helices[] = new int[]
{ 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
- StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(null);
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
new String[]
{ "A" }, "test/jalview/ext/jmol/1QCF.pdb",
"EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
Sequence sq1 = new Sequence(sq);
String inFile;
- StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(null);
// Associate the 1GAQ pdb file with the subsequence 'imported' from another
// source
StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
">FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor\nMATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGEVELQVPD\nDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKE\nEELTGA",
DataSourceType.PASTE, FileFormat.Fasta);
SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
- StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(null);
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
new String[]
{ null }, "examples/3W5V.pdb", DataSourceType.FILE);
// make it harder by shifting the copy vs the reference
newseq.setStart(refseq.getStart() + 25);
newseq.setEnd(refseq.getLength() + 25 + refseq.getStart());
- StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(null);
ssm.setProcessSecondaryStructure(true);
ssm.setAddTempFacAnnot(true);
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },