Serialized Form (com.hfg API Documentation)

Package com.hfg.bio
- Class com.hfg.bio.InvalidResidueException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.bio.Strand extends java.lang.Object implements Serializable
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
  - Serialized Fields
    - mSymbol
```
char mSymbol
```
    - mName
```
java.lang.String mName
```
    - mIndex
```
int mIndex
```
Package com.hfg.bio.seq
- Class com.hfg.bio.seq.SeqTopology extends java.lang.Object implements Serializable
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
  - Serialized Fields
    - mName
```
java.lang.String mName
```
Package com.hfg.bio.seq.alignment
- Class com.hfg.bio.seq.alignment.KMerBitSet extends java.util.BitSet implements Serializable
  - Serialized Fields
    - mSeqType
```
BioSequenceType mSeqType
```
    - mKMerSize
```
int mKMerSize
```
    - mResidueIndexLookup
```
int[] mResidueIndexLookup
```
    - mUnknownResidueIndex
```
int mUnknownResidueIndex
```
Package com.hfg.bio.seq.alignment.blast
- Class com.hfg.bio.seq.alignment.blast.BLAST_Database extends java.io.File implements Serializable
  - Serialized Fields
    - mType
```
BioSequenceType mType
```
    - mDescription
```
java.lang.String mDescription
```
    - mCacheDate
```
java.util.Date mCacheDate
```
    - mNumSequences
```
java.lang.Integer mNumSequences
```
Package com.hfg.bio.seq.format
- Class com.hfg.bio.seq.format.EMBL_DataClass extends java.lang.Object implements Serializable
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
  - Serialized Fields
    - mName
```
java.lang.String mName
```
    - mCode
```
java.lang.String mCode
```
- Class com.hfg.bio.seq.format.SeqFormatException extends SeqIOException implements Serializable
- Class com.hfg.bio.seq.format.SeqIOException extends java.lang.RuntimeException implements Serializable
Package com.hfg.bio.seq.format.feature.qualifier
- Class com.hfg.bio.seq.format.feature.qualifier.MolType extends java.lang.Object implements Serializable
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
  - Serialized Fields
    - mName
```
java.lang.String mName
```
    - mIsValid
```
boolean mIsValid
```
Package com.hfg.bio.seq.format.genbank
- Class com.hfg.bio.seq.format.genbank.InvalidGenBankKeywordException extends SeqIOException implements Serializable
- Class com.hfg.bio.seq.format.genbank.InvalidGenBankSubkeywordException extends SeqFormatException implements Serializable
Package com.hfg.bio.seq.pattern
- Class com.hfg.bio.seq.pattern.SeqPatternConfigurationException extends java.lang.RuntimeException implements Serializable
Package com.hfg.bio.seq.translation
- Class com.hfg.bio.seq.translation.TranslationException extends java.lang.RuntimeException implements Serializable
Package com.hfg.bio.taxonomy
- Class com.hfg.bio.taxonomy.EMBL_TaxonDivision extends java.lang.Object implements Serializable
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
  - Serialized Fields
    - mName
```
java.lang.String mName
```
    - mCode
```
java.lang.String mCode
```
- Class com.hfg.bio.taxonomy.NCBIGenBankDivision extends java.lang.Object implements Serializable
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
  - Serialized Fields
    - mName
```
java.lang.String mName
```
    - mCode
```
java.lang.String mCode
```
    - mId
```
java.lang.Integer mId
```
- Class com.hfg.bio.taxonomy.NCBITaxonNameClass extends java.lang.Object implements Serializable
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
  - Serialized Fields
    - mName
```
java.lang.String mName
```
- Class com.hfg.bio.taxonomy.NCBITaxonNodeRank extends java.lang.Object implements Serializable
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
  - Serialized Fields
    - mName
```
java.lang.String mName
```
    - mRank
```
int mRank
```
Package com.hfg.chem
- Class com.hfg.chem.ChemicalFormulaParseException extends java.lang.RuntimeException implements Serializable
Package com.hfg.chem.format
- Class com.hfg.chem.format.ChemIOException extends java.lang.RuntimeException implements Serializable
Package com.hfg.css
- Class com.hfg.css.CSSException extends java.lang.RuntimeException implements Serializable
Package com.hfg.datetime
- Class com.hfg.datetime.DateSortDirection extends java.lang.Object implements Serializable
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
  - Serialized Fields
    - mName
```
java.lang.String mName
```
    - mIndex
```
int mIndex
```
- Class com.hfg.datetime.ThreadSafeDateFormat extends java.text.SimpleDateFormat implements Serializable
  - Serialized Fields
    - mDateFormat
```
java.lang.ThreadLocal<T> mDateFormat
```
Package com.hfg.exception
- Class com.hfg.exception.CompressionException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.exception.ConfigurationException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.exception.DataIntegrityException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.exception.InsufficientConfigurationException extends ConfigurationException implements Serializable
- Class com.hfg.exception.InvalidValueException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.exception.LowMemoryException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.exception.ProgrammingException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.exception.UnimplementedFunctionalityException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.exception.UnimplementedMethodException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.exception.UnmodifyableObjectException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.exception.UserInputException extends java.lang.RuntimeException implements Serializable

Package com.hfg.graphics

Class com.hfg.graphics.BorderType extends java.lang.Object implements Serializable
- Serialization Methods
  - readResolve
```
private java.lang.Object readResolve()
```
    This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
- Serialized Fields
  - mName
```
java.lang.String mName
```
  - mIndex
```
int mIndex
```

Class com.hfg.graphics.Gene2D extends java.awt.Rectangle implements Serializable

Serialized Fields

mId
```
java.lang.String mId
```
mDescription
```
java.lang.String mDescription
```
mURLs
```
java.util.List<E> mURLs
```
mStartLocation
```
int mStartLocation
```
mEndLocation
```
int mEndLocation
```
mStrand
```
Strand mStrand
```
mExons
```
java.util.List<E> mExons
```
mSpecies
```
NCBITaxon mSpecies
```
mSeqMappingCoverage
```
SeqMappingCoverage mSeqMappingCoverage
```
mDisplayStart
```
int mDisplayStart
```
mDisplayEnd
```
int mDisplayEnd
```
mInDisplayRegion
```
boolean mInDisplayRegion
```
mShowId
```
boolean mShowId
```
mLabelWidthInPixels
```
int mLabelWidthInPixels
```
mColor
```
java.awt.Color mColor
```
mLabelFont
```
java.awt.Font mLabelFont
```
mXScalingFactor
```
double mXScalingFactor
```
mHeightInPixels
```
int mHeightInPixels
```

Class com.hfg.graphics.Track extends java.awt.Rectangle implements Serializable

Serialized Fields

mName
```
java.lang.String mName
```
mDescription
```
java.lang.String mDescription
```
mURL
```
java.lang.String mURL
```
mForwardGenes
```
java.util.List<E> mForwardGenes
```
mReverseGenes
```
java.util.List<E> mReverseGenes
```
mHighlightRegions
```
java.util.List<E> mHighlightRegions
```
mShowId
```
java.lang.Boolean mShowId
```
mShowSpeciesInTooltip
```
boolean mShowSpeciesInTooltip
```
mShowLocationInTooltip
```
boolean mShowLocationInTooltip
```
mBackgroundColor
```
java.awt.Color mBackgroundColor
```
mAxisColor
```
java.awt.Color mAxisColor
```
mLabelColor
```
java.awt.Color mLabelColor
```
mHighlightColor
```
java.awt.Color mHighlightColor
```
mLabelFont
```
java.awt.Font mLabelFont
```
mXAxisStartValue
```
int mXAxisStartValue
```
mXAxisEndValue
```
int mXAxisEndValue
```
mXScalingFactor
```
double mXScalingFactor
```
mForwardLineMap
```
java.util.Map<K,V> mForwardLineMap
```
mReverseLineMap
```
java.util.Map<K,V> mReverseLineMap
```
mNumForwardLines
```
int mNumForwardLines
```
mNumReverseLines
```
int mNumReverseLines
```
mForwardLineHeights
```
java.util.List<E> mForwardLineHeights
```
mReverseLineHeights
```
java.util.List<E> mReverseLineHeights
```
mImageWidthInPixels
```
int mImageWidthInPixels
```
mForwardImageHeightInPixels
```
int mForwardImageHeightInPixels
```
mReverseImageHeightInPixels
```
int mReverseImageHeightInPixels
```
mLineHeightInPixels
```
int mLineHeightInPixels
```
mLinePaddingInPixels
```
int mLinePaddingInPixels
```
mDescriptionWidthInPixels
```
int mDescriptionWidthInPixels
```
mMinimumBufferInPixels
```
int mMinimumBufferInPixels
```
mRightBufferInPixels
```
int mRightBufferInPixels
```
mXAxisImageHeightInPixels
```
int mXAxisImageHeightInPixels
```
mMajorTickStep
```
int mMajorTickStep
```
mMinorTickStep
```
int mMinorTickStep
```
mForwardImageMap
```
ImageMap mForwardImageMap
```
mReverseImageMap
```
ImageMap mReverseImageMap
```
mJavascript
```
Script mJavascript
```

Class com.hfg.graphics.Track2D extends java.awt.Rectangle implements Serializable

Serialized Fields

mName
```
java.lang.String mName
```
mDescription
```
java.lang.String mDescription
```
mURL
```
java.lang.String mURL
```
mForwardGenes
```
java.util.List<E> mForwardGenes
```
mReverseGenes
```
java.util.List<E> mReverseGenes
```
mHighlightRegions
```
java.util.List<E> mHighlightRegions
```
mShowId
```
java.lang.Boolean mShowId
```
mShowSpeciesInTooltip
```
boolean mShowSpeciesInTooltip
```
mShowLocationInTooltip
```
boolean mShowLocationInTooltip
```
mPctIdColorScale
```
ColorScale mPctIdColorScale
```
mBackgroundColor
```
java.awt.Color mBackgroundColor
```
mAxisColor
```
java.awt.Color mAxisColor
```
mLabelColor
```
java.awt.Color mLabelColor
```
mHighlightColor
```
java.awt.Color mHighlightColor
```
mLabelFont
```
java.awt.Font mLabelFont
```
mXAxisStartValue
```
int mXAxisStartValue
```
mXAxisEndValue
```
int mXAxisEndValue
```
mXScalingFactor
```
double mXScalingFactor
```
mForwardLineMap
```
java.util.Map<K,V> mForwardLineMap
```
mReverseLineMap
```
java.util.Map<K,V> mReverseLineMap
```
mNumForwardLines
```
int mNumForwardLines
```
mNumReverseLines
```
int mNumReverseLines
```
mForwardLineHeights
```
java.util.List<E> mForwardLineHeights
```
mReverseLineHeights
```
java.util.List<E> mReverseLineHeights
```
mImageWidthInPixels
```
int mImageWidthInPixels
```
mForwardImageHeightInPixels
```
int mForwardImageHeightInPixels
```
mReverseImageHeightInPixels
```
int mReverseImageHeightInPixels
```
mLineHeightInPixels
```
int mLineHeightInPixels
```
mLinePaddingInPixels
```
int mLinePaddingInPixels
```
mDescriptionWidthInPixels
```
int mDescriptionWidthInPixels
```
mMinimumBufferInPixels
```
int mMinimumBufferInPixels
```
mRightBufferInPixels
```
int mRightBufferInPixels
```
mXAxisImageHeightInPixels
```
int mXAxisImageHeightInPixels
```
mMajorTickStep
```
int mMajorTickStep
```
mMinorTickStep
```
int mMinorTickStep
```
mForwardImageMap
```
ImageMap mForwardImageMap
```
mReverseImageMap
```
ImageMap mReverseImageMap
```
mJavascript
```
Script mJavascript
```

Package com.hfg.html
- Class com.hfg.html.HTMLParseException extends java.lang.RuntimeException implements Serializable
Package com.hfg.html.attribute
- Class com.hfg.html.attribute.Align extends java.lang.Object implements Serializable
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
  - Serialized Fields
    - mName
```
java.lang.String mName
```
    - mIndex
```
int mIndex
```
- Class com.hfg.html.attribute.HTMLColor extends java.awt.Color implements Serializable
  - Serialized Fields
    - mName
```
java.lang.String mName
```
- Class com.hfg.html.attribute.Shape extends java.lang.Object implements Serializable
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
  - Serialized Fields
    - mName
```
java.lang.String mName
```
    - mIndex
```
int mIndex
```
- Class com.hfg.html.attribute.VAlign extends java.lang.Object implements Serializable
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      This method is called after de-serialization, allowing the object to nominate a replacement object to be used in the output graph instead of this object. We don't want multiple objects of each type to exist in a target VM, so instances replace themselves with local objects.
  - Serialized Fields
    - mName
```
java.lang.String mName
```
    - mIndex
```
int mIndex
```
Package com.hfg.javascript
- Class com.hfg.javascript.JsArray extends java.util.ArrayList<java.lang.Object> implements Serializable
- Class com.hfg.javascript.JsObjMap extends OrderedMap<java.lang.String,java.lang.Object> implements Serializable
  - Serialized Fields
    - mUnquotedValueKeys
```
java.util.Set<E> mUnquotedValueKeys
```
Package com.hfg.javascript.ext
- Class com.hfg.javascript.ext.ExtGridColList extends java.util.ArrayList<ExtGridCol> implements Serializable
  - Serialized Fields
    - mName
```
java.lang.String mName
```
Package com.hfg.ldap
- Class com.hfg.ldap.LDAP_Exception extends java.lang.RuntimeException implements Serializable
Package com.hfg.math
- Class com.hfg.math.Counter extends java.lang.Number implements Serializable
  - Serialized Fields
    - mValue
```
int mValue
```
- Class com.hfg.math.RomanNumeral extends java.lang.Number implements Serializable
  - Serialized Fields
    - mString
```
java.lang.String mString
```
    - mValue
```
int mValue
```
Package com.hfg.sql.jdbc
- Class com.hfg.sql.jdbc.JDBCException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.sql.jdbc.NoAvailableConnectionException extends JDBCException implements Serializable
Package com.hfg.svg
- Class com.hfg.svg.SvgException extends java.lang.RuntimeException implements Serializable
Package com.hfg.svg.path
- Class com.hfg.svg.path.SvgPathDataException extends SvgException implements Serializable
Package com.hfg.units
- Class com.hfg.units.UnitException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.units.UnitParseException extends UnitException implements Serializable
Package com.hfg.util
- Class com.hfg.util.ExecutorException extends java.lang.RuntimeException implements Serializable
Package com.hfg.util.collection
- Class com.hfg.util.collection.BiHashMap extends java.util.HashMap<K,V> implements Serializable
  - Serialized Fields
    - mReverseMap
```
java.util.Map<K,V> mReverseMap
```
- Class com.hfg.util.collection.DirtyList extends java.util.ArrayList<T> implements Serializable
  - Serialized Fields
    - mIsDirty
```
boolean mIsDirty
```
- Class com.hfg.util.collection.DirtyMap extends java.util.HashMap<K,V> implements Serializable
  - Serialized Fields
    - mIsDirty
```
boolean mIsDirty
```
    - mDirtyKeySet
```
java.util.Set<E> mDirtyKeySet
```
- Class com.hfg.util.collection.DirtyProperties extends java.util.Properties implements Serializable
  - Serialized Fields
    - mIsDirty
```
boolean mIsDirty
```
    - mDirtyProperties
```
java.util.HashSet<E> mDirtyProperties
```
- Class com.hfg.util.collection.OrderedMap extends java.util.HashMap<K,V> implements Serializable
  - Serialized Fields
    - mOrderedKeys
```
OrderedSet<E> mOrderedKeys
```
- Class com.hfg.util.collection.OrderedSet extends java.util.ArrayList<E> implements Serializable
- Class com.hfg.util.collection.SortedList extends java.util.ArrayList<T extends java.lang.Comparable<T>> implements Serializable
Package com.hfg.util.io
- Class com.hfg.util.io.RuntimeIOException extends java.lang.RuntimeException implements Serializable
Package com.hfg.util.mime
- Class com.hfg.util.mime.MimeException extends java.lang.RuntimeException implements Serializable
Package com.hfg.webapp
- Class com.hfg.webapp.HfgCookie extends javax.servlet.http.Cookie implements Serializable
  - Serialized Fields
    - mExpires
```
java.util.Date mExpires
```
    - mDecodedValue
```
java.lang.String mDecodedValue
```
Package com.hfg.webapp.filter.auth
- Class com.hfg.webapp.filter.auth.InvalidDomainException extends java.lang.RuntimeException implements Serializable
Package com.hfg.xml
- Class com.hfg.xml.XMLException extends java.lang.RuntimeException implements Serializable
- Class com.hfg.xml.XMLNamespaceSet extends java.util.HashSet<XMLNamespace> implements Serializable
  - Serialized Fields
    - mDefaultNamespace
```
XMLNamespace mDefaultNamespace
```
Package com.hfg.xml.msoffice2003.spreadsheetml
- Class com.hfg.xml.msoffice2003.spreadsheetml.ExcelFormatException extends java.lang.RuntimeException implements Serializable
Package com.hfg.xml.msofficexml
- Class com.hfg.xml.msofficexml.OfficeOpenXmlException extends java.lang.RuntimeException implements Serializable
Package com.hfg.xml.msofficexml.docx
- Class com.hfg.xml.msofficexml.docx.DocxException extends java.lang.RuntimeException implements Serializable
Package com.hfg.xml.msofficexml.xlsx
- Class com.hfg.xml.msofficexml.xlsx.ExcelIndexedColor extends java.awt.Color implements Serializable
  - Serialized Fields
    - mIndex
```
int mIndex
```
    - mName
```
java.lang.String mName
```

Serialized Form

Package com.hfg.bio

Class com.hfg.bio.InvalidResidueException extends java.lang.RuntimeException implements Serializable

Class com.hfg.bio.Strand extends java.lang.Object implements Serializable

Serialization Methods

readResolve

Serialized Fields

mSymbol

mName

mIndex

Package com.hfg.bio.seq

Class com.hfg.bio.seq.SeqTopology extends java.lang.Object implements Serializable

Serialization Methods

readResolve

Serialized Fields

mName

Package com.hfg.bio.seq.alignment

Class com.hfg.bio.seq.alignment.KMerBitSet extends java.util.BitSet implements Serializable

Serialized Fields

mSeqType

mKMerSize

mResidueIndexLookup

mUnknownResidueIndex

Package com.hfg.bio.seq.alignment.blast

Class com.hfg.bio.seq.alignment.blast.BLAST_Database extends java.io.File implements Serializable

Serialized Fields

mType

mDescription

mCacheDate

mNumSequences

Package com.hfg.bio.seq.format

Class com.hfg.bio.seq.format.EMBL_DataClass extends java.lang.Object implements Serializable

Serialization Methods

readResolve

Serialized Fields

mName

mCode

Class com.hfg.bio.seq.format.SeqFormatException extends SeqIOException implements Serializable

Class com.hfg.bio.seq.format.SeqIOException extends java.lang.RuntimeException implements Serializable

Package com.hfg.bio.seq.format.feature.qualifier

Class com.hfg.bio.seq.format.feature.qualifier.MolType extends java.lang.Object implements Serializable

Serialization Methods

readResolve

Serialized Fields

mName

mIsValid

Package com.hfg.bio.seq.format.genbank

Class com.hfg.bio.seq.format.genbank.InvalidGenBankKeywordException extends SeqIOException implements Serializable

Class com.hfg.bio.seq.format.genbank.InvalidGenBankSubkeywordException extends SeqFormatException implements Serializable

Package com.hfg.bio.seq.pattern

Class com.hfg.bio.seq.pattern.SeqPatternConfigurationException extends java.lang.RuntimeException implements Serializable

Package com.hfg.bio.seq.translation

Class com.hfg.bio.seq.translation.TranslationException extends java.lang.RuntimeException implements Serializable

Package com.hfg.bio.taxonomy

Class com.hfg.bio.taxonomy.EMBL_TaxonDivision extends java.lang.Object implements Serializable

Serialization Methods

readResolve

Serialized Fields

mName

mCode

Class com.hfg.bio.taxonomy.NCBIGenBankDivision extends java.lang.Object implements Serializable

Serialization Methods

readResolve

Serialized Fields

mName

mCode

mId

Class com.hfg.bio.taxonomy.NCBITaxonNameClass extends java.lang.Object implements Serializable

Serialization Methods

readResolve

Serialized Fields

mName

Class com.hfg.bio.taxonomy.NCBITaxonNodeRank extends java.lang.Object implements Serializable

Serialization Methods

readResolve

Serialized Fields

mName

mRank

Package com.hfg.chem

Class com.hfg.chem.ChemicalFormulaParseException extends java.lang.RuntimeException implements Serializable