SequenceRenderer sr = new SequenceRenderer(af.getViewport());
SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
- StructureSelectionManager ssm = new StructureSelectionManager();
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(null);
// need some mappings!
SequenceRenderer sr = new SequenceRenderer(af.getViewport());
SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
- StructureSelectionManager ssm = new StructureSelectionManager();
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(null);
/*
* map residues 1-10 to residues 21-30 (atoms 105-150) in structures
*/
- HashMap<Integer, int[]> map = new HashMap<Integer, int[]>();
+ HashMap<Integer, int[]> map = new HashMap<>();
for (int pos = 1; pos <= seq1.getLength(); pos++)
{
map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
String chainACommand = commands[0].commands[0];
// M colour is #82827d == (130, 130, 125) (see strand.html help page)
assertTrue(chainACommand
- .contains(";select 21:A/1.1;color[130,130,125]"));
+ .contains("select 21:A/1.1;color[130,130,125]")); // first one
// H colour is #60609f == (96, 96, 159)
assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]"));
// hidden columns are Gray (128, 128, 128)
String chainBCommand = commands[1].commands[0];
// M colour is #82827d == (130, 130, 125)
assertTrue(chainBCommand
- .contains(";select 21:B/2.1;color[130,130,125]"));
+ .contains("select 21:B/2.1;color[130,130,125]"));
// V colour is #ffff00 == (255, 255, 0)
assertTrue(chainBCommand
.contains(";select 22:B/2.1;color[255,255,0]"));