+ /**
+ * get an alphafold pAE for the given id, and add it to sequence 0 in
+ * pdbAlignment (assuming it came from structurefile parser).
+ *
+ * @param id
+ * @param pdbAlignment
+ * @param retrievalUrl
+ * - URL of .mmcif from EBI-AlphaFold - will be used to generate the
+ * pAE URL automatically
+ * @throws IOException
+ * @throws Exception
+ */
+ public static void retrieve_AlphaFold_pAE(String id,
+ AlignmentI pdbAlignment, String retrievalUrl) throws IOException
+ {
+ File pae = fetchAlphaFoldPAE(id, retrievalUrl);
+ addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false, null);
+ }
+
+ public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
+ int index, String id, boolean isStruct, boolean isStructId,
+ String label)
+ {
+ FileInputStream paeInput = null;
+ try
+ {
+ paeInput = new FileInputStream(pae);
+ } catch (FileNotFoundException e)
+ {
+ Console.error(
+ "Could not find pAE file '" + pae.getAbsolutePath() + "'", e);
+ return;
+ }
+
+ if (isStruct)
+ {
+ // ###### WRITE A TEST for this bit of the logic addAlphaFoldPAE with
+ // different params.
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (ssm != null)
+ {
+ String structFilename = isStructId ? ssm.findFileForPDBId(id) : id;
+ addPAEToStructure(ssm, structFilename, pae, label);
+ }
+
+ }
+ else
+ {
+ // attach to sequence?!
+ try
+ {
+ if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
+ index, id, label))
+ {
+ Console.warn("Could not import contact matrix from '"
+ + pae.getAbsolutePath() + "' to sequence.");
+ }
+ } catch (IOException e1)