X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdatamodel%2Falphafold%2FPAEContactMatrix.java;h=1ec856b67ac49045550cd5f0279008e17b19d4c1;hb=e134764b7eec841cb56a417250f2dd898680f985;hp=3298a9629d29b63b1c88064a670539899afc2551;hpb=892e857760e779796e156b4fa36d97d8d31e73e1;p=jalview.git diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java index 3298a96..1ec856b 100644 --- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java +++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java @@ -1,14 +1,22 @@ package jalview.ws.datamodel.alphafold; +import java.awt.Color; +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 jalview.analysis.AverageDistanceEngine; +import jalview.bin.Console; +import jalview.datamodel.BinaryNode; import jalview.datamodel.ContactListI; import jalview.datamodel.ContactListImpl; import jalview.datamodel.ContactListProviderI; import jalview.datamodel.ContactMatrixI; import jalview.datamodel.SequenceI; +import jalview.util.MapUtils; public class PAEContactMatrix implements ContactMatrixI { @@ -28,18 +36,23 @@ public class PAEContactMatrix implements ContactMatrixI float maxscore; - @SuppressWarnings("unchecked") - public PAEContactMatrix(SequenceI _refSeq, Map pae_obj) + private void setRefSeq(SequenceI _refSeq) { refSeq = _refSeq; while (refSeq.getDatasetSequence() != null) { refSeq = refSeq.getDatasetSequence(); } - // convert the lists to primitive arrays and store length = _refSeq.getEnd() - _refSeq.getStart() + 1; + } - if (!pae_obj.containsKey("predicted_aligned_error")) + @SuppressWarnings("unchecked") + public PAEContactMatrix(SequenceI _refSeq, Map pae_obj) + { + 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; @@ -51,25 +64,60 @@ public class PAEContactMatrix implements ContactMatrixI } /** + * 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 pae_obj) { - elements = new float[length][length]; // this is never going to be reached by the integer rounding.. or is it ? - maxscore = ((Double) pae_obj.get("max_predicted_aligned_error")) - .floatValue(); - Iterator> scoreRows = ((List>) pae_obj - .get("predicted_aligned_error")).iterator(); + maxscore = ((Double) MapUtils.getFirst(pae_obj, + "max_predicted_aligned_error", "max_pae")).floatValue(); + List> scoreRows = ((List>) MapUtils + .getFirst(pae_obj, "predicted_aligned_error", "pae")); + elements = new float[scoreRows.size()][scoreRows.size()]; int row = 0, col = 0; - while (scoreRows.hasNext()) + for (List scoreRow : scoreRows) { - Iterator scores = scoreRows.next().iterator(); + Iterator scores = scoreRow.iterator(); while (scores.hasNext()) { - elements[row][col++] = scores.next(); + 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; @@ -84,6 +132,7 @@ public class PAEContactMatrix implements ContactMatrixI * * @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 @@ -92,7 +141,7 @@ public class PAEContactMatrix implements ContactMatrixI Iterator cols = ((List) pae_obj.get("residue2")).iterator(); Iterator scores = ((List) pae_obj.get("distance")) .iterator(); - + // assume square matrix elements = new float[length][length]; while (scores.hasNext()) { @@ -110,8 +159,8 @@ 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 @@ -143,7 +192,6 @@ public class PAEContactMatrix implements ContactMatrixI { return -1; } - // TODO Auto-generated method stub return elements[_column][column]; } }); @@ -176,12 +224,176 @@ public class PAEContactMatrix implements ContactMatrixI @Override public String getAnnotDescr() { - return "Predicted Alignment Error for " + refSeq.getName(); + return "Predicted Alignment Error" + + ((refSeq == null) ? "" : (" for " + refSeq.getName())); } @Override public String getAnnotLabel() { - return "pAE Matrix"; + 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; + } + + List groups = null; + + @Override + public boolean hasGroups() + { + return groups != null; + } + + String newick = null; + + @Override + public String getNewick() + { + return newick; + } + + @Override + public boolean hasTree() + { + return newick != null && newick.length() > 0; + } + + boolean abs; + + double thresh; + + String treeType = null; + + public void makeGroups(float thresh, boolean abs) + { + AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null, + this); + double height = clusterer.findHeight(clusterer.getTopNode()); + newick = new jalview.io.NewickFile(clusterer.getTopNode(), false, true) + .print(); + treeType = "UPGMA"; + Console.trace("Newick string\n" + newick); + + List nodegroups; + if (abs ? height > thresh : 0 < thresh && thresh < 1) + { + float cut = abs ? (float) (thresh / height) : thresh; + Console.debug("Threshold " + cut + " for height=" + height); + + nodegroups = clusterer.groupNodes(cut); + } + else + { + nodegroups = new ArrayList(); + nodegroups.add(clusterer.getTopNode()); + } + this.abs = abs; + this.thresh = thresh; + groups = new ArrayList<>(); + for (BinaryNode root : nodegroups) + { + BitSet gpset = new BitSet(); + for (BinaryNode leaf : clusterer.findLeaves(root)) + { + gpset.set((Integer) leaf.element()); + } + groups.add(gpset); + } + } + + @Override + public void updateGroups(List colGroups) + { + if (colGroups != null) + { + groups = colGroups; + } + } + + @Override + public BitSet getGroupsFor(int column) + { + for (BitSet gp : groups) + { + if (gp.get(column)) + { + return gp; + } + } + return ContactMatrixI.super.getGroupsFor(column); + } + + HashMap colorMap = new HashMap<>(); + + @Override + public Color getColourForGroup(BitSet bs) + { + if (bs == null) + { + return Color.white; + } + Color groupCol = colorMap.get(bs); + if (groupCol == null) + { + return Color.white; + } + return groupCol; + } + + @Override + public void setColorForGroup(BitSet bs, Color color) + { + colorMap.put(bs, color); + } + + public void restoreGroups(List newgroups, String treeMethod, + String tree, double thresh2) + { + treeType = treeMethod; + groups = newgroups; + thresh = thresh2; + newick = tree; + + } + + @Override + public boolean hasCutHeight() + { + return groups != null && thresh != 0; + } + + @Override + public double getCutHeight() + { + return thresh; + } + + @Override + public String getTreeMethod() + { + return treeType; } }