1 package jalview.ws.datamodel.alphafold;
3 import java.util.Iterator;
7 import jalview.datamodel.ContactListI;
8 import jalview.datamodel.ContactListImpl;
9 import jalview.datamodel.ContactListProviderI;
10 import jalview.datamodel.ContactMatrixI;
11 import jalview.datamodel.SequenceI;
13 public class PAEContactMatrix implements ContactMatrixI
16 SequenceI refSeq = null;
19 * the length that refSeq is expected to be (excluding gaps, of course)
23 int maxrow = 0, maxcol = 0;
25 int[] indices1, indices2;
31 @SuppressWarnings("unchecked")
32 public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
36 while (refSeq.getDatasetSequence() != null)
38 refSeq = refSeq.getDatasetSequence();
40 // convert the lists to primitive arrays and store
41 length = _refSeq.getEnd() - _refSeq.getStart() + 1;
43 if (!pae_obj.containsKey("predicted_aligned_error"))
45 parse_version_1_pAE(pae_obj);
50 parse_version_2_pAE(pae_obj);
55 * parse a sane JSON representation of the pAE
59 private void parse_version_2_pAE(Map<String, Object> pae_obj)
61 elements = new float[length][length];
62 // this is never going to be reached by the integer rounding.. or is it ?
63 maxscore = ((Double) pae_obj.get("max_predicted_aligned_error"))
65 Iterator<List<Long>> scoreRows = ((List<List<Long>>) pae_obj
66 .get("predicted_aligned_error")).iterator();
68 while (scoreRows.hasNext())
70 Iterator<Long> scores = scoreRows.next().iterator();
71 while (scores.hasNext())
73 elements[row][col++] = scores.next();
83 * v1 format got ditched 28th July 2022 see
84 * https://alphafold.ebi.ac.uk/faq#:~:text=We%20updated%20the%20PAE%20JSON%20file%20format%20on%2028th%20July%202022
88 private void parse_version_1_pAE(Map<String, Object> pae_obj)
90 // assume indices are with respect to range defined by _refSeq on the
92 Iterator<Long> rows = ((List<Long>) pae_obj.get("residue1")).iterator();
93 Iterator<Long> cols = ((List<Long>) pae_obj.get("residue2")).iterator();
94 Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
97 elements = new float[length][length];
98 while (scores.hasNext())
100 float escore = scores.next().floatValue();
101 int row = rows.next().intValue();
102 int col = cols.next().intValue();
111 elements[row - 1][col - 1] = escore;
114 maxscore = ((Double) pae_obj.get("max_predicted_aligned_error"))
119 public ContactListI getContactList(final int _column)
121 if (_column < 0 || _column >= elements.length)
126 return new ContactListImpl(new ContactListProviderI()
129 public int getPosition()
135 public int getContactHeight()
141 public double getContactAt(int column)
143 if (column < 0 || column >= elements[_column].length)
147 // TODO Auto-generated method stub
148 return elements[_column][column];
154 public float getMin()
160 public float getMax()
166 public boolean hasReferenceSeq()
168 return (refSeq != null);
172 public SequenceI getReferenceSeq()