public class mergingMaps
extends java.lang.Object
Constructor and Description |
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mergingMaps() |
Modifier and Type | Method and Description |
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static void |
addMRNAs(SbmlDocument cd) |
static java.lang.String |
addPrefixToIds(java.lang.String text,
java.lang.String prefix) |
static void |
checkAliases(ReactionDocument.Reaction reaction,
java.lang.String id,
java.util.Vector speciesAliases,
java.util.Vector complexSpeciesAliases) |
static void |
checkAllTranslations(SbmlDocument cd) |
static void |
checkSpecies(ReactionDocument.Reaction reaction,
java.lang.String id,
java.util.Vector speciesIds,
java.util.Vector includedSpeciesIds) |
static void |
checkSpeciesAliases(SbmlDocument cd) |
static void |
countAll(SbmlDocument cd) |
static java.lang.String |
extractHUGO(java.lang.String name) |
static void |
flipDiagram(SbmlDocument cd) |
static CelldesignerLinkAnchorDocument.CelldesignerLinkAnchor.Position.Enum |
flipPosition(CelldesignerLinkAnchorDocument.CelldesignerLinkAnchor.Position.Enum position) |
static CelldesignerSpeciesAliasDocument.CelldesignerSpeciesAlias |
getAlias(SbmlDocument cd,
java.lang.String id) |
static CelldesignerGeneDocument.CelldesignerGene |
getGene(SbmlDocument cd,
java.lang.String id) |
static CelldesignerProteinDocument.CelldesignerProtein |
getProtein(SbmlDocument cd,
java.lang.String id) |
static java.lang.String |
getReactionString(ReactionDocument.Reaction r,
SbmlDocument sbmlDoc,
boolean realNames,
boolean addModifiers) |
static CelldesignerRNADocument.CelldesignerRNA |
getRNA(SbmlDocument cd,
java.lang.String id) |
static CelldesignerSpeciesAliasDocument.CelldesignerSpeciesAlias |
getRNAAliasBySpeciesId(SbmlDocument cd,
java.lang.String id) |
static SpeciesDocument.Species |
getSpecies(SbmlDocument cd,
java.lang.String id) |
static void |
listSpeciesForGeneList(SbmlDocument cd,
java.util.Vector<java.lang.String> geneList) |
static void |
main(java.lang.String[] args) |
static void |
mergeDiagrams(SbmlDocument cd,
SbmlDocument cd2) |
static void |
produceCandidateMergeLists(SbmlDocument cd,
SbmlDocument cd2,
java.lang.String prefix) |
static void |
rewireDiagram(SbmlDocument cd,
java.util.Vector<java.lang.String> subs,
java.util.Vector<java.lang.String> subsP) |
static void |
scaleDiagram(SbmlDocument cd,
float factor) |
public static void main(java.lang.String[] args)
public static void addMRNAs(SbmlDocument cd)
public static CelldesignerSpeciesAliasDocument.CelldesignerSpeciesAlias getAlias(SbmlDocument cd, java.lang.String id)
public static SpeciesDocument.Species getSpecies(SbmlDocument cd, java.lang.String id)
public static CelldesignerProteinDocument.CelldesignerProtein getProtein(SbmlDocument cd, java.lang.String id)
public static CelldesignerGeneDocument.CelldesignerGene getGene(SbmlDocument cd, java.lang.String id)
public static CelldesignerRNADocument.CelldesignerRNA getRNA(SbmlDocument cd, java.lang.String id)
public static CelldesignerSpeciesAliasDocument.CelldesignerSpeciesAlias getRNAAliasBySpeciesId(SbmlDocument cd, java.lang.String id)
public static void flipDiagram(SbmlDocument cd)
public static CelldesignerLinkAnchorDocument.CelldesignerLinkAnchor.Position.Enum flipPosition(CelldesignerLinkAnchorDocument.CelldesignerLinkAnchor.Position.Enum position)
public static void scaleDiagram(SbmlDocument cd, float factor)
public static java.lang.String extractHUGO(java.lang.String name)
public static void listSpeciesForGeneList(SbmlDocument cd, java.util.Vector<java.lang.String> geneList)
public static void rewireDiagram(SbmlDocument cd, java.util.Vector<java.lang.String> subs, java.util.Vector<java.lang.String> subsP)
public static java.lang.String getReactionString(ReactionDocument.Reaction r, SbmlDocument sbmlDoc, boolean realNames, boolean addModifiers)
public static java.lang.String addPrefixToIds(java.lang.String text, java.lang.String prefix)
public static void mergeDiagrams(SbmlDocument cd, SbmlDocument cd2)
public static void checkAllTranslations(SbmlDocument cd)
public static void checkSpeciesAliases(SbmlDocument cd)
public static void checkSpecies(ReactionDocument.Reaction reaction, java.lang.String id, java.util.Vector speciesIds, java.util.Vector includedSpeciesIds)
public static void checkAliases(ReactionDocument.Reaction reaction, java.lang.String id, java.util.Vector speciesAliases, java.util.Vector complexSpeciesAliases)
public static void countAll(SbmlDocument cd)
public static void produceCandidateMergeLists(SbmlDocument cd, SbmlDocument cd2, java.lang.String prefix) throws java.lang.Exception
java.lang.Exception