{
return "Contact Matrix";
}
--
- List<BitSet> groups = null;
-
- @Override
- public void updateGroups(List<BitSet> colGroups)
- {
- groups = colGroups;
- colorMap = new HashMap<>();
- }
-
- @Override
- public boolean hasGroups()
- {
- return groups != null && groups.size() > 0;
- }
-
- @Override
- public List<BitSet> getGroups()
- {
- return groups;
- }
-
- @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<>();
-
+ GroupSet grps = new GroupSet();
-
@Override
- public Color getColourForGroup(BitSet bs)
+ public GroupSetI getGroupSet()
{
- if (bs == null)
- {
- return Color.white;
- }
- Color groupCol = colorMap.get(bs);
- if (groupCol == null)
- {
- return Color.white;
- }
- return groupCol;
+ return grps;
}
--
@Override
- public void setColorForGroup(BitSet bs, Color color)
+ public void setGroupSet(GroupSet makeGroups)
{
- colorMap.put(bs, color);
+ grps = makeGroups;
}
--
public static String contactToFloatString(ContactMatrixI cm)
{
StringBuilder sb = new StringBuilder();
float[][] vals = new float[cols][rows];
StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
int c = 0, r = 0;
--
while (tabsep.hasMoreTokens())
{
double elem = Double.valueOf(tabsep.nextToken());
}
if (c >= vals.length)
{
--
break;
}
}
Console.warn(
"Ignoring additional elements for Float string to contact matrix parsing.");
}
--
return vals;
}
}
String getType();
int getWidth();
--
int getHeight();
-
+ public GroupSetI getGroupSet();
+
+ /// proxy methods to simplify use of the interface
+ /// Mappable contact matrices can override these to perform mapping
+
+ default public boolean hasGroupSet()
+ {
+ return getGroupSet() != null;
+ }
default boolean hasGroups()
{
default Color getColourForGroup(BitSet bs)
{
- return Color.white;
- };
+ if (hasGroupSet())
+ {
+ return getGroupSet().getColourForGroup(bs);
+ }
+ else
+ {
+ return Color.white;
+ }
+ }
+
+ void setGroupSet(GroupSet makeGroups);
-
}
import java.util.HashMap;
import java.util.List;
+import jalview.util.MapList;
+import jalview.ws.datamodel.alphafold.MappableContactMatrix;
-
/**
* Dummy contact matrix based on sequence distance
*
* @author jprocter
*
*/
-public class SeqDistanceContactMatrix implements ContactMatrixI
+public class SeqDistanceContactMatrix
+ extends MappableContactMatrix<SeqDistanceContactMatrix>
+ implements ContactMatrixI
{
private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
--
private int width = 0;
public SeqDistanceContactMatrix(int width)
{
return width;
}
--
- private List<BitSet> groups = null;
-
- @Override
- public void updateGroups(List<BitSet> colGroups)
- {
- groups = colGroups;
- }
-
@Override
- public boolean hasGroups()
+ protected double getElementAt(int _column, int i)
{
- return groups != null;
+ return Math.abs(_column - i);
}
--
- @Override
- public List<BitSet> getGroups()
- {
- return groups;
- }
-
- HashMap<BitSet, Color> colorMap = new HashMap<>();
-
@Override
- public Color getColourForGroup(BitSet bs)
+ protected SeqDistanceContactMatrix newMappableContactMatrix(
+ SequenceI newRefSeq, MapList newFromMapList)
{
- 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);
+ return new SeqDistanceContactMatrix(width);
}
}
super(inFile, sourceType, tempfacType);
}
+ public JmolParser(FileParse fp, boolean doXferSettings) throws IOException
+ {
+ super(fp, doXferSettings);
+ }
-
public JmolParser(FileParse fp) throws IOException
{
super(fp);
// add a PAEMatrix if set (either by above or otherwise)
if (hasPAEMatrix())
{
- Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
- EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
- null, false, false, null);
-
- if (al.getAlignmentAnnotation() != null)
+ try
{
- for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
+ Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
+ EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
- null, false, false);
++ null, false, false, null);
+
+ if (al.getAlignmentAnnotation() != null)
{
- annotations.add(alann);
+ for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
+ {
+ annotations.add(alann);
+ }
}
+ } catch (Throwable ff)
+ {
+ Console.error("Couldn't import PAE Matrix from " + getPAEMatrix(),
+ ff);
+ warningMessage += "Couldn't import PAE Matrix"
+ + getNewlineString() + ff.getLocalizedMessage()
+ + getNewlineString();
}
}
-
} catch (OutOfMemoryError er)
{
System.out.println(
return false;
}
ColumnSelection cs = av.getColumnSelection();
--
HiddenColumns hc = av.getAlignment().getHiddenColumns();
int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
: colm;
}
return false;
}
--
private BitSet createColumnGroupFor(Vector<BinaryNode> l, Color col)
{
BitSet gp = new BitSet();
{
continue;
}
+ // TODO - sort indices for faster lookup
-
ColumnSelection cs = av.getColumnSelection();
HiddenColumns hc = av.getAlignment().getHiddenColumns();
+ ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation);
+ MappableContactMatrixI mcm = null;
+ int offp;
+ if (cm instanceof MappableContactMatrixI)
+ {
+ mcm = (MappableContactMatrixI) cm;
+ int[] seqpos = mcm.getMappedPositionsFor(
+ tp.assocAnnotation.sequenceRef, colm);
+ if (seqpos == null)
+ {
+ // no mapping for this column.
+ continue;
+ }
+ // TODO: handle ranges...
+ offp = seqpos[0];
+ }
+ else
{
- int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
+ offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
: colm;
-
- if (!av.hasHiddenColumns() || hc.isVisible(offp - 1))
+ }
+ if (!av.hasHiddenColumns() || hc.isVisible(offp - 1))
+ {
+ if (cs.contains(offp - 1))
{
- if (cs.contains(offp - 1))
- {
- cs.removeElement(offp - 1);
- }
- else
- {
- cs.addElement(offp - 1);
- }
+ cs.removeElement(offp - 1);
+ }
+ else
+ {
+ cs.addElement(offp - 1);
}
}
}
{
xmlmat.setCutHeight(cm.getCutHeight());
}
--
// set/get properties
+ if (cm instanceof MappableContactMatrixI)
+ {
+ jalview.util.MapList mlst = ((MappableContactMatrixI) cm)
+ .getMapFor(annotation.sequenceRef);
+ if (mlst != null)
+ {
+ MapListType mp = new MapListType();
+ List<int[]> r = mlst.getFromRanges();
+ for (int[] range : r)
+ {
+ MapListFrom mfrom = new MapListFrom();
+ mfrom.setStart(range[0]);
+ mfrom.setEnd(range[1]);
+ // mp.addMapListFrom(mfrom);
+ mp.getMapListFrom().add(mfrom);
+ }
+ r = mlst.getToRanges();
+ for (int[] range : r)
+ {
+ MapListTo mto = new MapListTo();
+ mto.setStart(range[0]);
+ mto.setEnd(range[1]);
+ // mp.addMapListTo(mto);
+ mp.getMapListTo().add(mto);
+ }
+ mp.setMapFromUnit(
+ BigInteger.valueOf(mlst.getFromRatio()));
+ mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
+ xmlmat.setMapping(mp);
+ }
+ }
+ // and add to model
an.getContactmatrix().add(xmlmat);
}
}
}
+ private String stringifyBitset(BitSet gp)
+ {
+ StringBuilder sb = new StringBuilder();
+ for (long val : gp.toLongArray())
+ {
+ if (sb.length() > 0)
+ {
+ sb.append(",");
+ }
+ sb.append(val);
+ }
+ return sb.toString();
+ }
+
+ private BitSet deStringifyBitset(String stringified)
+ {
+ if ("".equals(stringified) || stringified == null)
+ {
+ return new BitSet();
+ }
+ String[] longvals = stringified.split(",");
+ long[] newlongvals = new long[longvals.length];
+ for (int lv = 0; lv < longvals.length; lv++)
+ {
+ try
+ {
+ newlongvals[lv] = Long.valueOf(longvals[lv]);
+ } catch (Exception x)
+ {
+ errorMessage += "Couldn't destringify bitset from: '" + stringified
+ + "'";
+ newlongvals[lv] = 0;
+ }
+ }
+ return BitSet.valueOf(newlongvals);
+
+ }
-
private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
{
AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
Console.log.info(
"Ignoring additional clusterings for contact matrix");
}
--
String treeMethod = xmlmat.getTreeMethod();
double thresh = xmlmat.getCutHeight() != null
? xmlmat.getCutHeight()
* shown when no data available from map
*/
Color no_data;
--
/**
* shown for region not currently visible - should normally not see this
*/
Color hidden;
--
/**
* linear shading scheme min/max
*/
x++;
continue;
}
+ // ContactListI from viewport can map column -> group
Color gpcol = (cm == null) ? Color.white
- : cm.getColourForGroup(cm.getGroupsFor(column));
+ : contacts.getColourForGroup(); // cm.getColourForGroup(cm.getGroupsFor(column));
-
// feature still in development - highlight or omit regions hidden in
// the alignment - currently marks them as red rows
boolean maskHiddenCols = false;
(int) (((float) (col.getBlue() + gpcol.getBlue())) / 2f));
}
g.setColor(col);
--
if (cgeom.pixels_step > 1)
{
g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
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
{
setRefSeq(_refSeq);
// convert the lists to primitive arrays and store
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;
}
@Override
- public ContactListI getContactList(final int _column)
+ 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)
+ if (column < 0 || column >= elements.length)
{
return null;
}
{
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)
+ public static void validateContactMatrixFile(String fileName)
+ throws FileFormatException, IOException
{
- 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)
+ FileInputStream infile = null;
+ try
{
- float cut = abs ? (float) (thresh / height) : thresh;
- Console.debug("Threshold " + cut + " for height=" + height);
-
- nodegroups = clusterer.groupNodes(cut);
- }
- else
+ infile = new FileInputStream(new File(fileName));
+ } catch (Throwable t)
{
- nodegroups = new ArrayList<BinaryNode>();
- nodegroups.add(clusterer.getTopNode());
+ new IOException("Couldn't open " + fileName, t);
}
-
- this.abs = abs;
- this.thresh = thresh;
- groups = new ArrayList<>();
- for (BinaryNode root : nodegroups)
+ JSONObject paeDict = null;
+ try
{
- 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)
+ paeDict = EBIAlfaFold.parseJSONtoPAEContactMatrix(infile);
+ } catch (Throwable t)
{
- groups = colGroups;
+ new FileFormatException("Couldn't parse " + fileName
+ + " as a JSON dict or array containing a dict");
}
- }
- @Override
- public BitSet getGroupsFor(int column)
- {
- for (BitSet gp : groups)
+ PAEContactMatrix matrix = new PAEContactMatrix(
+ new SequenceDummy("Predicted"), (Map<String, Object>) paeDict);
+ if (matrix.getWidth() <= 0)
{
- 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;
+ throw new FileFormatException(
+ "No data in PAE matrix read from '" + fileName + "'");
}
- 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()
+ protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
+ MapList newFromMapList)
{
- return treeType;
+ PAEContactMatrix pae = new PAEContactMatrix(newRefSeq, newFromMapList,
+ elements, new GroupSet(grps));
+ return pae;
}
}
}
ContactMatrixI matrix = new PAEContactMatrix(sequence,
(Map<String, Object>) paeDict);
- ((PAEContactMatrix) matrix).makeGroups(5f, true);
+ matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true));
AlignmentAnnotation cmannot = sequence.addContactList(matrix);
+ if (label != null)
+ cmannot.label = label;
pdbAlignment.addAnnotation(cmannot);
return true;
return false;
}
- ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
+ SequenceI seq = sm.getSequence();
+ ContactMatrixI matrix = new PAEContactMatrix(seq,
(Map<String, Object>) pae_obj);
- ((PAEContactMatrix) matrix).makeGroups(5f, true);
- AlignmentAnnotation cmannot = seq.addContactList(matrix);
+ matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true));
+ AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
- sm.getSequence().addAlignmentAnnotation(cmannot);
-
+ /* this already happens in Sequence.addContactList()
+ seq.addAlignmentAnnotation(cmannot);
+ */
return true;
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.03.17 at 05:31:44 PM GMT
+// Generated on: 2023.05.13 at 06:58:41 PM BST
//
++
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
++
/**
* <p>
* Java class for MatrixType complex type.
}
System.out.println("\\");
}
--
}
}
Assert.assertNotSame(dummyMat.getNewick(), "");
AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
al.addAnnotation(paeCm);
+ // verify store/restore of group bitsets
+ for (BitSet gp : dummyMat.getGroups())
+ {
+ StringBuilder sb = new StringBuilder();
+ for (long val : gp.toLongArray())
+ {
+ if (sb.length() > 0)
+ {
+ sb.append(",");
+ }
+ sb.append(val);
+ }
+ String[] longvals = sb.toString().split(",");
+ long[] newlongvals = new long[longvals.length];
+ for (int lv = 0; lv < longvals.length; lv++)
+ {
+ try
+ {
+ newlongvals[lv] = Long.valueOf(longvals[lv]);
+ } catch (Exception x)
+ {
+ Assert.fail("failed to deserialise bitset element ");
+ }
+ }
+ BitSet newGp = BitSet.valueOf(newlongvals);
+ assertTrue(gp.equals(newGp));
+ }
-
File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
".jvp");
new Jalview2XML(false).saveState(tfile);
ContactMatrixI restoredMat = newSeq
.getContactMatrixFor(newSeq.getAnnotation()[0]);
Assert.assertNotNull(restoredMat);
+ MapList oldMap = ((MappableContactMatrixI) dummyMat).getMapFor(sq);
+ MapList newMap = ((MappableContactMatrixI) restoredMat)
+ .getMapFor(newSeq);
+ Assert.assertEquals(oldMap.getFromRanges(), newMap.getFromRanges());
+ Assert.assertEquals(oldMap.getToRanges(), newMap.getToRanges());
+ Assert.assertEquals(oldMap.getFromRatio(), newMap.getFromRatio());
+ Assert.assertEquals(oldMap.getToRatio(), newMap.getToRatio());
-
for (i = sq.getLength() - 1; i >= 0; i--)
{
ContactListI oldCM = dummyMat.getContactList(i),
Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
--
}
}
git://source.jalview.org / jalview.git / commitdiff