Uses of Class
procope.tools.ProCopeException

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

Uses of ProCopeException in procope.data.complexes
 

Methods in procope.data.complexes that throw ProCopeException
 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 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 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 separator)
          Reads complexes from a given file.
 

Uses of ProCopeException in procope.data.networks
 

Methods in procope.data.networks that throw ProCopeException
 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 ProCopeException in procope.data.petrinets
 

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

Uses of ProCopeException in procope.methods.interologs.blast
 

Methods in procope.methods.interologs.blast that throw ProCopeException
static BlastHits BlastHitFileParser.parseBlastHits(File hitfile)
          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(String hitfile)
          Parse BLAST hits from a given BLAST hit file in tabular format.
 

Uses of ProCopeException in procope.tools
 

Methods in procope.tools that throw ProCopeException
 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 ProCopeException in procope.tools.namemapping
 

Methods in procope.tools.namemapping that throw ProCopeException
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.