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 extends MappableContactMatrix<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
{
+
+
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, Map<String, Object> pae_obj)
+ throws FileFormatException
{
setRefSeq(_refSeq);
// convert the lists to primitive arrays and store
/**
* new matrix with specific mapping to a reference sequence
+ *
* @param newRefSeq
* @param newFromMapList
* @param elements2
- * @param grps2
+ * @param grps2
*/
- public PAEContactMatrix(SequenceI newRefSeq,
- MapList newFromMapList, float[][] elements2, GroupSet grps2)
+ public PAEContactMatrix(SequenceI newRefSeq, MapList newFromMapList,
+ float[][] elements2, GroupSet grps2)
{
- this(newRefSeq,elements2);
+ this(newRefSeq, elements2);
toSeq = newFromMapList;
- grps= grps2;
+ grps = grps2;
}
/**
while (scores.hasNext())
{
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;
cols = ((List<Long>) pae_obj.get("residue2")).iterator();
Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
.iterator();
- elements = new float[maxrow][maxcol];
+ elements = new float[maxcol][maxrow];
while (scores.hasNext())
{
float escore = scores.next().floatValue();
{
maxcol = col;
}
- elements[row - 1][col - 1] = escore;
+ elements[col - 1][row-1] = escore;
}
maxscore = ((Double) MapUtils.getFirst(pae_obj,
"max_predicted_aligned_error", "max_pae")).floatValue();
}
+ /**
+ * getContactList(column) @returns the vector of predicted alignment errors
+ * for reference position given by column
+ */
@Override
public ContactListI getContactList(final int column)
{
-// final int _column;
-// if (toSeq != null)
-// {
-// int[] word = toSeq.locateInTo(column, column);
-// if (word == null)
-// {
-// return null;
-// }
-// _column = word[0];
-// }
-// else
-// {
-// _column = column;
-// }
if (column < 0 || column >= elements.length)
{
return null;
});
}
+ /**
+ * getElementAt(column, i) @returns the predicted superposition error for the
+ * ith position when column is used as reference
+ */
@Override
protected double getElementAt(int _column, int i)
{
return elements[_column][i];
}
+
@Override
public float getMin()
{
@Override
public String getAnnotDescr()
{
- return "Predicted Alignment Error"+((refSeq==null) ? "" : (" for " + refSeq.getName()));
+ return "Predicted Alignment Error"
+ + ((refSeq == null) ? "" : (" for " + refSeq.getName()));
}
@Override
public String getAnnotLabel()
{
StringBuilder label = new StringBuilder("PAE Matrix");
- //if (this.getReferenceSeq() != null)
- //{
- // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
- //}
+ // if (this.getReferenceSeq() != null)
+ // {
+ // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+ // }
return label.toString();
}
@Override
public int getWidth()
{
- return length;
+ return maxcol;
}
@Override
public int getHeight()
{
- return length;
+ return maxrow;
}
-
- public static void validateContactMatrixFile(String fileName) throws FileFormatException,IOException
+ public static void validateContactMatrixFile(String fileName)
+ throws FileFormatException, IOException
{
- FileInputStream infile=null;
- try {
+ FileInputStream infile = null;
+ try
+ {
infile = new FileInputStream(new File(fileName));
} catch (Throwable t)
{
- new IOException("Couldn't open "+fileName,t);
+ new IOException("Couldn't open " + fileName, t);
}
-
-
- JSONObject paeDict=null;
- try {
+ 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");
+ 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)
+
+ 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+"'");
+ throw new FileFormatException(
+ "No data in PAE matrix read from '" + fileName + "'");
}
}
-
@Override
- protected PAEContactMatrix newMappableContactMatrix(
- SequenceI newRefSeq, MapList newFromMapList)
+ protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
+ MapList newFromMapList)
{
- PAEContactMatrix pae=new PAEContactMatrix(newRefSeq, newFromMapList,
- elements, new GroupSet(grps));
+ PAEContactMatrix pae = new PAEContactMatrix(newRefSeq, newFromMapList,
+ elements, new GroupSet(grps));
return pae;
- }
+ }
}
git://source.jalview.org / jalview.git / blobdiff