+ return maxrow;
+ }
+ public static void validateContactMatrixFile(String fileName)
+ throws FileFormatException, IOException
+ {
+ FileInputStream infile = null;
+ try
+ {
+ infile = new FileInputStream(new File(fileName));
+ } catch (Throwable t)
+ {
+ new IOException("Couldn't open " + fileName, t);
+ }
+ JSONObject paeDict = null;
+ try
+ {
+ paeDict = EBIAlfaFold.parseJSONtoPAEContactMatrix(infile);
+ } catch (Throwable t)
+ {
+ new FileFormatException("Couldn't parse " + fileName
+ + " as a JSON dict or array containing a dict");
+ }
+
+ PAEContactMatrix matrix = new PAEContactMatrix(
+ new SequenceDummy("Predicted"), (Map<String, Object>) paeDict);
+ if (matrix.getWidth() <= 0)
+ {
+ throw new FileFormatException(
+ "No data in PAE matrix read from '" + fileName + "'");
+ }
+ }
+ @Override
+ protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
+ MapList newFromMapList)
+ {
+ PAEContactMatrix pae = new PAEContactMatrix(newRefSeq, newFromMapList,
+ elements, new GroupSet(grps));
+ return pae;