DetailsOptions (SMRT View)

java.lang.Object
- com.pacbio.secondary.vis.data.session.options.DetailsOptions

All Implemented Interfaces:: java.io.Serializable

public class DetailsOptions
extends java.lang.Object
implements java.io.Serializable

See Also:: Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`protected int`	`coverage_filter_value`
`static int`	`DEFAULT_DNA_FONT_HEIGTH`
`static int`	`DEFAULT_DNA_LETTER_TRACK_PIXELS`
`protected static int`	`DEFAULT_IPD_CONSENSUS_TRACK_HEIGHT`
`static int`	`DEFAULT_LANE_OFFSET_PIXELS`
`static int`	`DEFAULT_LANE_OFFSET_PIXELS_GRAPHS`
`protected int`	`details_coarse_mode`
`protected int`	`details_metrics_mode`
`protected int`	`details_range_mode`
`protected int`	`details_view_separator`
`static int`	`DNA_BASE_LETTER_EXTRA_PADDING`
`static int`	`DNA_BASE_RECTANGLE_EXTRA_PADDING`
`protected int`	`dna_char_height`
`protected int`	`dna_char_width`
`protected java.awt.Font`	`dna_font`
`static int`	`DNA_LETTER_TRACK_PADDING`
`protected boolean`	`enable_graph_structure`
`protected int`	`font_height`
`protected int`	`graph_structure_type`
`protected double`	`high_kin_threshold`
`protected int`	`high_qv_threshold`
`protected int`	`ipdconsensus_track_height`
`protected int`	`kinetics_scaling`
`static int`	`LANE_OFFSET_PIXELS`
`protected double`	`low_kin_threshold`
`protected int`	`low_qv_threshold`
`protected int`	`max_details_coverage`
`protected int`	`max_details_view_coverage`
`protected int`	`max_details_view_ordinate`
`protected static int`	`MAX_DNA_FONT_HEIGHT`
`protected int`	`max_dynamic_range`
`protected int`	`max_fixed_range`
`protected static int`	`MAX_IPD_CONSENSUS_TRACK_HEIGHT`
`protected static int`	`min_coverage_no_structures`
`protected static int`	`min_coverage_with_structures`
`protected static int`	`MIN_DNA_FONT_HEIGHT`
`protected static int`	`MIN_IPD_CONSENSUS_TRACK_HEIGHT`
`protected int`	`mods_filter_threshold`
`protected static long`	`serialVersionUID`
`protected boolean`	`show_graph_structure_only`
`protected boolean`	`show_tooltips`
`protected boolean`	`use_epipro_cutoff_filter`
`protected int`	`use_epipro_cutoff_threshold`
`protected int`	`use_epipro_mode`
`protected boolean`	`use_epipro_only_reads`
`protected boolean`	`use_events_coverage_filter`
`protected boolean`	`use_local_autoscale`
`protected boolean`	`use_mapqv_filter`
`protected boolean`	`use_mods_filter`
`protected boolean`	`use_monochrome_kinetic_palette`
`protected boolean`	`use_qv_filter`
`protected boolean`	`use_variants_confidence_filter`
`protected int`	`variants_filter_threshold`

Constructor Summary

Constructors
Modifier Constructor and Description

protected DetailsOptions()
de-serialization only

DetailsOptions(javax.swing.JComponent comp)

Constructors
Modifier	Constructor and Description
`protected`	`DetailsOptions()` de-serialization only
	`DetailsOptions(javax.swing.JComponent comp)`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`changeDNAFontSize(boolean bIncrement)`
`void`	`changeIPDConsensusHeight(boolean bIncrement)`
`int`	`getCoarseMode()`
`int`	`getDetails_view_separator()`
`int`	`getDetailsMetricsMode()`
`int`	`getDetailsRangeMode()`
`int`	`getDna_char_height()`
`int`	`getDna_char_width()`
`java.awt.Font`	`getDna_font()`
`boolean`	`getEnableGraphStructure()`
`int`	`getEventsCoverageFilterThreshold()`
`int`	`getGraphStructureType()`
`double`	`getHigh_kin_threshold()`
`double`	`getHigh_qv_threshold()`
`int`	`getIpdconsensus_track_height()`
`int`	`getKineticsScaling()`
`double`	`getLow_kin_threshold()`
`double`	`getLow_qv_threshold()`
`int`	`getMax_details_coverage()`
`int`	`getMax_details_view_coverage()`
`int`	`getMax_details_view_ordinate()`
`int`	`getMax_dynamic_range()`
`int`	`getMax_fixed_range()`
`int`	`getMaxDetailsViewRange()` Returns max genomic range of details view based on user options and max data coverage
`protected int`	`getMinCoverage()`
`int`	`getModsFilterThreshold()`
`boolean`	`getShowGraphStructureOnly()`
`boolean`	`getShowTooltips()`
`int`	`getUnmappedReadsCutoffThreshold()`
`int`	`getUseEpiProReadsMode()`
`boolean`	`getUseEpiProReadsOnly()`
`boolean`	`getUseEventsCoverageFilter()`
`boolean`	`getUseMapQVFilter()`
`boolean`	`getUseModsFilter()`
`boolean`	`getUseQVFilter()`
`boolean`	`getUseUnmappedReadsCutoffFilter()`
`boolean`	`getUseVariantsConfidenceFilter()`
`int`	`getVariantsConfFilterThreshold()`
`void`	`initDNAFont(javax.swing.JComponent comp)`
`static void`	`main(java.lang.String[] args)`
`void`	`readDetailsOptionsFromPropertiesFile()`
`void`	`setCoarseMode(int value)`
`void`	`setDetails_view_separator(int details_view_separator)`
`void`	`setDetailsMetricsMode(int value)`
`void`	`setDetailsRangeMode(int mode)`
`void`	`setDna_char_height(int dnaCharHeight)`
`void`	`setDna_font(java.awt.Font dnaFont)`
`void`	`setEnableGraphStructure(boolean b)`
`void`	`setEventsCoverageFilterThreshold(int coverageFilterValue)`
`void`	`setGraphStructureType(int n)`
`void`	`setHigh_kin_threshold(double highKinThreshold)`
`void`	`setHigh_qv_threshold(double highQvThreshold)`
`void`	`setIpdconsensus_track_height(int ipdconsensusTrackHeight)`
`void`	`setKineticsScaling(int value)`
`void`	`setLow_kin_threshold(double lowKinThreshold)`
`void`	`setLow_qv_threshold(double lowQvThreshold)`
`void`	`setMax_details_coverage(int max_details_coverage)`
`void`	`setMax_details_view_ordinate(int maxDetailsViewOrdinate)`
`void`	`setMax_dynamic_range(int max_dynamic_range)`
`void`	`setMax_fixed_range(int max_fixed_range)`
`void`	`setMaxSummaryCoverage(int max_coverage)` Called after summary file is first loaded (if available) to set max.
`void`	`setModsFilterThreshold(int value)`
`void`	`setShowGraphStructureOnly(boolean b)`
`void`	`setShowTooltips(boolean bShowTooltips)`
`void`	`setUnmappedReadsCutoffThreshold(int v)`
`void`	`setUseEpiProReadsMode(int b)`
`void`	`setUseEpiProReadsOnly(boolean b)`
`void`	`setUseEventsCoverageFilter(boolean bUseVariantsCoverageFilter)`
`void`	`setUseMapQVFilter(boolean bUseMapQVFilter)`
`void`	`setUseModsFilter(boolean b)`
`void`	`setUseQVFilter(boolean bUseQVFilter)`
`void`	`setUseUnmappedReadsCutoffFilter(boolean b)`
`void`	`setUseVariantsConfidenceFilter(boolean bUseVariantsConfidenceFilter)`
`void`	`setVariantsConfFilterThreshold(int value)`
`java.lang.String`	`toString()`
`protected void`	`updateLaneOffset()`
`void`	`writeDetailsOptionsToPropertiesFile()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

serialVersionUID
```
protected static final long serialVersionUID
```
See Also:
Constant Field Values

DEFAULT_LANE_OFFSET_PIXELS

public static final transient int DEFAULT_LANE_OFFSET_PIXELS

See Also:: Constant Field Values

DEFAULT_LANE_OFFSET_PIXELS_GRAPHS

public static final transient int DEFAULT_LANE_OFFSET_PIXELS_GRAPHS

See Also:: Constant Field Values

DEFAULT_DNA_LETTER_TRACK_PIXELS

public static final transient int DEFAULT_DNA_LETTER_TRACK_PIXELS

See Also:: Constant Field Values

LANE_OFFSET_PIXELS

public static transient int LANE_OFFSET_PIXELS

DNA_LETTER_TRACK_PADDING

public static transient int DNA_LETTER_TRACK_PADDING

DNA_BASE_RECTANGLE_EXTRA_PADDING

public static final transient int DNA_BASE_RECTANGLE_EXTRA_PADDING

See Also:: Constant Field Values

DNA_BASE_LETTER_EXTRA_PADDING

public static final transient int DNA_BASE_LETTER_EXTRA_PADDING

See Also:: Constant Field Values

DEFAULT_DNA_FONT_HEIGTH

public static final transient int DEFAULT_DNA_FONT_HEIGTH

See Also:: Constant Field Values

MIN_DNA_FONT_HEIGHT

protected static final transient int MIN_DNA_FONT_HEIGHT

See Also:: Constant Field Values

MAX_DNA_FONT_HEIGHT

protected static final transient int MAX_DNA_FONT_HEIGHT

See Also:: Constant Field Values

DEFAULT_IPD_CONSENSUS_TRACK_HEIGHT

protected static final transient int DEFAULT_IPD_CONSENSUS_TRACK_HEIGHT

See Also:: Constant Field Values

MIN_IPD_CONSENSUS_TRACK_HEIGHT

protected static final transient int MIN_IPD_CONSENSUS_TRACK_HEIGHT

See Also:: Constant Field Values

MAX_IPD_CONSENSUS_TRACK_HEIGHT

protected static final transient int MAX_IPD_CONSENSUS_TRACK_HEIGHT

See Also:: Constant Field Values

min_coverage_no_structures

protected static final transient int min_coverage_no_structures

See Also:: Constant Field Values

min_coverage_with_structures

protected static final transient int min_coverage_with_structures

See Also:: Constant Field Values

max_details_view_coverage

protected int max_details_view_coverage

max_details_view_ordinate

protected int max_details_view_ordinate

details_view_separator
```
protected int details_view_separator
```

show_tooltips
```
protected boolean show_tooltips
```

max_fixed_range
```
protected int max_fixed_range
```

max_dynamic_range
```
protected int max_dynamic_range
```

details_range_mode
```
protected int details_range_mode
```

max_details_coverage
```
protected int max_details_coverage
```

use_qv_filter
```
protected boolean use_qv_filter
```

use_mapqv_filter
```
protected boolean use_mapqv_filter
```

low_qv_threshold
```
protected int low_qv_threshold
```

high_qv_threshold
```
protected int high_qv_threshold
```

use_events_coverage_filter

protected boolean use_events_coverage_filter

coverage_filter_value
```
protected int coverage_filter_value
```

use_epipro_mode
```
protected int use_epipro_mode
```

use_epipro_only_reads

protected boolean use_epipro_only_reads

use_epipro_cutoff_filter

protected boolean use_epipro_cutoff_filter

use_epipro_cutoff_threshold

protected int use_epipro_cutoff_threshold

use_variants_confidence_filter

protected boolean use_variants_confidence_filter

variants_filter_threshold

protected int variants_filter_threshold

details_metrics_mode
```
protected int details_metrics_mode
```

kinetics_scaling
```
protected int kinetics_scaling
```

details_coarse_mode
```
protected int details_coarse_mode
```

low_kin_threshold
```
protected double low_kin_threshold
```

high_kin_threshold
```
protected double high_kin_threshold
```

use_local_autoscale
```
protected boolean use_local_autoscale
```

use_monochrome_kinetic_palette

protected boolean use_monochrome_kinetic_palette

dna_font
```
protected java.awt.Font dna_font
```

dna_char_width
```
protected int dna_char_width
```

dna_char_height
```
protected int dna_char_height
```

font_height
```
protected int font_height
```

enable_graph_structure

protected boolean enable_graph_structure

show_graph_structure_only

protected boolean show_graph_structure_only

graph_structure_type
```
protected int graph_structure_type
```

use_mods_filter
```
protected boolean use_mods_filter
```

mods_filter_threshold
```
protected int mods_filter_threshold
```

ipdconsensus_track_height

protected int ipdconsensus_track_height

Constructor Detail

DetailsOptions

public DetailsOptions(javax.swing.JComponent comp)

DetailsOptions
```
protected DetailsOptions()
```
de-serialization only

Method Detail

changeDNAFontSize

public void changeDNAFontSize(boolean bIncrement)

changeIPDConsensusHeight

public void changeIPDConsensusHeight(boolean bIncrement)

initDNAFont

public void initDNAFont(javax.swing.JComponent comp)

updateLaneOffset
```
protected void updateLaneOffset()
```

getDna_font
```
public java.awt.Font getDna_font()
```

setDna_font

public void setDna_font(java.awt.Font dnaFont)

getDna_char_height
```
public int getDna_char_height()
```

setDna_char_height

public void setDna_char_height(int dnaCharHeight)

getIpdconsensus_track_height

public int getIpdconsensus_track_height()

setIpdconsensus_track_height

public void setIpdconsensus_track_height(int ipdconsensusTrackHeight)

getLow_qv_threshold
```
public double getLow_qv_threshold()
```

setLow_qv_threshold

public void setLow_qv_threshold(double lowQvThreshold)

getHigh_qv_threshold
```
public double getHigh_qv_threshold()
```

setHigh_qv_threshold

public void setHigh_qv_threshold(double highQvThreshold)

getLow_kin_threshold
```
public double getLow_kin_threshold()
```

setLow_kin_threshold

public void setLow_kin_threshold(double lowKinThreshold)

getHigh_kin_threshold
```
public double getHigh_kin_threshold()
```

setHigh_kin_threshold

public void setHigh_kin_threshold(double highKinThreshold)

getDna_char_width
```
public int getDna_char_width()
```

getEventsCoverageFilterThreshold

public int getEventsCoverageFilterThreshold()

setEventsCoverageFilterThreshold

public void setEventsCoverageFilterThreshold(int coverageFilterValue)

getUseEventsCoverageFilter

public boolean getUseEventsCoverageFilter()

setUseEventsCoverageFilter

public void setUseEventsCoverageFilter(boolean bUseVariantsCoverageFilter)

getUseEpiProReadsMode
```
public int getUseEpiProReadsMode()
```

setUseEpiProReadsMode

public void setUseEpiProReadsMode(int b)

getUseEpiProReadsOnly

public boolean getUseEpiProReadsOnly()

setUseEpiProReadsOnly

public void setUseEpiProReadsOnly(boolean b)

getUseUnmappedReadsCutoffFilter

public boolean getUseUnmappedReadsCutoffFilter()

setUseUnmappedReadsCutoffFilter

public void setUseUnmappedReadsCutoffFilter(boolean b)

getUnmappedReadsCutoffThreshold

public int getUnmappedReadsCutoffThreshold()

setUnmappedReadsCutoffThreshold

public void setUnmappedReadsCutoffThreshold(int v)

getUseQVFilter
```
public boolean getUseQVFilter()
```

getUseMapQVFilter
```
public boolean getUseMapQVFilter()
```

setUseQVFilter

public void setUseQVFilter(boolean bUseQVFilter)

setUseMapQVFilter

public void setUseMapQVFilter(boolean bUseMapQVFilter)

getVariantsConfFilterThreshold

public int getVariantsConfFilterThreshold()

setVariantsConfFilterThreshold

public void setVariantsConfFilterThreshold(int value)

getUseVariantsConfidenceFilter

public boolean getUseVariantsConfidenceFilter()

setUseVariantsConfidenceFilter

public void setUseVariantsConfidenceFilter(boolean bUseVariantsConfidenceFilter)

getModsFilterThreshold
```
public int getModsFilterThreshold()
```

setModsFilterThreshold

public void setModsFilterThreshold(int value)

getUseModsFilter
```
public boolean getUseModsFilter()
```

setUseModsFilter

public void setUseModsFilter(boolean b)

getShowTooltips
```
public boolean getShowTooltips()
```

setShowTooltips

public void setShowTooltips(boolean bShowTooltips)

getDetailsMetricsMode
```
public int getDetailsMetricsMode()
```

setDetailsMetricsMode

public void setDetailsMetricsMode(int value)

getKineticsScaling
```
public int getKineticsScaling()
```

setKineticsScaling

public void setKineticsScaling(int value)

getCoarseMode
```
public int getCoarseMode()
```

setCoarseMode
```
public void setCoarseMode(int value)
```

getMax_fixed_range
```
public int getMax_fixed_range()
```

setMax_fixed_range

public void setMax_fixed_range(int max_fixed_range)

getMax_dynamic_range
```
public int getMax_dynamic_range()
```

setMax_dynamic_range

public void setMax_dynamic_range(int max_dynamic_range)

getDetailsRangeMode
```
public int getDetailsRangeMode()
```

setDetailsRangeMode

public void setDetailsRangeMode(int mode)

getMax_details_coverage
```
public int getMax_details_coverage()
```

setMax_details_coverage

public void setMax_details_coverage(int max_details_coverage)

getMaxDetailsViewRange
```
public int getMaxDetailsViewRange()
```
Returns max genomic range of details view based on user options and max data coverage

setMaxSummaryCoverage
```
public void setMaxSummaryCoverage(int max_coverage)
```
Called after summary file is first loaded (if available) to set max. data coverage

Parameters:
max_coverage -

getMinCoverage
```
protected int getMinCoverage()
```

getMax_details_view_coverage

public int getMax_details_view_coverage()

getMax_details_view_ordinate

public int getMax_details_view_ordinate()

setMax_details_view_ordinate

public void setMax_details_view_ordinate(int maxDetailsViewOrdinate)

getDetails_view_separator

public int getDetails_view_separator()

setDetails_view_separator

public void setDetails_view_separator(int details_view_separator)

getEnableGraphStructure

public boolean getEnableGraphStructure()

setEnableGraphStructure

public void setEnableGraphStructure(boolean b)

getShowGraphStructureOnly

public boolean getShowGraphStructureOnly()

setShowGraphStructureOnly

public void setShowGraphStructureOnly(boolean b)

getGraphStructureType
```
public int getGraphStructureType()
```

setGraphStructureType

public void setGraphStructureType(int n)

toString
```
public java.lang.String toString()
```
Overrides:

toString in class java.lang.Object

writeDetailsOptionsToPropertiesFile

public void writeDetailsOptionsToPropertiesFile()

readDetailsOptionsFromPropertiesFile

public void readDetailsOptionsFromPropertiesFile()

main

public static void main(java.lang.String[] args)

Parameters:: args -

Class DetailsOptions

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

DEFAULT_LANE_OFFSET_PIXELS

DEFAULT_LANE_OFFSET_PIXELS_GRAPHS

DEFAULT_DNA_LETTER_TRACK_PIXELS

LANE_OFFSET_PIXELS

DNA_LETTER_TRACK_PADDING

DNA_BASE_RECTANGLE_EXTRA_PADDING

DNA_BASE_LETTER_EXTRA_PADDING

DEFAULT_DNA_FONT_HEIGTH

MIN_DNA_FONT_HEIGHT

MAX_DNA_FONT_HEIGHT

DEFAULT_IPD_CONSENSUS_TRACK_HEIGHT

MIN_IPD_CONSENSUS_TRACK_HEIGHT

MAX_IPD_CONSENSUS_TRACK_HEIGHT

min_coverage_no_structures

min_coverage_with_structures

max_details_view_coverage

max_details_view_ordinate

details_view_separator

show_tooltips

max_fixed_range

max_dynamic_range

details_range_mode

max_details_coverage

use_qv_filter

use_mapqv_filter

low_qv_threshold

high_qv_threshold

use_events_coverage_filter

coverage_filter_value

use_epipro_mode

use_epipro_only_reads

use_epipro_cutoff_filter

use_epipro_cutoff_threshold

use_variants_confidence_filter

variants_filter_threshold

details_metrics_mode

kinetics_scaling

details_coarse_mode

low_kin_threshold

high_kin_threshold

use_local_autoscale

use_monochrome_kinetic_palette

dna_font

dna_char_width

dna_char_height

font_height

enable_graph_structure

show_graph_structure_only

graph_structure_type

use_mods_filter

mods_filter_threshold

ipdconsensus_track_height

Constructor Detail

DetailsOptions

DetailsOptions

Method Detail

changeDNAFontSize

changeIPDConsensusHeight

initDNAFont

updateLaneOffset

getDna_font

setDna_font

getDna_char_height

setDna_char_height

getIpdconsensus_track_height

setIpdconsensus_track_height

getLow_qv_threshold

setLow_qv_threshold

getHigh_qv_threshold

setHigh_qv_threshold

getLow_kin_threshold

setLow_kin_threshold

getHigh_kin_threshold