label.alignment_output_command = Alignment output - {0}
label.annotations = Annotations
label.structure_options = Structure Options
+label.structure_import_options = Structure Import Options
label.features = Features
label.overview_params = Overview {0}
label.paste_newick_file = Paste Newick file
label.tftype_plddt = pLDDT
label.optional = (optional)
label.choose_tempfac_type = Choose Temperature Factor type
+label.interpret_tempfac_as = Interpret Temperature Factor as
label.add_pae_matrix_file = Add PAE matrix file
label.nothing_selected = Nothing selected
+label.working_ellipsis = Working ...
\ No newline at end of file
<xs:element name="groups" type="xs:string" minOccurs="0"
maxOccurs="unbounded">
<xs:annotation>
- <xs:documentation>Comma separated series of BigIntegers formed from
+ <xs:documentation>Comma separated series of longs formed from
bitsets defining partitions on the rows/columns of the matrix
</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="property" type="vamsas:property"
minOccurs="0" maxOccurs="unbounded" />
+ <xs:element name="mapping" type="vamsas:mapListType"
+ minOccurs="0" maxOccurs="1">
+ <xs:annotation>
+ <xs:documentation>mapping from the matrix row and column positions to
+ associated reference frame</xs:documentation>
+ </xs:annotation>
+ </xs:element>
</xs:sequence>
<xs:attribute name="type" type="xs:string" use="required" />
/**
* Adds annotations to the top of the alignment annotations, in the same order
- * as their related sequences.
+ * as their related sequences. If you already have an annotation and want to
+ * add it to a sequence in an alignment use {@code addReferenceAnnotationTo}
*
* @param annotations
* the annotations to add
{
for (AlignmentAnnotation ann : annotations.get(seq))
{
- AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
- int startRes = 0;
- int endRes = ann.annotations.length;
- if (selectionGroup != null)
- {
- startRes = selectionGroup.getStartRes();
- endRes = selectionGroup.getEndRes();
- }
- copyAnn.restrict(startRes, endRes + 0);
+ addReferenceAnnotationTo(alignment, seq, ann, selectionGroup);
+ }
+ }
+ }
- /*
- * Add to the sequence (sets copyAnn.datasetSequence), unless the
- * original annotation is already on the sequence.
- */
- if (!seq.hasAnnotation(ann))
- {
- ContactMatrixI cm = seq.getDatasetSequence()
- .getContactMatrixFor(ann);
- if (cm != null)
- {
- seq.addContactListFor(copyAnn, cm);
- }
- seq.addAlignmentAnnotation(copyAnn);
- }
- // adjust for gaps
- copyAnn.adjustForAlignment();
- // add to the alignment and set visible
- alignment.addAnnotation(copyAnn);
- copyAnn.visible = true;
+ /**
+ * Make a copy of a reference annotation {@code ann} and add it to an
+ * alignment sequence {@code seq} in {@code alignment}, optionally limited to
+ * the extent of {@code selectionGroup}
+ *
+ * @param alignment
+ * @param seq
+ * @param ann
+ * @param selectionGroup
+ * - may be null
+ * @return annotation added to {@code seq and {@code alignment}
+ */
+ public static AlignmentAnnotation addReferenceAnnotationTo(
+ final AlignmentI alignment, final SequenceI seq,
+ final AlignmentAnnotation ann, final SequenceGroup selectionGroup)
+ {
+ AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
+ int startRes = 0;
+ int endRes = ann.annotations.length;
+ if (selectionGroup != null)
+ {
+ startRes = -1 + Math.min(seq.getEnd(), Math.max(seq.getStart(),
+ seq.findPosition(selectionGroup.getStartRes())));
+ endRes = -1 + Math.min(seq.getEnd(),
+ seq.findPosition(selectionGroup.getEndRes()));
+
+ }
+ copyAnn.restrict(startRes, endRes + 0);
+
+ /*
+ * Add to the sequence (sets copyAnn.datasetSequence), unless the
+ * original annotation is already on the sequence.
+ */
+ if (!seq.hasAnnotation(ann))
+ {
+ ContactMatrixI cm = seq.getDatasetSequence().getContactMatrixFor(ann);
+ if (cm != null)
+ {
+ seq.addContactListFor(copyAnn, cm);
}
+ seq.addAlignmentAnnotation(copyAnn);
}
+ // adjust for gaps
+ copyAnn.adjustForAlignment();
+ // add to the alignment and set visible
+ alignment.addAnnotation(copyAnn);
+ copyAnn.visible = true;
+ return copyAnn;
}
/**
{
distances.setValue(i, i, 0);
ContactListI jth = cm.getContactList(j);
+ if (jth == null)
+ {
+ break;
+ }
double prd = 0;
for (int indx = 0; indx < cm.getHeight(); indx++)
{
}
else
{
- _groupNodes(groups, (SequenceNode) nd.left(), threshold);
- _groupNodes(groups, (SequenceNode) nd.right(), threshold);
+ _groupNodes(groups, nd.left(), threshold);
+ _groupNodes(groups, nd.right(), threshold);
}
}
*/
SearchResultsI getSearchResults();
+ /**
+ * Retrieve a ContactListI corresponding to column in an annotation row in an
+ * alignment.
+ *
+ * @param _aa
+ * - annotation with associated matrix data
+ * @param column
+ * - column in alignment where _aa is associated
+ */
ContactListI getContactList(AlignmentAnnotation _aa, int column);
/**
}
if (cl == null && _aa.sequenceRef != null)
{
- int spos = _aa.sequenceRef.findPosition(column);
- if (spos >= _aa.sequenceRef.getStart()
- && spos <= 1 + _aa.sequenceRef.getEnd())
+ if (_aa.annotations[column] != null)
{
- cl = _aa.sequenceRef.getContactListFor(_aa,
- spos - _aa.sequenceRef.getStart());
+ // sequence associated
+ cl = _aa.sequenceRef.getContactListFor(_aa, column);
if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
{
- _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
- spos - _aa.sequenceRef.getStart());
+ int spos = _aa.sequenceRef.findPosition(column);
+ if (spos >= _aa.sequenceRef.getStart()
+ && spos <= 1 + _aa.sequenceRef.getEnd())
+ {
+ cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
+ spos - _aa.sequenceRef.getStart());
+ }
}
}
}
AlignmentAnnotation aa = cmholder.addContactList(cm);
Annotation _aa[] = new Annotation[getWidth()];
- Annotation dummy = new Annotation(0.0f);
- for (int i = 0; i < _aa.length; _aa[i++] = dummy)
+ for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
{
;
}
import java.awt.Color;
/**
- * DOCUMENT ME!
+ * Represent a node in a binary tree
*
- * @author $author$
+ * @author $mclamp (probably!)$
* @version $Revision$
*/
-public class BinaryNode
+public class BinaryNode<T>
{
- Object element;
+ T element;
String name;
- BinaryNode left;
+ BinaryNode<T> left;
- BinaryNode right;
+ BinaryNode<T> right;
- BinaryNode parent;
+ BinaryNode<T> parent;
/** Bootstrap value */
public int bootstrap;
/** DOCUMENT ME!! */
public Color color = Color.black;
- /** DOCUMENT ME!! */
+ /**
+ * if true, node is created to simulate polytomy between parent and its 3 or
+ * more children
+ */
public boolean dummy = false;
/**
* @param name
* DOCUMENT ME!
*/
- public BinaryNode(Object element, BinaryNode parent, String name,
+ public BinaryNode(T element, BinaryNode<T> parent, String name,
double dist)
{
this();
this.dist = dist;
}
- public BinaryNode(Object element, BinaryNode parent, String name,
+ public BinaryNode(T element, BinaryNode<T> parent, String name,
double dist, int bootstrap)
{
this(element, parent, name, dist);
this.bootstrap = bootstrap;
}
- public BinaryNode(Object val, BinaryNode parent, String name, double dist,
+ public BinaryNode(T val, BinaryNode<T> parent, String name, double dist,
int bootstrap, boolean dummy)
{
this(val, parent, name, dist, bootstrap);
*
* @return DOCUMENT ME!
*/
- public Object element()
+ public T element()
{
return element;
}
*
* @return DOCUMENT ME!
*/
- public Object setElement(Object v)
+ public T setElement(T v)
{
return element = v;
}
*
* @return DOCUMENT ME!
*/
- public BinaryNode left()
+ public BinaryNode<T> left()
{
return left;
}
*
* @return DOCUMENT ME!
*/
- public BinaryNode setLeft(BinaryNode n)
+ public BinaryNode<T> setLeft(BinaryNode<T> n)
{
return left = n;
}
*
* @return DOCUMENT ME!
*/
- public BinaryNode right()
+ public BinaryNode<T> right()
{
return right;
}
*
* @return DOCUMENT ME!
*/
- public BinaryNode setRight(BinaryNode n)
+ public BinaryNode<T> setRight(BinaryNode<T> n)
{
return right = n;
}
*
* @return DOCUMENT ME!
*/
- public BinaryNode parent()
+ public BinaryNode<T> parent()
{
return parent;
}
*
* @return DOCUMENT ME!
*/
- public BinaryNode setParent(BinaryNode n)
+ public BinaryNode<T> setParent(BinaryNode<T> n)
{
return parent = n;
}
* setChild(null), or detach() for this.
*
*/
- public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
+ public void SetChildren(BinaryNode<T> leftchild, BinaryNode<T> rightchild)
{
if (leftchild != null)
{
*
* @return BinaryNode The detached node.
*/
- public BinaryNode detach()
+ public BinaryNode<T> detach()
{
if (this.parent != null)
{
*
* @return BinaryNode
*/
- public BinaryNode ascendLeft()
+ public BinaryNode<T> ascendLeft()
{
- BinaryNode c = this;
+ BinaryNode<T> c = this;
do
{
*
* @return BinaryNode
*/
- public BinaryNode ascendRight()
+ public BinaryNode<T> ascendRight()
{
- BinaryNode c = this;
+ BinaryNode<T> c = this;
do
{
* ascends the tree but doesn't stop until a non-dummy node is discovered.
*
*/
- public BinaryNode AscendTree()
+ public BinaryNode<T> AscendTree()
{
- BinaryNode c = this;
+ BinaryNode<T> c = this;
do
{
}
/**
+ * add a series of start,end (inclusive) ranges to the column selection
+ *
+ * @param rng
+ * [start_0, end_0, start_1, end_1, ... ]
+ * @param baseOne
+ * - when true, ranges are base 1 and will be mapped to base 0
+ */
+ public void addRangeOfElements(int[] rng, boolean baseOne)
+ {
+ int base = baseOne ? -1 : 0;
+ for (int c = 0; c < rng.length; c += 2)
+ {
+ for (int p = rng[c]; p <= rng[c + 1]; p++)
+ {
+ selection.add(base + p);
+ }
+ }
+
+ }
+
+ /**
* clears column selection
*/
public void clear()
package jalview.datamodel;
+import java.awt.Color;
+
+import jalview.renderer.ContactGeometry.contactInterval;
+
public interface ContactListI extends ContactListProviderI
{
*/
ContactRange getRangeFor(int from_column, int to_column);
+ default Color getColourForGroup()
+ {
+ return null;
+ }
}
package jalview.datamodel;
+import java.awt.Color;
+
+import jalview.renderer.ContactGeometry.contactInterval;
+
/**
* helper class to compute min/max/mean for a range on a contact list
*
return cr;
}
+ @Override
+ public int[] getMappedPositionsFor(int cStart, int cEnd)
+ {
+ return clist.getMappedPositionsFor(cStart, cEnd);
+ }
+
+ @Override
+ public Color getColourForGroup()
+ {
+ return clist.getColourForGroup();
+ }
}
package jalview.datamodel;
+import java.awt.Color;
+
public interface ContactListProviderI
{
*/
double getContactAt(int column);
+ /**
+ * Return positions in local reference corresponding to cStart and cEnd in
+ * matrix data. Positions are base 1 column indices for sequence associated
+ * matrices.
+ *
+ * @param cStart
+ * @param cEnd
+ * @return int[] { start, end (inclusive) for each contiguous segment}
+ */
+ default int[] getMappedPositionsFor(int cStart, int cEnd)
+ {
+ return new int[] { cStart, cEnd };
+ }
+
+ default Color getColourForGroup()
+ {
+ return null;
+ }
+
}
import java.util.HashMap;
import java.util.Map;
+import jalview.ws.datamodel.MappableContactMatrixI;
+
public class ContactMapHolder implements ContactMapHolderI
{
{
return null;
}
+ if (cm instanceof MappableContactMatrixI)
+ {
+ if (_aa.sequenceRef != null)
+ {
+ return ((MappableContactMatrixI) cm)
+ .getMappableContactList(_aa.sequenceRef, column);
+ }
+ }
// TODO: could resolve sequence position to column position here
// TODO: what about for complexes - where contactMatrix may involve two or
// more sequences
contactmaps.put(aa.annotationId, cm);
// TODO: contact matrices could be intra or inter - more than one refseq
// possible!
- if (cm.hasReferenceSeq())
+ if (cm instanceof MappableContactMatrixI)
{
- aa.setSequenceRef(cm.getReferenceSeq());
+ aa.setSequenceRef(((MappableContactMatrixI) cm).getReferenceSeq());
}
return aa;
}
package jalview.datamodel;
import java.awt.Color;
+import java.math.BigInteger;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
import java.util.List;
+import java.util.Spliterator;
import java.util.StringTokenizer;
import jalview.bin.Console;
}
@Override
- public boolean hasReferenceSeq()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public SequenceI getReferenceSeq()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
public String getAnnotLabel()
{
return "Contact Matrix";
{
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;
}
}
float getMax();
- boolean hasReferenceSeq();
-
- SequenceI getReferenceSeq();
-
String getAnnotDescr();
String getAnnotLabel();
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()
{
- return false;
+ return hasGroupSet() && getGroupSet().hasGroups();
}
default BitSet getGroupsFor(int column)
{
- BitSet colbitset = new BitSet();
- colbitset.set(column);
- return colbitset;
+ if (!hasGroupSet())
+ {
+ BitSet colbitset = new BitSet();
+ colbitset.set(column);
+ return colbitset;
+ }
+ return getGroupSet().getGroupsFor(column);
}
default List<BitSet> getGroups()
{
- return Arrays.asList();
+ if (!hasGroupSet())
+ {
+ return Arrays.asList();
+ }
+ return getGroupSet().getGroups();
}
default boolean hasTree()
{
- return false;
+ return hasGroupSet() ? getGroupSet().hasTree() : false;
}
/**
*/
default String getNewick()
{
- return null;
+ return hasGroupSet() ? getGroupSet().getNewick() : null;
}
default String getTreeMethod()
{
- return null;
+ return hasGroupSet() ? getGroupSet().getTreeMethod() : null;
}
default boolean hasCutHeight()
{
- return false;
+ return hasGroupSet() ? getGroupSet().hasCutHeight() : false;
}
default double getCutHeight()
{
- return 0;
+ return hasGroupSet() ? getGroupSet().getCutHeight() : 0;
}
- void updateGroups(List<BitSet> colGroups);
+ default void updateGroups(List<BitSet> colGroups)
+ {
+ if (hasGroupSet())
+ {
+ getGroupSet().updateGroups(colGroups);
+ }
+ }
- void setColorForGroup(BitSet bs, Color color);
+ default void setColorForGroup(BitSet bs, Color color)
+ {
+ if (hasGroupSet())
+ {
+ getGroupSet().setColorForGroup(bs, color);
+ }
+ }
default Color getColourForGroup(BitSet bs)
{
- return Color.white;
- };
+ if (hasGroupSet())
+ {
+ return getGroupSet().getColourForGroup(bs);
+ }
+ else
+ {
+ return Color.white;
+ }
+ }
+
+ void setGroupSet(GroupSet makeGroups);
}
--- /dev/null
+package jalview.datamodel;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.List;
+
+import jalview.analysis.AverageDistanceEngine;
+import jalview.bin.Console;
+
+public class GroupSet implements GroupSetI
+{
+ List<BitSet> groups = Arrays.asList();
+
+ public GroupSet(GroupSet grps)
+ {
+ abs = grps.abs;
+ colorMap = new HashMap<BitSet, Color>(grps.colorMap);
+ groups = new ArrayList<BitSet>(grps.groups);
+ newick = grps.newick;
+ thresh = grps.thresh;
+ treeType = grps.treeType;
+ }
+
+ public GroupSet()
+ {
+ // TODO Auto-generated constructor stub
+ }
+
+ public GroupSet(boolean abs2, float thresh2, List<BitSet> groups2,
+ String treeType2, String newick2)
+ {
+ abs = abs2;
+ thresh = thresh2;
+ groups = groups2;
+ treeType = treeType2;
+ newick = newick2;
+ }
+
+ @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 = false;
+
+ double thresh = 0;
+
+ String treeType = null;
+
+ @Override
+ public void updateGroups(List<BitSet> colGroups)
+ {
+ if (colGroups != null)
+ {
+ groups = colGroups;
+ }
+ }
+
+ @Override
+ public BitSet getGroupsFor(int column)
+ {
+ if (groups != null)
+ {
+ for (BitSet gp : groups)
+ {
+ if (gp.get(column))
+ {
+ return gp;
+ }
+ }
+ }
+ // return singleton set;
+ BitSet bs = new BitSet();
+ bs.set(column);
+ return bs;
+ }
+
+ 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);
+ }
+
+ @Override
+ 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 GroupSet makeGroups(ContactMatrixI matrix, float thresh,
+ boolean abs)
+ {
+ AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
+ matrix);
+ double height = clusterer.findHeight(clusterer.getTopNode());
+ String newick = new jalview.io.NewickFile(clusterer.getTopNode(), false,
+ true).print();
+ String 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());
+ }
+ List<BitSet> 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);
+ }
+ GroupSet grps = new GroupSet(abs, thresh, groups, treeType, newick);
+ return grps;
+ }
+
+ @Override
+ public List<BitSet> getGroups()
+ {
+ return groups;
+ }
+}
--- /dev/null
+package jalview.datamodel;
+
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
+
+public interface GroupSetI
+{
+ boolean hasGroups();
+
+ String getNewick();
+
+ boolean hasTree();
+
+ void updateGroups(List<BitSet> colGroups);
+
+ BitSet getGroupsFor(int column);
+
+ Color getColourForGroup(BitSet bs);
+
+ void setColorForGroup(BitSet bs, Color color);
+
+ void restoreGroups(List<BitSet> newgroups, String treeMethod, String tree,
+ double thresh2);
+
+ boolean hasCutHeight();
+
+ double getCutHeight();
+
+ String getTreeMethod();
+
+ List<BitSet> getGroups();
+
+}
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)
}
@Override
- public boolean hasReferenceSeq()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public SequenceI getReferenceSeq()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
public String getAnnotDescr()
{
return "Sequence distance matrix";
{
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);
}
}
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
+import jalview.ws.datamodel.alphafold.MappableContactMatrix;
/**
*
AlignmentAnnotation aa = cmholder.addContactList(cm);
Annotation _aa[] = new Annotation[getLength()];
- Annotation dummy = new Annotation(0.0f);
- for (int i = 0; i < _aa.length; _aa[i++] = dummy)
+
+ for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
{
;
}
aa.annotations = _aa;
aa.setSequenceRef(this);
+ if (cm instanceof MappableContactMatrix
+ && !((MappableContactMatrix) cm).hasReferenceSeq())
+ {
+ ((MappableContactMatrix) cm).setRefSeq(this);
+ }
aa.createSequenceMapping(this, getStart(), false);
addAlignmentAnnotation(aa);
return aa;
* @author $author$
* @version $Revision$
*/
-public class SequenceNode extends BinaryNode
+public class SequenceNode extends BinaryNode<SequenceI>
{
private boolean placeholder = false;
super();
}
- public SequenceNode(SequenceI val, BinaryNode parent, String name,
- double dist, int bootstrap, boolean dummy)
+ public SequenceNode(SequenceI val, BinaryNode<SequenceI> parent,
+ String name, double dist, int bootstrap, boolean dummy)
{
super(val, parent, name, dist, bootstrap, dummy);
}
- public SequenceNode(SequenceI element, BinaryNode parent, String name,
- double dist, int bootstrap)
+ public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent,
+ String name, double dist, int bootstrap)
{
super(element, parent, name, dist, bootstrap);
}
- public SequenceNode(SequenceI element, BinaryNode parent, String name,
- double dist)
+ public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent,
+ String name, double dist)
{
super(element, parent, name, dist);
}
{
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);
+
+ 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)
{
final PAEContactMatrix cm = (PAEContactMatrix) av
.getContactMatrix(aa[selectedRow]);
- if (cm != null && cm.getNewick() != null
- && cm.getNewick().length() > 0)
+ if (cm != null && cm.hasTree())
{
item = new JMenuItem("Show Tree for Matrix");
item.addActionListener(new ActionListener()
fr = Math.min(cXci.cStart, cXci.cEnd);
to = Math.max(cXci.cStart, cXci.cEnd);
- if (evt.isControlDown())
+ // double click selects the whole group
+ if (evt.getClickCount() == 2)
{
ContactMatrixI matrix = av.getContactMatrix(clicked);
{
SequenceI rseq = clicked.sequenceRef;
BitSet grp = matrix.getGroupsFor(currentX);
+ // TODO: cXci needs to be mapped to real groups
for (int c = fr; c <= to; c++)
{
BitSet additionalGrp = matrix.getGroupsFor(c);
{
// select corresponding range in segment under mouse
{
- for (int c = fr; c <= to; c++)
+ int[] rng = forCurrentX.getMappedPositionsFor(fr, to);
+ if (rng != null)
{
- av.getColumnSelection().addElement(c);
+ av.getColumnSelection().addRangeOfElements(rng, true);
}
av.getColumnSelection().addElement(currentX);
}
// PAE SPECIFIC
// and also select everything lower than the max range adjacent
// (kind of works)
- if (PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
+ if (evt.isControlDown()
+ && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
{
int c = fr - 1;
ContactRange cr = forCurrentX.getRangeFor(fr, to);
if (// cr.getMin() <= cval &&
cval <= thresh)
{
- av.getColumnSelection().addElement(c--);
- }
- else
- {
- break;
+ int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+ if (cols != null)
+ {
+ av.getColumnSelection().addRangeOfElements(cols, true);
+ }
+ else
+ {
+ break;
+ }
}
+ c--;
}
c = to;
while (c < forCurrentX.getContactHeight())
if (// cr.getMin() <= cval &&
cval <= thresh)
{
- av.getColumnSelection().addElement(c++);
+ int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+ if (cols != null)
+ {
+ av.getColumnSelection().addRangeOfElements(cols, true);
+ }
}
else
{
break;
}
+ c++;
+
}
}
}
int fr, to;
fr = Math.min(lastXci.cStart, lastXci.cEnd);
to = Math.max(lastXci.cStart, lastXci.cEnd);
- jalview.bin.Console.trace("Marking " + fr + " to " + to);
- for (int c = fr; c <= to; c++)
+ int[] mappedPos = forFromX.getMappedPositionsFor(fr, to);
+ if (mappedPos != null)
{
- if (cma.sequenceRef != null)
+ jalview.bin.Console.trace("Marking " + fr + " to " + to
+ + " mapping to sequence positions " + mappedPos[0] + " to "
+ + mappedPos[1]);
+ for (int pair = 0; pair < mappedPos.length; pair += 2)
{
- int col = cma.sequenceRef.findIndex(c);
- av.getColumnSelection().addElement(col);
- }
- else
- {
- av.getColumnSelection().addElement(c);
+ for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++)
+ // {
+ // if (cma.sequenceRef != null)
+ // {
+ // int col = cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
+ // av.getColumnSelection().addElement(col);
+ // }
+ // else
+ {
+ av.getColumnSelection().addElement(c);
+ }
}
}
+ // and again for most recent corner of drag
fr = Math.min(cXci.cStart, cXci.cEnd);
to = Math.max(cXci.cStart, cXci.cEnd);
- jalview.bin.Console.trace("Marking " + fr + " to " + to);
- for (int c = fr; c <= to; c++)
+ mappedPos = forFromX.getMappedPositionsFor(fr, to);
+ if (mappedPos != null)
{
- if (cma.sequenceRef != null)
+ for (int pair = 0; pair < mappedPos.length; pair += 2)
{
- int col = cma.sequenceRef.findIndex(c);
- av.getColumnSelection().addElement(col);
- }
- else
- {
- av.getColumnSelection().addElement(c);
+ jalview.bin.Console.trace("Marking " + fr + " to " + to
+ + " mapping to sequence positions " + mappedPos[pair]
+ + " to " + mappedPos[pair + 1]);
+ for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++)
+ {
+ // if (cma.sequenceRef != null)
+ // {
+ // int col =
+ // cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
+ // av.getColumnSelection().addElement(col);
+ // }
+ // else
+ {
+ av.getColumnSelection().addElement(c);
+ }
+ }
}
}
fr = Math.min(lastX, currentX);
ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
+ " - " + ci.cEnd + "]" + "<br/>Mean:" + cr.getMean();
+
int col = ann.sequenceRef.findPosition(column);
+ int[][] highlightPos;
+ int[] mappedPos = clist.getMappedPositionsFor(ci.cStart, ci.cEnd);
+ if (mappedPos != null)
+ {
+ highlightPos = new int[1 + mappedPos.length][2];
+ highlightPos[0] = new int[] { col, col };
+ for (int p = 0, h = 0; p < mappedPos.length; h++, p += 2)
+ {
+ highlightPos[h][0] = ann.sequenceRef
+ .findPosition(mappedPos[p] - 1);
+ highlightPos[h][1] = ann.sequenceRef
+ .findPosition(mappedPos[p + 1] - 1);
+ }
+ }
+ else
+ {
+ highlightPos = new int[][] { new int[] { col, col } };
+ }
ap.getStructureSelectionManager()
- .highlightPositionsOn(ann.sequenceRef, new int[][]
- { new int[] { col, col },
- new int[]
- { ci.cStart, ci.cEnd } }, null);
+ .highlightPositionsOn(ann.sequenceRef, highlightPos, null);
}
}
return tooltip;
import jalview.gui.structurechooser.StructureChooserQuerySource;
import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.FilterOption;
import jalview.util.StringUtils;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
+import jalview.ws.dbsources.EBIAlfaFold;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.sifts.SiftsSettings;
}
/**
- * Handles action event for btn_pdbFromFile
+ * Handles action event for btn_paeMatrixFile
*/
@Override
protected void paeMatrixFile_actionPerformed()
"label.load_pae_matrix_file_associate_with_structure",
pdbFile.getName()));
+ // TODO convert to Callable/Promise
int value = chooser.showOpenDialog(null);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- localPdbPaeMatrixFileName = chooser.getSelectedFile().getPath();
+ String fileName = chooser.getSelectedFile().getPath();
+ try
+ {
+ PAEContactMatrix.validateContactMatrixFile(fileName);
+ } catch (Exception thr)
+ {
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_load_file", new Object[]
+ { fileName }) + "<br>" + thr.getLocalizedMessage(),
+ MessageManager.getString("label.error_loading_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ Console.error("Couldn't import " + fileName + " as a PAE matrix",
+ thr);
+ return;
+ }
+ localPdbPaeMatrixFileName = fileName;
Cache.setProperty("LAST_DIRECTORY", localPdbPaeMatrixFileName);
}
validateAssociationFromFile();
{
pdbFileString = MessageManager.getString("label.none");
pdbFileTooltip = MessageManager.getString("label.nothing_selected");
+ setPdbOptionsEnabled(false);
}
}
else
{
btn_pdbFromFile.setEnabled(false);
+ setPdbOptionsEnabled(false);
// lbl_fromFileStatus.setIcon(errorImage);
pdbFileString = MessageManager.getString("label.none");
pdbFileTooltip = MessageManager.getString("label.nothing_selected");
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
final int preferredHeight = pnl_filter.getHeight();
+ btn_add.setEnabled(false);
+ btn_newView.setEnabled(false);
+ btn_cancel.setEnabled(false);
+ actionsPanel.setEnabled(false);
+ final String progress = MessageManager
+ .getString("label.working_ellipsis");
+ setProgressBar(progress, progress.hashCode());
Runnable viewStruc = new Runnable()
{
@Override
.getCmb_assSeq().getSelectedItem();
SequenceI userSelectedSeq = assSeqOpt.getSequence();
if (userSelectedSeq != null)
+ {
selectedSequence = userSelectedSeq;
+ }
String pdbFilename = selectedPdbFileName;
StructureChooser.openStructureFileForSequence(ssm, sc, ap,
@Override
public void run()
{
+ setProgressBar("Complete.", progress.hashCode());
closeAction(preferredHeight);
mainFrame.dispose();
}
import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactMatrixI;
import jalview.structure.SelectionSource;
import jalview.util.Format;
import jalview.util.MessageManager;
+import jalview.ws.datamodel.MappableContactMatrixI;
/**
* DOCUMENT ME!
cm.setColorForGroup(gp, colors.get(gp));
}
}
+ // stash colors in linked annotation row.
+ // doesn't work yet. TESTS!
+ int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1
+ : 0;
+ Annotation ae;
+ Color gpcol = null;
+ int[] seqpos = null;
+ for (BitSet gp : colors.keySet())
+ {
+ gpcol = colors.get(gp);
+ for (int p = gp.nextSetBit(0); p >= 0
+ && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
+ {
+ if (cm instanceof MappableContactMatrixI)
+ {
+ MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
+ seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p);
+ if (seqpos == null)
+ {
+ // no mapping for this column.
+ continue;
+ }
+ // TODO: handle ranges...
+ ae = aa.getAnnotationForPosition(seqpos[0]);
+ }
+ else
+ {
+ ae = aa.getAnnotationForPosition(p + sstart);
+ }
+ if (ae != null)
+ {
+ ae.colour = gpcol.brighter().darker();
+ }
+ }
+ }
}
}
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);
}
}
}
}
if (jvseq instanceof SequenceI)
{
- leaf.setElement(jvseq);
+ leaf.setElement((SequenceI) jvseq);
leaf.setPlaceholder(false);
}
else
*/
protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB";
+ protected JPanel actionsPanel;
+
protected JPanel statusPanel = new JPanel();
public JLabel statusBar = new JLabel();
protected StringBuilder errorWarning = new StringBuilder();
+ protected JButton btn_cancel;
+
protected JButton btn_add;
protected JButton btn_newView;
}
});
- JButton btn_cancel = new JButton(
- MessageManager.getString("action.cancel"));
+ btn_cancel = new JButton(MessageManager.getString("action.cancel"));
btn_cancel.setFont(VERDANA_12);
btn_cancel.addActionListener(new ActionListener()
{
lbl_pdbFile.setFont(VERDANA_10);
lbl_chooseTempFacType.setFont(VERDANA_12);
- lbl_chooseTempFacType.setText(new StringBuilder()
- .append(MessageManager.getString("label.choose_tempfac_type"))
- .append(" ").append(MessageManager.getString("label.optional"))
- .toString());
+ lbl_chooseTempFacType.setText(
+ MessageManager.getString("label.interpret_tempfac_as"));
combo_tempFacAs.setFont(VERDANA_12);
for (TFType t : TFType.values())
});
btn_paeMatrixFile.setFont(VERDANA_12);
- btn_paeMatrixFile.setText(new StringBuilder()
- .append(MessageManager.getString("label.add_pae_matrix_file"))
- .append(" ").append(MessageManager.getString("label.optional"))
- .toString());
+ btn_paeMatrixFile
+ .setText(MessageManager.getString("label.add_pae_matrix_file"));
btn_paeMatrixFile.addActionListener(new ActionListener()
{
@Override
targetView.setVisible(false);
- JPanel actionsPanel = new JPanel(new MigLayout());
+ actionsPanel = new JPanel(new MigLayout());
actionsPanel.add(targetView, "left");
actionsPanel.add(btn_add, "wrap");
actionsPanel.add(chk_superpose, "left");
gbc.insets = new Insets(0, 0, 18, 0);
pnl_fileOptions.add(lbl_pdbFile, gbc);
gbc.gridy++;
+
gbc.insets = new Insets(0, 0, 2, 0);
+ pnl_fileOptions.add(new JLabel(
+ MessageManager.getString("label.structure_import_options")),
+ gbc);
+ gbc.gridy++;
+
+ gbc.insets = new Insets(0, 0, 6, 0);
pnl_fileOptions.add(lbl_chooseTempFacType, gbc);
gbc.gridy++;
gbc.insets = new Insets(0, 0, 18, 0);
pnl_fileOptions.add(combo_tempFacAs, gbc);
gbc.gridy++;
- gbc.insets = new Insets(0, 0, 2, 0);
+ gbc.insets = new Insets(0, 0, 6, 0);
pnl_fileOptions.add(btn_paeMatrixFile, gbc);
gbc.gridy++;
+ gbc.insets = new Insets(0, 0, 2, 0);
gbc.weighty = 1.0;
pnl_fileOptions.add(lbl_paeFile, gbc);
lbl_chooseTempFacType.setEnabled(b);
combo_tempFacAs.setEnabled(b);
btn_paeMatrixFile.setEnabled(b);
+ lbl_paeFile.setEnabled(b);
}
}
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
+import jalview.datamodel.GroupSet;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+import jalview.ws.datamodel.MappableContactMatrixI;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.xml.binding.jalview.JalviewModel.Viewport.Overview;
import jalview.xml.binding.jalview.JalviewUserColours;
import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.MapListType;
import jalview.xml.binding.jalview.MapListType.MapListFrom;
import jalview.xml.binding.jalview.MapListType.MapListTo;
import jalview.xml.binding.jalview.Mapping;
{
for (BitSet gp : cm.getGroups())
{
- BigInteger val = new BigInteger(gp.toByteArray());
- xmlmat.getGroups().add(val.toString());
+ xmlmat.getGroups().add(stringifyBitset(gp));
}
}
if (cm.hasTree())
{
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);
.fromFloatStringToContacts(xmlmat.getElements(),
xmlmat.getCols().intValue(),
xmlmat.getRows().intValue());
+ jalview.util.MapList mapping = null;
+ if (xmlmat.getMapping() != null)
+ {
+ MapListType m = xmlmat.getMapping();
+ // Mapping m = dr.getMapping();
+ int fr[] = new int[m.getMapListFrom().size() * 2];
+ Iterator<MapListFrom> from = m.getMapListFrom()
+ .iterator();// enumerateMapListFrom();
+ for (int _i = 0; from.hasNext(); _i += 2)
+ {
+ MapListFrom mf = from.next();
+ fr[_i] = mf.getStart();
+ fr[_i + 1] = mf.getEnd();
+ }
+ int fto[] = new int[m.getMapListTo().size() * 2];
+ Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
+ for (int _i = 0; to.hasNext(); _i += 2)
+ {
+ MapListTo mf = to.next();
+ fto[_i] = mf.getStart();
+ fto[_i + 1] = mf.getEnd();
+ }
- PAEContactMatrix newpae = new PAEContactMatrix(
- jaa.sequenceRef, elements);
+ mapping = new jalview.util.MapList(fr, fto,
+ m.getMapFromUnit().intValue(),
+ m.getMapToUnit().intValue());
+ }
List<BitSet> newgroups = new ArrayList<BitSet>();
if (xmlmat.getGroups().size() > 0)
{
for (String sgroup : xmlmat.getGroups())
{
- try
- {
- BigInteger group = new BigInteger(sgroup);
- newgroups.add(BitSet.valueOf(group.toByteArray()));
- } catch (NumberFormatException nfe)
- {
- Console.error(
- "Problem parsing groups for a contact matrix (\""
- + sgroup + "\"",
- nfe);
- }
+ newgroups.add(deStringifyBitset(sgroup));
}
}
String nwk = xmlmat.getNewick().size() > 0
Console.log.info(
"Ignoring additional clusterings for contact matrix");
}
-
String treeMethod = xmlmat.getTreeMethod();
double thresh = xmlmat.getCutHeight() != null
? xmlmat.getCutHeight()
: 0;
- newpae.restoreGroups(newgroups, treeMethod, nwk, thresh);
+ GroupSet grpset = new GroupSet();
+ grpset.restoreGroups(newgroups, treeMethod, nwk, thresh);
+ PAEContactMatrix newpae = new PAEContactMatrix(
+ jaa.sequenceRef, mapping, elements, grpset);
jaa.sequenceRef.addContactListFor(jaa, newpae);
}
}
import java.util.Iterator;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactListI;
-
+import jalview.datamodel.HiddenColumns;
+import jalview.renderer.ContactGeometry.contactInterval;
+
+/**
+ * encapsulate logic for mapping between positions in a ContactList and their
+ * rendered representation in a given number of pixels.
+ *
+ * @author jprocter
+ *
+ */
public class ContactGeometry
{
+
+ final ContactListI contacts;
+
final int pixels_step;
final double contacts_per_pixel;
final int graphHeight;
- public ContactGeometry(ContactListI contacts, int graphHeight)
+ public ContactGeometry(final ContactListI contacts, int graphHeight)
{
+ this.contacts = contacts;
this.graphHeight = graphHeight;
contact_height = contacts.getContactHeight();
// fractional number of contacts covering each pixel
public final int pStart;
public final int pEnd;
+
+ }
+
+ /**
+ *
+ * @param columnSelection
+ * @param ci
+ * @param visibleOnly
+ * - when true, only test intersection of visible columns given
+ * matrix range
+ * @return true if the range on the matrix specified by ci intersects with
+ * selected columns in the ContactListI's reference frame.
+ */
+
+ boolean intersects(contactInterval ci, ColumnSelection columnSelection,
+ HiddenColumns hiddenColumns, boolean visibleOnly)
+ {
+ boolean rowsel = false;
+ final int[] mappedRange = contacts.getMappedPositionsFor(ci.cStart,
+ ci.cEnd);
+ if (mappedRange == null)
+ {
+ return false;
+ }
+ for (int p = 0; p < mappedRange.length && !rowsel; p += 2)
+ {
+ boolean containsHidden = false;
+ if (visibleOnly && hiddenColumns != null
+ && hiddenColumns.hasHiddenColumns())
+ {
+ // TODO: turn into function on hiddenColumns and create test !!
+ Iterator<int[]> viscont = hiddenColumns.getVisContigsIterator(
+ mappedRange[p], mappedRange[p + 1], false);
+ containsHidden = !viscont.hasNext();
+ if (!containsHidden)
+ {
+ for (int[] interval = viscont.next(); viscont
+ .hasNext(); rowsel |= columnSelection
+ .intersects(interval[p], interval[p + 1]))
+ ;
+ }
+ }
+ else
+ {
+ rowsel = columnSelection.intersects(mappedRange[p],
+ mappedRange[p + 1]);
+ }
+ }
+ return rowsel;
+
}
/**
* 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;
- // TODO: pass visible column mask to the ContactGeometry object so it maps
+ // TODO: optionally pass visible column mask to the ContactGeometry object
+ // so it maps
// only visible contacts to geometry
// Bean holding mapping from contact list to pixels
+ // TODO: allow bracketing/limiting of range on contacts to render (like
+ // visible column mask but more flexible?)
+
+ // COntactListI provides mapping for column -> cm-groupmapping
final ContactGeometry cgeom = new ContactGeometry(contacts,
_aa.graphHeight);
boolean rowsel = false, containsHidden = false;
if (columnSelection != null)
{
- if (_aa.sequenceRef == null)
- {
- rowsel = columnSelection.intersects(ci.cStart, ci.cEnd);
- }
- else
- {
- // TODO check we have correctly mapped cstart to local sequence
- // numbering
- int s = _aa.sequenceRef.findIndex(ci.cStart);
- int e = _aa.sequenceRef.findIndex(ci.cEnd);
- if (maskHiddenCols && hasHiddenColumns)
- {
- // TODO: turn into function and create test !!
- Iterator<int[]> viscont = hiddenColumns
- .getVisContigsIterator(s, e, false);
- containsHidden = !viscont.hasNext();
- }
- if (s > 0 && s < _aa.sequenceRef.getLength())
- {
- rowsel = columnSelection.intersects(s, e);
- }
-
- }
+ rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns,
+ maskHiddenCols);
}
// TODO: show selected region
if (colsel || rowsel)
(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);
}
List<StructureCommandI> finalView = commandGenerator
.centerViewOn(models);
- executeCommands(finalView, false, "Centered on Superposition");
+ if (finalView != null && finalView.size() > 0)
+ {
+ executeCommands(finalView, false, "Centered on Superposition");
+ }
}
return error;
}
--- /dev/null
+package jalview.ws.datamodel;
+
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceI;
+import jalview.util.MapList;
+
+public interface MappableContactMatrixI extends ContactMatrixI
+{
+
+ boolean hasReferenceSeq();
+
+ SequenceI getReferenceSeq();
+
+ /**
+ * remaps the matrix to a new reference sequence
+ *
+ * @param dsq
+ * @param sqmpping
+ * - mapping from current reference to new reference - 1:1 only
+ * @return new ContactMatrixI instance with updated mapping
+ */
+ MappableContactMatrixI liftOver(SequenceI dsq, Mapping sqmpping);
+
+ /**
+ * like ContactMatrixI.getContactList(int column) but
+ *
+ * @param localFrame
+ * - sequence or other object that this contact matrix is associated
+ * with
+ * @param column
+ * - position in localFrame
+ * @return ContactListI that returns contacts w.r.t. localFrame
+ */
+
+ ContactListI getMappableContactList(SequenceI localFrame, int column);
+
+ /**
+ *
+ * Similar to AlignedCodonFrame.getMappingBetween
+ *
+ * @param sequenceRef
+ * - a reference sequence mappable to this contactMatrix - may be
+ * null
+ * @return null or the MapList mapping to the coordinates of the reference
+ * sequence (or if hasReferenceSeq() is false, and sequenceRef is
+ * null, any mapping present)
+ *
+ */
+ MapList getMapFor(SequenceI sequenceRef);
+
+ /**
+ * Locate a position in the mapped sequence for a column in the matrix - use
+ * this to resolve positions corresponding to column clusters
+ *
+ * @param localFrame
+ * - sequence derivced from reference sequence
+ * @param column
+ * - matrix row/column
+ * @return sequence position(s) corresponding to column in contact matrix
+ */
+ int[] getMappedPositionsFor(SequenceI localFrame, int column);
+}
--- /dev/null
+package jalview.ws.datamodel.alphafold;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.BitSet;
+
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactListImpl;
+import jalview.datamodel.ContactListProviderI;
+import jalview.datamodel.GroupSet;
+import jalview.datamodel.GroupSetI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceI;
+import jalview.util.MapList;
+import jalview.ws.datamodel.MappableContactMatrixI;
+
+public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>>
+ implements MappableContactMatrixI
+{
+ SequenceI refSeq = null;
+
+ MapList toSeq = null;
+
+ /**
+ * the length that refSeq is expected to be (excluding gaps, of course)
+ */
+ int length;
+
+ @Override
+ public boolean hasReferenceSeq()
+ {
+ return (refSeq != null);
+ }
+
+ @Override
+ public SequenceI getReferenceSeq()
+ {
+ return refSeq;
+ }
+
+ /**
+ * container for groups - defined on matrix columns
+ */
+ GroupSet grps = new GroupSet();
+
+ @Override
+ public GroupSetI getGroupSet()
+ {
+ return grps;
+ };
+
+ @Override
+ public void setGroupSet(GroupSet makeGroups)
+ {
+ grps = makeGroups;
+ }
+
+ @Override
+ public MapList getMapFor(SequenceI mapSeq)
+ {
+ if (refSeq != null)
+ {
+ while (mapSeq != refSeq && mapSeq.getDatasetSequence() != null)
+ {
+ mapSeq = mapSeq.getDatasetSequence();
+ }
+ if (mapSeq != refSeq)
+ {
+ return null;
+ }
+ }
+ else
+ {
+ if (mapSeq != null)
+ {
+ // our MapList does not concern this seq
+ return null;
+ }
+ }
+
+ return toSeq;
+ }
+
+ /**
+ * set the reference sequence and construct the mapping between the start-end
+ * positions of given sequence and row/columns of contact matrix
+ *
+ * @param _refSeq
+ */
+ public void setRefSeq(SequenceI _refSeq)
+ {
+ refSeq = _refSeq;
+ while (refSeq.getDatasetSequence() != null)
+ {
+ refSeq = refSeq.getDatasetSequence();
+ }
+ length = _refSeq.getEnd() - _refSeq.getStart() + 1;
+ // if (length!=refSeq.getLength() || _refSeq.getStart()!=1)
+ {
+ toSeq = new MapList(
+ new int[]
+ { _refSeq.getStart(), _refSeq.getEnd() },
+ new int[]
+ { 0, length - 1 }, 1, 1);
+ }
+ }
+
+ public T liftOver(SequenceI newRefSeq, Mapping sp2sq)
+ {
+ if (sp2sq.getMappedWidth() != sp2sq.getWidth())
+ {
+ // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
+ // Protein reference frames
+ throw new Error(
+ "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
+ }
+ boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == refSeq) : false;
+
+ /**
+ * map from matrix to toSeq's coordinate frame
+ */
+ int[] refMap = toSeq.locateInFrom(0, length - 1);
+ ArrayList<Integer> newFromMap = new ArrayList<Integer>();
+ int last = -1;
+ for (int i = 0; i < refMap.length; i += 2)
+ {
+ /*
+ * for each contiguous range in toSeq, locate corresponding range in sequence mapped to toSeq by sp2sq
+ */
+ int[] sp2map = mapIsTo
+ ? sp2sq.getMap().locateInFrom(refMap[i], refMap[i + 1])
+ : sp2sq.getMap().locateInTo(refMap[i], refMap[i + 1]);
+ if (sp2map == null)
+ {
+ continue;
+ }
+
+ for (int spm = 0; spm < sp2map.length; spm += 2)
+ {
+
+ if (last > -1)
+ {
+ if (sp2map[spm] != last + 1)
+ {
+ newFromMap.add(sp2map[spm]);
+ }
+ else
+ {
+ newFromMap.remove(newFromMap.size() - 1);
+ }
+ }
+ else
+ {
+ newFromMap.add(sp2map[spm]);
+ }
+ last = sp2map[spm + 1];
+ newFromMap.add(last);
+ }
+ }
+ if ((newFromMap.size() % 2) != 0)
+ {
+ // should have had an even number of int ranges!
+ throw new Error("PAEMatrix liftover failed.");
+ }
+ int fromIntMap[] = new int[newFromMap.size()];
+ int ipos = 0;
+ for (Integer i : newFromMap)
+ {
+ fromIntMap[ipos++] = i;
+ }
+ MapList newFromMapList = new MapList(fromIntMap,
+ new int[]
+ { 0, length - 1 }, 1, 1);
+
+ T newCM = newMappableContactMatrix(newRefSeq, newFromMapList);
+ return newCM;
+ }
+
+ protected abstract T newMappableContactMatrix(SequenceI newRefSeq,
+ MapList newFromMapList);
+
+ @Override
+ public int[] getMappedPositionsFor(final SequenceI localFrame,
+ final int column)
+ {
+ return getMappedPositionsFor(localFrame, column, column);
+ }
+
+ public int[] getMappedPositionsFor(final SequenceI localFrame, int from,
+ int to)
+ {
+ if (localFrame == null)
+ {
+ throw new Error("Unimplemented when no local sequence given.");
+ }
+ // return a ContactListI for column
+ // column is index into localFrame
+ // 1. map column to corresponding column in matrix
+
+ final int _lcolumn = localFrame.findPosition(from);
+ final int _rcolumn = (from == to) ? _lcolumn
+ : localFrame.findPosition(to);
+ if (toSeq == null)
+ {
+ // no mapping
+ return new int[] { _lcolumn, _rcolumn };
+ }
+
+ SequenceI lf = localFrame, uf = refSeq;
+
+ // just look for dataset sequences and check they are the same.
+ // in future we could use DBRefMappings/whatever.
+ while (lf.getDatasetSequence() != null
+ || uf.getDatasetSequence() != null)
+ {
+ if (lf.getDatasetSequence() != null)
+ {
+ lf = lf.getDatasetSequence();
+ }
+ if (uf.getDatasetSequence() != null)
+ {
+ uf = uf.getDatasetSequence();
+ }
+ }
+ if (lf != uf)
+ {
+ // could try harder to find a mapping
+ throw new Error("This Matrix associated with '" + refSeq.getName()
+ + "' is not mappable for the given localFrame sequence. ("
+ + localFrame.getName() + ")");
+ }
+
+ int[] mappedPositions = toSeq.locateInFrom(_lcolumn, _rcolumn);
+ // TODO - trim to localFrame ?
+ // if (mappedPositions!=null) {
+ // int s=-1,e=-1;
+ // for (int p=0;p<mappedPositions.length;p++)
+ // {
+ // if (s==-1 && mappedPositions[p]>=localFrame.getStart())
+ // {
+ // s=p; // remember first position within local frame
+ // }
+ // if (e==-1 || mappedPositions[p]<=localFrame.getEnd())
+ // {
+ // // update end pointer
+ // e=p;
+ // // compute local map
+ // mappedPositions[p] = localFrame.findIndex(mappedPositions[p]);
+ // }
+ // }
+ // }
+ return mappedPositions;
+ }
+
+ @Override
+ public ContactListI getMappableContactList(final SequenceI localFrame,
+ final int column)
+ {
+ final int _column;
+ final int _lcolumn;
+ if (localFrame == null)
+ {
+ throw new Error("Unimplemented when no local sequence given.");
+ }
+ // return a ContactListI for column
+ // column is index into localFrame
+ // 1. map column to corresponding column in matrix
+ final MappableContactMatrix us = this;
+ _lcolumn = localFrame.findPosition(column);
+
+ if (toSeq != null)
+ {
+ SequenceI lf = localFrame, uf = refSeq;
+
+ // just look for dataset sequences and check they are the same.
+ // in future we could use DBRefMappings/whatever.
+ while (lf.getDatasetSequence() != null
+ || uf.getDatasetSequence() != null)
+ {
+ if (lf.getDatasetSequence() != null)
+ {
+ lf = lf.getDatasetSequence();
+ }
+ if (uf.getDatasetSequence() != null)
+ {
+ uf = uf.getDatasetSequence();
+ }
+ }
+ if (lf != uf)
+ {
+ // could try harder to find a mapping
+ throw new Error("This Matrix associated with '" + refSeq.getName()
+ + "' is not mappable for the given localFrame sequence. ("
+ + localFrame.getName() + ")");
+ }
+ // check the mapping to see if localFrame _lcolumn exists
+ int[] word = toSeq.locateInTo(_lcolumn, _lcolumn);
+ if (word == null)
+ {
+ return null;
+ }
+ _column = word[0];
+ }
+ else
+ {
+ // no mapping
+ _column = _lcolumn;
+ }
+
+ // TODO - remove ? this may be a redundant check
+ if (_column < 0 || ((toSeq != null && _column > toSeq.getToHighest())
+ || (toSeq == null && getHeight() <= _column)))
+ {
+ return null;
+ }
+
+ // 2. resolve ranges in matrix corresponding to range in localFrame
+ final int[] matrixRange = toSeq == null
+ ? new int[]
+ { localFrame.getStart(), localFrame.getEnd() }
+ : toSeq.locateInTo(localFrame.getStart(), localFrame.getEnd());
+
+ int h = 0;
+ for (int p = 0; p < matrixRange.length; p += 2)
+ {
+ h += 1 + Math.abs(matrixRange[p + 1] - matrixRange[p]);
+ }
+ final int rangeHeight = h;
+ // 3. Construct ContactListImpl instance for just those segments.
+
+ return new ContactListImpl(new ContactListProviderI()
+ {
+
+ public int getColumn()
+ {
+ return column;
+ }
+
+ @Override
+ public int getPosition()
+ {
+ return _column;
+ }
+
+ @Override
+ public int getContactHeight()
+ {
+ return rangeHeight;
+ }
+
+ @Override
+ public double getContactAt(int mcolumn)
+ {
+ if (mcolumn < 0 || mcolumn >= rangeHeight)
+ {
+ return -1;
+ }
+ return getElementAt(_column, locateInRange(mcolumn));
+
+ // this code maps from mcolumn to localFrame - but that isn't what's
+ // needed
+ // int loccolumn = localFrame.findPosition(mcolumn);
+ // int[] lcolumn=(toSeq==null) ? new int[] {mcolumn} :
+ // toSeq.locateInTo(loccolumn,loccolumn);
+ // if (lcolumn==null || lcolumn[0] < 0 || lcolumn[0] >= rangeHeight)
+ // {
+ // return -1;
+ // }
+ // return getElementAt(_column,lcolumn[0]);
+ }
+
+ @Override
+ public int[] getMappedPositionsFor(int cStart, int cEnd)
+ {
+ if (!hasReferenceSeq())
+ {
+ return ContactListProviderI.super.getMappedPositionsFor(cStart,
+ cEnd);
+ }
+ // map into segment of matrix being shown
+ int realCstart = locateInRange(cStart);
+ int realCend = locateInRange(cEnd);
+
+ // TODO account for discontinuities in the mapping
+
+ int[] mappedPositions = toSeq.locateInFrom(realCstart, realCend);
+ if (mappedPositions != null)
+ {
+ int s = -1, e = -1;
+ for (int p = 0; p < mappedPositions.length; p++)
+ {
+ if (s == -1 && mappedPositions[p] >= localFrame.getStart())
+ {
+ s = p; // remember first position within local frame
+ }
+ if (e == -1 || mappedPositions[p] <= localFrame.getEnd())
+ {
+ // update end pointer
+ e = p;
+ // compute local map
+ mappedPositions[p] = localFrame.findIndex(mappedPositions[p]);
+ }
+ }
+ }
+ return mappedPositions;
+ }
+
+ /**
+ * @return the mcolumn'th position in the matrixRange window on the matrix
+ */
+ private int locateInRange(int mcolumn)
+ {
+
+ int h = 0, p = 0;
+ while (h < mcolumn && p + 2 < matrixRange.length)
+ {
+ h += 1 + Math.abs(matrixRange[p + 1] - matrixRange[p]);
+ p += 2;
+ }
+ return matrixRange[p] + mcolumn - h;
+ }
+
+ @Override
+ public Color getColourForGroup()
+ {
+ BitSet gp = us.getGroupsFor(_column);
+ Color col = us.getColourForGroup(gp);
+ return col;
+ }
+ });
+ }
+
+ /**
+ * get a specific element of the contact matrix in its data-local coordinates
+ * rather than the mapped frame. Implementations are allowed to throw
+ * RunTimeExceptions if _column/i are out of bounds
+ *
+ * @param _column
+ * @param i
+ * @return
+ */
+ protected abstract double getElementAt(int _column, int i);
+
+}
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 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
}
/**
+ * 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
@SuppressWarnings("unchecked")
private void parse_version_2_pAE(Map<String, Object> pae_obj)
{
- // this is never going to be reached by the integer rounding.. or is it ?
- maxscore = ((Double) MapUtils.getFirst(pae_obj,
- "max_predicted_aligned_error", "max_pae")).floatValue();
+ maxscore = -1;
+ // look for a maxscore element - if there is one...
+ try
+ {
+ // this is never going to be reached by the integer rounding.. or is it ?
+ maxscore = ((Double) MapUtils.getFirst(pae_obj,
+ "max_predicted_aligned_error", "max_pae")).floatValue();
+ } catch (Throwable t)
+ {
+ // ignore if a key is not found.
+ }
List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
.getFirst(pae_obj, "predicted_aligned_error", "pae"));
elements = new float[scoreRows.size()][scoreRows.size()];
{
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;
// dataset refSeq
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
+ while (rows.hasNext())
+ {
+ int row = rows.next().intValue();
+ int col = cols.next().intValue();
+ if (maxrow < row)
+ {
+ maxrow = row;
+ }
+ if (maxcol < col)
+ {
+ maxcol = col;
+ }
+
+ }
+ rows = ((List<Long>) pae_obj.get("residue1")).iterator();
+ cols = ((List<Long>) pae_obj.get("residue2")).iterator();
Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
.iterator();
- // assume square matrix
- elements = new float[length][length];
+ elements = new float[maxrow][maxcol];
while (scores.hasNext())
{
float escore = scores.next().floatValue();
}
@Override
- public ContactListI getContactList(final int _column)
+ public ContactListI getContactList(final int column)
{
- if (_column < 0 || _column >= elements.length)
+ 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
- public float getMin()
+ protected double getElementAt(int _column, int i)
{
- return 0;
+ return elements[_column][i];
}
@Override
- public float getMax()
- {
- return maxscore;
- }
-
- @Override
- public boolean hasReferenceSeq()
+ public float getMin()
{
- return (refSeq != null);
+ return 0;
}
@Override
- public SequenceI getReferenceSeq()
+ public float getMax()
{
- return refSeq;
+ return maxscore;
}
@Override
{
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;
}
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GroupSet;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
}
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)
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);
/* this already happens in Sequence.addContactList()
seq.addAlignmentAnnotation(cmannot);
*/
// 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 05:31:45 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.embl;
// 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 05:31:45 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.embl;
// 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 05:31:45 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.embl;
// 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 05:31:45 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.embl;
// 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 05:31:45 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.embl;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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.
* <element name="groups" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
* <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
* <element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="mapping" type="{www.vamsas.ac.uk/jalview/version2}mapListType" minOccurs="0"/>
* </sequence>
* <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="rows" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
@XmlType(
name = "MatrixType",
propOrder =
- { "elements", "groups", "newick", "property" })
+ { "elements", "groups", "newick", "property", "mapping" })
public class MatrixType
{
protected List<Property> property;
+ protected MapListType mapping;
+
@XmlAttribute(name = "type", required = true)
protected String type;
}
/**
+ * Gets the value of the mapping property.
+ *
+ * @return possible object is {@link MapListType }
+ *
+ */
+ public MapListType getMapping()
+ {
+ return mapping;
+ }
+
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is {@link MapListType }
+ *
+ */
+ public void setMapping(MapListType value)
+ {
+ this.mapping = value;
+ }
+
+ /**
* Gets the value of the type property.
*
* @return possible object is {@link String }
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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;
// 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
//
@javax.xml.bind.annotation.XmlSchema(
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
package jalview.xml.binding.uniprot;
// 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 05:31:46 PM GMT
+// Generated on: 2023.05.13 at 06:58:42 PM BST
//
@javax.xml.bind.annotation.XmlSchema(
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureMapping;
import jalview.util.Comparison;
+import jalview.ws.datamodel.MappableContactMatrixI;
public class PDBChain
{
ana = new AlignmentAnnotation(ana);
ana.liftOver(dsq, sqmpping);
dsq.addAlignmentAnnotation(ana);
- if (cm != null)
+ if (cm != null && cm instanceof MappableContactMatrixI)
{
- dsq.addContactListFor(ana, cm);
+ dsq.addContactListFor(ana, ((MappableContactMatrixI) cm)
+ .liftOver(dsq, sqmpping));
}
}
else
*/
package jalview.analysis;
+import static org.testng.Assert.assertNotEquals;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import jalview.datamodel.SeqDistanceContactMatrix;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.gff.SequenceOntologyI;
+import jalview.util.Comparison;
import jalview.util.MapList;
import jalview.util.MappingUtils;
}
@Test(groups = "Functional")
+ public void testAddReferenceAnnotations()
+ {
+ SequenceI longseq = new Sequence("longA", "ASDASDASDASDAASDASDASDASDA");
+ Annotation[] aa = new Annotation[longseq.getLength()];
+
+ for (int p = 0; p < aa.length; p++)
+ {
+ aa[p] = new Annotation("P", "pos " + (p + 1), (char) 0,
+ (float) p + 1);
+ }
+ AlignmentAnnotation refAnnot = new AlignmentAnnotation("LongSeqAnnot",
+ "Annotations", aa);
+ refAnnot.setCalcId("Test");
+ longseq.addAlignmentAnnotation(refAnnot);
+ verifyExpectedSequenceAnnotation(refAnnot);
+
+ Alignment ourAl = new Alignment(
+ new SequenceI[]
+ { longseq.getSubSequence(5, 10),
+ longseq.getSubSequence(7, 12) });
+ ourAl.createDatasetAlignment();
+
+ // transfer annotation
+ SortedMap<String, String> tipEntries = new TreeMap<>();
+ Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+
+ AlignmentUtils.findAddableReferenceAnnotations(ourAl.getSequences(),
+ tipEntries, candidates, ourAl);
+ AlignmentUtils.addReferenceAnnotations(candidates, ourAl, null);
+
+ assertNotNull(ourAl.getAlignmentAnnotation());
+ assertEquals(ourAl.getAlignmentAnnotation().length, 2);
+
+ for (AlignmentAnnotation alan : ourAl.getAlignmentAnnotation())
+ {
+ verifyExpectedSequenceAnnotation(alan);
+ }
+ // Everything above works for 2.11.3 and 2.11.2.x.
+ // now simulate copy/paste to new alignment
+ SequenceI[] newSeqAl = new SequenceI[2];
+ // copy sequences but no annotation
+ newSeqAl[0] = new Sequence(ourAl.getSequenceAt(0),
+ ourAl.getSequenceAt(0).getAnnotation());
+ newSeqAl[1] = new Sequence(ourAl.getSequenceAt(1),
+ ourAl.getSequenceAt(1).getAnnotation());
+
+ Alignment newAl = new Alignment(newSeqAl);
+ // delete annotation
+ for (SequenceI sq : newAl.getSequences())
+ {
+ sq.setAlignmentAnnotation(new AlignmentAnnotation[0]);
+ }
+ // JAL-4182 scenario test
+ SequenceGroup sg = new SequenceGroup(Arrays.asList(newSeqAl));
+ sg.setStartRes(0);
+ sg.setEndRes(newAl.getWidth());
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0],
+ newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1],
+ newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
+ for (AlignmentAnnotation alan : newAl.getAlignmentAnnotation())
+ {
+ verifyExpectedSequenceAnnotation(alan);
+ }
+ }
+
+ /**
+ * helper - tests annotation is mapped to position it was originally created
+ * for
+ *
+ * @param alan
+ */
+ private void verifyExpectedSequenceAnnotation(AlignmentAnnotation alan)
+ {
+ for (int c = 0; c < alan.annotations.length; c++)
+ {
+ Annotation a = alan.annotations[c];
+ if (a != null)
+ {
+ assertEquals("Misaligned annotation at " + c,
+ (float) alan.sequenceRef.findPosition(c), a.value);
+ }
+ else
+ {
+ assertTrue("Unexpected Null at position " + c,
+ c >= alan.sequenceRef.getLength()
+ || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
+ }
+ }
+ }
+
+ @Test(groups = "Functional")
public void testAddReferenceContactMap()
{
SequenceI sq = new Sequence("a", "SSSQ");
&& al.getAlignmentAnnotation().length == 1);
AlignmentAnnotation alan = al.findAnnotations(sq, null, cm_aan.label)
.iterator().next();
+ ContactMatrixI t_cm = al.getContactMatrixFor(alan);
+ assertNotNull("No contact map for the transferred annotation row.",
+ t_cm);
+ assertTrue(t_cm instanceof SeqDistanceContactMatrix);
+ assertTrue(((SeqDistanceContactMatrix) t_cm).hasReferenceSeq());
+
ContactListI cl = al.getContactListFor(alan, 1);
assertNotNull(
"No contact matrix recovered after reference annotation transfer",
Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
}
- @Test
+ @Test(groups = { "Functional" })
public void testUPGMAEngine() throws Exception
{
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
}
System.out.println("\\");
}
-
}
}
--- /dev/null
+package jalview.datamodel;
+
+import static org.testng.Assert.*;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.SeqsetUtils;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
+import jalview.ws.datamodel.MappableContactMatrixI;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
+
+public class PAEContactMatrixTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ static float[][] PAEdata = { { 1.0f, 2.0f, 3.0f, 4.0f, 5.0f },
+ { 2.0f, 1.0f, 2.0f, 3.0f, 4.0f },
+ { 3.0f, 2.0f, 1.0f, 2.0f, 3.0f },
+ { 4.0f, 3.0f, 2.0f, 1.0f, 2.0f },
+ { 5.0f, 4.0f, 3.0f, 2.0f, 1.0f } };
+
+ /**
+ * test associations for a PAE matrix
+ */
+ @Test(groups = { "Functional" })
+ public void testSeqAssociatedPAEMatrix()
+ {
+ Sequence seq = new Sequence("Seq", "ASDQE");
+ AlignmentAnnotation aa = seq
+ .addContactList(new PAEContactMatrix(seq, PAEdata));
+ assertNotNull(seq.getContactListFor(aa, 0));
+ assertEquals(seq.getContactListFor(aa, 0).getContactAt(0), 1.0);
+ assertNotNull(seq.getContactListFor(aa, 1));
+ assertEquals(seq.getContactListFor(aa, 1).getContactAt(1), 1.0);
+ assertNotNull(seq.getContactListFor(aa, 2));
+ assertEquals(seq.getContactListFor(aa, 2).getContactAt(2), 1.0);
+ assertNotNull(seq.getContactListFor(aa, 3));
+ assertEquals(seq.getContactListFor(aa, 3).getContactAt(3), 1.0);
+ assertNotNull(seq.getContactListFor(aa, 4));
+ assertEquals(seq.getContactListFor(aa, 4).getContactAt(4), 1.0);
+
+ assertNotNull(seq.getContactListFor(aa, seq.getEnd() - 1));
+ assertNull(seq.getContactListFor(aa, seq.getEnd()));
+
+ ContactListI cm = seq.getContactListFor(aa, seq.getStart());
+ assertEquals(cm.getContactAt(seq.getStart()), 1d);
+ verifyPAEmatrix(seq, aa, 0, 0, 4);
+
+ // Now associated with sequence not starting at 1
+ seq = new Sequence("Seq/5-9", "ASDQE");
+ ContactMatrixI paematrix = new PAEContactMatrix(seq, PAEdata);
+ aa = seq.addContactList(paematrix);
+ assertNotNull(aa);
+ // individual annotation elements need to be distinct for Matrix associated
+ // rows
+ Annotation ae5 = aa.getAnnotationForPosition(5);
+ Annotation ae6 = aa.getAnnotationForPosition(6);
+ assertNotNull(ae5);
+ assertNotNull(ae6);
+ assertTrue(ae5 != ae6);
+
+ cm = seq.getContactListFor(aa, 0);
+ assertEquals(cm.getContactAt(0), 1d);
+ verifyPAEmatrix(seq, aa, 0, 0, 4);
+
+ // test clustering
+ paematrix.setGroupSet(GroupSet.makeGroups(paematrix, 0.1f, false));
+
+ // remap - test the MappableContactMatrix.liftOver method
+ SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+ Mapping sqmap = new Mapping(seq,
+ new MapList(new int[]
+ { 5, 8, 10, 10 }, new int[] { 5, 9 }, 1, 1));
+ assertTrue(paematrix instanceof MappableContactMatrixI);
+
+ MappableContactMatrixI remapped = ((MappableContactMatrixI) paematrix)
+ .liftOver(newseq, sqmap);
+ assertTrue(remapped instanceof PAEContactMatrix);
+
+ AlignmentAnnotation newaa = newseq.addContactList(remapped);
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(1)));
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(4)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(5)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(6)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(7)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(8)));
+ // no mapping for position 9
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
+ // last column
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(10)));
+
+ // verify MappedPositions includes discontinuity
+ int[] mappedCl = newseq.getContactListFor(newaa, 5)
+ .getMappedPositionsFor(0, 4);
+ assertEquals(4, mappedCl.length,
+ "getMappedPositionsFor doesn't support discontinuous mappings to contactList");
+
+ // make it harder.
+
+ SequenceI alseq = newseq.getSubSequence(6, 10);
+ alseq.insertCharAt(2, 2, '-');
+ AlignmentI alForSeq = new Alignment(new SequenceI[] { alseq });
+ newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
+ null);
+ ContactListI alcl = alForSeq.getContactListFor(newaa, 1);
+ assertNotNull(alcl);
+ mappedCl = alcl.getMappedPositionsFor(0, 4);
+ assertNotNull(mappedCl);
+ assertEquals(4, mappedCl.length,
+ "getMappedPositionsFor doesn't support discontinuous mappings to contactList");
+
+ // remap2 - test with original matrix map from 1-5 remapped to 5-9
+
+ seq = new Sequence("Seq/1-5", "ASDQE");
+ paematrix = new PAEContactMatrix(seq, PAEdata);
+ assertTrue(paematrix instanceof MappableContactMatrixI);
+ aa = seq.addContactList(paematrix);
+
+ newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+ sqmap = new Mapping(seq,
+ new MapList(new int[]
+ { 5, 9 }, new int[] { 1, 5 }, 1, 1));
+
+ remapped = ((MappableContactMatrixI) paematrix).liftOver(newseq, sqmap);
+ assertTrue(remapped instanceof PAEContactMatrix);
+
+ newaa = newseq.addContactList(remapped);
+ verify_mapping(newseq, newaa);
+
+ // remap3 - remap2 but mapping sense in liftover is reversed
+
+ seq = new Sequence("Seq/1-5", "ASDQE");
+ paematrix = new PAEContactMatrix(seq, PAEdata);
+ assertTrue(paematrix instanceof MappableContactMatrixI);
+ aa = seq.addContactList(paematrix);
+
+ newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+ sqmap = new Mapping(newseq,
+ new MapList(new int[]
+ { 1, 5 }, new int[] { 5, 9 }, 1, 1));
+
+ remapped = ((MappableContactMatrixI) paematrix).liftOver(newseq, sqmap);
+ assertTrue(remapped instanceof PAEContactMatrix);
+
+ newaa = newseq.addContactList(remapped);
+ verify_mapping(newseq, newaa);
+ }
+
+ /**
+ * checks that the PAE matrix is located at positions 1-9 in newseq, and
+ * columns are not truncated.
+ *
+ * @param newseq
+ * @param newaa
+ */
+ private void verify_mapping(SequenceI newseq, AlignmentAnnotation newaa)
+ {
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(1)));
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(4)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(5)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(6)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(7)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(8)));
+ assertNotNull(
+ newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
+ // last column should be null this time
+ assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(10)));
+
+ verifyPAEmatrix(newseq, newaa, 4, 4, 8);
+ }
+
+ private void verifyPAEmatrix(SequenceI seq, AlignmentAnnotation aa,
+ int topl, int rowl, int rowr)
+ {
+ int[] mappedCl;
+ for (int f = rowl; f <= rowr; f++)
+ {
+ ContactListI clist = seq.getContactListFor(aa, f);
+ assertNotNull(clist, "No ContactListI for position " + (f));
+ assertEquals(clist.getContactAt(0), (double) f - topl + 1,
+ "for column " + f + " relative to " + topl);
+ mappedCl = clist.getMappedPositionsFor(0, 0);
+ assertNotNull(mappedCl);
+ assertEquals(mappedCl[0], mappedCl[1]);
+ assertEquals(mappedCl[0], seq.findIndex(seq.getStart() + topl));
+ assertEquals(clist.getContactAt(f - topl), 1d,
+ "for column and row " + f + " relative to " + topl);
+ }
+ }
+
+}
import java.awt.Rectangle;
import java.io.File;
import java.io.IOException;
+import java.math.BigInteger;
import java.util.ArrayList;
+import java.util.BitSet;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLocus;
+import jalview.datamodel.GroupSet;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import jalview.ws.datamodel.MappableContactMatrixI;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
@Test(singleThreaded = true)
float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
sq.getLength(), sq.getLength());
assertEquals(vals[3][4], paevals[3][4]);
- dummyMat.makeGroups(0.5f, false);
+ dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, 0.5f, false));
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),
newCM = restoredMat.getContactList(i);
for (int j = oldCM.getContactHeight(); j >= 0; j--)
{
- Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j));
+ double old_j = oldCM.getContactAt(j);
+ double new_j = newCM.getContactAt(j);
+ Assert.assertEquals(old_j, new_j);
}
}
Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups());
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