package jalview.ws.datamodel.alphafold;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import org.json.simple.JSONObject;
+
import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactListImpl;
import jalview.datamodel.ContactListProviderI;
import jalview.datamodel.ContactMatrixI;
-import jalview.datamodel.ContactRange;
+import jalview.datamodel.FloatContactMatrix;
+import jalview.datamodel.GroupSet;
+import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceI;
+import jalview.io.FileFormatException;
+import jalview.util.MapList;
+import jalview.util.MapUtils;
+import jalview.ws.dbsources.EBIAlfaFold;
-public class PAEContactMatrix implements ContactMatrixI
+/**
+ * routines and class for holding predicted alignment error matrices as produced
+ * by alphafold et al.
+ *
+ * getContactList(column) returns the vector of predicted alignment errors for
+ * reference position given by column getElementAt(column, i) returns the
+ * predicted superposition error for the ith position when column is used as
+ * reference
+ *
+ * Many thanks to Ora Schueler Furman for noticing that earlier development
+ * versions did not show the PAE oriented correctly
+ *
+ * @author jprocter
+ *
+ */
+public class PAEContactMatrix extends
+ MappableContactMatrix<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 FileFormatException
+ {
+ setRefSeq(_refSeq);
+ // convert the lists to primitive arrays and store
+
+ 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)
+ {
+ mappedMatrix=new FloatContactMatrix(matrix);
+ setRefSeq(_refSeq);
+ }
+
+ /**
+ * 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, new FloatContactMatrix(elements2,grps2));
+ toSeq = newFromMapList;
+ }
+
+ public PAEContactMatrix(SequenceI _refSeq,
+ ContactMatrixI floatContactMatrix)
+ {
+ mappedMatrix = floatContactMatrix;
+ setRefSeq(_refSeq);
+ }
+ public PAEContactMatrix(SequenceI _refSeq, MapList newFromMapList,
+ ContactMatrixI floatContactMatrix)
+ {
+ mappedMatrix = floatContactMatrix;
+ setRefSeq(_refSeq);
+ toSeq = newFromMapList;
+ }
+ @Override
+ protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
+ MapList newFromMapList)
+ {
+ return new PAEContactMatrix(newRefSeq, newFromMapList, mappedMatrix);
+ }
+
+ /**
+ * parse a sane JSON representation of the pAE and update the mappedMatrix
+ *
+ * @param pae_obj
+ */
@SuppressWarnings("unchecked")
- public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj) throws Exception
+ private void parse_version_2_pAE(Map<String, Object> pae_obj)
{
- refSeq = _refSeq;
- while (refSeq.getDatasetSequence()!=null)
+ float maxscore = -1;
+ // look for a maxscore element - if there is one...
+ try
+ {
+ // 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();
+ } catch (Throwable t)
{
- refSeq=refSeq.getDatasetSequence();
+ // ignore if a key is not found.
}
- // 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)
+ List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
+ .getFirst(pae_obj, "predicted_aligned_error", "pae"));
+ float[][] 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())
{
- maxcol=col;
+ Object d = scores.next();
+ if (d instanceof Double)
+ {
+ elements[col][row] = ((Double) d).longValue();
+ }
+ else
+ {
+ elements[col][row] = (float) ((Long) d).longValue();
+ }
+
+ if (maxscore < elements[col][row])
+ {
+ maxscore = elements[col][row];
+ }
+ col++;
}
- elements[row-1][col-1]=escore;
+ row++;
+ col = 0;
}
-
- maxscore = ((Double) pae_obj.get("max_predicted_aligned_error")).floatValue();
+ mappedMatrix=new FloatContactMatrix(elements);
}
- @Override
- public ContactListI getContactList(final int _column)
+ /**
+ * 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();
+ // two pass - to allocate the elements array
- return new ContactListImpl(new ContactListProviderI()
+ int maxrow=-1,maxcol=-1;
+ while (rows.hasNext())
{
- @Override
- public int getContactHeight()
+ int row = rows.next().intValue();
+ int col = cols.next().intValue();
+ if (maxrow < row)
{
- return maxcol-1;
+ maxrow = row;
}
-
- @Override
- public double getContactAt(int column)
+ if (maxcol < col)
{
- if (column<0 || column>=elements[_column].length)
- {
- return -1;
- }
- // TODO Auto-generated method stub
- return elements[_column][column];
+ maxcol = col;
}
- });
+
+ }
+ rows = ((List<Long>) pae_obj.get("residue1")).iterator();
+ cols = ((List<Long>) pae_obj.get("residue2")).iterator();
+ Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
+ .iterator();
+ float[][] elements = new float[maxcol][maxrow];
+ 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[col - 1][row-1] = escore;
+ }
+
+ mappedMatrix=new FloatContactMatrix(elements);
}
@Override
- public float getMin()
+ public String getAnnotDescr()
{
- return 0;
+ return "Predicted Alignment Error"
+ + ((refSeq == null) ? "" : (" for " + refSeq.getName()));
}
@Override
- public float getMax()
+ public String getAnnotLabel()
{
- return maxscore;
+ 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 boolean hasReferenceSeq()
+ public String getType()
{
- return (refSeq!=null);
+ return PAEMATRIX;
}
+
+ 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
- public SequenceI getReferenceSeq()
+ public boolean equals(Object obj)
{
- return refSeq;
+ return super.equals(obj);
+ }
+ @Override
+ public int hashCode()
+ {
+ return super.hashCode();
}
-
}
git://source.jalview.org / jalview.git / blobdiff