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.FloatContactMatrix;
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;
+/**
+ * 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
{
- int maxrow = 0, maxcol = 0;
-
-
- float[][] elements;
-
- float maxscore;
-
-
@SuppressWarnings("unchecked")
public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
throws FileFormatException
*/
public PAEContactMatrix(SequenceI _refSeq, float[][] matrix)
{
+ mappedMatrix=new FloatContactMatrix(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;
-
}
/**
public PAEContactMatrix(SequenceI newRefSeq, MapList newFromMapList,
float[][] elements2, GroupSet grps2)
{
- this(newRefSeq, elements2);
+ 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;
- grps = grps2;
+ }
+
+ @Override
+ protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
+ MapList newFromMapList)
+ {
+ return new PAEContactMatrix(newRefSeq, newFromMapList, mappedMatrix);
}
/**
- * parse a sane JSON representation of the pAE
+ * parse a sane JSON representation of the pAE and update the mappedMatrix
*
* @param pae_obj
*/
@SuppressWarnings("unchecked")
private void parse_version_2_pAE(Map<String, Object> pae_obj)
{
- maxscore = -1;
+ float maxscore = -1;
// look for a maxscore element - if there is one...
try
{
}
List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
.getFirst(pae_obj, "predicted_aligned_error", "pae"));
- elements = new float[scoreRows.size()][scoreRows.size()];
+ float[][] elements = new float[scoreRows.size()][scoreRows.size()];
int row = 0, col = 0;
for (List<Long> scoreRow : scoreRows)
{
Object d = scores.next();
if (d instanceof Double)
{
- elements[row][col++] = ((Double) d).longValue();
+ elements[col][row] = ((Double) d).longValue();
}
else
{
- elements[row][col++] = (float) ((Long) d).longValue();
+ elements[col][row] = (float) ((Long) d).longValue();
}
- if (maxscore < elements[row][col - 1])
+ if (maxscore < elements[col][row])
{
- maxscore = elements[row][col - 1];
+ maxscore = elements[col][row];
}
+ col++;
}
row++;
col = 0;
}
- maxcol = length;
- maxrow = length;
+ mappedMatrix=new FloatContactMatrix(elements);
}
/**
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
+
+ int maxrow=-1,maxcol=-1;
while (rows.hasNext())
{
int row = rows.next().intValue();
cols = ((List<Long>) pae_obj.get("residue2")).iterator();
Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
.iterator();
- elements = new float[maxrow][maxcol];
+ float[][] elements = new float[maxcol][maxrow];
while (scores.hasNext())
{
float escore = scores.next().floatValue();
{
maxcol = col;
}
- elements[row - 1][col - 1] = escore;
- }
-
- maxscore = ((Double) MapUtils.getFirst(pae_obj,
- "max_predicted_aligned_error", "max_pae")).floatValue();
- }
-
- @Override
- public ContactListI getContactList(final int column)
- {
- if (column < 0 || column >= elements.length)
- {
- return null;
+ elements[col - 1][row-1] = escore;
}
- return new ContactListImpl(new ContactListProviderI()
- {
- @Override
- public int getPosition()
- {
- return column;
- }
-
- @Override
- public int getContactHeight()
- {
- return maxcol - 1;
- }
-
- @Override
- public double getContactAt(int mcolumn)
- {
- if (mcolumn < 0 || mcolumn >= elements[column].length)
- {
- return -1;
- }
- return elements[column][mcolumn];
- }
- });
- }
-
- @Override
- protected double getElementAt(int _column, int i)
- {
- return elements[_column][i];
- }
-
- @Override
- public float getMin()
- {
- return 0;
- }
-
- @Override
- public float getMax()
- {
- return maxscore;
+ mappedMatrix=new FloatContactMatrix(elements);
}
@Override
return PAEMATRIX;
}
- @Override
- public int getWidth()
- {
- return length;
- }
- @Override
- public int getHeight()
- {
- return length;
- }
public static void validateContactMatrixFile(String fileName)
throws FileFormatException, IOException
{
}
}
@Override
- protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
- MapList newFromMapList)
+ public boolean equals(Object obj)
+ {
+ return super.equals(obj);
+ }
+ @Override
+ public int hashCode()
{
- PAEContactMatrix pae = new PAEContactMatrix(newRefSeq, newFromMapList,
- elements, new GroupSet(grps));
- return pae;
+ return super.hashCode();
}
}
git://source.jalview.org / jalview.git / blobdiff