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| === Code Notes === * '''Feb 12 2007:''' Cytoscape API changes: * CyNet.set*AttributeValue (where *=[Node,Edge]) and CyNet.get*Attribute (* = [Integer,Double,...]) is deprecated as of v2.2 - replaced with CyAttributes instead (CytoscapeUtil.java) * '''Feb 21 2007:''' Resolved some issues running new plugin jar in Cytoscape 2.4: * ''TO RESOLVE:'' 'bytecode.jar' for biojava-1.5-beta2.jar was causing java.lang.IllegalAccessError exception when loading ; had to revert back to biojava-1.4.jar and bytecode.jar dated Oct 13 2004 * ''TO RESOLVE:'' NoClassDefFound exception due to missing org.mskcc.dataservices.vocab.CommonVocab referenced in CytoscapeUtil.java. This class is contained in data-aux.jar which was removed as of Cytoscape 2.4 due to CPath package reorganization. Copied data-aux.jar in plugins folder to overcome this for now. * ''TO RESOLVE:'' "Link Out" feature from node context menu fails to open selected database in web browser. This error only occurs when searching mammalian RefSeq db I downloaded, apparently because of the format of the FASTA file header, e.g. ''gi|119943093|ref|NP_001073324.1| glycogenin 2 isoform a [Homo sapiens]''. The file "smallDB.fasta" in the PDZ testData folder does not present this error. It's format is ''YAL001C TFC3 SGDID:S0000001, Chr I from 151168-151099,151008-147596, reverse complement, Verified ORF'' ---- |
Moyez Dharsee
Email: MailTo(mdharsee AT SPAMFREE infochromics DOT com)
416-889-1624 (mobile)
Skype Name: moe_dee
Code Notes
Feb 12 2007: Cytoscape API changes:
CyNet.set*AttributeValue (where *=[Node,Edge]) and CyNet.get*Attribute (* = [Integer,Double,...]) is deprecated as of v2.2 - replaced with CyAttributes instead (CytoscapeUtil.java)
Feb 21 2007: Resolved some issues running new plugin jar in Cytoscape 2.4:
TO RESOLVE: 'bytecode.jar' for biojava-1.5-beta2.jar was causing java.lang.IllegalAccessError exception when loading ; had to revert back to biojava-1.4.jar and bytecode.jar dated Oct 13 2004
TO RESOLVE: NoClassDefFound exception due to missing org.mskcc.dataservices.vocab.CommonVocab referenced in CytoscapeUtil.java. This class is contained in data-aux.jar which was removed as of Cytoscape 2.4 due to CPath package reorganization. Copied data-aux.jar in plugins folder to overcome this for now.
TO RESOLVE: "Link Out" feature from node context menu fails to open selected database in web browser. This error only occurs when searching mammalian RefSeq db I downloaded, apparently because of the format of the FASTA file header, e.g. gi|119943093|ref|NP_001073324.1| glycogenin 2 isoform a [Homo sapiens]. The file "smallDB.fasta" in the PDZ testData folder does not present this error. It's format is YAL001C TFC3 SGDID:S0000001, Chr I from 151168-151099,151008-147596, reverse complement, Verified ORF