sbgn/libsbgn

Issues

• Improve Usability with SBML models

  #65 opened 2 years ago by shoepfl
  4

• Use `emptyset` rather than `source and sink`

  #62 opened 3 years ago by fbergmann
  0

• v0.3-SNAPSHOT

  #35 opened 5 years ago by matthiaskoenig
  3

• Conflicting library version in maven dependency.

  #57 opened 5 years ago by piotr-gawron
  0

• Switch to Github Packages

  #56 opened 5 years ago by cannin
  0

• Incorrect SBGN file format following writing the render information

  #54 opened 5 years ago by ibalaur
  5

• Suggestion: Font style property to be exposed via the RenderUtil class

  #52 opened 5 years ago by ibalaur
  3

• Problems writing render extension, set DocumentBuilderFactory in SbgnUtil.addAnnotation namespace aware?

  #53 opened 5 years ago by tczauderna
  2

• SbgnUtil.readFrom(InputStream is) fails when conversion from Milestone 1 or 2 necessary

  #49 opened 6 years ago by tczauderna
  2

• Question on high level validation, ruleId=pd10112: if there are compartments defined, top-level glyphs must have a compartmentRef.

  #51 opened 6 years ago by ibalaur
  2

• Suggestion: function to convert from 3.0 to 2.0 to be provided

  #50 opened 6 years ago by ibalaur
  0

• Proposal to allow double colon (i.e. "::") to be used inside a glyph id

  #47 opened 6 years ago by ibalaur
  4

• maven build not working on some systems

  #46 opened 6 years ago by fbergmann
  1

• Compile problem: error: Source option 1.5 is no longer supported. Use 1.6 or later

  #41 opened 6 years ago by ibalaur
  1

• port ant script to maven

  #45 opened 6 years ago by fbergmann
  3

• utility classes for creating / accessing render elements

  #44 opened 6 years ago by fbergmann
  0

• clone / notes examples

  #43 opened 6 years ago by fbergmann
  0

• More flexible parse functions with support for InputStreams

  #39 opened 6 years ago by draeger
  1

• Schema not found

  #42 opened 6 years ago by yun-vis
  1

• Ant tests failing

  #38 opened 6 years ago by matthiaskoenig
  3

• Implement submaps

  #13 opened 14 years ago by cannin
  10

• Create javadocs for v0.2 and v0.3-SNAPSHOT & host somewhere

  #33 opened 8 years ago by matthiaskoenig
  1

• Create specification docs for v0.3-SNAPSHOT

  #34 opened 8 years ago by matthiaskoenig
  1

• Proposal for text styles

  #21 opened 14 years ago by cannin
  2

• Add license

  #31 opened 8 years ago by matthiaskoenig
  2

• drawing order of overlapping compartments in PD

  #27 opened 8 years ago by cannin
  6

• Second notation for state variables

  #14 opened 8 years ago by cannin
  2

• State variables: 3rd notation not supported

  #9 opened 14 years ago by cannin
  4

• Serializations not created in C++ bindings

  #30 opened 8 years ago by cannin
  5

• phenotype / observable class for ER maps

  #29 opened 8 years ago by cannin
  1

• Custom Annotations warrant higher priority

  #28 opened 8 years ago by cannin
  1

• enum with string constants

  #26 opened 8 years ago by cannin
  2

• ids on arcs?

  #25 opened 8 years ago by cannin
  6

• STAT1 alpha get's converted to STAT1α

  #24 opened 8 years ago by cannin
  6

• Compartment containment

  #23 opened 8 years ago by cannin
  2

• Unit of information label = prefix + value

  #22 opened 14 years ago by cannin
  2

• definition of starting point / end point for arcs

  #20 opened 8 years ago by cannin
  3

• mismatch betw. def. of bounding box in schema and test files

  #19 opened 8 years ago by cannin
  3

• Recommend a mime type

  #18 opened 14 years ago by cannin
  1

• Complex Glyphs depicting elements on the inside

  #17 opened 8 years ago by cannin
  3

• Bug in compartments.xml or how to do associations

  #16 opened 8 years ago by cannin
  5

• Proposal for Label bounds

  #15 opened 8 years ago by cannin
  4

• Port position information duplicated

  #12 opened 8 years ago by cannin
  4

• Submap is missing

  #11 opened 8 years ago by cannin
  2

• All logical operators are missing

  #10 opened 8 years ago by cannin
  2

• Underdefined glyphs

  #8 opened 14 years ago by cannin
  2

• Discussion xsd Process Description

  #7 opened 8 years ago by cannin
  3

• The value "perturbating agent" should be "perturbing agent".

  #6 opened 8 years ago by cannin
  3

• Missing glyphs for Process Description

  #5 opened 8 years ago by cannin
  3

• Explicit bounding box for (some/all?) labels

  #4 opened 8 years ago by cannin
  5