+ public static void addPAEToStructure(StructureSelectionManager ssm,
+ String structFilename, File pae)
+ {
+ FileInputStream paeInput = null;
+ try
+ {
+ paeInput = new FileInputStream(pae);
+ } catch (FileNotFoundException e)
+ {
+ Console.error(
+ "Could not find pAE file '" + pae.getAbsolutePath() + "'", e);
+ return;
+ }
+ if (ssm == null)
+ {
+ ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ }
+ if (ssm != null)
+ {
+ StructureMapping[] smArray = ssm.getMapping(structFilename);
+
+ try
+ {
+ if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput))
+ {
+ Console.warn("Could not import contact matrix from '"
+ + pae.getAbsolutePath() + "' to structure.");
+ }
+ } catch (IOException e1)
+ {
+ Console.error("Error when importing pAE file '"
+ + pae.getAbsolutePath() + "'", e1);
+ } catch (ParseException e2)
+ {
+ Console.error("Error when parsing pAE file '"
+ + pae.getAbsolutePath() + "'", e2);
+ }
+ }
+ }
+