public interface EscherOptions
extends de.zbit.util.prefs.KeyProvider
Modifier and Type | Interface and Description |
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static class |
EscherOptions.InputFormat
Enumeration of allowable input file formats.
|
static class |
EscherOptions.OutputFormat
Enumeration of allowable output file formats.
|
Modifier and Type | Field and Description |
---|---|
static java.util.ResourceBundle |
bundle
Localization support.
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static de.zbit.util.prefs.Option<java.lang.Double> |
CANVAS_DEFAULT_HEIGHT
Just as in the case of the width of the canvas, this value needs to be
specified for cases where the JSON input file lacks an explicit
specification of the canvas height.
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static de.zbit.util.prefs.Option<java.lang.Double> |
CANVAS_DEFAULT_WIDTH
This value is used when no width has been defined for the canvas.
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static de.zbit.util.prefs.Option<java.lang.Boolean> |
COMBINE
Whether to combine layouts of an SBML file, if more than one.
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static de.zbit.util.prefs.Option<java.lang.String> |
COMPARTMENT_ID
A compartment needs to have a unique identifier, which needs to be a
machine-readable Sting that must start with a letter or underscore and
can only contain ASCII characters.
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static de.zbit.util.prefs.Option<java.lang.String> |
COMPARTMENT_NAME
With this option it is possible to define a name for the default
compartment can be that needs to be generated for the conversion to SBML.
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static de.zbit.util.prefs.Option<java.lang.Boolean> |
EXTRACT_COBRA
Whether to extract CoBRA model, if FBC present on SBML file.
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static de.zbit.util.prefs.Option<EscherOptions.OutputFormat> |
FORMAT
The desired format for the conversion, e.g., SBML.
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static de.zbit.util.prefs.OptionGroup<?> |
GROUP_LAYOUT
The options in this group allow you to influence how large certain
elements should be displayed.
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static de.zbit.util.prefs.OptionGroup<?> |
GROUP_NAMING
Here you can influence how elements in the layout are called or
identified.
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static de.zbit.util.prefs.Option<java.lang.Boolean> |
INFER_COMPARTMENT_BOUNDS
This converter can infer where the boundaries of compartments could be
drawn.
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static de.zbit.util.prefs.Option<java.lang.Double> |
LABEL_HEIGHT
With this option you can specify the height of the bounding box of text
labels.
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static de.zbit.util.prefs.Option<java.lang.Double> |
LABEL_WIDTH
This option defines the width of bounding boxes for text labels.
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static de.zbit.util.prefs.Option<java.lang.String> |
LAYOUT_ID
In contrast to the name, this identifier does not have to be
human-readable.
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static de.zbit.util.prefs.Option<java.lang.String> |
LAYOUT_NAME
This should be a human-readable name for the layout that is to be
created.
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static de.zbit.util.prefs.Option<java.lang.Double> |
NODE_DEPTH
The length of nodes along z-coordinate.
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static de.zbit.util.prefs.Option<java.lang.Double> |
NODE_LABEL_HEIGHT
Node labels can have a size different from general labels in the graph.
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static de.zbit.util.prefs.Option<java.lang.Double> |
PRIMARY_NODE_HEIGHT
The primary node should be bigger than the secondary node.
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static de.zbit.util.prefs.Option<java.lang.Double> |
PRIMARY_NODE_WIDTH
Escher maps distinguish between primary and secondary nodes.
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static de.zbit.util.prefs.Option<java.lang.Double> |
REACTION_LABEL_HEIGHT
This option allows you to specify the height of labels for reactions.
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static de.zbit.util.prefs.Option<java.lang.Double> |
REACTION_NODE_RATIO
This value is used as a conversion factor to determine the size of the
reaction display box depending on the size of primary nodes.
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static de.zbit.util.prefs.Range<EscherOptions.OutputFormat> |
SBML_CONDITION
Helper constant for internal use.
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static de.zbit.util.prefs.Option<java.lang.Double> |
SECONDARY_NODE_RATIO
Similar to the reaction node ratio, the size of secondary nodes (width
and height) is determined by dividing the corresponding values from the
primary nodes by this value.
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static de.zbit.util.prefs.Option<java.lang.Double> |
Z
The position on the z-axis where the entire two-dimensional graph should
be drawn.
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static final de.zbit.util.prefs.Range<EscherOptions.OutputFormat> SBML_CONDITION
static final java.util.ResourceBundle bundle
static final de.zbit.util.prefs.Option<java.lang.Boolean> INFER_COMPARTMENT_BOUNDS
static final de.zbit.util.prefs.Option<EscherOptions.OutputFormat> FORMAT
static final de.zbit.util.prefs.Option<java.lang.Boolean> COMBINE
static final de.zbit.util.prefs.Option<java.lang.Boolean> EXTRACT_COBRA
static final de.zbit.util.prefs.Option<java.lang.Double> CANVAS_DEFAULT_WIDTH
static final de.zbit.util.prefs.Option<java.lang.Double> CANVAS_DEFAULT_HEIGHT
static final de.zbit.util.prefs.Option<java.lang.String> COMPARTMENT_ID
static final de.zbit.util.prefs.Option<java.lang.String> COMPARTMENT_NAME
static final de.zbit.util.prefs.Option<java.lang.String> LAYOUT_NAME
static final de.zbit.util.prefs.Option<java.lang.String> LAYOUT_ID
static final de.zbit.util.prefs.Option<java.lang.Double> LABEL_WIDTH
static final de.zbit.util.prefs.Option<java.lang.Double> LABEL_HEIGHT
static final de.zbit.util.prefs.Option<java.lang.Double> NODE_DEPTH
static final de.zbit.util.prefs.Option<java.lang.Double> Z
static final de.zbit.util.prefs.Option<java.lang.Double> NODE_LABEL_HEIGHT
static final de.zbit.util.prefs.Option<java.lang.Double> REACTION_LABEL_HEIGHT
static final de.zbit.util.prefs.Option<java.lang.Double> PRIMARY_NODE_WIDTH
static final de.zbit.util.prefs.Option<java.lang.Double> PRIMARY_NODE_HEIGHT
static final de.zbit.util.prefs.Option<java.lang.Double> REACTION_NODE_RATIO
static final de.zbit.util.prefs.Option<java.lang.Double> SECONDARY_NODE_RATIO
static final de.zbit.util.prefs.OptionGroup<?> GROUP_LAYOUT
static final de.zbit.util.prefs.OptionGroup<?> GROUP_NAMING