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<PAEContactMatrix> implements ContactMatrixI
{
-
- SequenceI refSeq = null;
-
- /**
- * the length that refSeq is expected to be (excluding gaps, of course)
- */
- int length;
-
int maxrow = 0, maxcol = 0;
- int[] indices1, indices2;
-
float[][] elements;
float maxscore;
- private void setRefSeq(SequenceI _refSeq)
- {
- refSeq = _refSeq;
- while (refSeq.getDatasetSequence() != null)
- {
- refSeq = refSeq.getDatasetSequence();
- }
- length = _refSeq.getEnd() - _refSeq.getStart() + 1;
- }
@SuppressWarnings("unchecked")
public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj) throws FileFormatException
}
/**
+ * 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
}
@Override
- public ContactListI getContactList(final int _column)
+ public ContactListI getContactList(final int column)
{
- if (_column < 0 || _column >= elements.length)
+// 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;
}
@Override
public int getPosition()
{
- return _column;
+ return column;
}
@Override
}
@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;
}
- 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;
}
@Override
- public boolean hasReferenceSeq()
- {
- return (refSeq != null);
- }
-
- @Override
- public SequenceI getReferenceSeq()
- {
- return refSeq;
- }
-
- @Override
public String getAnnotDescr()
{
return "Predicted Alignment Error"+((refSeq==null) ? "" : (" for " + refSeq.getName()));
{
return length;
}
- List<BitSet> 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<BinaryNode> 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<BinaryNode>();
- 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<BitSet> 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<BitSet,Color> 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<BitSet> 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;
- }
-
+
public static void validateContactMatrixFile(String fileName) throws FileFormatException,IOException
{
FileInputStream infile=null;
{
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;
}
}
git://source.jalview.org / jalview.git / blobdiff