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| 1. | * '''Apr 11 2007:''' * Added new node attributes Motif Start, Motif End, SNPs (Motif Hit) (CytoscapeUtil::addSequenceSearchResultSetToCytoscape, CytoscapeUtil::addGenPeptFeaturesToNode) * Added "Unique peptides" checkbox in profile chooser panel (BrainParameterChangeDialog) * new boolean parameter ''uniquePeptides'' and getter/setter in BrainParameterSet * '''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) === Code ToDo === * '''Feb 12 2007:''' BiNGO 2.0 * Tried using the latest BiNGO v2.0 but method MultipleTestingCorrection (among others) not supported; reverted back to previously used version * '''Feb 21 2007:''' Plugin issues to resolve in Cytoscape 2.4: * '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 * 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. * "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
Apr 11 2007:
Added new node attributes Motif Start, Motif End, SNPs (Motif Hit) (CytoscapeUtil::addSequenceSearchResultSetToCytoscape, CytoscapeUtil::addGenPeptFeaturesToNode)
Added "Unique peptides" checkbox in profile chooser panel (BrainParameterChangeDialog)
new boolean parameter uniquePeptides and getter/setter in BrainParameterSet
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)
Code ToDo
Feb 12 2007: BiNGO 2.0
Tried using the latest BiNGO v2.0 but method MultipleTestingCorrection (among others) not supported; reverted back to previously used version
Feb 21 2007: Plugin issues to resolve in Cytoscape 2.4:
'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
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.
"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