Uses of Class
tools.LibraryNameException

Packages that use LibraryNameException
data.complexes   
data.networks   
data.petrinets   
methods.interologs.blast   
tools   
tools.namemapping   
 

Uses of LibraryNameException in data.complexes
 

Methods in data.complexes that throw LibraryNameException
 void ComplexSet.addComplex(Complex toAdd)
          Adds a complex to the complex set.
static ComplexSet ComplexSetReader.readComplexes(File file)
          Reads complexes from a given file.
static ComplexSet ComplexSetReader.readComplexes(File file, String organism)
          Reads complexes from a given file.
static ComplexSet ComplexSetReader.readComplexes(File file, String organism, String separator)
          Reads complexes from a given file.
static ComplexSet ComplexSetReader.readComplexes(InputStream input)
          Reads complexes from a given InputStream.
static ComplexSet ComplexSetReader.readComplexes(InputStream input, String organism)
          Reads complexes from a given InputStream.
static ComplexSet ComplexSetReader.readComplexes(InputStream input, String organism, String separator)
          Reads complexes from a given InputStream.
static ComplexSet ComplexSetReader.readComplexes(String file)
          Reads complexes from a given file.
static ComplexSet ComplexSetReader.readComplexes(String file, String organism)
          Reads complexes from a given file.
static ComplexSet ComplexSetReader.readComplexes(String file, String organism, String separator)
          Reads complexes from a given file.
 

Uses of LibraryNameException in data.networks
 

Methods in data.networks that throw LibraryNameException
 PurificationData ProteinNetwork.derivePurificationData(boolean poolBaits)
          Creates a purification data object from a directed network.
 void ProteinNetwork.setEdge(int prot1, int prot2, float weight)
          Sets a weighted edge between two given proteins.
 void ProteinNetwork.setEdgeAnnotation(int prot1, int prot2, String key, Object value)
          Labels an edge between two proteins with a given key/value pair.
 void ProteinNetwork.setEdgeAnnotations(int prot1, int prot2, Map<String,Object> annotations)
          Labels an edge in the network with a given set of annotations.
 

Uses of LibraryNameException in data.petrinets
 

Methods in data.petrinets that throw LibraryNameException
static Place PetriNetCreator.parsePlace(String line)
          Parses a place from a given Petri net input line
 

Uses of LibraryNameException in methods.interologs.blast
 

Methods in methods.interologs.blast that throw LibraryNameException
static BlastHits BlastHitFileParser.parseBlastHits(File hitfile)
          Parse BLAST hits from a given BLAST hit file in tabular format.
static BlastHits BlastHitFileParser.parseBlastHits(File hitfile, String organism1, String organism2)
          Parse BLAST hits from a given BLAST hit file in tabular format.
static BlastHits BlastHitFileParser.parseBlastHits(InputStream input)
          Parse BLAST hits from a given input stream.
static BlastHits BlastHitFileParser.parseBlastHits(InputStream input, String organism1, String organism2)
          Parse BLAST hits from a given input stream.
static BlastHits BlastHitFileParser.parseBlastHits(String hitfile)
          Parse BLAST hits from a given BLAST hit file in tabular format.
static BlastHits BlastHitFileParser.parseBlastHits(String hitfile, String organism1, String organism2)
          Parse BLAST hits from a given BLAST hit file in tabular format.
 

Uses of LibraryNameException in tools
 

Methods in tools that throw LibraryNameException
 jaligner.Alignment SequenceAligner.getAlignment(int protein1, int protein2)
          Returns the local sequence alignment for two given proteins.
 void SequenceAligner.setMatrix(String matrixName)
          Sets the substitution matrix.
static void Tools.verifyAnnotationType(Object value)
          Checks whether a given object is an Integer, a Float or a List.
 

Uses of LibraryNameException in tools.namemapping
 

Methods in tools.namemapping that throw LibraryNameException
static Object ProteinManager.addAnnotation(int internalID, String key, Object value)
          Adds an annotation to the protein with a given internal ID.
static void ProteinManager.addAnnotations(int internalID, Map<String,Object> newAnnotations)
          Adds set of annotations to a protein with a given internal ID.
static Object ProteinManager.getAnnotation(int internalID, String key)
          Retrieves an annotation for a given protein.
static Map<String,Object> ProteinManager.getAnnotations(int internalID)
          Retrieves all annotations for a given protein.
static void ProteinManager.loadProteinAnnotations(String file)
          Load protein annotations from a given file.