Fix multiple structure alignment example II

lafita · web-flow · commit 40917abd648b · 2016-11-23T16:03:01.000+01:00
biojava#14
diff --git a/structure/alignment.md b/structure/alignment.md
@@ -333,11 +333,13 @@ example of how to create and display a multiple alignment:
 //Specify the structures to align: some ASP-proteinases
 List<String> names = Arrays.asList("3app", "4ape", "5pep", "1psn", "4cms", "1bbs.A", "1smr.A");
 
-//Load the CA atoms of the structures
+//Load the CA atoms of the structures and create the structure identifiers
 AtomCache cache = new AtomCache();
 List<Atom[]> atomArrays = new ArrayList<Atom[]>();
+List<StructureIdentifier> identifiers = new ArrayList<StructureIdentifier>();
 for (String name:names)	{
   atomArrays.add(cache.getAtoms(name));
+  identifiers.add(new SubstructureIdentifier(name));
 }
 
 //Generate the multiple alignment algorithm with the chosen pairwise algorithm
@@ -347,6 +349,9 @@ MultipleMcMain multiple = new MultipleMcMain(pairwise);
 //Perform the alignment
 MultipleAlignment result = multiple.align(atomArrays);
 
+// Set the structure identifiers, so that each atom array can be identified in the outputs
+result.getEnsemble().setStructureIdentifiers(identifiers);
+
 //Output the FASTA sequence alignment
 System.out.println(MultipleAlignmentWriter.toFASTA(result));
 
