/**
* Converts the {@link MultipleAlignment} into a FatCat String format. Includes summary
* information about the alignment in the top and a multiple sequence alignment at the bottom.
*
* @param alignment MultipleAlignment
* @return String multiple sequence alignment in FASTA format
*/
public static String toFatCat(MultipleAlignment alignment) {
// Initialize the String and put the summary information
StringWriter fatcat = new StringWriter();
fatcat.append(alignment.toString() + "\n\n");
// Get the alignment sequences and the mapping
List<Integer> mapSeqToStruct = new ArrayList<Integer>();
List<String> alnSequences =
MultipleAlignmentTools.getSequenceAlignment(alignment, mapSeqToStruct);
// Get the String of the Block Numbers for Position
String blockNumbers = "";
for (int pos = 0; pos < alnSequences.get(0).length(); pos++) {
int blockNr =
MultipleAlignmentTools.getBlockForSequencePosition(alignment, mapSeqToStruct, pos);
if (blockNr != -1) blockNumbers = blockNumbers.concat("" + (blockNr + 1));
else blockNumbers = blockNumbers.concat(" ");
}
// Write the Sequence Alignment
for (int str = 0; str < alignment.size(); str++) {
if (str < 9) fatcat.append("Chain 0" + (str + 1) + ": " + alnSequences.get(str) + "\n");
else fatcat.append("Chain " + (str + 1) + ": " + alnSequences.get(str) + "\n");
if (str != alignment.size() - 1) fatcat.append(" " + blockNumbers + "\n");
}
return fatcat.toString();
}
/**
* Converts the {@link MultipleAlignment} into a multiple sequence alignment String in FASTA
* format.
*
* @param alignment MultipleAlignment
* @return String multiple sequence alignment in FASTA format
*/
public static String toFASTA(MultipleAlignment alignment) {
// Get the alignment sequences
List<String> alnSequences = MultipleAlignmentTools.getSequenceAlignment(alignment);
String fasta = "";
for (int st = 0; st < alignment.size(); st++) {
// Add the structure identifier as the head of the FASTA
fasta +=
">"
+ alignment.getEnsemble().getStructureNames().get(st)
+ "\n"
+ alnSequences.get(st)
+ "\n";
}
return fasta;
}
