+ if (!transferred)\r
+ {\r
+ // report the ID/sequence mismatches\r
+ sbuffer.append(messages);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * loop thru and collect additional sequences in Map.\r
+ * \r
+ * @param sequencesArray\r
+ * @return\r
+ */\r
+ private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)\r
+ {\r
+ Vector nseq = new Vector();\r
+ for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)\r
+ {\r
+ nseq.addElement(sequencesArray[i]);\r
+ DBRefEntry dbr[] = sequencesArray[i].getDBRef();\r
+ jalview.datamodel.Mapping map = null;\r
+ for (int r = 0; (dbr != null) && r < dbr.length; r++)\r
+ {\r
+ if ((map = dbr[r].getMap()) != null)\r
+ {\r
+ if (map.getTo() != null && !nseq.contains(map.getTo()))\r
+ {\r
+ nseq.addElement(map.getTo());\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (nseq.size() > 0)\r
+ {\r
+ sequencesArray = new SequenceI[nseq.size()];\r
+ nseq.toArray(sequencesArray);\r
+ }\r
+ return sequencesArray;\r