public class EscherReaction extends AbstractEscherBase implements Element
Modifier and Type | Field and Description |
---|---|
static java.util.ResourceBundle |
bundle
Localization support.
|
Constructor and Description |
---|
EscherReaction()
Creates a new reaction object where all properties are initialized with
null values. |
EscherReaction(EscherReaction escherReaction) |
Modifier and Type | Method and Description |
---|---|
void |
addGene(Gene gene) |
void |
addMetabolite(Metabolite metabolite) |
void |
addSegment(Segment segment) |
EscherReaction |
clone() |
boolean |
contains(java.lang.String nodeId) |
boolean |
equals(java.lang.Object obj) |
Node |
findMidmarker(EscherMap map) |
java.lang.String |
getBiggId() |
int |
getGeneCount() |
java.util.List<Gene> |
getGeneList() |
java.lang.String |
getGeneReactionRule() |
java.util.Map<java.lang.String,Gene> |
getGenes() |
java.lang.String |
getId() |
java.lang.Double |
getLabelX() |
java.lang.Double |
getLabelY() |
Metabolite |
getMetabolite(java.lang.String biggId) |
int |
getMetaboliteCount() |
java.util.List<Metabolite> |
getMetaboliteList() |
java.util.Map<java.lang.String,Metabolite> |
getMetabolites()
Gives you the mapping between BiGG ids and the metabolites with that
BiGG id that participate in this reaction.
|
Node |
getMidmarker() |
java.lang.String |
getName() |
java.util.Set<java.lang.String> |
getNodes() |
java.lang.Boolean |
getReversibility() |
Segment |
getSegment(java.lang.String id) |
int |
getSegmentCount() |
java.util.Map<java.lang.String,Segment> |
getSegments() |
int |
hashCode() |
java.util.Set<Node> |
intersect(java.util.Set<Node> nodes) |
boolean |
isSetBiggId() |
boolean |
isSetGeneReactionRule() |
boolean |
isSetId() |
boolean |
isSetLabelX() |
boolean |
isSetLabelY() |
boolean |
isSetMidmarker() |
boolean |
isSetName() |
boolean |
isSetReversibility() |
Segment |
removeSegment(java.lang.String key) |
java.util.Set<java.util.Map.Entry<java.lang.String,Segment>> |
segments() |
void |
setBiggId(java.lang.String biggId) |
void |
setGeneList(java.util.List<Gene> geneList) |
void |
setGeneReactionRule(java.lang.String geneReactionRule) |
void |
setId(java.lang.String id) |
void |
setLabelX(java.lang.Double labelX) |
void |
setLabelY(java.lang.Double labelY) |
void |
setMetaboliteList(java.util.List<Metabolite> metaboliteList) |
void |
setMidmarker(Node midmarker) |
void |
setName(java.lang.String name) |
void |
setReversibility(java.lang.Boolean reversibility) |
void |
setSegments(java.util.Map<java.lang.String,Segment> segments) |
java.lang.String |
toString() |
getUserObject, putUserObject, userObjectEntrySet, userObjectKeys
finalize, getClass, notify, notifyAll, wait, wait, wait
getUserObject, putUserObject, userObjectEntrySet, userObjectKeys
public EscherReaction()
null
values.public EscherReaction(EscherReaction escherReaction)
escherReaction
- public void addGene(Gene gene)
gene
- public void addMetabolite(Metabolite metabolite)
metabolite
- public void addSegment(Segment segment)
segment
- public EscherReaction clone()
clone
in class AbstractEscherBase
public boolean contains(java.lang.String nodeId)
nodeId
- Set.contains(Object)
public boolean equals(java.lang.Object obj)
equals
in class AbstractEscherBase
public java.lang.String getBiggId()
public int getGeneCount()
public java.lang.String getGeneReactionRule()
public java.util.Map<java.lang.String,Gene> getGenes()
public java.util.List<Gene> getGeneList()
public java.lang.Double getLabelX()
public java.lang.Double getLabelY()
public Metabolite getMetabolite(java.lang.String biggId)
biggId
- public int getMetaboliteCount()
public java.util.Map<java.lang.String,Metabolite> getMetabolites()
public java.util.List<Metabolite> getMetaboliteList()
public Node getMidmarker()
public java.lang.String getName()
public java.lang.Boolean getReversibility()
public java.util.Map<java.lang.String,Segment> getSegments()
public Segment getSegment(java.lang.String id)
id
- public int getSegmentCount()
public java.util.Set<java.lang.String> getNodes()
public int hashCode()
hashCode
in class AbstractEscherBase
public java.util.Set<Node> intersect(java.util.Set<Node> nodes)
nodes
- public boolean isSetBiggId()
true
if the requested property is not null
.public boolean isSetGeneReactionRule()
public boolean isSetId()
public boolean isSetLabelX()
true
if the requested property is not null
.public boolean isSetLabelY()
true
if the requested property is not null
.public boolean isSetMidmarker()
public boolean isSetName()
true
if the requested property is not null
.public boolean isSetReversibility()
true
if the requested property is not null
.public Segment removeSegment(java.lang.String key)
key
- public java.util.Set<java.util.Map.Entry<java.lang.String,Segment>> segments()
public void setBiggId(java.lang.String biggId)
biggId
- the biggId to setpublic void setGeneReactionRule(java.lang.String geneReactionRule)
geneReactionRule
- the geneReactionRule to setpublic void setId(java.lang.String id)
public void setLabelX(java.lang.Double labelX)
labelX
- the labelX to setpublic void setLabelY(java.lang.Double labelY)
labelY
- the labelY to setpublic void setMidmarker(Node midmarker)
midmarker
- the midmarker to setpublic void setName(java.lang.String name)
name
- the name to setpublic void setReversibility(java.lang.Boolean reversibility)
reversibility
- the reversibility to setpublic void setGeneList(java.util.List<Gene> geneList)
public void setMetaboliteList(java.util.List<Metabolite> metaboliteList)
public void setSegments(java.util.Map<java.lang.String,Segment> segments)
public java.lang.String toString()
toString
in class java.lang.Object