super();\r
}\r
/**\r
- * set this to false to *not* add protein products to alignment dataset.\r
- */\r
- public boolean getProteinProducts=false;\r
- /**\r
* retrieve and parse an emblxml file\r
* @param emprefx either EMBL or EMBLCDS strings are allowed - anything else will not retrieve emblxml\r
* @param query\r
}\r
if (reply != null && reply.exists())\r
{\r
+ efile=null;\r
file = reply.getAbsolutePath();\r
- efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);\r
+ if (reply.length()>25)\r
+ {\r
+ efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);\r
+ } else {\r
+ result.append("# No EMBL record retrieved for "+emprefx.toLowerCase()+":"+query.trim());\r
+ }\r
}\r
if (efile!=null) {\r
for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {\r
EmblEntry entry = (EmblEntry) i.next();\r
- SequenceI[] seqparts = entry.getSequences(false,!getProteinProducts, emprefx);\r
+ SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO: use !fetchNa,!fetchPeptide here instead - see todo in emblEntry\r
if (seqparts!=null) {\r
SequenceI[] newseqs = null;\r
int si=0;\r