--- /dev/null
+package jalview.ws.datamodel.alphafold;
+
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactListImpl;
+import jalview.datamodel.ContactListProviderI;
+import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.ContactRange;
+import jalview.datamodel.SequenceI;
+
+public class PAEContactMatrix implements ContactMatrixI
+{
+
+ SequenceI refSeq=null;
+ int maxrow=0,maxcol=0;
+ int[] indices1,indices2;
+ float[][] elements;
+ float maxscore;
+
+ @SuppressWarnings("unchecked")
+ public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj) throws Exception
+ {
+ refSeq = _refSeq;
+ while (refSeq.getDatasetSequence()!=null)
+ {
+ refSeq=refSeq.getDatasetSequence();
+ }
+ // convert the lists to primitive arrays and store
+ int length = _refSeq.getEnd()-_refSeq.getStart()+1;
+
+ // 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();
+
+ elements=new float[length][length];
+ while (scores.hasNext()) {
+ float escore=scores.next().floatValue();
+ int row=rows.next().intValue();
+ int col=cols.next().intValue();
+ if (maxrow<row)
+ {
+ maxrow=row;
+ }
+ if (maxcol<col)
+ {
+ maxcol=col;
+ }
+ elements[row-1][col-1]=escore;
+ }
+
+ maxscore = ((Double) pae_obj.get("max_predicted_aligned_error")).floatValue();
+ }
+
+ @Override
+ public ContactListI getContactList(final int _column)
+ {
+
+ return new ContactListImpl(new ContactListProviderI()
+ {
+ @Override
+ public int getContactHeight()
+ {
+ return maxcol-1;
+ }
+
+ @Override
+ public double getContactAt(int column)
+ {
+ if (column<0 || column>=elements[_column].length)
+ {
+ return -1;
+ }
+ // TODO Auto-generated method stub
+ return elements[_column][column];
+ }
+ });
+ }
+
+ @Override
+ public float getMin()
+ {
+ return 0;
+ }
+
+ @Override
+ public float getMax()
+ {
+ return maxscore;
+ }
+
+ @Override
+ public boolean hasReferenceSeq()
+ {
+ return (refSeq!=null);
+ }
+
+ @Override
+ public SequenceI getReferenceSeq()
+ {
+ return refSeq;
+ }
+
+}