SynBioDex-archive libSBOLj issues

SynBioDex-archive / libSBOLj

deprecated libSBOL Java library

http://SynBioDex.github.com/libSBOLj

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issues

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changing displayId of loaded SequenceFeature has strange outcome when later writing to rdf

#42 nroehner opened 12 years ago
0
encrypted ID of SequenceFeature not loaded when using IOTools.fromRdfXml()

#41 nroehner opened 12 years ago
0
java.lang.NoSuchMethodError: java.util.Properties.load(Ljava/io/Reader;)V

#40 mgaldzic opened 13 years ago
3
consider new name for SbolService

#39 mgaldzic opened 13 years ago
0
fulfill all test cases

#38 mgaldzic opened 13 years ago
0
remove system.out debug calls

#37 mgaldzic closed 13 years ago
0
SBOLutil.fromRDF returns null Library when Library in RDF file points directly to sequence features

#36 nroehner closed 13 years ago
1
remove the dependency on BioJava

#35 mgaldzic opened 13 years ago
0
Could Use Method for Returning All Libraries Stored in SBOLservice

#34 nroehner closed 13 years ago
4
DNARef in DNASequence should be mutually exclusive with DNASequence

#33 mgaldzic opened 13 years ago
1
remove type from DnaComponent

#32 mgaldzic closed 13 years ago
0
consider renaming SBOlutil to IOtools

#31 mgaldzic closed 13 years ago
0
add read Json method to IOTools

#30 mgaldzic opened 13 years ago
0
add optional uri references to the DNAComponent

#29 mgaldzic opened 13 years ago
0
doc should explain why SO type a is a URI

#28 mgaldzic opened 13 years ago
0
the "reference" type for dnaRef is underdefined

#27 mgaldzic opened 13 years ago
0
addComponent method of Library has no explicit scope

#26 mgaldzic closed 13 years ago
1
Document and test the minimal object cases

#25 mgaldzic closed 13 years ago
1
using SBOLutil.toJson or .toRDF should work for any SBOL object

#24 mgaldzic opened 13 years ago
0
Tests are bogus - ignore until real tests are implemented

#23 mgaldzic closed 13 years ago
2
plan an Exceptions scheme

#22 mgaldzic opened 13 years ago
0
DnaComponent.equals, "getClass() != obj.getClass()" should be > "obj instanceof DnaComponent"

#21 mgaldzic opened 13 years ago
1
consider java.security.MessageDigest for hash calc

#20 mgaldzic closed 13 years ago
1
change insertXXX methods to add(object)

#19 mgaldzic opened 13 years ago
0
change SBOLservice as it is not an intuitive name

#18 mgaldzic closed 13 years ago
0
Standardize to camel case - toJson and toRdf

#17 mgaldzic closed 13 years ago
0
SBOLservice class name does not match java file name

#16 nroehner closed 13 years ago
4
use Ham's Naming Convention for Sequence Starts

#15 mgaldzic opened 13 years ago
0
fix namespace for SO terms

#14 mgaldzic closed 13 years ago
0
make SBOLutil static

#13 mgaldzic closed 13 years ago
0
Rename SbolService to SBOLservice

#12 mgaldzic closed 13 years ago
0
upgrade to BioJava 3

#11 mgaldzic opened 13 years ago
0
start using a logger

#10 mgaldzic closed 13 years ago
2
Main class should have a package name

#9 mgaldzic closed 13 years ago
1
SBOLutil class needs documentation

#8 mgaldzic closed 13 years ago
0
Main class needs documentation

#7 mgaldzic closed 13 years ago
0
Library class needs documentation

#6 mgaldzic closed 13 years ago
0
SbolService doesnt have a createLibrary method

#5 mgaldzic closed 13 years ago
0
SequenceAnnotation.setFeature should be removed

#4 mgaldzic closed 13 years ago
3
SequenceAnnotation.getFeature should be removed

#3 mgaldzic closed 13 years ago
1
SequenceAnnotation start, stop coordinates

#2 mgaldzic opened 13 years ago
0
Identifier system discrepancy between RdfId and Id

#1 mgaldzic closed 13 years ago
1