X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdatamodel%2Falphafold%2FPAEContactMatrix.java;h=ce072e06a0477b8b3245154dae6548758618a568;hb=beb2fee66dde629e3bbb7febb38d0116e1a64df2;hp=af8dfc3b327c4358ad66a3e743c0b3f6a4386f53;hpb=59f8f1014e5ef09bf93c8a2cabe11b846012a521;p=jalview.git diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java index af8dfc3..ce072e0 100644 --- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java +++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java @@ -1,48 +1,200 @@ package jalview.ws.datamodel.alphafold; +import java.awt.Color; +import java.io.BufferedInputStream; +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.util.ArrayList; +import java.util.BitSet; +import java.util.HashMap; import java.util.Iterator; import java.util.List; import java.util.Map; +import java.util.Map.Entry; +import org.json.simple.JSONObject; + +import jalview.analysis.AverageDistanceEngine; +import jalview.bin.Console; +import jalview.datamodel.Annotation; +import jalview.datamodel.BinaryNode; import jalview.datamodel.ContactListI; import jalview.datamodel.ContactListImpl; import jalview.datamodel.ContactListProviderI; import jalview.datamodel.ContactMatrixI; +import jalview.datamodel.GroupSet; +import jalview.datamodel.GroupSetI; +import jalview.datamodel.Mapping; +import jalview.datamodel.SequenceDummy; import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; +import jalview.io.FileFormatException; +import jalview.io.FileParse; +import jalview.util.MapList; +import jalview.util.MapUtils; +import jalview.ws.dbsources.EBIAlfaFold; -public class PAEContactMatrix implements ContactMatrixI +public class PAEContactMatrix extends + MappableContactMatrix implements ContactMatrixI { - SequenceI refSeq = null; int maxrow = 0, maxcol = 0; - int[] indices1, indices2; float[][] elements; float maxscore; + @SuppressWarnings("unchecked") public PAEContactMatrix(SequenceI _refSeq, Map pae_obj) - throws Exception + throws FileFormatException { - refSeq = _refSeq; - while (refSeq.getDatasetSequence() != null) + setRefSeq(_refSeq); + // convert the lists to primitive arrays and store + + if (!MapUtils.containsAKey(pae_obj, "predicted_aligned_error", "pae")) { - refSeq = refSeq.getDatasetSequence(); + parse_version_1_pAE(pae_obj); + return; } - // convert the lists to primitive arrays and store - int length = _refSeq.getEnd() - _refSeq.getStart() + 1; + 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; + + } + + /** + * 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; + } + /** + * parse a sane JSON representation of the pAE + * + * @param pae_obj + */ + @SuppressWarnings("unchecked") + private void parse_version_2_pAE(Map pae_obj) + { + 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) + { + // ignore if a key is not found. + } + List> scoreRows = ((List>) MapUtils + .getFirst(pae_obj, "predicted_aligned_error", "pae")); + elements = new float[scoreRows.size()][scoreRows.size()]; + int row = 0, col = 0; + for (List scoreRow : scoreRows) + { + Iterator 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(); + } + + if (maxscore < elements[row][col - 1]) + { + maxscore = elements[row][col - 1]; + } + } + 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 pae_obj) + { // assume indices are with respect to range defined by _refSeq on the // dataset refSeq Iterator rows = ((List) pae_obj.get("residue1")).iterator(); Iterator cols = ((List) pae_obj.get("residue2")).iterator(); + // two pass - to allocate the elements array + while (rows.hasNext()) + { + int row = rows.next().intValue(); + int col = cols.next().intValue(); + if (maxrow < row) + { + maxrow = row; + } + if (maxcol < col) + { + maxcol = col; + } + + } + rows = ((List) pae_obj.get("residue1")).iterator(); + cols = ((List) pae_obj.get("residue2")).iterator(); Iterator scores = ((List) pae_obj.get("distance")) .iterator(); - - elements = new float[length][length]; + elements = new float[maxrow][maxcol]; while (scores.hasNext()) { float escore = scores.next().floatValue(); @@ -59,14 +211,14 @@ public class PAEContactMatrix implements ContactMatrixI 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 - public ContactListI getContactList(final int _column) + public ContactListI getContactList(final int column) { - if (_column < 0 || _column >= elements.length) + if (column < 0 || column >= elements.length) { return null; } @@ -74,25 +226,36 @@ public class PAEContactMatrix implements ContactMatrixI return new ContactListImpl(new ContactListProviderI() { @Override + public int getPosition() + { + return column; + } + + @Override public int getContactHeight() { return maxcol - 1; } @Override - public double getContactAt(int column) + public double getContactAt(int mcolumn) { - if (column < 0 || column >= elements[_column].length) + if (mcolumn < 0 || mcolumn >= elements[column].length) { return -1; } - // TODO Auto-generated method stub - return elements[_column][column]; + return elements[column][mcolumn]; } }); } @Override + protected double getElementAt(int _column, int i) + { + return elements[_column][i]; + } + + @Override public float getMin() { return 0; @@ -105,15 +268,77 @@ public class PAEContactMatrix implements ContactMatrixI } @Override - public boolean hasReferenceSeq() + public String getAnnotDescr() { - return (refSeq != null); + return "Predicted Alignment Error" + + ((refSeq == null) ? "" : (" for " + refSeq.getName())); } @Override - public SequenceI getReferenceSeq() + public String getAnnotLabel() { - return refSeq; + 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; + } + 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) paeDict); + if (matrix.getWidth() <= 0) + { + throw new FileFormatException( + "No data in PAE matrix read from '" + fileName + "'"); + } + } + @Override + protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq, + MapList newFromMapList) + { + PAEContactMatrix pae = new PAEContactMatrix(newRefSeq, newFromMapList, + elements, new GroupSet(grps)); + return pae; + } }