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Packages that use ProCopeException | |
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data.complexes | |
data.networks | |
data.petrinets | |
methods.interologs.blast | |
tools | |
tools.namemapping |
Uses of ProCopeException in data.complexes |
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Methods in data.complexes that throw ProCopeException | |
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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 ProCopeException in data.networks |
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Methods in data.networks that throw ProCopeException | |
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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 data.petrinets |
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Methods in data.petrinets that throw ProCopeException | |
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static Place |
PetriNetCreator.parsePlace(String line)
Parses a place from a given Petri net input line |
Uses of ProCopeException in methods.interologs.blast |
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Methods in methods.interologs.blast that throw ProCopeException | |
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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 ProCopeException in tools |
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Methods in tools that throw ProCopeException | |
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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 tools.namemapping |
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Methods in tools.namemapping that throw ProCopeException | |
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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. |
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