info.bioinfweb.libralign.model.factory

Class NewAlignmentModelParameterMap

java.lang.Object

java.util.AbstractMap<K,V>

java.util.TreeMap<java.lang.String,java.lang.Object>

info.bioinfweb.commons.collections.ParameterMap

info.bioinfweb.libralign.model.factory.NewAlignmentModelParameterMap

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.util.Map<java.lang.String,java.lang.Object>, java.util.NavigableMap<java.lang.String,java.lang.Object>, java.util.SortedMap<java.lang.String,java.lang.Object>

public class NewAlignmentModelParameterMap
extends ParameterMap

Parameter map that stores information used to create new instances of alignment models by implementations of AlignmentModelFactory.

Since:

0.4.0

Author:

Ben Stöver

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class java.util.AbstractMap

java.util.AbstractMap.SimpleEntry<K,V>, java.util.AbstractMap.SimpleImmutableEntry<K,V>

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	KEY_ALIGNMENT_ID Key used to store the ID of the alignment model to be created.
static java.lang.String	KEY_ALIGNMENT_LABEL Key used to store the label of the alignment model to be created.
static java.lang.String	KEY_CHARACTER_STATE_COUNT Key used to store an Integer or Long value defining the maximum number of states to be supported by the new model.
static java.lang.String	KEY_CHARACTER_STATE_SET_TYPE Key used to store the return value of getCharacterStateSetType().
static java.lang.String	KEY_DEFINED_TOKENS Key used to store the return value of getDefinedTokens().
static java.lang.String	KEY_END_INDEX Key used to store the first column index after the end of the model to be created in its parent concatenated alignment model.
static java.lang.String	KEY_IS_PART_MODEL Key used to store a Boolean value defining whether the model to be created will be part of a concatenated alignment model.
static java.lang.String	KEY_PREFIX The prefix of predefined keys used in this map.
static java.lang.String	KEY_START_INDEX Key used to store the first column index of the model to be created in its parent concatenated alignment model.

Constructor Summary

Constructors

Constructor and Description
NewAlignmentModelParameterMap()

Method Summary

Modifier and Type	Method and Description
CharacterStateSetType	getCharacterStateSetType() Returns the character set type the alignment model to be created shall have.
java.util.List<TokenDefinition>	getDefinedTokens() Returns a list of defined Tokens (e.g.
void	setCharacterStateSetType(CharacterStateSetType type) Sets or replaces the character set type in this map.

Methods inherited from class info.bioinfweb.commons.collections.ParameterMap

getApplicationLogger, getApplicationLogger, getBoolean, getDouble, getFile, getFile, getFloat, getInteger, getLong, getObject, getObject, getString, getString

Methods inherited from class java.util.TreeMap

ceilingEntry, ceilingKey, clear, clone, comparator, containsKey, containsValue, descendingKeySet, descendingMap, entrySet, firstEntry, firstKey, floorEntry, floorKey, forEach, get, headMap, headMap, higherEntry, higherKey, keySet, lastEntry, lastKey, lowerEntry, lowerKey, navigableKeySet, pollFirstEntry, pollLastEntry, put, putAll, remove, replace, replace, replaceAll, size, subMap, subMap, tailMap, tailMap, values

Methods inherited from class java.util.AbstractMap

equals, hashCode, isEmpty, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Map

compute, computeIfAbsent, computeIfPresent, equals, getOrDefault, hashCode, isEmpty, merge, putIfAbsent, remove

Field Detail

KEY_PREFIX

public static final java.lang.String KEY_PREFIX

The prefix of predefined keys used in this map.

See Also:

Constant Field Values

KEY_ALIGNMENT_ID

public static final java.lang.String KEY_ALIGNMENT_ID

Key used to store the ID of the alignment model to be created.

See Also:

Constant Field Values

KEY_ALIGNMENT_LABEL

public static final java.lang.String KEY_ALIGNMENT_LABEL

Key used to store the label of the alignment model to be created.

See Also:

Constant Field Values

KEY_CHARACTER_STATE_SET_TYPE

public static final java.lang.String KEY_CHARACTER_STATE_SET_TYPE

Key used to store the return value of getCharacterStateSetType().

See Also:

Constant Field Values

KEY_DEFINED_TOKENS

public static final java.lang.String KEY_DEFINED_TOKENS

Key used to store the return value of getDefinedTokens().

See Also:

Constant Field Values

KEY_CHARACTER_STATE_COUNT

public static final java.lang.String KEY_CHARACTER_STATE_COUNT

Key used to store an Integer or Long value defining the maximum number of states to be supported by the new model.

See Also:

Constant Field Values

KEY_IS_PART_MODEL

public static final java.lang.String KEY_IS_PART_MODEL

Key used to store a Boolean value defining whether the model to be created will be part of a concatenated alignment model.

This key is currently not in use, but is already defined for future support of concatenated alignment models.

See Also:

Constant Field Values

KEY_START_INDEX

public static final java.lang.String KEY_START_INDEX

Key used to store the first column index of the model to be created in its parent concatenated alignment model.

This key is currently not in use, but is already defined for future support of concatenated alignment models.

See Also:

Constant Field Values

KEY_END_INDEX

public static final java.lang.String KEY_END_INDEX

Key used to store the first column index after the end of the model to be created in its parent concatenated alignment model.

This key is currently not in use, but is already defined for future support of concatenated alignment models.

See Also:

Constant Field Values

Constructor Detail

NewAlignmentModelParameterMap

public NewAlignmentModelParameterMap()

Method Detail

getCharacterStateSetType

public CharacterStateSetType getCharacterStateSetType()

Returns the character set type the alignment model to be created shall have.

Returns:

the character set type (TokenSetType#UNKNOWN is also returned if no value is stored for the key #KEY_CHARACTER_SET_TYPE in this instance.)

setCharacterStateSetType

public void setCharacterStateSetType(CharacterStateSetType type)

Sets or replaces the character set type in this map.

Parameters:

type - the character set type the alignment model to be created shall have

getDefinedTokens

public java.util.List<TokenDefinition> getDefinedTokens()

Returns a list of defined Tokens (e.g. for gaps or unknown characters).

After calling this method, it is guaranteed that this maps contains an list to KEY_DEFINED_TOKENS which is returned. The returned list may be modified.

Returns:

the list of according single token definition events (Maybe empty but is never null.)