+ StringTokenizer st;\r
+ for (int i = 0; i < sequences.size(); i++)\r
+ {\r
+ SequenceI restore = (SequenceI) sequences.elementAt(i);\r
+\r
+\r
+ if (restore.getLength() == 0)\r
+ {\r
+ //This is for edits which remove all residues in a sequence\r
+ alignment.getSequences().insertElementAt(restore,\r
+ Integer.parseInt(alignIndex.elementAt(i).toString()));\r
+ }\r
+\r
+ st = new StringTokenizer(seqAsString.elementAt(i).toString());\r
+ restore.setStart(Integer.parseInt(st.nextToken()));\r
+ restore.setEnd(Integer.parseInt(st.nextToken()));\r
+ restore.setSequence(st.nextToken());\r
+ }\r
+\r
+ if(hiddenSeqs!=null)\r
+ {\r
+ for(int hs=0; hs<hiddenSeqs.size(); hs++)\r
+ {\r
+ SequenceI key = (SequenceI) hiddenSeqs.elementAt(hs);\r
+ key.setSequence(hiddenSeqsAsString.elementAt(hs).toString());\r
+ }\r
+ }\r
+\r
+ if (type == HistoryItem.PASTE)\r
+ {\r
+ for (int i = alignment.getHeight() - 1;\r
+ i > (sequences.size() - 1); i--)\r
+ {\r
+ alignment.deleteSequence(i);\r
+ }\r
+ }\r