public class MakeCanonicalView
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
java.util.Vector<java.lang.String> |
aliasesToKeep |
SbmlDocument |
cd |
java.lang.String |
fileNameGeneList |
java.lang.String |
fileNameIn |
java.lang.String |
fileNameOut |
java.lang.String |
fileNameReactionsToKeep |
java.lang.String |
fileNameReferenceGraph |
java.lang.String |
fileNameSpeciesToKeep |
int |
fontSize |
java.util.HashSet<java.lang.String> |
foundEntities |
java.util.HashSet<java.lang.String> |
foundGenes |
java.util.Vector<java.lang.String> |
geneList |
java.util.Vector<java.lang.String> |
geneTypes |
GMTFile |
gmtFile |
boolean |
makenamelayer |
boolean |
makesubmap |
java.util.HashSet<java.lang.String> |
mappedEntities |
java.util.HashMap<java.lang.String,java.lang.String> |
nameType |
Graph |
reactionGraph |
Graph |
referenceGraph |
int |
scale |
boolean |
select |
java.util.Vector<java.lang.String> |
selectedIds |
Constructor and Description |
---|
MakeCanonicalView() |
Modifier and Type | Method and Description |
---|---|
void |
detectSimpleSpeciesFromGeneList() |
void |
loadCellDesigner() |
void |
loadGeneList() |
void |
loadReactions() |
void |
loadReferenceGraph() |
void |
loadSpecies() |
static void |
main(java.lang.String[] args) |
void |
makeGMTEntityHUGO() |
void |
makeNameLayer() |
void |
makeNameLayerImage(java.util.Vector<java.lang.String> geneIds,
java.util.HashMap<java.lang.String,java.lang.String> nameType) |
void |
makeReactionGraph() |
void |
makeSubMap() |
void |
saveCellDesigner() |
void |
selectSpeciesAndReactions() |
public java.lang.String fileNameIn
public java.lang.String fileNameOut
public java.lang.String fileNameReferenceGraph
public java.lang.String fileNameSpeciesToKeep
public java.lang.String fileNameReactionsToKeep
public java.lang.String fileNameGeneList
public Graph reactionGraph
public Graph referenceGraph
public GMTFile gmtFile
public boolean select
public boolean makenamelayer
public boolean makesubmap
public SbmlDocument cd
public int fontSize
public int scale
public java.util.Vector<java.lang.String> geneList
public java.util.Vector<java.lang.String> geneTypes
public java.util.Vector<java.lang.String> aliasesToKeep
public java.util.Vector<java.lang.String> selectedIds
public java.util.HashMap<java.lang.String,java.lang.String> nameType
public java.util.HashSet<java.lang.String> foundGenes
public java.util.HashSet<java.lang.String> foundEntities
public java.util.HashSet<java.lang.String> mappedEntities
public static void main(java.lang.String[] args)
public void loadCellDesigner()
public void loadSpecies()
public void makeReactionGraph()
public void makeGMTEntityHUGO()
public void loadReactions()
public void saveCellDesigner()
public void selectSpeciesAndReactions()
public void detectSimpleSpeciesFromGeneList()
public void makeNameLayer()
public void makeNameLayerImage(java.util.Vector<java.lang.String> geneIds, java.util.HashMap<java.lang.String,java.lang.String> nameType)
public void makeSubMap()
public void loadGeneList()
public void loadReferenceGraph()