Author: kono Date: 2010-02-18 15:02:24 -0800 (Thu, 18 Feb 2010) New Revision: 19377
Modified: coreplugins/trunk/NCBIClient/manifest/plugin.props coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClient.java Log: Bug ID 2182: Attributes are missing for genes in original query (NCBI Clinet) is fixed. Modified: coreplugins/trunk/NCBIClient/manifest/plugin.props =================================================================== --- coreplugins/trunk/NCBIClient/manifest/plugin.props 2010-02-18 23:01:57 UTC (rev 19376) +++ coreplugins/trunk/NCBIClient/manifest/plugin.props 2010-02-18 23:02:24 UTC (rev 19377) @@ -8,7 +8,7 @@ pluginDescription=<p>Web Service client module for <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html";>NCBI Entrez Utilities Web Service</a>.</p><p>For more information, please visit the following pages:</p><ul><li><a href="http://www.cytoscape.org/cgi-bin/moin.cgi/SampleWebServiceClients";>Sample clients</a></li><li><a href="http://www.cytoscape.org/cgi-bin/moin.cgi/WebServiceWorkflow";>Sample workflow</a></li></ul><p><strong><font color="red">To use this function from Cytoscape Desktop, <u>NCBI Entrez Gene User Interface</u> plugin is required. This plugin works with Cytoscape 2.7.0 or later.</font></strong> # Plugin version number, this must be two numbers separated by a decimlal. Ex. 0.2, 14.03 -pluginVersion=0.96 +pluginVersion=0.97 # Compatible Cytoscape version cytoscapeVersion=2.7 Modified: coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClient.java =================================================================== --- coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClient.java 2010-02-18 23:01:57 UTC (rev 19376) +++ coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClient.java 2010-02-18 23:02:24 UTC (rev 19377) @@ -579,10 +579,10 @@ Object attrVal; for (String key : nodeAltName.keySet()) { - nodeAttr.setAttribute(key, "Alt Name", nodeAltName - .get(key)); - nodeAttr.setAttribute(key, "Interactor Type", nodeTypes - .get(key)); + if (nodeAltName.get(key) != null) + nodeAttr.setAttribute(key, "Alt Name", nodeAltName.get(key)); + if (nodeTypes.get(key) != null) + nodeAttr.setAttribute(key, "Interactor Type", nodeTypes.get(key)); } for (String[] key : attrMap.keySet()) { @@ -755,6 +755,12 @@ .getEntrezgeneSet().getEntrezgene().get(i) .getEntrezgeneTrackInfo().getGeneTrack() .getGeneTrackGeneid().toString(), true); + // Add attributes + final String centerNodeAltName = res.getEntrezgeneSet().getEntrezgene().get(i).getEntrezgeneGene().getGeneRef().getGeneRefLocus(); + if(centerNodeAltName != null) + nodeAltName.put(centerNode.getIdentifier(), centerNodeAltName); + // Center node is always a gene in Entrez Gene Database. + nodeTypes.put(centerNode.getIdentifier(), "GeneID"); System.out.println("Got Interactions for: " + centerNode.getIdentifier()); } catch (Exception e) { @@ -931,8 +937,6 @@ this.ids = ids; } - private void parseAnnotation(EFetchResult res) { - } public Object call() { StringBuilder builder = new StringBuilder(); -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/cytoscape-cvs?hl=en.
