public class CellDesignerToCytoscapeConverter
extends java.lang.Object
Modifier and Type | Class and Description |
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static class |
CellDesignerToCytoscapeConverter.Graph
Simple container for GraphDocument and SbmlDocument objects
|
Modifier and Type | Field and Description |
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static boolean |
addSuffixForMultipleAliases |
static boolean |
alwaysMentionCompartment
If checked, the compartment name will appear in all species names,
otherwide the compartment name will be omited for that compartment
containing majority of the species
|
CellDesigner |
celldesigner
Auxiliary BiNoM wrapper of CellDesigner
|
static java.util.Vector |
comp_ids |
static java.util.Vector |
comp_ids_n |
static java.util.HashMap<java.lang.String,CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias> |
complexSpeciesAliasIdMap |
static java.util.HashMap<java.lang.String,java.util.Vector<CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias>> |
complexSpeciesAliasMap |
static java.util.HashMap<java.lang.String,java.util.Vector<CelldesignerSpeciesDocument.CelldesignerSpecies>> |
complexSpeciesMap |
static java.lang.String |
defcomp_id |
static java.util.HashMap<java.lang.String,CelldesignerSpeciesDocument.CelldesignerSpecies> |
includedSpeciesMap |
static java.util.HashMap<java.lang.String,CelldesignerProteinDocument.CelldesignerProtein> |
proteinMap |
org.sbml.x2001.ns.celldesigner.SbmlDocument |
sbml
Java xml-beans mapping of CellDesigner file
|
static java.util.HashMap<java.lang.String,CelldesignerSpeciesAliasDocument.CelldesignerSpeciesAlias> |
speciesAliasIdMap |
static java.util.HashMap<java.lang.String,java.util.Vector<CelldesignerSpeciesAliasDocument.CelldesignerSpeciesAlias>> |
speciesAliasMap |
static java.util.HashMap<java.lang.String,SpeciesDocument.Species> |
speciesMap |
static java.util.HashMap |
takenaliases
Map from a key in the form reaction_id+"_"+species_alias_id
to ReactionDocument.Reaction object
|
Constructor and Description |
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CellDesignerToCytoscapeConverter() |
Modifier and Type | Method and Description |
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static java.lang.String |
checkAndModifyEntitiesIDs(SbmlDocument sb,
SbmlDocument sbbase) |
static java.lang.String |
checkAndModifySpeciesIDs(SbmlDocument sb,
SbmlDocument sbbase)
Utility function.
|
static CellDesignerToCytoscapeConverter.Graph |
convert(java.lang.String file)
Principal conversion function used from outside
|
static java.lang.String |
convertSpeciesToName(SbmlDocument.Sbml sbml,
java.lang.String speciesID,
boolean addCompartmentName,
boolean addModifications) |
static java.lang.String |
convertSpeciesToName(SbmlDocument.Sbml sbml,
java.lang.String speciesID,
boolean addCompartmentName,
boolean addModifications,
boolean uniqueName)
Generates a unique name for a species speciesID
|
static java.lang.String |
convertSpeciesToName(SbmlDocument.Sbml sbml,
java.lang.String speciesID,
boolean addCompartmentName,
boolean addModifications,
boolean uniqueName,
java.lang.String alias)
Generates a name for a species speciesID
|
static java.lang.String |
convertSpeciesToName(SbmlDocument sbmlDoc,
java.lang.String speciesID,
boolean addCompartmentName,
boolean addModifications)
Generates a unique name for a species speciesID
|
static java.lang.String |
convertSpeciesToName(SbmlDocument sbmlDoc,
java.lang.String speciesID,
boolean addCompartmentName,
boolean addModifications,
boolean uniqueName) |
static void |
createSpeciesMap(SbmlDocument.Sbml sbml) |
static java.util.Vector<java.util.Vector<java.lang.String>> |
extractAttributesFromNotes(CelldesignerNotes notes) |
static java.util.Vector<java.util.Vector<java.lang.String>> |
extractAttributesFromNotes(Notes notes) |
static java.util.Vector |
findAllAliasesForSpecies(SbmlDocument.Sbml sbml,
java.lang.String spid)
Finds all CellDesigner species aliases
|
static java.lang.String |
getCelldesignerSpeciesName(SbmlDocument.Sbml sbml,
java.lang.String speciesID) |
static java.lang.String |
getEntityId(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity spid) |
static java.lang.String |
getEntityName(java.lang.String spid,
CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity ident,
SbmlDocument.Sbml sbml) |
static java.lang.String |
getEntityName(java.lang.String spid,
CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity ident,
SbmlDocument sbmlDoc) |
static java.util.Vector |
getIncludedSpeciesInComplex(SbmlDocument.Sbml sbml,
java.lang.String complexid) |
static java.util.Vector |
getIncludedSpeciesInComplex(SbmlDocument sbmlDoc,
java.lang.String complexid) |
static java.lang.String |
getNameOfIncludedSpecies(SbmlDocument.Sbml sbml,
CelldesignerSpeciesDocument.CelldesignerSpecies sp,
java.lang.String alias) |
static java.lang.String |
getNameOfIncludedSpecies(SbmlDocument sbmlDoc,
CelldesignerSpeciesDocument.CelldesignerSpecies sp,
java.lang.String alias) |
static java.lang.String |
getNameOfModificationResidue(SbmlDocument.Sbml sbml,
CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity ident,
java.lang.String residueID) |
static java.lang.String |
getNameOfModificationResidue(SbmlDocument sbmlDoc,
CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity ident,
java.lang.String residueID) |
static java.util.Vector<CelldesignerProteinDocument.CelldesignerProtein> |
getProteinsInComplex(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml,
java.lang.String id) |
static java.lang.String |
getReactionString(ReactionDocument.Reaction r,
SbmlDocument sbmlDoc,
boolean realNames)
Function for printing the CellDesigner reactions
|
static java.util.HashMap |
getSpecies(SbmlDocument.Sbml sbml)
Creates the map from species id to SpeciesDocument.Species
|
static java.lang.String |
getSpeciesAliasInReaction(ReactionDocument.Reaction r,
java.lang.String id,
java.lang.String role)
Finds CellDesigner alias of species 'id' in the reation r
|
static java.lang.String |
getSpeciesName(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity spi,
java.lang.String sp_id,
java.lang.String sp_name,
java.lang.String compartment,
boolean addModifications,
boolean addCompartmentName,
java.lang.String defcomp_id,
SbmlDocument.Sbml sbml) |
static java.lang.String |
getSpeciesName(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity spi,
java.lang.String sp_id,
java.lang.String sp_name,
java.lang.String compartment,
boolean addModifications,
boolean addCompartmentName,
java.lang.String defcomp_id,
SbmlDocument.Sbml sbml,
java.lang.String alias) |
static java.lang.String |
getSpeciesName(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity spi,
java.lang.String sp_id,
java.lang.String sp_name,
java.lang.String compartment,
boolean addModifications,
boolean addCompartmentName,
java.lang.String defcomp_id,
SbmlDocument sbmlDoc) |
static java.lang.String |
getSuffixForMultipleAliases(SbmlDocument.Sbml sbml,
java.lang.String spid,
java.lang.String alias)
Axillary function, adds ' (prime) to Cytoscape node name to distinguish multiple CellDesigner species aliases
|
static GraphDocument |
getXGMMLGraph(java.lang.String name,
org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml)
The converter itself
|
static java.util.HashMap |
MapEntitiesId(SbmlDocument sbb) |
static java.util.HashMap |
MapSpeciesAliases(SbmlDocument sbb) |
static java.util.HashMap |
MapSpeciesId(SbmlDocument sbb) |
static void |
mergeCellDesignerFiles(SbmlDocument sbout,
SbmlDocument sbin)
Merges two CellDesigner SbmlDocuments, the result of merging is in sbout
|
static void |
setAveragePositionForXGMML(GraphicNode nod,
java.util.Vector nodes,
java.util.HashMap speciesNodes)
Place node 'nod' into the average of 'nodes' positions
|
static void |
setEntityId(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity spid,
java.lang.String id) |
static void |
setSpeciesPositionForXGMML(java.lang.String spalias,
GraphicNode nod,
SbmlDocument.Sbml sbml)
Reads the position information for a node from CellDesigner
|
static void |
substituteEntityId(SbmlDocument sb,
java.lang.String idold,
java.lang.String idnew) |
static void |
substituteSpeciesId(SbmlDocument sb,
java.lang.String idold,
java.lang.String idnew) |
public org.sbml.x2001.ns.celldesigner.SbmlDocument sbml
public CellDesigner celldesigner
public static java.util.HashMap takenaliases
public static boolean alwaysMentionCompartment
public static java.util.HashMap<java.lang.String,SpeciesDocument.Species> speciesMap
public static java.util.HashMap<java.lang.String,CelldesignerSpeciesDocument.CelldesignerSpecies> includedSpeciesMap
public static java.util.HashMap<java.lang.String,java.util.Vector<CelldesignerSpeciesDocument.CelldesignerSpecies>> complexSpeciesMap
public static java.util.HashMap<java.lang.String,java.util.Vector<CelldesignerSpeciesAliasDocument.CelldesignerSpeciesAlias>> speciesAliasMap
public static java.util.HashMap<java.lang.String,java.util.Vector<CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias>> complexSpeciesAliasMap
public static java.util.HashMap<java.lang.String,CelldesignerSpeciesAliasDocument.CelldesignerSpeciesAlias> speciesAliasIdMap
public static java.util.HashMap<java.lang.String,CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias> complexSpeciesAliasIdMap
public static java.util.HashMap<java.lang.String,CelldesignerProteinDocument.CelldesignerProtein> proteinMap
public static java.lang.String defcomp_id
public static java.util.Vector comp_ids
public static java.util.Vector comp_ids_n
public static boolean addSuffixForMultipleAliases
public static CellDesignerToCytoscapeConverter.Graph convert(java.lang.String file)
public static GraphDocument getXGMMLGraph(java.lang.String name, org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml)
public static void setSpeciesPositionForXGMML(java.lang.String spalias, GraphicNode nod, SbmlDocument.Sbml sbml)
spalias
- nod
- sbml
- public static void setAveragePositionForXGMML(GraphicNode nod, java.util.Vector nodes, java.util.HashMap speciesNodes)
public static java.lang.String getSpeciesAliasInReaction(ReactionDocument.Reaction r, java.lang.String id, java.lang.String role)
r
- id
- role
- can be 'reactant' or 'product' or 'modifier'public static java.util.Vector findAllAliasesForSpecies(SbmlDocument.Sbml sbml, java.lang.String spid)
sbml
- spid
- public static java.lang.String getSuffixForMultipleAliases(SbmlDocument.Sbml sbml, java.lang.String spid, java.lang.String alias)
sbml
- spid
- species idalias
- public static java.util.HashMap getSpecies(SbmlDocument.Sbml sbml)
sbml
- public static java.lang.String convertSpeciesToName(SbmlDocument sbmlDoc, java.lang.String speciesID, boolean addCompartmentName, boolean addModifications)
public static java.lang.String convertSpeciesToName(SbmlDocument.Sbml sbml, java.lang.String speciesID, boolean addCompartmentName, boolean addModifications)
public static java.lang.String convertSpeciesToName(SbmlDocument.Sbml sbml, java.lang.String speciesID, boolean addCompartmentName, boolean addModifications, boolean uniqueName)
sbml
- speciesID
- addCompartmentName
- addModifications
- public static java.lang.String convertSpeciesToName(SbmlDocument sbmlDoc, java.lang.String speciesID, boolean addCompartmentName, boolean addModifications, boolean uniqueName)
public static java.lang.String getCelldesignerSpeciesName(SbmlDocument.Sbml sbml, java.lang.String speciesID)
sbml
- speciesID
- species SBML idpublic static java.lang.String convertSpeciesToName(SbmlDocument.Sbml sbml, java.lang.String speciesID, boolean addCompartmentName, boolean addModifications, boolean uniqueName, java.lang.String alias)
public static java.lang.String getSpeciesName(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity spi, java.lang.String sp_id, java.lang.String sp_name, java.lang.String compartment, boolean addModifications, boolean addCompartmentName, java.lang.String defcomp_id, SbmlDocument sbmlDoc)
public static java.lang.String getSpeciesName(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity spi, java.lang.String sp_id, java.lang.String sp_name, java.lang.String compartment, boolean addModifications, boolean addCompartmentName, java.lang.String defcomp_id, SbmlDocument.Sbml sbml)
public static java.lang.String getSpeciesName(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity spi, java.lang.String sp_id, java.lang.String sp_name, java.lang.String compartment, boolean addModifications, boolean addCompartmentName, java.lang.String defcomp_id, SbmlDocument.Sbml sbml, java.lang.String alias)
public static java.util.Vector getIncludedSpeciesInComplex(SbmlDocument sbmlDoc, java.lang.String complexid)
public static java.util.Vector getIncludedSpeciesInComplex(SbmlDocument.Sbml sbml, java.lang.String complexid)
public static java.lang.String getNameOfIncludedSpecies(SbmlDocument sbmlDoc, CelldesignerSpeciesDocument.CelldesignerSpecies sp, java.lang.String alias)
public static java.lang.String getNameOfIncludedSpecies(SbmlDocument.Sbml sbml, CelldesignerSpeciesDocument.CelldesignerSpecies sp, java.lang.String alias)
public static java.lang.String getNameOfModificationResidue(SbmlDocument sbmlDoc, CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity ident, java.lang.String residueID)
public static java.lang.String getNameOfModificationResidue(SbmlDocument.Sbml sbml, CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity ident, java.lang.String residueID)
public static java.lang.String getReactionString(ReactionDocument.Reaction r, SbmlDocument sbmlDoc, boolean realNames)
r
- sbmlDoc
- realNames
- public static java.lang.String getEntityName(java.lang.String spid, CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity ident, SbmlDocument sbmlDoc)
public static java.lang.String getEntityName(java.lang.String spid, CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity ident, SbmlDocument.Sbml sbml)
public static void mergeCellDesignerFiles(SbmlDocument sbout, SbmlDocument sbin)
sbout
- sbin
- public static java.lang.String checkAndModifySpeciesIDs(SbmlDocument sb, SbmlDocument sbbase)
sb
- sbbase
- public static java.lang.String checkAndModifyEntitiesIDs(SbmlDocument sb, SbmlDocument sbbase)
public static java.util.HashMap MapEntitiesId(SbmlDocument sbb)
public static java.lang.String getEntityId(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity spid)
public static void setEntityId(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity spid, java.lang.String id)
public static java.util.HashMap MapSpeciesId(SbmlDocument sbb)
public static java.util.HashMap MapSpeciesAliases(SbmlDocument sbb)
public static void substituteEntityId(SbmlDocument sb, java.lang.String idold, java.lang.String idnew)
public static void substituteSpeciesId(SbmlDocument sb, java.lang.String idold, java.lang.String idnew)
public static void createSpeciesMap(SbmlDocument.Sbml sbml)
public static java.util.Vector<java.util.Vector<java.lang.String>> extractAttributesFromNotes(Notes notes)
public static java.util.Vector<java.util.Vector<java.lang.String>> extractAttributesFromNotes(CelldesignerNotes notes)
public static java.util.Vector<CelldesignerProteinDocument.CelldesignerProtein> getProteinsInComplex(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml, java.lang.String id)