<xs:element name="contactmatrix" type="vamsas:MatrixType"
maxOccurs="unbounded" minOccurs="0">
</xs:element>
- <xs:element name="property" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="name" type="xs:string" />
- <xs:attribute name="value" type="xs:string" />
- </xs:complexType>
- </xs:element>
+ <xs:element name="property" type="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="graph" type="xs:boolean" use="required" />
<xs:attribute name="graphType" type="xs:int" use="optional" />
<xs:attribute name="description" type="xs:string"/>
</xs:complexType>
<xs:complexType name="MatrixType">
- <xs:simpleContent><xs:extension base="xs:string">
- <xs:attribute name="id" type="xs:string"/>
- <xs:attribute name="type" type="xs:string" use="required"/>
- <xs:attribute name="rows" type="xs:integer" use="required"/>
- <xs:attribute name="cols" type="xs:integer" use="required"/>
- </xs:extension>
- </xs:simpleContent>
+ <xs:sequence>
+ <xs:element name="elements" type="xs:string" minOccurs="1"
+ maxOccurs="1">
+ <xs:annotation>
+ <xs:documentation>serialised representation of matrix as one or
+ more sets of comma separated values</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="groups" type="xs:string" minOccurs="0"
+ maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Comma separated series of BigIntegers formed from
+ bitsets defining partitions on the rows/columns of the matrix
+ </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="newick" type="xs:string" minOccurs="0"
+ maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>tree computed for this</xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="property" type="vamsas:property"
+ minOccurs="0" maxOccurs="unbounded" />
+ </xs:sequence>
+
+ <xs:attribute name="type" type="xs:string" use="required" />
+ <xs:attribute name="rows" type="xs:integer"
+ use="required" />
+ <xs:attribute name="cols" type="xs:integer"
+ use="required" />
+ <xs:attribute name="treeMethod" type="xs:string"
+ use="optional" />
+ <xs:attribute name="cutHeight" type="xs:double"
+ use="optional" />
+ <xs:attribute name="id" type="xs:string" use="optional" />
+
</xs:complexType>
+ <xs:complexType name="property">
+ <xs:attribute name="name" type="xs:string" />
+ <xs:attribute name="value" type="xs:string" />
+ </xs:complexType>
+
</xs:schema>
package jalview.datamodel;
+import java.util.Arrays;
import java.util.BitSet;
+import java.util.List;
public interface ContactMatrixI
{
return colbitset;
}
+ default List<BitSet> getGroups() {
+ return Arrays.asList();
+ }
+
+ default boolean hasTree() {
+ return false;
+ }
+
+ /**
+ * Newick representation of clustered matrix
+ * @return null unless hasTree is true
+ */
+ default String getNewick() {
+ return null;
+ }
+
+ default String getTreeMethod() {
+ return null;
+ }
+
+ default boolean hasCutHeight() {
+ return false;
+ }
+
+ default double getCutHeight() {
+ return 0;
+ }
}
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.BitSet;
import java.util.Collections;
import java.util.Enumeration;
import java.util.GregorianCalendar;
xmlmat.setType(cm.getType());
xmlmat.setRows(BigInteger.valueOf(cm.getWidth()));
xmlmat.setCols(BigInteger.valueOf(cm.getHeight()));
- xmlmat.setValue(ContactMatrix.contactToFloatString(cm));
+ // consider using an opaque to/from -> allow instance to control its representation ?
+ xmlmat.setElements(ContactMatrix.contactToFloatString(cm));
+ if (cm.hasGroups())
+ {
+ for (BitSet gp: cm.getGroups())
+ {
+ BigInteger val = new BigInteger(gp.toByteArray());
+ xmlmat.getGroups().add(val.toString());
+ }
+ }
+ if (cm.hasTree())
+ {
+ // provenance object for tree ?
+ xmlmat.getNewick().add(cm.getNewick());
+ xmlmat.setTreeMethod(cm.getTreeMethod());
+ }
+ if (cm.hasCutHeight())
+ {
+ xmlmat.setCutHeight(cm.getCutHeight());
+ }
+
+ // set/get properties
an.getContactmatrix().add(xmlmat);
}
}
{
for (String pr : annotation.getProperties())
{
- jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
+ jalview.xml.binding.jalview.Property prop = new jalview.xml.binding.jalview.Property();
prop.setName(pr);
prop.setValue(annotation.getProperty(pr));
- // an.addProperty(prop);
an.getProperty().add(prop);
}
}
jaa.setCalcId(annotation.getCalcId());
if (annotation.getProperty().size() > 0)
{
- for (Annotation.Property prop : annotation.getProperty())
+ for (jalview.xml.binding.jalview.Property prop : annotation.getProperty())
{
jaa.setProperty(prop.getName(), prop.getValue());
}
else
{
float[][] elements = ContactMatrix
- .fromFloatStringToContacts(xmlmat.getValue(),
+ .fromFloatStringToContacts(xmlmat.getElements(),
xmlmat.getCols().intValue(),
xmlmat.getRows().intValue());
PAEContactMatrix newpae = new PAEContactMatrix(
jaa.sequenceRef, elements);
+ 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);
+ }
+ }
+ }
+ String nwk=xmlmat.getNewick().size()>0 ? xmlmat.getNewick().get(0):null;
+ if (xmlmat.getNewick().size()>1)
+ {
+ 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);
jaa.sequenceRef.addContactListFor(jaa, newpae);
}
}
@Override
public String getAnnotLabel()
{
- StringBuilder label = new StringBuilder("pAE Matrix");
+ StringBuilder label = new StringBuilder("PAE Matrix");
if (this.getReferenceSeq() != null)
+ {
label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+ }
return label.toString();
}
{
return newick;
}
+ boolean abs;
+ double thresh;
+ String treeType=null;
public void makeGroups(float thresh,boolean abs)
{
AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null, this);
double height = clusterer.findHeight(clusterer.getTopNode());
newick = new jalview.io.NewickFile(clusterer.getTopNode(),false,true).print();
-
+ treeType = "UPGMA";
Console.trace("Newick string\n"+newick);
List<BinaryNode> nodegroups;
nodegroups = new ArrayList<BinaryNode>();
nodegroups.add(clusterer.getTopNode());
}
-
+ this.abs=abs;
+ this.thresh=thresh;
groups = new ArrayList<>();
for (BinaryNode root:nodegroups)
{
}
return ContactMatrixI.super.getGroupsFor(column);
}
+
+ 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;
+ }
}
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:03 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:03 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:03 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:03 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:03 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
* </complexType>
* </element>
* <element name="contactmatrix" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="property" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
+ * <element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/>
* </sequence>
* <attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
* <attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
protected String description;
protected Annotation.ThresholdLine thresholdLine;
protected List<MatrixType> contactmatrix;
- protected List<Annotation.Property> property;
+ protected List<Property> property;
@XmlAttribute(name = "graph", required = true)
protected boolean graph;
@XmlAttribute(name = "graphType")
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link Annotation.Property }
+ * {@link Property }
*
*
*/
- public List<Annotation.Property> getProperty() {
+ public List<Property> getProperty() {
if (property == null) {
- property = new ArrayList<Annotation.Property>();
+ property = new ArrayList<Property>();
}
return this.property;
}
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Property {
-
- @XmlAttribute(name = "name")
- protected String name;
- @XmlAttribute(name = "value")
- protected String value;
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
* <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
* <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
package jalview.xml.binding.jalview;
import java.math.BigInteger;
+import java.util.ArrayList;
+import java.util.List;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-import javax.xml.bind.annotation.XmlValue;
/**
*
* <pre>
* <complexType name="MatrixType">
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="elements" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <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"/>
+ * </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" />
* <attribute name="cols" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * </extension>
- * </simpleContent>
+ * <attribute name="treeMethod" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="cutHeight" type="{http://www.w3.org/2001/XMLSchema}double" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
* </complexType>
* </pre>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "MatrixType", propOrder = {
- "value"
+ "elements",
+ "groups",
+ "newick",
+ "property"
})
public class MatrixType {
- @XmlValue
- protected String value;
- @XmlAttribute(name = "id")
- protected String id;
+ @XmlElement(required = true)
+ protected String elements;
+ protected List<String> groups;
+ protected List<String> newick;
+ protected List<Property> property;
@XmlAttribute(name = "type", required = true)
protected String type;
@XmlAttribute(name = "rows", required = true)
protected BigInteger rows;
@XmlAttribute(name = "cols", required = true)
protected BigInteger cols;
+ @XmlAttribute(name = "treeMethod")
+ protected String treeMethod;
+ @XmlAttribute(name = "cutHeight")
+ protected Double cutHeight;
+ @XmlAttribute(name = "id")
+ protected String id;
/**
- * Gets the value of the value property.
+ * Gets the value of the elements property.
*
* @return
* possible object is
* {@link String }
*
*/
- public String getValue() {
- return value;
+ public String getElements() {
+ return elements;
}
/**
- * Sets the value of the value property.
+ * Sets the value of the elements property.
*
* @param value
* allowed object is
* {@link String }
*
*/
- public void setValue(String value) {
- this.value = value;
+ public void setElements(String value) {
+ this.elements = value;
}
/**
- * Gets the value of the id property.
+ * Gets the value of the groups property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the groups property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getGroups().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getId() {
- return id;
+ public List<String> getGroups() {
+ if (groups == null) {
+ groups = new ArrayList<String>();
+ }
+ return this.groups;
}
/**
- * Sets the value of the id property.
+ * Gets the value of the newick property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the newick property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getNewick().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setId(String value) {
- this.id = value;
+ public List<String> getNewick() {
+ if (newick == null) {
+ newick = new ArrayList<String>();
+ }
+ return this.newick;
+ }
+
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Property }
+ *
+ *
+ */
+ public List<Property> getProperty() {
+ if (property == null) {
+ property = new ArrayList<Property>();
+ }
+ return this.property;
}
/**
this.cols = value;
}
+ /**
+ * Gets the value of the treeMethod property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTreeMethod() {
+ return treeMethod;
+ }
+
+ /**
+ * Sets the value of the treeMethod property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTreeMethod(String value) {
+ this.treeMethod = value;
+ }
+
+ /**
+ * Gets the value of the cutHeight property.
+ *
+ * @return
+ * possible object is
+ * {@link Double }
+ *
+ */
+ public Double getCutHeight() {
+ return cutHeight;
+ }
+
+ /**
+ * Sets the value of the cutHeight property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Double }
+ *
+ */
+ public void setCutHeight(Double value) {
+ this.cutHeight = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
}
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
}
/**
- * Create an instance of {@link Annotation.Property }
+ * Create an instance of {@link jalview.xml.binding.jalview.Property }
*
*/
- public Annotation.Property createAnnotationProperty() {
- return new Annotation.Property();
+ public jalview.xml.binding.jalview.Property createProperty() {
+ return new jalview.xml.binding.jalview.Property();
}
/**
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
// 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: 2023.02.22 at 10:08:57 PM GMT
+// Generated on: 2023.03.09 at 07:45:02 AM GMT
//
@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
// 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: 2023.02.22 at 10:08:58 PM GMT
+// Generated on: 2023.03.09 at 07:45:04 AM GMT
//
@javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1
float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength());
assertEquals(vals[3][4],paevals[3][4]);
-
+ dummyMat.makeGroups(0.5f, false);
AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
al.addAnnotation(paeCm);
File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j));
}
}
+ Assert.assertEquals(dummyMat.hasGroups(), restoredMat.hasGroups());
+ Assert.assertEquals(dummyMat.getGroups(), restoredMat.getGroups());
+ Assert.assertEquals(dummyMat.hasTree(), restoredMat.hasTree());
+ Assert.assertEquals(dummyMat.getNewick(), restoredMat.getNewick());
+
}
git://source.jalview.org / jalview.git / commitdiff