+\r
+ public void setNucleotide(boolean b)\r
+ {\r
+ if(b)\r
+ type = NUCLEOTIDE;\r
+ else\r
+ type = PROTEIN;\r
+ }\r
+\r
+ public boolean isNucleotide()\r
+ {\r
+ if(type==NUCLEOTIDE)\r
+ return true;\r
+ else\r
+ return false;\r
+ }\r
+\r
+ public void setDataset(Alignment data)\r
+ {\r
+ if(dataset==null && data==null)\r
+ {\r
+ // Create a new dataset for this alignment.\r
+ // Can only be done once, if dataset is not null\r
+ // This will not be performed\r
+ Sequence[] seqs = new Sequence[getHeight()];\r
+ for (int i = 0; i < getHeight(); i++)\r
+ {\r
+\r
+ seqs[i] = new Sequence(getSequenceAt(i).getName(),\r
+ AlignSeq.extractGaps(\r
+ jalview.util.Comparison.GapChars,\r
+ getSequenceAt(i).getSequence()\r
+ ),\r
+ getSequenceAt(i).getStart(),\r
+ getSequenceAt(i).getEnd());\r
+\r
+ getSequenceAt(i).setDatasetSequence(seqs[i]);\r
+ }\r
+\r
+ dataset = new Alignment(seqs);\r
+ }\r
+ else if(dataset==null && data!=null)\r
+ {\r
+ dataset = data;\r
+ }\r
+ }\r
+\r
+ public Alignment getDataset()\r
+ {\r
+ return dataset;\r
+ }\r
+\r
+ public boolean padGaps() {\r
+ boolean modified=false;\r
+\r
+ //Remove excess gaps from the end of alignment\r
+ int maxLength = -1;\r
+\r
+ SequenceI current;\r
+ for (int i = 0; i < sequences.size(); i++)\r
+ {\r
+ current = getSequenceAt(i);\r
+ for (int j = current.getLength(); j > maxLength; j--)\r
+ {\r
+ if (j > maxLength && !jalview.util.Comparison.isGap(\r
+ current.getCharAt(j)))\r
+ {\r
+ maxLength = j;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+\r
+ maxLength++;\r
+\r
+ for (int i = 0; i < sequences.size();\r
+ i++)\r
+ {\r
+ current = getSequenceAt(i);\r
+\r
+ if (current.getLength() < maxLength)\r
+ {\r
+ current.insertCharAt(maxLength - 1, gapCharacter);\r
+ modified=true;\r
+ }\r
+ else if(current.getLength() > maxLength)\r
+ {\r
+ current.deleteChars(maxLength, current.getLength());\r
+ }\r
+ }\r
+ return modified;\r
+ }\r
+\r
+ public HiddenSequences getHiddenSequences()\r
+ {\r
+ return hiddenSequences;\r
+ }\r
+\r