Serialized Form (SMRT View)

Package com.pacbio.secondary.vis.common.utils
- Class com.pacbio.secondary.vis.common.utils.PropertiesHelper extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - appVisualFilter
```
java.lang.String appVisualFilter
```
    - useTableViewFilter
```
boolean useTableViewFilter
```
    - alwaysShowMemoryInfo
```
boolean alwaysShowMemoryInfo
```
    - fitGenomicTableToPanel
```
boolean fitGenomicTableToPanel
```
    - lockGenomeRegionPanels
```
boolean lockGenomeRegionPanels
```
    - lockRegionDetailsPanels
```
boolean lockRegionDetailsPanels
```
    - viewSubReadsData
```
boolean viewSubReadsData
```
    - lockRangeExpand
```
boolean lockRangeExpand
```
    - useLogScaling
```
boolean useLogScaling
```
Package com.pacbio.secondary.vis.common.utils.constants
- Class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - EpiProReadsPalettes
```
java.util.ArrayList<E> EpiProReadsPalettes
```
- Class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.ColorInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - start
```
float start
```
    - end
```
float end
```
- Class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - contig_start
```
int contig_start
```
    - contig_end
```
int contig_end
```
    - contig_length
```
int contig_length
```
    - color_info
```
EpiProPalette.ColorInfo color_info
```
Package com.pacbio.secondary.vis.common.utils.exception
- Class com.pacbio.secondary.vis.common.utils.exception.FileFormatException extends java.lang.Exception implements Serializable
- Class com.pacbio.secondary.vis.common.utils.exception.InsertNodeException extends IntervalTreeException implements Serializable
- Class com.pacbio.secondary.vis.common.utils.exception.IntervalTreeException extends java.lang.Exception implements Serializable
Package com.pacbio.secondary.vis.data.db
- Class com.pacbio.secondary.vis.data.db.IdeogramDB extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - num_contigs
```
int num_contigs
```
    - tree
```
IntervalTree[] tree
```
    - isAutoGenerated
```
boolean isAutoGenerated
```
    - autoIdeogramUsesFixedNumBands
```
boolean autoIdeogramUsesFixedNumBands
```
    - autoIdeogramNumBands
```
int autoIdeogramNumBands
```
    - autoIdeogramBandSize
```
int autoIdeogramBandSize
```
Package com.pacbio.secondary.vis.data.graph
- Class com.pacbio.secondary.vis.data.graph.GraphPrimitive extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - nodes
```
int[][] nodes
```
- Class com.pacbio.secondary.vis.data.graph.GraphStructure extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - type
```
int type
```
    - primitives
```
GraphPrimitive[] primitives
```
Package com.pacbio.secondary.vis.data.session
- Class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  10L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      specialized serialization includes colors
      
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      specialized serialization includes: version
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - regions
```
java.util.LinkedList<E> regions
```
    - session_id
```
java.lang.String session_id
```
- Class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - image
```
byte[] image
```
    - workspace
```
byte[] workspace
```
    - session
```
byte[] session
```
    - timestamp
```
long timestamp
```
    - info
```
java.lang.String info
```
    - user_data
```
java.lang.String user_data
```
- Class com.pacbio.secondary.vis.data.session.SessionDataHelper extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  210L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      specialized serialization includes colors
      
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
    - writeObject
```
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException
```
      specialized serialization includes: version, views, detailsoptions and colors
      
      Throws:
      
      java.io.IOException
  - Serialized Fields
    - details_options
```
DetailsOptions details_options
```
    - app_options
```
PropertiesHelper app_options
```
    - currentContig
```
int currentContig
```
    - num_tracks
```
int num_tracks
```
    - region_interval
```
Interval region_interval
```
    - details_interval
```
Interval details_interval
```
    - view_intervals
```
java.util.ArrayList<E> view_intervals
```
    - slots_colors
```
java.util.ArrayList<E> slots_colors
```
    - slots_max_values
```
java.util.ArrayList<E> slots_max_values
```
    - details_tracks_height
```
int details_tracks_height
```
    - region_tracks_height
```
int region_tracks_height
```
    - epipro_palette
```
EpiProPalette epipro_palette
```

Package com.pacbio.secondary.vis.data.session.options

Class com.pacbio.secondary.vis.data.session.options.DetailsOptions extends java.lang.Object implements Serializable

serialVersionUID:: 1L

Serialized Fields

max_details_view_coverage
```
int max_details_view_coverage
```
max_details_view_ordinate
```
int max_details_view_ordinate
```
details_view_separator
```
int details_view_separator
```
show_tooltips
```
boolean show_tooltips
```
max_fixed_range
```
int max_fixed_range
```
max_dynamic_range
```
int max_dynamic_range
```
details_range_mode
```
int details_range_mode
```
max_details_coverage
```
int max_details_coverage
```
use_qv_filter
```
boolean use_qv_filter
```
use_mapqv_filter
```
boolean use_mapqv_filter
```
low_qv_threshold
```
int low_qv_threshold
```
high_qv_threshold
```
int high_qv_threshold
```
use_events_coverage_filter
```
boolean use_events_coverage_filter
```
coverage_filter_value
```
int coverage_filter_value
```
use_epipro_mode
```
int use_epipro_mode
```
use_epipro_only_reads
```
boolean use_epipro_only_reads
```
use_epipro_cutoff_filter
```
boolean use_epipro_cutoff_filter
```
use_epipro_cutoff_threshold
```
int use_epipro_cutoff_threshold
```
use_variants_confidence_filter
```
boolean use_variants_confidence_filter
```
variants_filter_threshold
```
int variants_filter_threshold
```
details_metrics_mode
```
int details_metrics_mode
```
kinetics_scaling
```
int kinetics_scaling
```
details_coarse_mode
```
int details_coarse_mode
```
low_kin_threshold
```
double low_kin_threshold
```
high_kin_threshold
```
double high_kin_threshold
```
use_local_autoscale
```
boolean use_local_autoscale
```
use_monochrome_kinetic_palette
```
boolean use_monochrome_kinetic_palette
```
dna_font
```
java.awt.Font dna_font
```
dna_char_width
```
int dna_char_width
```
dna_char_height
```
int dna_char_height
```
font_height
```
int font_height
```
enable_graph_structure
```
boolean enable_graph_structure
```
show_graph_structure_only
```
boolean show_graph_structure_only
```
graph_structure_type
```
int graph_structure_type
```
use_mods_filter
```
boolean use_mods_filter
```
mods_filter_threshold
```
int mods_filter_threshold
```
ipdconsensus_track_height
```
int ipdconsensus_track_height
```

Package com.pacbio.secondary.vis.data.table.model
- Class com.pacbio.secondary.vis.data.table.model.TableModelAnnotations extends TableModelBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - num_total_rows
```
int num_total_rows
```
    - global_rows_cache
```
int[][] global_rows_cache
```
    - slots_rows_cache
```
int[] slots_rows_cache
```
    - column_names
```
java.lang.String[] column_names
```
    - contig_column_index
```
int contig_column_index
```
    - qv_column_index
```
int qv_column_index
```
    - column_names_multicontig
```
java.lang.String[] column_names_multicontig
```
    - column_names_singlecontig
```
java.lang.String[] column_names_singlecontig
```
- Class com.pacbio.secondary.vis.data.table.model.TableModelBase extends javax.swing.table.AbstractTableModel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - str_temp
```
java.lang.String str_temp
```
    - int_temp
```
java.lang.Integer int_temp
```
    - d_temp
```
java.lang.Double d_temp
```
    - main_app
```
VioletApp main_app
```
- Class com.pacbio.secondary.vis.data.table.model.TableModelDeNovo extends TableModelBase implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.data.table.model.TableModelGenomicInterval extends TableModelBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - current_view
```
GenomicViewEvents current_view
```
    - num_total_rows
```
int num_total_rows
```
    - global_rows_cache
```
int[] global_rows_cache
```
    - column_names
```
java.lang.String[] column_names
```
- Class com.pacbio.secondary.vis.data.table.model.TableModelTrack extends TableModelBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - current_view
```
GenomicViewEvents current_view
```
    - track_index
```
int track_index
```
    - column_names
```
java.lang.String[] column_names
```
Package com.pacbio.secondary.vis.data.variableresolution.model.gff
- Class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
```
VariableResolutionDataSetValues.VariableResolutionDataSetValue[] data
```
    - hasCoverage
```
boolean hasCoverage
```
    - hasVariants
```
boolean hasVariants
```
    - hasBaseMods
```
boolean hasBaseMods
```
    - motifs
```
java.util.ArrayList<E> motifs
```
    - basemods
```
java.util.ArrayList<E> basemods
```
- Class com.pacbio.secondary.vis.data.variableresolution.model.gff.VariableResolutionDataSetValues.VariableResolutionDataSetValue extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - max_coverage
```
double max_coverage
```
    - max_variants
```
int max_variants
```
    - max_norm_ipd_fwd
```
double[] max_norm_ipd_fwd
```
    - max_norm_ipd_rev
```
double[] max_norm_ipd_rev
```
Package com.pacbio.secondary.vis.gui.control
- Class com.pacbio.secondary.vis.gui.control.JCheckBoxMenuItemEx extends javax.swing.JCheckBoxMenuItem implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.control.JComboBoxCtrl extends javax.swing.JComboBox implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.control.JHyperlinksHtmlTooltip extends javax.swing.JToolTip implements Serializable
  
  serialVersionUID:
  
  6708029193343619228L
  - Serialized Fields
    - htmlPane
```
javax.swing.JEditorPane htmlPane
```
    - bIsEmpty
```
boolean bIsEmpty
```
- Class com.pacbio.secondary.vis.gui.control.JLabelCtrl extends javax.swing.JLabel implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.control.JMultiLineHtmlToolTip extends javax.swing.JToolTip implements Serializable
  
  serialVersionUID:
  
  -6496373185775134673L
- Class com.pacbio.secondary.vis.gui.control.JMultiLineToolTip extends javax.swing.JToolTip implements Serializable
  - Serialized Fields
    - tipText
```
java.lang.String tipText
```
    - component
```
javax.swing.JComponent component
```
    - columns
```
int columns
```
    - fixedwidth
```
int fixedwidth
```
- Class com.pacbio.secondary.vis.gui.control.JRadioButtonMenuItemEx extends javax.swing.JRadioButtonMenuItem implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.control.JToolbarToggleButton extends javax.swing.JToggleButton implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.control.PaletteCtrl extends javax.swing.JComponent implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - genomicViewDetails
```
GenomicViewDetails genomicViewDetails
```
- Class com.pacbio.secondary.vis.gui.control.VioletStatusBar extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - m_Font
```
java.awt.Font m_Font
```
    - m_StatusLabel
```
javax.swing.JLabel m_StatusLabel
```
    - m_SysInfoLabel
```
javax.swing.JLabel m_SysInfoLabel
```
    - m_DataInfoLabel
```
javax.swing.JLabel m_DataInfoLabel
```
    - NUM_SECTIONS
```
int NUM_SECTIONS
```
    - m_ProgressBar
```
javax.swing.JProgressBar m_ProgressBar
```
    - m_GridBagContraints
```
java.awt.GridBagConstraints m_GridBagContraints
```
- Class com.pacbio.secondary.vis.gui.control.VioletToolBar extends javax.swing.JToolBar implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - toolbar_items
```
java.lang.String[][] toolbar_items
```
- Class com.pacbio.secondary.vis.gui.control.VioletToolBarTest extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - textArea
```
javax.swing.JTextArea textArea
```
    - newline
```
java.lang.String newline
```
Package com.pacbio.secondary.vis.gui.control.treetable
- Class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable extends javax.swing.JTable implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - tree
```
JTreeTable.TreeTableCellRenderer tree
```
- Class com.pacbio.secondary.vis.gui.control.treetable.JTreeTable.TreeTableCellRenderer extends javax.swing.JTree implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - visibleRow
```
int visibleRow
```
      Last table/tree row asked to renderer.
Package com.pacbio.secondary.vis.gui.dialogs
- Class com.pacbio.secondary.vis.gui.dialogs.AboutDialog extends SMRTViewDialog implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.dialogs.DNAColorsOptionsPane extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.dialogs.EpiProColorOptionsPane extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.dialogs.EpiProColorOptionsPane.EpiProOptionsTable extends javax.swing.JTable implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.dialogs.GoToDialog extends SMRTViewDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - app
```
VioletApp app
```
    - font_height
```
int font_height
```
    - contigs
```
java.lang.String[] contigs
```
    - contigs_list
```
javax.swing.JComboBox<E> contigs_list
```
    - close_btn
```
javax.swing.JButton close_btn
```
    - genome_panel
```
GoToDialog.GoToDialogPanel genome_panel
```
    - region_panel
```
GoToDialog.GoToDialogPanel region_panel
```
    - details_panel
```
GoToDialog.GoToDialogPanel details_panel
```
- Class com.pacbio.secondary.vis.gui.dialogs.GoToDialog.GoToDialogPanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - link
```
java.lang.String link
```
    - min_field
```
javax.swing.JFormattedTextField min_field
```
    - max_field
```
javax.swing.JFormattedTextField max_field
```
    - goto_btn
```
javax.swing.JButton goto_btn
```
    - link_checkbox
```
javax.swing.JCheckBox link_checkbox
```
- Class com.pacbio.secondary.vis.gui.dialogs.InspectDataDialog extends SMRTViewDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - center_location
```
long center_location
```
    - popupmenu
```
javax.swing.JPopupMenu popupmenu
```
- Class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase extends javax.swing.JFrame implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - app
```
VioletApp app
```
    - tabbed_pane
```
javax.swing.JTabbedPane tabbed_pane
```
    - variants_tab
```
javax.swing.JPanel variants_tab
```
    - qv_tab
```
javax.swing.JPanel qv_tab
```
    - kinetics_tab
```
javax.swing.JPanel kinetics_tab
```
    - structures_tab
```
javax.swing.JPanel structures_tab
```
    - details_tab
```
javax.swing.JPanel details_tab
```
    - program_tab
```
javax.swing.JPanel program_tab
```
    - epipro_tab
```
javax.swing.JPanel epipro_tab
```
    - variants_close_btn
```
javax.swing.JButton variants_close_btn
```
    - qv_close_btn
```
javax.swing.JButton qv_close_btn
```
    - kinetics_close_btn
```
javax.swing.JButton kinetics_close_btn
```
    - structures_close_btn
```
javax.swing.JButton structures_close_btn
```
    - epipro_close_btn
```
javax.swing.JButton epipro_close_btn
```
    - details_close_btn
```
javax.swing.JButton details_close_btn
```
    - program_close_btn
```
javax.swing.JButton program_close_btn
```
    - variants_save_btn
```
javax.swing.JButton variants_save_btn
```
    - qv_save_btn
```
javax.swing.JButton qv_save_btn
```
    - kinetics_save_btn
```
javax.swing.JButton kinetics_save_btn
```
    - structures_save_btn
```
javax.swing.JButton structures_save_btn
```
    - epipro_save_btn
```
javax.swing.JButton epipro_save_btn
```
    - details_save_btn
```
javax.swing.JButton details_save_btn
```
    - program_save_btn
```
javax.swing.JButton program_save_btn
```
    - variants_help_btn
```
javax.swing.JButton variants_help_btn
```
    - qv_help_btn
```
javax.swing.JButton qv_help_btn
```
    - kinetics_help_btn
```
javax.swing.JButton kinetics_help_btn
```
    - structures_help_btn
```
javax.swing.JButton structures_help_btn
```
    - epipro_help_btn
```
javax.swing.JButton epipro_help_btn
```
    - details_help_btn
```
javax.swing.JButton details_help_btn
```
    - program_help_btn
```
javax.swing.JButton program_help_btn
```
    - reset_btn
```
javax.swing.JButton reset_btn
```
    - close_text
```
java.lang.String close_text
```
    - save_text
```
java.lang.String save_text
```
    - btn_inset
```
int btn_inset
```
    - baseqv_checkbox
```
javax.swing.JCheckBox baseqv_checkbox
```
    - mapqv_checkbox
```
javax.swing.JCheckBox mapqv_checkbox
```
    - qv_thresholds_panel
```
QVThresholdOptionsPane qv_thresholds_panel
```
    - dna_colors_panel
```
DNAColorsOptionsPane dna_colors_panel
```
    - cov_filter_checkbox
```
javax.swing.JCheckBox cov_filter_checkbox
```
    - cov_filter_threshold
```
javax.swing.JFormattedTextField cov_filter_threshold
```
    - conf_filter_checkbox
```
javax.swing.JCheckBox conf_filter_checkbox
```
    - conf_filter_threshold
```
javax.swing.JFormattedTextField conf_filter_threshold
```
    - kinetics_checkbox
```
javax.swing.JCheckBox kinetics_checkbox
```
    - basemods_filter_checkbox
```
javax.swing.JCheckBox basemods_filter_checkbox
```
    - basemods_options_cb
```
JComboBoxCtrl basemods_options_cb
```
    - kinetics_palette
```
PaletteCtrl kinetics_palette
```
    - kinetics_min_slider
```
PreferencesDialogBase.JDoubleSlider kinetics_min_slider
```
    - kinetics_max_slider
```
PreferencesDialogBase.JDoubleSlider kinetics_max_slider
```
    - kinetics_min_text
```
javax.swing.JFormattedTextField kinetics_min_text
```
    - kinetics_max_text
```
javax.swing.JFormattedTextField kinetics_max_text
```
    - basemods_filter_threshold
```
javax.swing.JFormattedTextField basemods_filter_threshold
```
    - kinetics_scaling_cb
```
JComboBoxCtrl kinetics_scaling_cb
```
    - kinetics_scaling_label
```
javax.swing.JLabel kinetics_scaling_label
```
    - kinetics_min_label
```
javax.swing.JLabel kinetics_min_label
```
    - kinetics_max_label
```
javax.swing.JLabel kinetics_max_label
```
    - kinetics_ann_label
```
javax.swing.JLabel kinetics_ann_label
```
    - details_view_range_mode_cb
```
JComboBoxCtrl details_view_range_mode_cb
```
    - details_view_dynamic_range
```
javax.swing.JFormattedTextField details_view_dynamic_range
```
    - details_view_fixed_range
```
javax.swing.JFormattedTextField details_view_fixed_range
```
    - details_view_max_coverage
```
javax.swing.JFormattedTextField details_view_max_coverage
```
    - fixed_range_label
```
javax.swing.JLabel fixed_range_label
```
    - dynamic_range_label
```
javax.swing.JLabel dynamic_range_label
```
    - details_view_coarse_cb
```
JComboBoxCtrl details_view_coarse_cb
```
    - show_tooltip_checkbox
```
javax.swing.JCheckBox show_tooltip_checkbox
```
    - epipro_only_checkbox
```
javax.swing.JCheckBox epipro_only_checkbox
```
    - epipro_cutoff_filter_checkbox
```
javax.swing.JCheckBox epipro_cutoff_filter_checkbox
```
    - epipro_view_mode_cb
```
JComboBoxCtrl epipro_view_mode_cb
```
    - epipro_cutoff_filter_threshold
```
javax.swing.JFormattedTextField epipro_cutoff_filter_threshold
```
    - epipro_pane
```
EpiProColorOptionsPane epipro_pane
```
    - show_graph_structures_checkbox
```
javax.swing.JCheckBox show_graph_structures_checkbox
```
    - show_structures_only_checkbox
```
javax.swing.JCheckBox show_structures_only_checkbox
```
    - structures_listbox
```
javax.swing.JList<E> structures_listbox
```
    - always_show_mem_stats_checkbox
```
javax.swing.JCheckBox always_show_mem_stats_checkbox
```
    - link_genome_region_checkbox
```
javax.swing.JCheckBox link_genome_region_checkbox
```
    - link_region_details_checkbox
```
javax.swing.JCheckBox link_region_details_checkbox
```
- Class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogBase.JDoubleSlider extends javax.swing.JSlider implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - scale
```
float scale
```
- Class com.pacbio.secondary.vis.gui.dialogs.PreferencesDialogEx extends PreferencesDialogBase implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.dialogs.PrintOptionsDialog extends SMRTViewDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - dlg_data
```
java.lang.Boolean[] dlg_data
```
    - whole_genome_box
```
javax.swing.JCheckBox whole_genome_box
```
    - region_view_box
```
javax.swing.JCheckBox region_view_box
```
    - details_view_box
```
javax.swing.JCheckBox details_view_box
```
- Class com.pacbio.secondary.vis.gui.dialogs.ProgressDialog extends javax.swing.JFrame implements Serializable
  - Serialized Fields
    - progress
```
javax.swing.JProgressBar progress
```
    - model
```
javax.swing.BoundedRangeModel model
```
    - timer
```
javax.swing.Timer timer
```
    - info
```
javax.swing.JLabel info
```
    - cancel
```
javax.swing.JButton cancel
```
    - cancelled
```
boolean cancelled
```
- Class com.pacbio.secondary.vis.gui.dialogs.PropertiesDialog extends SMRTViewDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - htmlPane
```
javax.swing.JEditorPane htmlPane
```
- Class com.pacbio.secondary.vis.gui.dialogs.QVThresholdOptionsPane extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - view
```
GenomicViewDetails view
```
    - model
```
com.pacbio.secondary.vis.gui.dialogs.QVThresholdOptionsPane.QVOptionsTableModel model
```
    - thresholds
```
java.lang.Double[] thresholds
```
    - colors
```
java.awt.Color[][] colors
```
    - table_width
```
int table_width
```
- Class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog extends SMRTViewDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - htmlPane
```
RegionsOfInterestDialog.BookmarksEditorPane htmlPane
```
- Class com.pacbio.secondary.vis.gui.dialogs.RegionsOfInterestDialog.BookmarksEditorPane extends javax.swing.JEditorPane implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - tooltip
```
java.lang.String tooltip
```
- Class com.pacbio.secondary.vis.gui.dialogs.RemoveTrackDialog extends SMRTViewDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - selected_track
```
java.lang.Object selected_track
```
- Class com.pacbio.secondary.vis.gui.dialogs.SelectFileDialog extends SMRTViewDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - file_path
```
java.lang.String file_path
```
- Class com.pacbio.secondary.vis.gui.dialogs.SMRTViewDialog extends javax.swing.JDialog implements Serializable
  
  serialVersionUID:
  
  1L
Package com.pacbio.secondary.vis.gui.draw.views
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewBase extends javax.swing.JComponent implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - minViewGenomicRange
```
int minViewGenomicRange
```
    - default_view_height
```
int default_view_height
```
    - default_view_width
```
int default_view_width
```
    - default_ideogram_width
```
int default_ideogram_width
```
    - default_ideogram_height
```
int default_ideogram_height
```
    - default_ideogram_label_width
```
int default_ideogram_label_width
```
    - default_left_info_width
```
int default_left_info_width
```
    - default_tracks_width
```
int default_tracks_width
```
    - default_border_width
```
int default_border_width
```
    - default_y_top_ideogram
```
int default_y_top_ideogram
```
    - default_height_top_axis
```
int default_height_top_axis
```
    - default_y_bottom_ideogram
```
int default_y_bottom_ideogram
```
    - default_feature_size
```
int default_feature_size
```
    - currentViewContig
```
int currentViewContig
```
    - bHorizontal
```
boolean bHorizontal
```
    - bCircular
```
boolean bCircular
```
    - bDetails
```
boolean bDetails
```
    - bInspection
```
boolean bInspection
```
    - leftVisible
```
java.util.BitSet leftVisible
```
    - rightVisible
```
java.util.BitSet rightVisible
```
    - scaleX
```
double scaleX
```
    - scaleY
```
double scaleY
```
    - selectedSlotIndex
```
int selectedSlotIndex
```
    - selectedTrackIndex
```
int selectedTrackIndex
```
    - showGenes
```
java.lang.Boolean showGenes
```
    - showLabels
```
boolean showLabels
```
    - showMarkers
```
boolean showMarkers
```
    - showMarkerLabels
```
boolean showMarkerLabels
```
    - minWidth
```
int minWidth
```
    - maxWidth
```
int maxWidth
```
    - selectionChangedListeners
```
java.util.LinkedList<E> selectionChangedListeners
```
    - rangeSelection
```
Interval rangeSelection
```
    - beginPoint
```
java.awt.Point beginPoint
```
    - endPoint
```
java.awt.Point endPoint
```
    - viewHistory
```
java.util.LinkedList<E> viewHistory
```
    - dim_ideogramview
```
java.awt.Dimension dim_ideogramview
```
    - markers
```
java.util.ArrayList<E> markers
```
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewCircular extends GenomicViewEvents implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - main_app
```
VioletApp main_app
```
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewData extends GenomicViewBase implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetails extends GenomicViewDetailsDraw implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsData extends GenomicViewHorizontal implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - details_options
```
DetailsOptions details_options
```
    - details_data
```
DetailsStorage details_data
```
    - data_request_queue
```
Locus data_request_queue
```
    - reference_data
```
ReferenceSequenceStorage reference_data
```
    - reference_request_queue
```
Locus reference_request_queue
```
    - ipd_consensus_data
```
IPDConsensusStorage ipd_consensus_data
```
    - ipd_consensus_request_queue
```
Locus ipd_consensus_request_queue
```
    - data_on_demand_queue
```
Locus data_on_demand_queue
```
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDetailsDraw extends GenomicViewDetailsData implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewDraw extends GenomicViewData implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - end_last_upper_label_x
```
int end_last_upper_label_x
```
    - end_last_lower_label_x
```
int end_last_lower_label_x
```
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewEvents extends GenomicViewDraw implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream stream)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Necessary actions for deserializing the object.
      
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewHorizontal extends GenomicViewEvents implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - default_tracks_height
```
int default_tracks_height
```
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewInspect extends GenomicViewDetails implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - end_first_insertion
```
int end_first_insertion
```
    - end_insertion_reference
```
int end_insertion_reference
```
    - insertion_width
```
int insertion_width
```
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewRegion extends GenomicViewHorizontal implements Serializable
  
  serialVersionUID:
  
  2L
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewSingleContig extends GenomicViewVertical implements Serializable
  
  serialVersionUID:
  
  2L
- Class com.pacbio.secondary.vis.gui.draw.views.GenomicViewVertical extends GenomicViewEvents implements Serializable
  
  serialVersionUID:
  
  1L
Package com.pacbio.secondary.vis.gui.evt
- Class com.pacbio.secondary.vis.gui.evt.GenomicViewChangeEvent extends javax.swing.event.ChangeEvent implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - event_type
```
GenomicViewChangeEvent.GenomicViewEventType event_type
```
Package com.pacbio.secondary.vis.gui.frame
- Class com.pacbio.secondary.vis.gui.frame.VioletFrame extends VioletFrameCreate implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.frame.VioletFrameActions extends VioletFrameIO implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - table_menu
```
javax.swing.JMenu table_menu
```
    - statusBar
```
VioletStatusBar statusBar
```
    - toolBar
```
VioletToolBar toolBar
```
    - preferences_dlg
```
PreferencesDialogEx preferences_dlg
```
    - goto_dlg
```
GoToDialog goto_dlg
```
- Class com.pacbio.secondary.vis.gui.frame.VioletFrameBase extends javax.swing.JFrame implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pageFormat
```
java.awt.print.PageFormat pageFormat
```
    - printerJob
```
java.awt.print.PrinterJob printerJob
```
    - popmenu
```
javax.swing.JPopupMenu popmenu
```
    - main_app
```
VioletApp main_app
```
    - currentMainFrameContig
```
int currentMainFrameContig
```
    - bFitToWindow
```
boolean bFitToWindow
```
    - bFitRegionViewToWindowHeight
```
boolean bFitRegionViewToWindowHeight
```
    - docking_desktop
```
DockingDesktop docking_desktop
```
    - default_workspace_layout
```
java.lang.String default_workspace_layout
```
    - chromosomes_views
```
GenomicViewSingleContig[] chromosomes_views
```
    - chromosomes_panel
```
WholeGenomePanel chromosomes_panel
```
    - chromosomes_scroller
```
DockableScrollPaneBase chromosomes_scroller
```
    - region_view
```
GenomicViewRegion region_view
```
    - region_scroller
```
DockableScrollPaneBase region_scroller
```
    - details_view
```
GenomicViewDetails details_view
```
    - details_scroller
```
DockableScrollPaneBase details_scroller
```
    - circular_view
```
GenomicViewCircular circular_view
```
    - circular_scroller
```
DockableScrollPaneBase circular_scroller
```
    - denovo_table_panel
```
DeNovoTablePanel denovo_table_panel
```
    - genomic_table_panel
```
GenomicTablePanel genomic_table_panel
```
    - browser_panel
```
WebBrowserPanel browser_panel
```
    - selection_panel
```
SelectionInfoPanel selection_panel
```
- Class com.pacbio.secondary.vis.gui.frame.VioletFrameChanges extends VioletFrameBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - last_selected_dockable_view
```
Dockable last_selected_dockable_view
```
- Class com.pacbio.secondary.vis.gui.frame.VioletFrameCreate extends VioletFrameActions implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.frame.VioletFrameDesktop extends VioletFrame implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.frame.VioletFrameIO extends VioletFrameChanges implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.frame.VioletFrameSummary extends VioletFrame implements Serializable
  
  serialVersionUID:
  
  1L
Package com.pacbio.secondary.vis.gui.panels
- Class com.pacbio.secondary.vis.gui.panels.DeNovoTablePanel extends TablePanelBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - denovo_model
```
TableModelDeNovo denovo_model
```
    - denovo_table
```
GenomicTableDeNovo denovo_table
```
    - popupmenu
```
javax.swing.JPopupMenu popupmenu
```
- Class com.pacbio.secondary.vis.gui.panels.GenomicTablePanel extends TablePanelBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data_table
```
GenomicTableBase data_table
```
    - model_annotations
```
TableModelAnnotations model_annotations
```
    - model_interval
```
TableModelGenomicInterval model_interval
```
    - model_track
```
TableModelTrack model_track
```
    - popupmenu
```
javax.swing.JPopupMenu popupmenu
```
- Class com.pacbio.secondary.vis.gui.panels.SelectionInfoPanel extends DockablePaneBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - main_app
```
VioletApp main_app
```
    - infoPanel
```
javax.swing.JTextPane infoPanel
```
    - popupmenu
```
javax.swing.JPopupMenu popupmenu
```
    - lastSource
```
GenomicViewEvents lastSource
```
    - lastMarker
```
Marker lastMarker
```
- Class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel extends DockablePaneBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - editorPane
```
WebBrowserPanel.WebBrowserEditorPane editorPane
```
    - use_external_browser
```
boolean use_external_browser
```
    - main_app
```
VioletApp main_app
```
    - toolBar
```
WebBrowserPanel.WebBrowserToolBar toolBar
```
- Class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserEditorPane extends javax.swing.JEditorPane implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - history
```
java.util.List<E> history
```
    - historyIndex
```
int historyIndex
```
    - toolbar
```
WebBrowserPanel.WebBrowserToolBar toolbar
```
- Class com.pacbio.secondary.vis.gui.panels.WebBrowserPanel.WebBrowserToolBar extends javax.swing.JToolBar implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - webBrowserPane
```
WebBrowserPanel.WebBrowserEditorPane webBrowserPane
```
    - backButton
```
javax.swing.JButton backButton
```
    - forwardButton
```
javax.swing.JButton forwardButton
```
    - refreshButton
```
javax.swing.JButton refreshButton
```
    - urlTextField
```
javax.swing.JTextField urlTextField
```
- Class com.pacbio.secondary.vis.gui.panels.WholeGenomePanel extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - app
```
VioletApp app
```
Package com.pacbio.secondary.vis.gui.panels.base
- Class com.pacbio.secondary.vis.gui.panels.base.DockablePaneBase extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - key
```
DockKey key
```
- Class com.pacbio.secondary.vis.gui.panels.base.DockableScrollPaneBase extends javax.swing.JScrollPane implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - key
```
DockKey key
```
- Class com.pacbio.secondary.vis.gui.panels.base.TablePanelBase extends DockablePaneBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - filter_text_field
```
javax.swing.JTextField filter_text_field
```
    - filter_view_btn
```
JToolbarToggleButton filter_view_btn
```
    - panel_status_text
```
javax.swing.JLabel panel_status_text
```
    - sorter
```
javax.swing.table.TableRowSorter<M extends javax.swing.table.TableModel> sorter
```
    - main_app
```
VioletApp main_app
```
    - enable_filter
```
boolean enable_filter
```
Package com.pacbio.secondary.vis.gui.table
- Class com.pacbio.secondary.vis.gui.table.GenomicTableBase extends javax.swing.JTable implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.table.GenomicTableDeNovo extends GenomicTableBase implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.table.GenomicTableInterval extends GenomicTableBase implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.table.GenomicTableTrack extends GenomicTableBase implements Serializable
  
  serialVersionUID:
  
  1L
Package com.pacbio.secondary.vis.gui.table.renderer
- Class com.pacbio.secondary.vis.gui.table.renderer.ColorEditor extends javax.swing.AbstractCellEditor implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.table.renderer.ColorRenderer extends javax.swing.JLabel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - selectedBorder
```
javax.swing.border.Border selectedBorder
```
    - unselectedBorder
```
javax.swing.border.Border unselectedBorder
```
    - isBordered
```
boolean isBordered
```
- Class com.pacbio.secondary.vis.gui.table.renderer.EpiProPaletteRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - palette_display
```
EpiProPaletteRenderer.EpiProPaletteDisplay palette_display
```
- Class com.pacbio.secondary.vis.gui.table.renderer.EpiProPaletteRenderer.EpiProPaletteDisplay extends javax.swing.JLabel implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.table.renderer.IntegerRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - nf
```
java.text.NumberFormat nf
```
- Class com.pacbio.secondary.vis.gui.table.renderer.IntervalRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.gui.table.renderer.LongRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - nf
```
java.text.NumberFormat nf
```
Package com.pacbio.secondary.vis.io.hdf.exception
- Class com.pacbio.secondary.vis.io.hdf.exception.HDF5ExceptionEx extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1L
Package com.pacbio.secondary.vis.io.indexer.gff.metadata
- Class com.pacbio.secondary.vis.io.indexer.gff.metadata.GFFMetadataInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - file_path
```
java.lang.String file_path
```
    - indexes
```
java.util.ArrayList<E> indexes
```
    - avg_row_lenght
```
int avg_row_lenght
```
    - max_read_length
```
int max_read_length
```
    - gff_slice_size
```
long gff_slice_size
```
Package com.pacbio.secondary.vis.io.indexer.indexinfo
- Class com.pacbio.secondary.vis.io.indexer.indexinfo.ASCIIFileIndexInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - contig
```
int contig
```
    - sequence_position
```
long sequence_position
```
    - file_offset
```
long file_offset
```
- Class com.pacbio.secondary.vis.io.indexer.indexinfo.FASTAFileIndexInfo extends ASCIIFileIndexInfo implements Serializable
  
  serialVersionUID:
  
  1L
- Class com.pacbio.secondary.vis.io.indexer.indexinfo.GFFIndexInfo extends ASCIIFileIndexInfo implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - read_qv
```
double read_qv
```
    - read_num_annotations
```
int read_num_annotations
```
Package com.pacbio.secondary.vis.svc.server.data
- Class com.pacbio.secondary.vis.svc.server.data.WsContigInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - m_name
```
java.lang.String m_name
```
    - m_id
```
java.lang.String m_id
```
    - m_header
```
java.lang.String m_header
```
    - m_sequence_file
```
java.lang.String m_sequence_file
```
    - m_contig_length
```
int m_contig_length
```
- Class com.pacbio.secondary.vis.svc.server.data.WsFastaSequenceInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - m_info
```
java.lang.String m_info
```
    - m_sequence
```
byte[] m_sequence
```
- Class com.pacbio.secondary.vis.svc.server.data.WsFileInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - length
```
long length
```
    - timestamp
```
long timestamp
```
    - isdirectory
```
boolean isdirectory
```
    - directory
```
java.lang.String directory
```
    - name
```
java.lang.String name
```
- Class com.pacbio.secondary.vis.svc.server.data.WsIntervalSvc extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - ctg
```
int ctg
```
    - star
```
int star
```
    - end
```
int end
```
    - strn
```
byte strn
```
- Class com.pacbio.secondary.vis.svc.server.data.WsIPDConsensusInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - m_info
```
java.lang.String m_info
```
    - m_ipd_ratio
```
int[] m_ipd_ratio
```
- Class com.pacbio.secondary.vis.svc.server.data.WsJobMetadataInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - m_reference_info
```
WsReferenceInfo m_reference_info
```
    - m_tracks_info_array
```
WsTrackInfo[] m_tracks_info_array
```
    - m_data_file
```
java.lang.String m_data_file
```
    - m_job_title
```
java.lang.String m_job_title
```
- Class com.pacbio.secondary.vis.svc.server.data.WsRead extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - name
```
java.lang.String name
```
    - intv
```
WsIntervalSvc intv
```
    - lane
```
int lane
```
    - scor
```
int scor
```
    - seq
```
java.lang.String seq
```
    - ann
```
byte[] ann
```
    - qv
```
byte[] qv
```
    - molid
```
int molid
```
    - structid
```
int structid
```
- Class com.pacbio.secondary.vis.svc.server.data.WsReadEx extends WsRead implements Serializable
  
  serialVersionUID:
  
  2L
- Class com.pacbio.secondary.vis.svc.server.data.WsReferenceInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - m_num_contigs
```
int m_num_contigs
```
    - m_max_contig_length
```
int m_max_contig_length
```
    - m_path
```
java.lang.String m_path
```
    - m_name
```
java.lang.String m_name
```
    - m_id
```
java.lang.String m_id
```
    - m_ideogram_file
```
java.lang.String m_ideogram_file
```
    - m_web_url
```
java.lang.String m_web_url
```
    - m_sequence_file
```
java.lang.String m_sequence_file
```
    - m_sequence_index_file
```
java.lang.String m_sequence_index_file
```
    - m_image_file
```
java.lang.String m_image_file
```
    - m_contigs_info_array
```
WsContigInfo[] m_contigs_info_array
```
- Class com.pacbio.secondary.vis.svc.server.data.WsResults extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - info
```
WsResultsInfo info
```
    - reads
```
WsRead[] reads
```
    - graph
```
GraphStructure graph
```
- Class com.pacbio.secondary.vis.svc.server.data.WsResultsInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - status
```
java.lang.String status
```
    - mode
```
int mode
```
    - strobe
```
boolean strobe
```
    - start
```
long start
```
    - end
```
long end
```
    - ctg
```
int ctg
```
    - lanes
```
int lanes
```
    - lanes_separator
```
int lanes_separator
```
    - reads
```
int reads
```
    - bases
```
long bases
```
    - time_io
```
double time_io
```
    - time_bld
```
double time_bld
```
- Class com.pacbio.secondary.vis.svc.server.data.WsTrackInfo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - m_name
```
java.lang.String m_name
```
    - m_file
```
java.lang.String m_file
```
    - m_web_search
```
java.lang.String m_web_search
```
Package pub.vlsolutions.swing.docking
- Class pub.vlsolutions.swing.docking.AutoHideButton extends javax.swing.JLabel implements Serializable
  - Serialized Fields
    - selected
```
boolean selected
```
    - key
```
DockKey key
```
    - dockable
```
Dockable dockable
```
    - zone
```
int zone
```
    - isNotification
```
boolean isNotification
```
    - notificationTimer
```
javax.swing.Timer notificationTimer
```
    - blinkCount
```
int blinkCount
```
    - MAX_BLINKS
```
int MAX_BLINKS
```
    - keyListener
```
java.beans.PropertyChangeListener keyListener
```
- Class pub.vlsolutions.swing.docking.AutoHideButtonPanel extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - border
```
int border
```
      <=> Zone
    - buttonHighlighter
```
pub.vlsolutions.swing.docking.AutoHideButtonPanel.ButtonHighlighter buttonHighlighter
```
      highlight effect (rollover) on the contained buttons
    - expandPanel
```
AutoHideExpandPanel expandPanel
```
      expansion management
- Class pub.vlsolutions.swing.docking.AutoHideExpandPanel extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - expansionTimer
```
javax.swing.Timer expansionTimer
```
    - isRolloverTimer
```
boolean isRolloverTimer
```
    - isExpanding
```
boolean isExpanding
```
    - savedDimensions
```
java.util.HashMap<K,V> savedDimensions
```
    - controler
```
pub.vlsolutions.swing.docking.AutoHideExpandPanel.ExpandControler controler
```
    - selectedButton
```
AutoHideButton selectedButton
```
    - expandedComponent
```
java.awt.Component expandedComponent
```
    - desk
```
DockingDesktop desk
```
    - topDragger
```
javax.swing.JPanel topDragger
```
    - leftDragger
```
javax.swing.JPanel leftDragger
```
    - bottomDragger
```
javax.swing.JPanel bottomDragger
```
    - rightDragger
```
javax.swing.JPanel rightDragger
```
    - lastDragger
```
javax.swing.JPanel lastDragger
```
    - content
```
javax.swing.JPanel content
```
    - heavyPanel
```
java.awt.Panel heavyPanel
```
    - titleBar
```
DockViewTitleBar titleBar
```
    - animationControler
```
pub.vlsolutions.swing.docking.AutoHideExpandPanel.AnimationControler animationControler
```
    - expandFromTopBorder
```
javax.swing.border.Border expandFromTopBorder
```
    - expandFromLeftBorder
```
javax.swing.border.Border expandFromLeftBorder
```
    - expandFromBottomBorder
```
javax.swing.border.Border expandFromBottomBorder
```
    - expandFromRightBorder
```
javax.swing.border.Border expandFromRightBorder
```
    - shouldCollapse
```
boolean shouldCollapse
```
      this boolean is used to disable auto-hiding temporarily, especially during drag operation (where mouse can leave the component)
    - isHeavyPanelInstalled
```
boolean isHeavyPanelInstalled
```
      flag used when heavywieght usage + single heavyweight component
    - lastTimeMouseWasIn
```
long lastTimeMouseWasIn
```
      Used by the collapse timer
    - canUseMouseInfo
```
boolean canUseMouseInfo
```
    - collapser
```
pub.vlsolutions.swing.docking.AutoHideExpandPanel.FocusCollapser collapser
```
    - collapseTimer
```
javax.swing.Timer collapseTimer
```
      Timer used to collapse the expand panel (when mouse is out of bounds). (only for java > 1.5)
- Class pub.vlsolutions.swing.docking.CompoundDockingPanel extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - dockable
```
CompoundDockable dockable
```
- Class pub.vlsolutions.swing.docking.DetachedDockView extends DockView implements Serializable
- Class pub.vlsolutions.swing.docking.DockablePanel extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - key
```
DockKey key
```
- Class pub.vlsolutions.swing.docking.DockableStoreButton extends javax.swing.JButton implements Serializable
  - Serialized Fields
    - dockable
```
Dockable dockable
```
    - emptyText
```
java.lang.String emptyText
```
    - emptyTooltip
```
java.lang.String emptyTooltip
```
    - emptyIcon
```
javax.swing.Icon emptyIcon
```
    - fullText
```
java.lang.String fullText
```
    - fullTooltip
```
java.lang.String fullTooltip
```
- Class pub.vlsolutions.swing.docking.DockingDesktop extends javax.swing.JLayeredPane implements Serializable
  - Serialized Fields
    - context
```
DockingContext context
```
      contextual data that can be shared by multiple desktops
    - contentPane
```
javax.swing.JPanel contentPane
```
      panel containing autohidepanels on borders and dockingpanel at center
    - dockingPanel
```
DockingPanel dockingPanel
```
      main central container for dockables
    - expandPanel
```
AutoHideExpandPanel expandPanel
```
      container responsible for auto-hidden components expansion
    - topBorderPane
```
AutoHideButtonPanel topBorderPane
```
      panel used to display autohide buttons
    - leftBorderPane
```
AutoHideButtonPanel leftBorderPane
```
      panel used to display autohide buttons
    - bottomBorderPane
```
AutoHideButtonPanel bottomBorderPane
```
      panel used to display autohide buttons
    - rightBorderPane
```
AutoHideButtonPanel rightBorderPane
```
      panel used to display autohide buttons
    - borderPanes
```
AutoHideButtonPanel[] borderPanes
```
      array containing the border panes
    - autoHideButtons
```
java.util.HashMap<K,V> autoHideButtons
```
    - dragControler
```
DragControler dragControler
```
    - dummyMaximedReplacer
```
pub.vlsolutions.swing.docking.MaximizedComponentReplacer dummyMaximedReplacer
```
      a component used to track position of the current maximized component
    - maximizedComponent
```
java.awt.Component maximizedComponent
```
      the current maximized component
    - currentMaximizedComponentIsHeavyWeight
```
boolean currentMaximizedComponentIsHeavyWeight
```
      a flag set when adding a maximized component : true is this one is heavyweight Only used with heavyweight support AND singleHeavyWeightComponent
    - mouseMotionGrabber
```
javax.swing.JComponent mouseMotionGrabber
```
    - mouseOutOfExpandedPanelTimer
```
javax.swing.Timer mouseOutOfExpandedPanelTimer
```
      this timer is only used when the java version is < 1.5 (version>=1.5 uses the MouseInfo component)
    - tabbedGroups
```
java.util.HashMap<K,V> tabbedGroups
```
      groups of tabs (used to re-tab autohidden dockable)
    - focusHandler
```
pub.vlsolutions.swing.docking.DockingDesktop.FocusHandler focusHandler
```
    - previousFloatingDockableStates
```
java.util.HashMap<K,V> previousFloatingDockableStates
```
      return state for floating dockables
    - desktopName
```
java.lang.String desktopName
```
      Unique name for this desktop : used since 2.1 to support multiple desktops
    - lastWindowLocation
```
java.awt.Point lastWindowLocation
```
    - windowMovementListener
```
java.awt.event.ComponentAdapter windowMovementListener
```
    - windowListener
```
java.awt.event.WindowListener windowListener
```
    - closeAction
```
javax.swing.AbstractAction closeAction
```
      Action used for keyboard binding : closes the current dockable
    - maximizeAction
```
javax.swing.AbstractAction maximizeAction
```
      Action used for keyboard binding : maximize/restore the current dockable
    - dockAction
```
javax.swing.AbstractAction dockAction
```
      Action used for keyboard binding : autohide/dock the current dockable
    - floatAction
```
javax.swing.AbstractAction floatAction
```
      Action used for keyboard binding : float/attach the current dockable
    - cancelAction
```
javax.swing.AbstractAction cancelAction
```
      Action used for keyboard binding : cancel the current operation
- Class pub.vlsolutions.swing.docking.DockingPanel extends javax.swing.JPanel implements Serializable
- Class pub.vlsolutions.swing.docking.DockingSelectorDialog extends javax.swing.JDialog implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - model
```
pub.vlsolutions.swing.docking.DockingSelectorDialog.DockablesTableModel model
```
    - desktop
```
DockingDesktop desktop
```
    - confirmButton
```
javax.swing.JButton confirmButton
```
    - cancelButton
```
javax.swing.JButton cancelButton
```
    - table
```
javax.swing.JTable table
```
    - wizardLabel
```
javax.swing.JLabel wizardLabel
```
    - wizardLabelText
```
java.lang.String wizardLabelText
```
    - closingState
```
int closingState
```
    - visibleViews
```
java.util.HashMap<K,V> visibleViews
```
- Class pub.vlsolutions.swing.docking.DockTabbedPane extends javax.swing.JTabbedPane implements Serializable
  - Serialized Fields
    - lastDropBounds
```
java.awt.Rectangle lastDropBounds
```
      cache for reusing the general path lastDropPath between calls to getDropShape
    - lastDropTabBounds
```
java.awt.Rectangle lastDropTabBounds
```
      cache for reusing the general path lastDropPath between calls to getDropShape
    - lastDropPath
```
java.awt.geom.GeneralPath lastDropPath
```
    - draggedDockable
```
SingleDockableContainer draggedDockable
```
      set by a drag operation
    - isMultipleDrag
```
boolean isMultipleDrag
```
      True when the whole tabbedpane is dragged
    - desktop
```
DockingDesktop desktop
```
    - popup
```
javax.swing.JPopupMenu popup
```
      The pop-up menu used to provide fast "close" shortcuts (close all, close others)
    - popupTab
```
int popupTab
```
      the tab currently associated with the pop-up
    - previousSelectedDockable
```
int previousSelectedDockable
```
      The tab that was selected before the current one
    - closeActions
```
java.util.HashMap<K,V> closeActions
```
    - selfDockable
```
Dockable selfDockable
```
    - keyChangeListener
```
java.beans.PropertyChangeListener keyChangeListener
```
- Class pub.vlsolutions.swing.docking.DockView extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - title
```
DockViewTitleBar title
```
    - desktop
```
DockingDesktop desktop
```
      the desktop managing this view
    - dockable
```
Dockable dockable
```
      the dockable managed by this view
    - lastDropShape
```
java.awt.Shape lastDropShape
```
      remember the last drop position to cache the shape used for showing the drop position
    - lastDropGeneralPath
```
java.awt.Shape lastDropGeneralPath
```
      remember the last drop position to cache the shape used for showing the drop position
    - listener
```
java.beans.PropertyChangeListener listener
```
      listen to the titlebar actions
- Class pub.vlsolutions.swing.docking.DockViewAsTab extends DockView implements Serializable
  - Serialized Fields
    - tabHeader
```
DockViewAsTab.TabHeader tabHeader
```
      The tab container in which the components are added
    - tpManager
```
JTabbedPaneSmartIconManager tpManager
```
      smart icon manager
    - smartIcon
```
JTabbedPaneSmartIcon smartIcon
```
      smart icon used to display the title
    - closeAction
```
javax.swing.AbstractAction closeAction
```
    - closeSmartIcon
```
SmartIconJButton closeSmartIcon
```
    - maximizeAction
```
javax.swing.AbstractAction maximizeAction
```
    - maximizeSmartIcon
```
SmartIconJButton maximizeSmartIcon
```
    - hideAction
```
javax.swing.AbstractAction hideAction
```
    - hideSmartIcon
```
SmartIconJButton hideSmartIcon
```
    - floatAction
```
javax.swing.AbstractAction floatAction
```
    - floatSmartIcon
```
SmartIconJButton floatSmartIcon
```
    - isCloseButtonDisplayed
```
boolean isCloseButtonDisplayed
```
    - isHideButtonDisplayed
```
boolean isHideButtonDisplayed
```
    - isDockButtonDisplayed
```
boolean isDockButtonDisplayed
```
    - isMaximizeButtonDisplayed
```
boolean isMaximizeButtonDisplayed
```
    - isRestoreButtonDisplayed
```
boolean isRestoreButtonDisplayed
```
    - isFloatButtonDisplayed
```
boolean isFloatButtonDisplayed
```
    - isAttachButtonDisplayed
```
boolean isAttachButtonDisplayed
```
    - keyListener
```
java.beans.PropertyChangeListener keyListener
```
      listen to the key changes
    - currentPopUp
```
javax.swing.JPopupMenu currentPopUp
```
    - titleMouseListener
```
java.awt.event.MouseListener titleMouseListener
```
      reacts to single and double click on title bar
    - actionListener
```
java.awt.event.ActionListener actionListener
```
- Class pub.vlsolutions.swing.docking.DockViewAsTab.TabHeader extends javax.swing.JTabbedPane implements Serializable
- Class pub.vlsolutions.swing.docking.DockViewTitleBar extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - titleLabel
```
javax.swing.JLabel titleLabel
```
    - sortButton
```
javax.swing.JToggleButton sortButton
```
    - helpButton
```
javax.swing.JButton helpButton
```
    - closeButton
```
javax.swing.JButton closeButton
```
    - dockButton
```
javax.swing.JButton dockButton
```
    - maximizeButton
```
javax.swing.JButton maximizeButton
```
    - floatButton
```
javax.swing.JButton floatButton
```
    - active
```
boolean active
```
    - actionListener
```
java.awt.event.ActionListener actionListener
```
    - target
```
Dockable target
```
    - isNotification
```
boolean isNotification
```
      used to have a state of blinking (notification)
    - currentPopUp
```
javax.swing.JPopupMenu currentPopUp
```
    - blinkCount
```
int blinkCount
```
      current blinking count (the limit to the notification timer)
    - MAX_BLINKS
```
int MAX_BLINKS
```
    - titleMouseListener
```
java.awt.event.MouseListener titleMouseListener
```
      reacts to single and double click on title bar
    - dockKeyListener
```
java.beans.PropertyChangeListener dockKeyListener
```
      listen to the key changes
    - notificationTimer
```
javax.swing.Timer notificationTimer
```
      Timer used to trigger repaint event for notification (blinking title bar)
    - desktop
```
DockingDesktop desktop
```
- Class pub.vlsolutions.swing.docking.DragControlerGlassPane extends javax.swing.JComponent implements Serializable
  - Serialized Fields
    - stopDragCursor
```
java.awt.Cursor stopDragCursor
```
    - dragCursor
```
java.awt.Cursor dragCursor
```
    - floatCursor
```
java.awt.Cursor floatCursor
```
    - swapDragCursor
```
java.awt.Cursor swapDragCursor
```
    - innerColor
```
java.awt.Color innerColor
```
    - textColor
```
java.awt.Color textColor
```
    - textFillColor
```
java.awt.Color textFillColor
```
    - textBorderColor
```
java.awt.Color textBorderColor
```
    - paintShapes
```
boolean paintShapes
```
    - labelPainter
```
pub.vlsolutions.swing.docking.DragControlerGlassPane.ShapeLabelPainter labelPainter
```
    - outlinePainer
```
pub.vlsolutions.swing.docking.ShapeOutlinePainter outlinePainer
```
    - controler
```
DragControler controler
```
- Class pub.vlsolutions.swing.docking.FloatingDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - titleHeight
```
int titleHeight
```
      the drag header height
    - activeCaptionColor
```
java.awt.Color activeCaptionColor
```
    - inactiveCaptionColor
```
java.awt.Color inactiveCaptionColor
```
    - activeCaptionBorderColor
```
java.awt.Color activeCaptionBorderColor
```
    - inactiveCaptionBorderColor
```
java.awt.Color inactiveCaptionBorderColor
```
    - activeBorder
```
javax.swing.border.Border activeBorder
```
    - inactiveBorder
```
javax.swing.border.Border inactiveBorder
```
    - title
```
javax.swing.JComponent title
```
    - left
```
FloatingDialog.Resizer left
```
    - right
```
FloatingDialog.Resizer right
```
    - bottom
```
FloatingDialog.Resizer bottom
```
    - desktop
```
DockingDesktop desktop
```
- Class pub.vlsolutions.swing.docking.FloatingDialog.Resizer extends javax.swing.JComponent implements Serializable
- Class pub.vlsolutions.swing.docking.FloatingDialog.TitlePanel extends javax.swing.JComponent implements Serializable
- Class pub.vlsolutions.swing.docking.MaximizedDockView extends DockView implements Serializable
- Class pub.vlsolutions.swing.docking.MaximizedDockViewAsTab extends DockViewAsTab implements Serializable
- Class pub.vlsolutions.swing.docking.MaximizedDockViewAsTab.MaximizedTabHeader extends DockViewAsTab.TabHeader implements Serializable
- Class pub.vlsolutions.swing.docking.SplitContainer extends javax.swing.JSplitPane implements Serializable
  - Serialized Fields
    - isPainted
```
boolean isPainted
```
    - hasProportionalLocation
```
boolean hasProportionalLocation
```
    - proportionalLocation
```
double proportionalLocation
```
- Class pub.vlsolutions.swing.docking.TabbedDockView extends DockView implements Serializable
Package pub.vlsolutions.swing.docking.ws
- Class pub.vlsolutions.swing.docking.ws.WorkspaceButton extends javax.swing.JButton implements Serializable
  - Serialized Fields
    - workspace
```
Workspace workspace
```
    - ctx
```
DockingContext ctx
```
    - actionListener
```
java.awt.event.ActionListener actionListener
```
- Class pub.vlsolutions.swing.docking.ws.WorkspaceException extends java.lang.Exception implements Serializable
- Class pub.vlsolutions.swing.docking.ws.WorkspaceMenuItem extends javax.swing.JMenuItem implements Serializable
  - Serialized Fields
    - workspace
```
Workspace workspace
```
    - ctx
```
DockingContext ctx
```
    - actionListener
```
java.awt.event.ActionListener actionListener
```
Package pub.vlsolutions.swing.toolbars
- Class pub.vlsolutions.swing.toolbars.ToolBarContainer extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - componentsByContraints
```
java.util.Map<K,V> componentsByContraints
```
    - contraintsByComponents
```
java.util.Map<K,V> contraintsByComponents
```
    - toolBarsByName
```
java.util.Map<K,V> toolBarsByName
```
- Class pub.vlsolutions.swing.toolbars.ToolBarGripper extends javax.swing.JComponent implements Serializable
  - Serialized Fields
    - orientation
```
int orientation
```
    - collapsible
```
boolean collapsible
```
    - collapsed
```
boolean collapsed
```
- Class pub.vlsolutions.swing.toolbars.ToolBarPanel extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - orientation
```
int orientation
```
    - painter
```
BackgroundPainter painter
```
      an optionnal background painter
- Class pub.vlsolutions.swing.toolbars.VLToolBar extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - gripper
```
ToolBarGripper gripper
```
    - rolloverBorderPainted
```
boolean rolloverBorderPainted
```
    - rolloverContentAreaFilled
```
boolean rolloverContentAreaFilled
```
    - useCustomUI
```
boolean useCustomUI
```
    - orientation
```
int orientation
```
    - buttonMouseHandler
```
java.awt.event.MouseListener buttonMouseHandler
```
    - gripperListener
```
pub.vlsolutions.swing.toolbars.VLToolBar.GripperHandler gripperListener
```
      The mouse listener in charge for toolbar drag and drop
    - draggedBorder
```
javax.swing.border.Border draggedBorder
```
      The border used during DnD to show that the toolbar is selected
    - horizontalLayout
```
VLToolBarLayout horizontalLayout
```
    - verticalLayout
```
VLToolBarLayout verticalLayout
```
    - isInAnimationCycle
```
boolean isInAnimationCycle
```

Serialized Form

Package com.pacbio.secondary.vis.common.utils

Class com.pacbio.secondary.vis.common.utils.PropertiesHelper extends java.lang.Object implements Serializable

Serialized Fields

appVisualFilter

useTableViewFilter

alwaysShowMemoryInfo

fitGenomicTableToPanel

lockGenomeRegionPanels

lockRegionDetailsPanels

viewSubReadsData

lockRangeExpand

useLogScaling

Package com.pacbio.secondary.vis.common.utils.constants

Class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette extends java.lang.Object implements Serializable

Serialized Fields

EpiProReadsPalettes

Class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.ColorInfo extends java.lang.Object implements Serializable

Serialized Fields

start

end

Class com.pacbio.secondary.vis.common.utils.constants.EpiProPalette.EpiProContigPalette extends java.lang.Object implements Serializable

Serialized Fields

contig_start

contig_end

contig_length

color_info

Package com.pacbio.secondary.vis.common.utils.exception

Class com.pacbio.secondary.vis.common.utils.exception.FileFormatException extends java.lang.Exception implements Serializable

Class com.pacbio.secondary.vis.common.utils.exception.InsertNodeException extends IntervalTreeException implements Serializable

Class com.pacbio.secondary.vis.common.utils.exception.IntervalTreeException extends java.lang.Exception implements Serializable

Package com.pacbio.secondary.vis.data.db

Class com.pacbio.secondary.vis.data.db.IdeogramDB extends java.lang.Object implements Serializable

Serialized Fields

num_contigs

tree

isAutoGenerated

autoIdeogramUsesFixedNumBands

autoIdeogramNumBands

autoIdeogramBandSize

Package com.pacbio.secondary.vis.data.graph

Class com.pacbio.secondary.vis.data.graph.GraphPrimitive extends java.lang.Object implements Serializable

Serialized Fields

nodes

Class com.pacbio.secondary.vis.data.graph.GraphStructure extends java.lang.Object implements Serializable

Serialized Fields

type

primitives

Package com.pacbio.secondary.vis.data.session

Class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage extends java.lang.Object implements Serializable

Serialization Methods

readObject

writeObject

Serialized Fields

regions

session_id

Class com.pacbio.secondary.vis.data.session.RegionsOfInterestStorage.RegionOfInterest extends java.lang.Object implements Serializable

Serialized Fields

image

workspace

session

timestamp

info

user_data

Class com.pacbio.secondary.vis.data.session.SessionDataHelper extends java.lang.Object implements Serializable

Serialization Methods

readObject

writeObject

Serialized Fields

details_options

app_options

currentContig

num_tracks

region_interval

details_interval

view_intervals

slots_colors

slots_max_values

details_tracks_height

region_tracks_height