+ * construct a sequence associated PAE matrix directly from a float array
+ *
+ * @param _refSeq
+ * @param matrix
+ */
+ public PAEContactMatrix(SequenceI _refSeq, float[][] matrix)
+ {
+ setRefSeq(_refSeq);
+ maxcol = 0;
+ for (float[] row : matrix)
+ {
+ if (row.length > maxcol)
+ {
+ maxcol = row.length;
+ }
+ maxscore = row[0];
+ for (float f : row)
+ {
+ if (maxscore < f)
+ {
+ maxscore = f;
+ }
+ }
+ }
+ maxrow = matrix.length;
+ elements = matrix;
+
+ }
+
+ /**
+ * new matrix with specific mapping to a reference sequence
+ * @param newRefSeq
+ * @param newFromMapList
+ * @param elements2
+ * @param grps2
+ */
+ public PAEContactMatrix(SequenceI newRefSeq,
+ MapList newFromMapList, float[][] elements2, GroupSet grps2)
+ {
+ this(newRefSeq,elements2);
+ toSeq = newFromMapList;
+ grps= grps2;
+ }
+
+ /**