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<A NAME="_F_"><!-- --></A><H2>
<B>F</B></H2>
<DL>
<DT><A HREF="../org/biopax/paxtools/io/BioPAXIOHandlerAdapter.html#factory"><B>factory</B></A> - 
Variable in class org.biopax.paxtools.io.<A HREF="../org/biopax/paxtools/io/BioPAXIOHandlerAdapter.html" title="class in org.biopax.paxtools.io">BioPAXIOHandlerAdapter</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/controller/Fetcher.html#fetch(org.biopax.paxtools.model.BioPAXElement, org.biopax.paxtools.model.Model)"><B>fetch(BioPAXElement, Model)</B></A> - 
Method in class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/Fetcher.html" title="class in org.biopax.paxtools.controller">Fetcher</A>
<DD>Adds the element and all its children to the model.
<DT><A HREF="../org/biopax/paxtools/controller/Fetcher.html#fetch(org.biopax.paxtools.model.BioPAXElement)"><B>fetch(BioPAXElement)</B></A> - 
Method in class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/Fetcher.html" title="class in org.biopax.paxtools.controller">Fetcher</A>
<DD>Recursively finds and collects all child objects.
<DT><A HREF="../org/biopax/paxtools/controller/Fetcher.html#fetch(org.biopax.paxtools.model.BioPAXElement, int)"><B>fetch(BioPAXElement, int)</B></A> - 
Method in class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/Fetcher.html" title="class in org.biopax.paxtools.controller">Fetcher</A>
<DD>Recursively finds and collects all child objects.
<DT><A HREF="../org/biopax/paxtools/controller/Fetcher.html#fetch(org.biopax.paxtools.model.BioPAXElement, java.lang.Class)"><B>fetch(BioPAXElement, Class&lt;T&gt;)</B></A> - 
Method in class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/Fetcher.html" title="class in org.biopax.paxtools.controller">Fetcher</A>
<DD>Recursively goes over child objects of the given biopax element, 
 its child's child objects, etc., but collects only biopax 
 elements of the specified type (including its sub-classes).
<DT><A HREF="../org/biopax/paxtools/controller/Fetcher.html" title="class in org.biopax.paxtools.controller"><B>Fetcher</B></A> - Class in <A HREF="../org/biopax/paxtools/controller/package-summary.html">org.biopax.paxtools.controller</A><DD>This class is used to fetch an element (traverse it to obtain
 its dependent elements) and to add this element into a model
 using the visitor and traverse functions.<DT><A HREF="../org/biopax/paxtools/controller/Fetcher.html#Fetcher(org.biopax.paxtools.controller.EditorMap, org.biopax.paxtools.util.Filter...)"><B>Fetcher(EditorMap, Filter&lt;PropertyEditor&gt;...)</B></A> - 
Constructor for class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/Fetcher.html" title="class in org.biopax.paxtools.controller">Fetcher</A>
<DD>Constructor.
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FIELD_AVAILABILITY"><B>FIELD_AVAILABILITY</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FIELD_COMMENT"><B>FIELD_COMMENT</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FIELD_DATASOURCE"><B>FIELD_DATASOURCE</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FIELD_ECNUMBER"><B>FIELD_ECNUMBER</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FIELD_KEYWORD"><B>FIELD_KEYWORD</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FIELD_NAME"><B>FIELD_NAME</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FIELD_ORGANISM"><B>FIELD_ORGANISM</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FIELD_PATHWAY"><B>FIELD_PATHWAY</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FIELD_SEQUENCE"><B>FIELD_SEQUENCE</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FIELD_TERM"><B>FIELD_TERM</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FIELD_XREFDB"><B>FIELD_XREFDB</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FIELD_XREFID"><B>FIELD_XREFID</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/controller/ModelFilter.html#filter(org.biopax.paxtools.model.Model)"><B>filter(Model)</B></A> - 
Method in interface org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/ModelFilter.html" title="interface in org.biopax.paxtools.controller">ModelFilter</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/controller/Traverser.html#filter(org.biopax.paxtools.controller.PropertyEditor)"><B>filter(PropertyEditor&lt;?, ?&gt;)</B></A> - 
Method in class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/Traverser.html" title="class in org.biopax.paxtools.controller">Traverser</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/converter/LevelUpgrader.html#filter(org.biopax.paxtools.model.Model)"><B>filter(Model)</B></A> - 
Method in class org.biopax.paxtools.converter.<A HREF="../org/biopax/paxtools/converter/LevelUpgrader.html" title="class in org.biopax.paxtools.converter">LevelUpgrader</A>
<DD>Converts a BioPAX Model, Level 1 or 2, to the Level 3.
<DT><A HREF="../org/biopax/paxtools/converter/OneTwoThree.html#filter(org.biopax.paxtools.model.Model)"><B>filter(Model)</B></A> - 
Method in class org.biopax.paxtools.converter.<A HREF="../org/biopax/paxtools/converter/OneTwoThree.html" title="class in org.biopax.paxtools.converter">OneTwoThree</A>
<DD><B>Deprecated.</B>&nbsp;Converts a BioPAX Model, Level 1 or 2, to the Level 3.
<DT><A HREF="../org/biopax/paxtools/util/ClassFilterSet.html#filter(E)"><B>filter(E)</B></A> - 
Method in class org.biopax.paxtools.util.<A HREF="../org/biopax/paxtools/util/ClassFilterSet.html" title="class in org.biopax.paxtools.util">ClassFilterSet</A>
<DD>This filter method implementation filters based on isInstance function.
<DT><A HREF="../org/biopax/paxtools/util/Filter.html" title="interface in org.biopax.paxtools.util"><B>Filter</B></A>&lt;<A HREF="../org/biopax/paxtools/util/Filter.html" title="type parameter in Filter">T</A>&gt; - Interface in <A HREF="../org/biopax/paxtools/util/package-summary.html">org.biopax.paxtools.util</A><DD>Generic interface for defining filter decorators.<DT><A HREF="../org/biopax/paxtools/util/Filter.html#filter(T)"><B>filter(T)</B></A> - 
Method in interface org.biopax.paxtools.util.<A HREF="../org/biopax/paxtools/util/Filter.html" title="interface in org.biopax.paxtools.util">Filter</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FILTER_BY_DATASOURCE"><B>FILTER_BY_DATASOURCE</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html#FILTER_BY_ORGANISM"><B>FILTER_BY_ORGANISM</B></A> - 
Static variable in class org.biopax.paxtools.impl.<A HREF="../org/biopax/paxtools/impl/BioPAXElementImpl.html" title="class in org.biopax.paxtools.impl">BioPAXElementImpl</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/util/ClassFilterSet.html#filterClass"><B>filterClass</B></A> - 
Variable in class org.biopax.paxtools.util.<A HREF="../org/biopax/paxtools/util/ClassFilterSet.html" title="class in org.biopax.paxtools.util">ClassFilterSet</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/controller/FilteredPropertyAccessor.html" title="class in org.biopax.paxtools.controller"><B>FilteredPropertyAccessor</B></A>&lt;<A HREF="../org/biopax/paxtools/controller/FilteredPropertyAccessor.html" title="type parameter in FilteredPropertyAccessor">D</A> extends <A HREF="../org/biopax/paxtools/model/BioPAXElement.html" title="interface in org.biopax.paxtools.model">BioPAXElement</A>,<A HREF="../org/biopax/paxtools/controller/FilteredPropertyAccessor.html" title="type parameter in FilteredPropertyAccessor">R</A>&gt; - Class in <A HREF="../org/biopax/paxtools/controller/package-summary.html">org.biopax.paxtools.controller</A><DD>This class is a decorating property accessor that filters values with a given class.<DT><A HREF="../org/biopax/paxtools/controller/PropertyFilterBilinked.html#filterInverse(org.biopax.paxtools.controller.PropertyEditor)"><B>filterInverse(PropertyEditor)</B></A> - 
Method in interface org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/PropertyFilterBilinked.html" title="interface in org.biopax.paxtools.controller">PropertyFilterBilinked</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/controller/TraverserBilinked.html#filterInverse(org.biopax.paxtools.controller.PropertyEditor)"><B>filterInverse(PropertyEditor)</B></A> - 
Method in class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/TraverserBilinked.html" title="class in org.biopax.paxtools.controller">TraverserBilinked</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/controller/Traverser.html#filters"><B>filters</B></A> - 
Variable in class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/Traverser.html" title="class in org.biopax.paxtools.controller">Traverser</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/model/level2/XReferrable.html#findCommonPublications(org.biopax.paxtools.model.level2.XReferrable)"><B>findCommonPublications(XReferrable)</B></A> - 
Method in interface org.biopax.paxtools.model.level2.<A HREF="../org/biopax/paxtools/model/level2/XReferrable.html" title="interface in org.biopax.paxtools.model.level2">XReferrable</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/model/level2/XReferrable.html#findCommonRelationships(org.biopax.paxtools.model.level2.XReferrable)"><B>findCommonRelationships(XReferrable)</B></A> - 
Method in interface org.biopax.paxtools.model.level2.<A HREF="../org/biopax/paxtools/model/level2/XReferrable.html" title="interface in org.biopax.paxtools.model.level2">XReferrable</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/model/level2/XReferrable.html#findCommonUnifications(org.biopax.paxtools.model.level2.XReferrable)"><B>findCommonUnifications(XReferrable)</B></A> - 
Method in interface org.biopax.paxtools.model.level2.<A HREF="../org/biopax/paxtools/model/level2/XReferrable.html" title="interface in org.biopax.paxtools.model.level2">XReferrable</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/util/SetEquivalenceChecker.html#findEquivalentIntersection(java.util.Set, java.util.Set)"><B>findEquivalentIntersection(Set&lt;? extends T&gt;, Set&lt;? extends T&gt;)</B></A> - 
Static method in class org.biopax.paxtools.util.<A HREF="../org/biopax/paxtools/util/SetEquivalenceChecker.html" title="class in org.biopax.paxtools.util">SetEquivalenceChecker</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/controller/ModelUtils.html#findFeaturesAddedToSecond(org.biopax.paxtools.model.level3.PhysicalEntity, org.biopax.paxtools.model.level3.PhysicalEntity, boolean)"><B>findFeaturesAddedToSecond(PhysicalEntity, PhysicalEntity, boolean)</B></A> - 
Static method in class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/ModelUtils.html" title="class in org.biopax.paxtools.controller">ModelUtils</A>
<DD>TODO annotate
<DT><A HREF="../org/biopax/paxtools/controller/ObjectPropertyEditor.html#findInverseGetMethod()"><B>findInverseGetMethod()</B></A> - 
Method in class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/ObjectPropertyEditor.html" title="class in org.biopax.paxtools.controller">ObjectPropertyEditor</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/controller/ModelUtils.html#fixDanglingInverseProperties(org.biopax.paxtools.model.BioPAXElement, org.biopax.paxtools.model.Model)"><B>fixDanglingInverseProperties(BioPAXElement, Model)</B></A> - 
Static method in class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/ModelUtils.html" title="class in org.biopax.paxtools.controller">ModelUtils</A>
<DD>Unlinks <em>inverse properties</em> of the BioPAX object
 from values the other model does not have.
<DT><A HREF="../org/biopax/paxtools/controller/ModelUtils.html#fixDanglingObjectProperties(org.biopax.paxtools.model.BioPAXElement, org.biopax.paxtools.model.Model)"><B>fixDanglingObjectProperties(BioPAXElement, Model)</B></A> - 
Static method in class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/ModelUtils.html" title="class in org.biopax.paxtools.controller">ModelUtils</A>
<DD>Unlinks <em>object properties</em> of the BioPAX object
 from values the model does not have.
<DT><A HREF="../org/biopax/paxtools/controller/ReusedPEPHelper.html#fixReusedPEP(org.biopax.paxtools.model.level2.physicalEntityParticipant, org.biopax.paxtools.model.BioPAXElement)"><B>fixReusedPEP(physicalEntityParticipant, BioPAXElement)</B></A> - 
Method in class org.biopax.paxtools.controller.<A HREF="../org/biopax/paxtools/controller/ReusedPEPHelper.html" title="class in org.biopax.paxtools.controller">ReusedPEPHelper</A>
<DD>&nbsp;
<DT><A HREF="../org/biopax/paxtools/io/BioPAXIOHandler.html#fixReusedPEPs(boolean)"><B>fixReusedPEPs(boolean)</B></A> - 
Method in interface org.biopax.paxtools.io.<A HREF="../org/biopax/paxtools/io/BioPAXIOHandler.html" title="interface in org.biopax.paxtools.io">BioPAXIOHandler</A>
<DD>This option is only applicable two level 2 models.
<DT><A HREF="../org/biopax/paxtools/io/BioPAXIOHandlerAdapter.html#fixReusedPEPs(boolean)"><B>fixReusedPEPs(boolean)</B></A> - 
Method in class org.biopax.paxtools.io.<A HREF="../org/biopax/paxtools/io/BioPAXIOHandlerAdapter.html" title="class in org.biopax.paxtools.io">BioPAXIOHandlerAdapter</A>
<DD>Enables (true) or disables (false) the fixing of reused peps.
<DT><A HREF="../org/biopax/paxtools/model/level3/FragmentFeature.html" title="interface in org.biopax.paxtools.model.level3"><B>FragmentFeature</B></A> - Interface in <A HREF="../org/biopax/paxtools/model/level3/package-summary.html">org.biopax.paxtools.model.level3</A><DD>Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or
 degradation event.<DT><A HREF="../org/biopax/paxtools/impl/level3/FragmentFeatureImpl.html" title="class in org.biopax.paxtools.impl.level3"><B>FragmentFeatureImpl</B></A> - Class in <A HREF="../org/biopax/paxtools/impl/level3/package-summary.html">org.biopax.paxtools.impl.level3</A><DD>&nbsp;<DT><A HREF="../org/biopax/paxtools/impl/level3/FragmentFeatureImpl.html#FragmentFeatureImpl()"><B>FragmentFeatureImpl()</B></A> - 
Constructor for class org.biopax.paxtools.impl.level3.<A HREF="../org/biopax/paxtools/impl/level3/FragmentFeatureImpl.html" title="class in org.biopax.paxtools.impl.level3">FragmentFeatureImpl</A>
<DD>&nbsp;
</DL>
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