import jalview.datamodel.ContactListProviderI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.SequenceI;
+import jalview.util.MapUtils;
public class PAEContactMatrix implements ContactMatrixI
{
SequenceI refSeq = null;
+ /**
+ * the length that refSeq is expected to be (excluding gaps, of course)
+ */
+ int length;
+
int maxrow = 0, maxcol = 0;
int[] indices1, indices2;
float maxscore;
- @SuppressWarnings("unchecked")
- public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
- throws Exception
+ private void setRefSeq(SequenceI _refSeq)
{
refSeq = _refSeq;
while (refSeq.getDatasetSequence() != null)
{
refSeq = refSeq.getDatasetSequence();
}
+ length = _refSeq.getEnd() - _refSeq.getStart() + 1;
+ }
+
+ @SuppressWarnings("unchecked")
+ public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
+ {
+ setRefSeq(_refSeq);
// convert the lists to primitive arrays and store
- int length = _refSeq.getEnd() - _refSeq.getStart() + 1;
+ if (!MapUtils.containsAKey(pae_obj, "predicted_aligned_error", "pae"))
+ {
+ parse_version_1_pAE(pae_obj);
+ return;
+ }
+ else
+ {
+ parse_version_2_pAE(pae_obj);
+ }
+ }
+
+ /**
+ * 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;
+
+ }
+
+ /**
+ * parse a sane JSON representation of the pAE
+ *
+ * @param pae_obj
+ */
+ @SuppressWarnings("unchecked")
+ private void parse_version_2_pAE(Map<String, Object> pae_obj)
+ {
+ // this is never going to be reached by the integer rounding.. or is it ?
+ maxscore = ((Double) MapUtils.getFirst(pae_obj,
+ "max_predicted_aligned_error", "max_pae")).floatValue();
+ List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
+ .getFirst(pae_obj, "predicted_aligned_error", "pae"));
+ elements = new float[scoreRows.size()][scoreRows.size()];
+ int row = 0, col = 0;
+ for (List<Long> scoreRow : scoreRows)
+ {
+ Iterator<Long> scores = scoreRow.iterator();
+ while (scores.hasNext())
+ {
+ Object d = scores.next();
+ if (d instanceof Double)
+ elements[row][col++] = ((Double) d).longValue();
+ else
+ elements[row][col++] = (float) ((Long) d).longValue();
+ }
+ row++;
+ col = 0;
+ }
+ maxcol = length;
+ maxrow = length;
+ }
+
+ /**
+ * v1 format got ditched 28th July 2022 see
+ * https://alphafold.ebi.ac.uk/faq#:~:text=We%20updated%20the%20PAE%20JSON%20file%20format%20on%2028th%20July%202022
+ *
+ * @param pae_obj
+ */
+ @SuppressWarnings("unchecked")
+ private void parse_version_1_pAE(Map<String, Object> pae_obj)
+ {
// assume indices are with respect to range defined by _refSeq on the
// dataset refSeq
Iterator<Long> rows = ((List<Long>) pae_obj.get("residue1")).iterator();
Iterator<Long> cols = ((List<Long>) pae_obj.get("residue2")).iterator();
Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
.iterator();
-
+ // assume square matrix
elements = new float[length][length];
while (scores.hasNext())
{
elements[row - 1][col - 1] = escore;
}
- maxscore = ((Double) pae_obj.get("max_predicted_aligned_error"))
- .floatValue();
+ maxscore = ((Double) MapUtils.getFirst(pae_obj,
+ "max_predicted_aligned_error", "max_pae")).floatValue();
}
@Override
return new ContactListImpl(new ContactListProviderI()
{
@Override
+ public int getPosition()
+ {
+ return _column;
+ }
+
+ @Override
public int getContactHeight()
{
return maxcol - 1;
{
return -1;
}
- // TODO Auto-generated method stub
return elements[_column][column];
}
});
return refSeq;
}
+ @Override
+ public String getAnnotDescr()
+ {
+ return "Predicted Alignment Error for " + refSeq.getName();
+ }
+
+ @Override
+ public String getAnnotLabel()
+ {
+ StringBuilder label = new StringBuilder("pAE Matrix");
+ // if (this.getReferenceSeq() != null)
+ // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+ return label.toString();
+ }
+
+ public static final String PAEMATRIX = "PAE_MATRIX";
+
+ @Override
+ public String getType()
+ {
+ return PAEMATRIX;
+ }
+
+ @Override
+ public int getWidth()
+ {
+ return length;
+ }
+
+ @Override
+ public int getHeight()
+ {
+ return length;
+ }
}