Serialized Form (genoviz tutorial 1.1.9 API)

Package com.affymetrix.genoviz.demo

Class com.affymetrix.genoviz.demo.GraphDemo extends JApplet implements Serializable

Serialized Fields

map

com.affymetrix.genoviz.widget.NeoMap map

xzoomer

com.affymetrix.genoviz.awt.AdjustableJSlider xzoomer

yzoomer

com.affymetrix.genoviz.awt.AdjustableJSlider yzoomer

selected
```
Vector<E> selected
```

Class com.affymetrix.genoviz.demo.NeoAssemblerDemo extends JApplet implements Serializable

Serialized Fields

tryUniString
```
boolean tryUniString
```
simulateTrimmedEdges
```
boolean simulateTrimmedEdges
```
no_reverse
```
boolean no_reverse
```

map

com.affymetrix.genoviz.widget.NeoAssembler map

hzoom
```
JScrollBar hzoom
```
mapframe
```
Frame mapframe
```
propframe
```
Frame propframe
```
zoomframe
```
Frame zoomframe
```
editMenu
```
Menu editMenu
```
propertiesMenuItem
```
MenuItem propertiesMenuItem
```
addConsMenuItem
```
MenuItem addConsMenuItem
```
addNextMenuItem
```
MenuItem addNextMenuItem
```
addAlignMenuItem
```
MenuItem addAlignMenuItem
```
addGapsMenuItem
```
MenuItem addGapsMenuItem
```
addBasesMenuItem
```
MenuItem addBasesMenuItem
```
addNegMenuItem
```
MenuItem addNegMenuItem
```
addAllAligns
```
MenuItem addAllAligns
```
internalSortItem
```
MenuItem internalSortItem
```
externalSortItem
```
MenuItem externalSortItem
```
switchFontTypeItem
```
MenuItem switchFontTypeItem
```
switchFontStyleItem
```
MenuItem switchFontStyleItem
```
switchFontSizeItem
```
MenuItem switchFontSizeItem
```
externalColorRectItem
```
MenuItem externalColorRectItem
```
externalColorFontItem
```
MenuItem externalColorFontItem
```
label_width
```
int label_width
```
pixel_width
```
int pixel_width
```
pixel_height
```
int pixel_height
```
use_label_arrows
```
boolean use_label_arrows
```
use_internal_zoomer
```
boolean use_internal_zoomer
```
show_half_first
```
boolean show_half_first
```
external_rect_coloring
```
boolean external_rect_coloring
```
external_font_coloring
```
boolean external_font_coloring
```
optimize_scrolling
```
boolean optimize_scrolling
```
optimize_damage
```
boolean optimize_damage
```
isTimed
```
boolean isTimed
```
isMemed
```
boolean isMemed
```
consensus_added
```
boolean consensus_added
```
currentSeq
```
int currentSeq
```
firstSeq
```
Object firstSeq
```
selectedDataModels
```
Vector<E> selectedDataModels
```
negstart
```
int negstart
```
negend
```
int negend
```
ref_start
```
int ref_start
```
ref_end
```
int ref_end
```

bg_painter

com.affymetrix.genoviz.bioviews.ResiduePainter bg_painter

fg_painter

com.affymetrix.genoviz.bioviews.ResiduePainter fg_painter

assem
```
genoviz.demo.datamodel.Assembly assem
```

consensus

com.affymetrix.genoviz.datamodel.Mapping consensus

backgroundImage
```
Image backgroundImage
```
clicking
```
boolean clicking
```

customizer

com.affymetrix.genoviz.widget.NeoAssemblerCustomizer customizer

framesShowing
```
boolean framesShowing
```
going
```
boolean going
```
nicePaleBlue
```
Color nicePaleBlue
```

consglyph

com.affymetrix.genoviz.glyph.AlignmentGlyph consglyph

font_name_index
```
int font_name_index
```
font_styles
```
int[] font_styles
```
font_style_index
```
int font_style_index
```

Class com.affymetrix.genoviz.demo.NeoAssemblerDemo2 extends JApplet implements Serializable
- Serialized Fields
  - assem
```
genoviz.demo.datamodel.Assembly assem
```
  - map
```
com.affymetrix.genoviz.widget.NeoAssembler map
```
  - seq_URL
```
URL seq_URL
```
  - align_URL
```
URL align_URL
```

Class com.affymetrix.genoviz.demo.NeoMapDemo extends JApplet implements Serializable

Serialized Fields

map

com.affymetrix.genoviz.widget.NeoMap map

propframe
```
JFrame propframe
```
fileMenu
```
JMenu fileMenu
```
editMenu
```
JMenu editMenu
```
optionsMenu
```
JMenu optionsMenu
```
selectionMenu
```
JMenu selectionMenu
```
reshapeMenu
```
JMenu reshapeMenu
```
zoomingMenu
```
JMenu zoomingMenu
```
fuzzinessMenu
```
JMenu fuzzinessMenu
```
printMenuItem
```
JMenuItem printMenuItem
```
exitMenuItem
```
JMenuItem exitMenuItem
```
clearMenuItem
```
JMenuItem clearMenuItem
```
deleteMenuItem
```
JMenuItem deleteMenuItem
```
hideMenuItem
```
JMenuItem hideMenuItem
```
unhideMenuItem
```
JMenuItem unhideMenuItem
```
optionsMenuItem
```
JMenuItem optionsMenuItem
```
noSelection
```
JCheckBoxMenuItem noSelection
```
highlightSelection
```
JCheckBoxMenuItem highlightSelection
```
outlineSelection
```
JCheckBoxMenuItem outlineSelection
```
selectRed
```
JCheckBoxMenuItem selectRed
```
selectOrange
```
JCheckBoxMenuItem selectOrange
```
selectYellow
```
JCheckBoxMenuItem selectYellow
```

fitHorizontallyMenuItem

JCheckBoxMenuItem fitHorizontallyMenuItem

fitVerticallyMenuItem
```
JCheckBoxMenuItem fitVerticallyMenuItem
```
zoomTopMenuItem
```
JCheckBoxMenuItem zoomTopMenuItem
```
zoomMiddleMenuItem
```
JCheckBoxMenuItem zoomMiddleMenuItem
```
zoomBottomMenuItem
```
JCheckBoxMenuItem zoomBottomMenuItem
```
zoomLeftMenuItem
```
JCheckBoxMenuItem zoomLeftMenuItem
```
zoomCenterMenuItem
```
JCheckBoxMenuItem zoomCenterMenuItem
```
zoomRightMenuItem
```
JCheckBoxMenuItem zoomRightMenuItem
```

sharpPrecisionMenuItem

JCheckBoxMenuItem sharpPrecisionMenuItem

normalPrecisionMenuItem

JCheckBoxMenuItem normalPrecisionMenuItem

fuzzyPrecisionMenuItem

JCheckBoxMenuItem fuzzyPrecisionMenuItem

pixel_width
```
int pixel_width
```
pixel_height
```
int pixel_height
```
seq_start
```
int seq_start
```
seq_end
```
int seq_end
```
offset_start
```
int offset_start
```
offset_end
```
int offset_end
```
hidden
```
Vector<E> hidden
```
selectionColor
```
Color selectionColor
```
selectionType
```
int selectionType
```
backgroundImage
```
Image backgroundImage
```
clicking
```
boolean clicking
```

customizer

com.affymetrix.genoviz.widget.NeoMapCustomizer customizer

framesShowing
```
boolean framesShowing
```
going
```
boolean going
```
nicePaleBlue
```
Color nicePaleBlue
```
placeholder
```
Label placeholder
```

Class com.affymetrix.genoviz.demo.NeoQuallerDemo extends Applet implements Serializable

Serialized Fields

widg_pan

com.affymetrix.genoviz.awt.NeoPanel widg_pan

clone_in_same_frame
```
boolean clone_in_same_frame
```
framed
```
boolean framed
```

read_conf

com.affymetrix.genoviz.datamodel.ReadConfidence read_conf

widget

com.affymetrix.genoviz.widget.NeoQualler widget

oneClone

com.affymetrix.genoviz.widget.NeoQualler oneClone

pixel_width
```
int pixel_width
```
pixel_height
```
int pixel_height
```
posText
```
TextField posText
```
strText
```
TextField strText
```
posLabel
```
Label posLabel
```
strLabel
```
Label strLabel
```
descLabel
```
Label descLabel
```
searchChoice
```
Choice searchChoice
```
cloneButton
```
Button cloneButton
```
controlPanel
```
Panel controlPanel
```
editMenu
```
Menu editMenu
```
propertiesMenuItem
```
MenuItem propertiesMenuItem
```
propFrame
```
Frame propFrame
```
propFrameShowing
```
boolean propFrameShowing
```
prevSearchPosition
```
int prevSearchPosition
```

Class com.affymetrix.genoviz.demo.NeoQuallerDemo2 extends JApplet implements Serializable

Serialized Fields

widg_pan
```
JPanel widg_pan
```

read_conf

com.affymetrix.genoviz.datamodel.ReadConfidence read_conf

widget

com.affymetrix.genoviz.widget.NeoQualler widget

oneClone

com.affymetrix.genoviz.widget.NeoQualler oneClone

pixel_width
```
int pixel_width
```
pixel_height
```
int pixel_height
```
posText
```
TextField posText
```
strText
```
TextField strText
```
posLabel
```
Label posLabel
```
strLabel
```
Label strLabel
```
descLabel
```
Label descLabel
```
searchChoice
```
Choice searchChoice
```
controlPanel
```
Panel controlPanel
```
editMenu
```
Menu editMenu
```
propertiesMenuItem
```
MenuItem propertiesMenuItem
```
propFrame
```
Frame propFrame
```
propFrameShowing
```
boolean propFrameShowing
```
prevSearchPosition
```
int prevSearchPosition
```

Class com.affymetrix.genoviz.demo.NeoSeqDemo extends Applet implements Serializable

Serialized Fields

seqview

com.affymetrix.genoviz.widget.NeoSeq seqview

mapframe
```
Frame mapframe
```
propframe
```
Frame propframe
```

seqmodel

com.affymetrix.genoviz.datamodel.Sequence seqmodel

annotations
```
Vector<E> annotations
```
seq
```
String seq
```
use_real_seq
```
boolean use_real_seq
```
fake_seq
```
String fake_seq
```
showComp
```
boolean showComp
```
pixel_width
```
int pixel_width
```
pixel_height
```
int pixel_height
```
text_annot_color
```
Color text_annot_color
```
back_annot_color
```
Color back_annot_color
```
out_annot_color
```
Color out_annot_color
```
backgroundImage
```
Image backgroundImage
```
clicking
```
boolean clicking
```

customizer

com.affymetrix.genoviz.widget.NeoSeqCustomizer customizer

framesShowing
```
boolean framesShowing
```
going
```
boolean going
```
nicePaleBlue
```
Color nicePaleBlue
```
colorMenu
```
Menu colorMenu
```
blueMenuItem
```
MenuItem blueMenuItem
```
greenMenuItem
```
MenuItem greenMenuItem
```
magentaMenuItem
```
MenuItem magentaMenuItem
```
whiteMenuItem
```
MenuItem whiteMenuItem
```
editMenu
```
Menu editMenu
```
seqToggleMenuItem
```
MenuItem seqToggleMenuItem
```
clearWidgetMenuItem
```
MenuItem clearWidgetMenuItem
```
undoMenuItem
```
MenuItem undoMenuItem
```
selectMenuItem
```
MenuItem selectMenuItem
```
fontAnnotMenuItem
```
MenuItem fontAnnotMenuItem
```
backAnnotMenuItem
```
MenuItem backAnnotMenuItem
```
outAnnotMenuItem
```
MenuItem outAnnotMenuItem
```
printAnnotMenuItem
```
MenuItem printAnnotMenuItem
```
toFrontMenuItem
```
MenuItem toFrontMenuItem
```
visTestMenuItem
```
MenuItem visTestMenuItem
```
showSelectedEndsMenuItem
```
MenuItem showSelectedEndsMenuItem
```
showVisibleEndsMenuItem
```
MenuItem showVisibleEndsMenuItem
```
propertiesMenuItem
```
MenuItem propertiesMenuItem
```
showMenu
```
Menu showMenu
```
compCBMenuItem
```
CheckboxMenuItem compCBMenuItem
```
transOneCBMenuItem
```
CheckboxMenuItem transOneCBMenuItem
```
transTwoCBMenuItem
```
CheckboxMenuItem transTwoCBMenuItem
```
transThreeCBMenuItem
```
CheckboxMenuItem transThreeCBMenuItem
```
transNegOneCBMenuItem
```
CheckboxMenuItem transNegOneCBMenuItem
```
transNegTwoCBMenuItem
```
CheckboxMenuItem transNegTwoCBMenuItem
```

transNegThreeCBMenuItem

CheckboxMenuItem transNegThreeCBMenuItem

fontMenu
```
Menu fontMenu
```
defaultFontCBMenuItem
```
CheckboxMenuItem defaultFontCBMenuItem
```
serifFontCBMenuItem
```
CheckboxMenuItem serifFontCBMenuItem
```

sansSerifFontCBMenuItem

CheckboxMenuItem sansSerifFontCBMenuItem

monospacedFontCBMenuItem

CheckboxMenuItem monospacedFontCBMenuItem

dialogFontCBMenuItem
```
CheckboxMenuItem dialogFontCBMenuItem
```

dialogInputFontCBMenuItem

CheckboxMenuItem dialogInputFontCBMenuItem

fontSizesMenu
```
Menu fontSizesMenu
```
smallFontCBMenuItem
```
CheckboxMenuItem smallFontCBMenuItem
```
mediumFontCBMenuItem
```
CheckboxMenuItem mediumFontCBMenuItem
```
largeFontCBMenuItem
```
CheckboxMenuItem largeFontCBMenuItem
```
stripesMenu
```
Menu stripesMenu
```
vertStripesCBMenuItem
```
CheckboxMenuItem vertStripesCBMenuItem
```
horizStripesCBMenuItem
```
CheckboxMenuItem horizStripesCBMenuItem
```
noStripesCBMenuItem
```
CheckboxMenuItem noStripesCBMenuItem
```
stripeSizesMenu
```
Menu stripeSizesMenu
```
smallStripesCBMenuItem
```
CheckboxMenuItem smallStripesCBMenuItem
```

mediumStripesCBMenuItem

CheckboxMenuItem mediumStripesCBMenuItem

largeStripesCBMenuItem
```
CheckboxMenuItem largeStripesCBMenuItem
```
lineSpacingMenu
```
Menu lineSpacingMenu
```

smallLineSpacingCBMenuItem

CheckboxMenuItem smallLineSpacingCBMenuItem

mediumLineSpacingCBMenuItem

CheckboxMenuItem mediumLineSpacingCBMenuItem

largeLineSpacingCBMenuItem

CheckboxMenuItem largeLineSpacingCBMenuItem

transFormatMenu
```
Menu transFormatMenu
```
oneLetterCBMenuItem
```
CheckboxMenuItem oneLetterCBMenuItem
```
threeLetterCBMenuItem
```
CheckboxMenuItem threeLetterCBMenuItem
```
fileMenu
```
Menu fileMenu
```
saveAsMenuItem
```
MenuItem saveAsMenuItem
```
exitMenuItem
```
MenuItem exitMenuItem
```

Class com.affymetrix.genoviz.demo.NeoTracerDemo extends Applet implements Serializable

Serialized Fields

appl
```
AppletContext appl
```
app
```
Applet app
```

widg_pan

com.affymetrix.genoviz.awt.NeoPanel widg_pan

clone_in_same_frame
```
boolean clone_in_same_frame
```
optScrolling
```
boolean optScrolling
```
optDamage
```
boolean optDamage
```
external_zoomers
```
boolean external_zoomers
```

trace

com.affymetrix.genoviz.datamodel.TraceI trace

widget

com.affymetrix.genoviz.widget.NeoTracer widget

oneClone

com.affymetrix.genoviz.widget.NeoTracer oneClone

xzoomer
```
Adjustable xzoomer
```
yzoomer
```
Adjustable yzoomer
```
zoomframe
```
Frame zoomframe
```
pixel_width
```
int pixel_width
```
pixel_height
```
int pixel_height
```
next_or_prev
```
int next_or_prev
```
scroll_value
```
int scroll_value
```
xzoom_value
```
float xzoom_value
```
yzoom_value
```
float yzoom_value
```
scrollLeftB
```
Button scrollLeftB
```
scrollRightB
```
Button scrollRightB
```
optDamageB
```
Button optDamageB
```
optScrollingB
```
Button optScrollingB
```
toggleTraceB
```
Button toggleTraceB
```
toggleRevCompB
```
Button toggleRevCompB
```
xzoomB
```
Button xzoomB
```
yzoomB
```
Button yzoomB
```
clipper
```
Button clipper
```
properties
```
Button properties
```
posText
```
TextField posText
```
findButton
```
Button findButton
```
strText
```
TextField strText
```
posLabel
```
Label posLabel
```
descLabel
```
Label descLabel
```
cloneButton
```
Button cloneButton
```
controlPanel
```
Panel controlPanel
```
editMenu
```
Menu editMenu
```
propertiesMenuItem
```
MenuItem propertiesMenuItem
```
propFrame
```
Frame propFrame
```
propFrameShowing
```
boolean propFrameShowing
```
nextAction
```
ActionListener nextAction
```
prevAction
```
ActionListener prevAction
```
propAction
```
ActionListener propAction
```
prevSearchPosition
```
int prevSearchPosition
```

Class com.affymetrix.genoviz.demo.ShadowDemo extends JApplet implements Serializable

Serialized Fields

mapview

com.affymetrix.genoviz.widget.NeoMap mapview

seqview

com.affymetrix.genoviz.widget.NeoSeq seqview

shadowRect

com.affymetrix.genoviz.bioviews.GlyphI shadowRect

mapframe
```
Panel mapframe
```
annotations
```
Vector<E> annotations
```
sizeL
```
Label sizeL
```
spacingL
```
Label spacingL
```
stripeL
```
Label stripeL
```
firstL
```
Label firstL
```
lastL
```
Label lastL
```
sizeT
```
TextField sizeT
```
spacingT
```
TextField spacingT
```
stripeT
```
TextField stripeT
```
visibleB
```
Button visibleB
```
selectedB
```
Button selectedB
```
removeAnnotB
```
Button removeAnnotB
```
addTextAnnotB
```
Button addTextAnnotB
```
addBackAnnotB
```
Button addBackAnnotB
```
orientL
```
Label orientL
```
orientC
```
Choice orientC
```
fontL
```
Label fontL
```
fontC
```
Choice fontC
```
seq
```
String seq
```
seq2
```
String seq2
```
seq3
```
String seq3
```
newseq
```
String newseq
```
num_left
```
boolean num_left
```
mapframe_active
```
boolean mapframe_active
```
text_annot_color
```
Color text_annot_color
```
back_annot_color
```
Color back_annot_color
```
shadowActive
```
boolean shadowActive
```

hzoom

com.affymetrix.genoviz.awt.AdjustableJSlider hzoom

SEQVIEW_WIDTH
```
int SEQVIEW_WIDTH
```
SEQVIEW_HEIGHT
```
int SEQVIEW_HEIGHT
```
MAP_WIDTH
```
int MAP_WIDTH
```
MAP_HEIGHT
```
int MAP_HEIGHT
```
mouse_offset
```
double mouse_offset
```

Class com.affymetrix.genoviz.demo.TieredMapDemo extends Applet implements Serializable

Serialized Fields

pixel_width
```
int pixel_width
```
pixel_height
```
int pixel_height
```
seq_start
```
int seq_start
```
seq_end
```
int seq_end
```
offset_start
```
int offset_start
```
offset_end
```
int offset_end
```
selectionColor
```
Color selectionColor
```

map

com.affymetrix.genoviz.widget.TieredNeoMap map

yscroll
```
JScrollBar yscroll
```

axisTier

com.affymetrix.genoviz.widget.tieredmap.MapTierGlyph axisTier

squiggleTier

com.affymetrix.genoviz.widget.tieredmap.MapTierGlyph squiggleTier

fillrectTier

com.affymetrix.genoviz.widget.tieredmap.MapTierGlyph fillrectTier

roundrectTier

com.affymetrix.genoviz.widget.tieredmap.MapTierGlyph roundrectTier

selectedTier

com.affymetrix.genoviz.widget.tieredmap.MapTierGlyph selectedTier

squiggleFactory

com.affymetrix.genoviz.bioviews.MapGlyphFactory squiggleFactory

fillRectFactory

com.affymetrix.genoviz.bioviews.MapGlyphFactory fillRectFactory

roundRectFactory

com.affymetrix.genoviz.bioviews.MapGlyphFactory roundRectFactory

labelmap

com.affymetrix.genoviz.widget.TieredLabelMap labelmap

frame
```
Frame frame
```
popup
```
PopupMenu popup
```
exit
```
MenuItem exit
```
showall
```
MenuItem showall
```
backgroundImage
```
Image backgroundImage
```

Class com.affymetrix.genoviz.demo.VerticalMapDemo extends JApplet implements Serializable
- Serialized Fields
  - panel1
```
JPanel panel1
```
  - panel2
```
JPanel panel2
```

Package com.affymetrix.genoviz.demo.datamodel
- Class com.affymetrix.genoviz.demo.datamodel.Assembly extends Object implements Serializable
Package com.affymetrix.genoviz.tutorial
- Class com.affymetrix.genoviz.tutorial.BedSequenceDemo extends JFrame implements Serializable
  - Serialized Fields
    - mapPanel
```
JPanel mapPanel
```
    - map
```
com.affymetrix.genoviz.widget.NeoMap map
```
    - bedVector
```
HashMap<K,V> bedVector
```
    - pb
```
JProgressBar pb
```
    - progress
```
JLabel progress
```
    - map_length
```
int map_length
```
- Class com.affymetrix.genoviz.tutorial.GlyphTestMap extends JApplet implements Serializable
  - Serialized Fields
    - map
```
com.affymetrix.genoviz.widget.NeoMap map
```
    - clear
```
JButton clear
```
    - add
```
JButton add
```
    - start_field
```
JTextField start_field
```
    - end_field
```
JTextField end_field
```
    - glyph_field
```
JComboBox<E> glyph_field
```
    - color_field
```
JComboBox<E> color_field
```
    - glyphtypes
```
String[] glyphtypes
```
    - colors
```
String[] colors
```
- Class com.affymetrix.genoviz.tutorial.HairMap extends SimpleMap3 implements Serializable
  - Serialized Fields
    - zoomPoint
```
com.affymetrix.genoviz.widget.VisibleRange zoomPoint
```
- Class com.affymetrix.genoviz.tutorial.HelloMap extends JApplet implements Serializable
  - Serialized Fields
    - map
```
com.affymetrix.genoviz.widget.NeoMap map
```
- Class com.affymetrix.genoviz.tutorial.NeoDraw extends JApplet implements Serializable
  - Serialized Fields
    - glyphMenu
```
JMenu glyphMenu
```
    - arrowMenuItem
```
JCheckBoxMenuItem arrowMenuItem
```
    - boundedPointMenuItem
```
JCheckBoxMenuItem boundedPointMenuItem
```
    - centeredCircleMenuItem
```
JCheckBoxMenuItem centeredCircleMenuItem
```
    - fillRectMenuItem
```
JCheckBoxMenuItem fillRectMenuItem
```
    - fillOvalMenuItem
```
JCheckBoxMenuItem fillOvalMenuItem
```
    - lineContainerMenuItem
```
JCheckBoxMenuItem lineContainerMenuItem
```
    - outlineRectMenuItem
```
JCheckBoxMenuItem outlineRectMenuItem
```
    - squiggleMenuItem
```
JCheckBoxMenuItem squiggleMenuItem
```
    - triBarGlyphMenuItem
```
JCheckBoxMenuItem triBarGlyphMenuItem
```
    - triangleMenuItem
```
JCheckBoxMenuItem triangleMenuItem
```
    - colorMenu
```
JMenu colorMenu
```
    - blackMenuItem
```
JCheckBoxMenuItem blackMenuItem
```
    - blueMenuItem
```
JCheckBoxMenuItem blueMenuItem
```
    - redMenuItem
```
JCheckBoxMenuItem redMenuItem
```
    - grayMenuItem
```
JCheckBoxMenuItem grayMenuItem
```
    - magentaMenuItem
```
JCheckBoxMenuItem magentaMenuItem
```
    - editMenu
```
JMenu editMenu
```
    - clearMenuItem
```
JMenuItem clearMenuItem
```
    - repackMenuItem
```
JMenuItem repackMenuItem
```
    - map
```
com.affymetrix.genoviz.widget.NeoMap map
```
- Class com.affymetrix.genoviz.tutorial.ParseOne extends Applet implements Serializable
  - Serialized Fields
    - widget
```
com.affymetrix.genoviz.widget.NeoAbstractWidget widget
```
    - parser
```
com.affymetrix.genoviz.parser.ContentParser parser
```
    - pan
```
com.affymetrix.genoviz.awt.NeoPanel pan
```
- Class com.affymetrix.genoviz.tutorial.SequenceMap0 extends SimpleMap4 implements Serializable
  - Serialized Fields
    - seq
```
com.affymetrix.genoviz.widget.NeoSeq seq
```
    - seqFrame
```
Frame seqFrame
```
    - pan
```
com.affymetrix.genoviz.awt.NeoPanel pan
```
- Class com.affymetrix.genoviz.tutorial.SequenceMap1 extends SequenceMap0 implements Serializable
  - Serialized Fields
    - mouser
```
MouseListener mouser
```
- Class com.affymetrix.genoviz.tutorial.SimpleMap extends JApplet implements Serializable
  - Serialized Fields
    - map
```
com.affymetrix.genoviz.widget.NeoMap map
```
- Class com.affymetrix.genoviz.tutorial.SimpleMap0 extends Applet implements Serializable
  - Serialized Fields
    - map
```
com.affymetrix.genoviz.widget.NeoMap map
```
    - pan
```
com.affymetrix.genoviz.awt.NeoPanel pan
```
- Class com.affymetrix.genoviz.tutorial.SimpleMap1 extends GlyphTestMap implements Serializable
- Class com.affymetrix.genoviz.tutorial.SimpleMap2 extends SimpleMap0 implements Serializable
  - Serialized Fields
    - positions
```
Hashtable<K,V> positions
```
    - labelFactory
```
com.affymetrix.genoviz.bioviews.MapGlyphFactory labelFactory
```
- Class com.affymetrix.genoviz.tutorial.SimpleMap3 extends SimpleMap1 implements Serializable
  - Serialized Fields
    - zoomer
```
com.affymetrix.genoviz.awt.AdjustableJSlider zoomer
```
    - scroller
```
JScrollBar scroller
```
- Class com.affymetrix.genoviz.tutorial.SimpleMap4 extends SimpleMap3 implements Serializable
  - Serialized Fields
    - featureTypes
```
Hashtable<K,V> featureTypes
```
- Class com.affymetrix.genoviz.tutorial.SimpleMap5 extends Applet implements Serializable
  - Serialized Fields
    - parser
```
NarcissusParser parser
```
    - pan
```
com.affymetrix.genoviz.awt.NeoPanel pan
```
- Class com.affymetrix.genoviz.tutorial.SimpleMap6 extends Applet implements Serializable
  - Serialized Fields
    - parser
```
MapHandler parser
```
    - pan
```
com.affymetrix.genoviz.awt.NeoPanel pan
```
- Class com.affymetrix.genoviz.tutorial.SimpleSelectableMap extends GlyphTestMap implements Serializable
  - Serialized Fields
    - isApplet
```
boolean isApplet
```
    - ml
```
MouseListener ml
```
- Class com.affymetrix.genoviz.tutorial.TutorialAssmblr extends JApplet implements Serializable
  - Serialized Fields
    - assmblr
```
com.affymetrix.genoviz.widget.NeoAssembler assmblr
```
- Class com.affymetrix.genoviz.tutorial.TutorialGlyphDemo extends Applet implements Serializable
- Class com.affymetrix.genoviz.tutorial.TutorialGlyphDemo2 extends Applet implements Serializable
- Class com.affymetrix.genoviz.tutorial.TutorialQualler extends Applet implements Serializable
  - Serialized Fields
    - framed
```
boolean framed
```
    - read_conf
```
com.affymetrix.genoviz.datamodel.ReadConfidence read_conf
```
    - widget
```
com.affymetrix.genoviz.widget.NeoQualler widget
```
    - oneClone
```
com.affymetrix.genoviz.widget.NeoQualler oneClone
```
    - pan
```
com.affymetrix.genoviz.awt.NeoPanel pan
```
    - pixel_width
```
int pixel_width
```
    - pixel_height
```
int pixel_height
```
    - posText
```
TextField posText
```
    - strText
```
TextField strText
```
    - posLabel
```
Label posLabel
```
    - strLabel
```
Label strLabel
```
    - descLabel
```
Label descLabel
```
    - searchChoice
```
Choice searchChoice
```
    - cloneButton
```
Button cloneButton
```
    - controlPanel
```
Panel controlPanel
```
    - editMenu
```
Menu editMenu
```
    - propertiesMenuItem
```
MenuItem propertiesMenuItem
```
    - propFrame
```
Frame propFrame
```
    - propFrameShowing
```
boolean propFrameShowing
```
    - hider
```
WindowListener hider
```
    - mouser
```
MouseListener mouser
```
    - prevSearchPosition
```
int prevSearchPosition
```
- Class com.affymetrix.genoviz.tutorial.TutorialTracer extends Applet implements Serializable
  - Serialized Fields
    - trace
```
com.affymetrix.genoviz.datamodel.TraceI trace
```
    - widget
```
com.affymetrix.genoviz.widget.NeoTracer widget
```
    - xzoomer
```
Adjustable xzoomer
```
    - yzoomer
```
Adjustable yzoomer
```
    - zoomframe
```
Frame zoomframe
```
    - pan1
```
com.affymetrix.genoviz.awt.NeoPanel pan1
```
    - pan2
```
com.affymetrix.genoviz.awt.NeoPanel pan2
```
    - optScrolling
```
boolean optScrolling
```
    - optDamage
```
boolean optDamage
```
    - pixel_width
```
int pixel_width
```
    - pixel_height
```
int pixel_height
```
    - scroll_value
```
int scroll_value
```
    - xzoom_value
```
float xzoom_value
```
    - yzoom_value
```
float yzoom_value
```
    - scrollLeftB
```
Button scrollLeftB
```
    - scrollRightB
```
Button scrollRightB
```
    - optDamageB
```
Button optDamageB
```
    - optScrollingB
```
Button optScrollingB
```
    - toggleTraceB
```
Button toggleTraceB
```
    - toggleRevCompB
```
Button toggleRevCompB
```
    - xzoomB
```
Button xzoomB
```
    - yzoomB
```
Button yzoomB
```
    - posText
```
TextField posText
```
    - strText
```
TextField strText
```
    - posLabel
```
Label posLabel
```
    - strLabel
```
Label strLabel
```
    - descLabel
```
Label descLabel
```
    - searchChoice
```
Choice searchChoice
```
    - controlPanel
```
Panel controlPanel
```
    - editMenu
```
Menu editMenu
```
    - propertiesMenuItem
```
MenuItem propertiesMenuItem
```
    - propFrame
```
Frame propFrame
```
    - propFrameShowing
```
boolean propFrameShowing
```
    - hider
```
WindowListener hider
```
    - mouser
```
MouseListener mouser
```
    - prevSearchPosition
```
int prevSearchPosition
```

Serialized Form

Package com.affymetrix.genoviz.demo

Class com.affymetrix.genoviz.demo.GraphDemo extends JApplet implements Serializable

Serialized Fields

map

xzoomer

yzoomer

selected

Class com.affymetrix.genoviz.demo.NeoAssemblerDemo extends JApplet implements Serializable

Serialized Fields

tryUniString

simulateTrimmedEdges

no_reverse

map

hzoom

mapframe

propframe

zoomframe

editMenu

propertiesMenuItem

addConsMenuItem

addNextMenuItem

addAlignMenuItem

addGapsMenuItem

addBasesMenuItem

addNegMenuItem

addAllAligns

internalSortItem

externalSortItem

switchFontTypeItem

switchFontStyleItem

switchFontSizeItem

externalColorRectItem

externalColorFontItem

label_width

pixel_width

pixel_height

use_label_arrows

use_internal_zoomer

show_half_first

external_rect_coloring

external_font_coloring

optimize_scrolling

optimize_damage

isTimed

isMemed

consensus_added

currentSeq

firstSeq

selectedDataModels

negstart

negend

ref_start

ref_end

bg_painter

fg_painter

assem

consensus

backgroundImage

clicking

customizer

framesShowing

going

nicePaleBlue

consglyph

font_name_index

font_styles

font_style_index

Class com.affymetrix.genoviz.demo.NeoAssemblerDemo2 extends JApplet implements Serializable

Serialized Fields

assem

map

seq_URL

align_URL

Class com.affymetrix.genoviz.demo.NeoMapDemo extends JApplet implements Serializable

Serialized Fields

map

propframe

fileMenu

editMenu