey
 public abstract java.lang.String getBiodockey(java.lang.String field)
 o addDocLine
 public abstract void addDocLine(java.lang.String line)
 o addDocLine
 public void addDocLine(flybase.OpenString line)
 o getBiodockey
 public static java.lang.String getBiodockey(int kind)
 o getBiodoclabel
 public static java.lang.String getBiodoclabel(int kind)
 o getBiodocInteger
 public java.lang.Integer getBiodocInteger(java.lang.String field)
 o getBiodocKind
 public int getBiodocKind(java.lang.String field)
 o clone
 public java.lang.Object clone()
Overrides:
clone in class java.lang.Object
 o getID
 public java.lang.String getID()
 o getTitle
 public java.lang.String getTitle()
 o hasFeatures
 public boolean hasFeatures()
 o hasDocument
 public boolean hasDocument()
 o documents
 public flybase.FastVector documents()
 o features
 public flybase.FastVector features()
 o setSourceDoc
 public void setSourceDoc(iubio.readseq.BioseqDoc source)
 o getDocField
 public final java.lang.String getDocField(int kind)
 o getDocField
 public final java.lang.String getDocField(flybase.FastVector doc,
                                           int kind,
                                           int which)
 o deleteDocItem
 public void deleteDocItem(int kind)
 o deleteDocItem
 public void deleteDocItem(flybase.FastVector doc,
                           int kind,
                           int which)
 o replaceDocItem
 public final void replaceDocItem(int kind,
                                  iubio.readseq.DocItem newitem)
 o findDocItem
 public final iubio.readseq.DocItem findDocItem(int kind,
                                                int which)
 o findDocItem
 public iubio.readseq.DocItem findDocItem(flybase.FastVector doc,
                                          int kind,
                                          int which)
 o getDocField
 public final java.lang.String getDocField(java.lang.String field)
 o getFeature
 public final java.lang.String getFeature(java.lang.String field)
 o getDocField
 public final java.lang.String getDocField(java.lang.String field,
                                           int which)
 o getDocField
 public final java.lang.String getDocField(flybase.FastVector doc,
                                           java.lang.String field,
                                           int which)
 o findDocItem
 public iubio.readseq.DocItem findDocItem(flybase.FastVector doc,
                                          java.lang.String field,
                                          int which)
 o getCurFieldItem
 public iubio.readseq.FeatureItem getCurFieldItem()
 o setCurFieldItem
 public void setCurFieldItem(iubio.readseq.FeatureItem fi)
 o setKeepField
 public void setKeepField(int kind)
 o setSkipDocs
 public void setSkipDocs(boolean turnon)
 o addBasicName
 public void addBasicName(java.lang.String desc)
 o addComment
 public void addComment(java.lang.String comment)
 o addDate
 public void addDate(java.util.Date date)
 o addSequenceStats
 public void addSequenceStats(iubio.bioseq.Bioseq seq)
 o addDocText
 public void addDocText(java.lang.String text)
 o addFeatureText
 public void addFeatureText(java.lang.String text)
 o addDocField
 public void addDocField(iubio.readseq.DocItem di)
 o addDocField
 public void addDocField(int fieldId,
                         java.lang.String value)
 o replaceDocField
 public void replaceDocField(int fieldId,
                             java.lang.String value)
 o addDocField
 public void addDocField(java.lang.String field,
                         java.lang.String value,
                         int level,
                         boolean append)
 o addDocField
 public void addDocField(java.lang.String field,
                         java.lang.String value,
                         int kind,
                         int level,
                         boolean append)
 o addFeatureNote
 public void addFeatureNote(iubio.readseq.FeatureItem featItem,
                            java.lang.String key,
                            java.lang.String value)
 o addFeatureNote
 public void addFeatureNote(iubio.readseq.FeatureItem featItem,
                            java.lang.String value)
 o addFeatureNote
 public void addFeatureNote(java.lang.String key,
                            java.lang.String value)
 o addFeatureNote
 public void addFeatureNote(java.lang.String value)
 o addFeature
 public void addFeature(iubio.readseq.FeatureItem fi)
 o addFeature
 public iubio.readseq.FeatureItem addFeature(java.lang.String name,
                                             iubio.bioseq.SeqRange sr)
 o addFeatures
 public void addFeatures(flybase.FastVector addfeats)
 o addFeature
 public void addFeature(java.lang.String field,
                        java.lang.String value,
                        int level,
                        boolean append)
 o deleteFeature
 public void deleteFeature(java.lang.String name,
                           iubio.bioseq.SeqRange sr)
 o findFeature
 public iubio.readseq.FeatureItem findFeature(java.lang.String name,
                                              iubio.bioseq.SeqRange sr)
 o findFeature
 public iubio.readseq.FeatureItem findFeature(java.lang.String name)
 o findFeature
 public iubio.readseq.FeatureItem findFeature(java.lang.Object item)
 o findFeatures
 public final iubio.readseq.FeatureItem[] findFeatures(iubio.bioseq.SeqRange sr)
 o findFeatures
 public final iubio.readseq.FeatureItem[] findFeatures(java.lang.String name)
 o findFeatures
 public iubio.readseq.FeatureItem[] findFeatures(java.lang.String name,
                                                 iubio.bioseq.SeqRange sr)
 o findFeatures
 public final java.util.Vector findFeatures(iubio.bioseq.SeqRange sr,
                                            java.util.Vector addto)
 o findFeatures
 public final java.util.Vector findFeatures(java.lang.String name,
                                            java.util.Vector addto)
 o findFeatures
 public java.util.Vector findFeatures(java.lang.String name,
                                      iubio.bioseq.SeqRange sr,
                                      java.util.Vector addto)
 o findFeatures
 public java.util.Vector findFeatures(java.util.Hashtable wantfeatures,
                                      iubio.bioseq.SeqRange sr,
                                      java.util.Vector addto)
 o getFeaturesAt
 public java.lang.String[] getFeaturesAt(iubio.bioseq.SeqRange sr)
 o updateRange
 public void updateRange(int changeflags,
                         int start,
                         int length,
                         byte changes[])
changeflags: SeqRange.kDelete = 1, kInsert = 2, kReorder = 4, kChange = 8;

 o removeRange
 public final void removeRange(iubio.bioseq.SeqRange sr)
 o insertRange
 public final void insertRange(iubio.bioseq.SeqRange sr)
 o wantedFeatures
 public java.util.Hashtable wantedFeatures()
 o wantedRange
 public iubio.bioseq.SeqRange wantedRange()
 o isNotWantedFeature
 public boolean isNotWantedFeature()
 o setWantedFeatures
 public void setWantedFeatures(java.util.Hashtable wantfeatures)
 o setWantedFeatures
 public void setWantedFeatures(java.util.Hashtable wantfeatures,
                               iubio.bioseq.SeqRange wantedrange)
 o setWantedFeatures
 public void setWantedFeatures(boolean extract,
                               java.util.Hashtable wantfeatures,
                               iubio.bioseq.SeqRange wantedrange)
 o getFeatureRanges
 public final iubio.bioseq.SeqRange getFeatureRanges(int offset,
                                                     int seqlen)
 o getFeatureRanges
 public iubio.bioseq.SeqRange getFeatureRanges(java.util.Hashtable wantfeatures,
                                               int offset,
                                               int seqlen)
 o linesWritten
 public int linesWritten()
 o getIndent
 public int getIndent()
 o getContinueLabel
 public java.lang.String getContinueLabel(iubio.readseq.DocItem di)
 o setOutput
 public void setOutput(java.io.Writer outs)
 o setOutput
 public void setOutput(java.io.OutputStream outs)
 o writeTo
 public int writeTo(java.io.Writer outs)
 o writeTo
 public int writeTo(java.io.Writer outs,
                    boolean doId)
 o writeAllText
 public void writeAllText()
 o writeDocumentText
 public void writeDocumentText()
 o writeFeatureText
 public void writeFeatureText()
 o getDocumentText
 public java.lang.String getDocumentText()
 o getFeatureText
 public java.lang.String getFeatureText()
 o writeWrapText
 public java.lang.String writeWrapText(java.lang.String val)

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