Bug 332772 - Support problem filters for API Use Scan Task

10 files changed, 643 insertions, 511 deletions

diff --git a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/ApiFilterStore.java b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/ApiFilterStore.java
index 0b6bafe755..2c300a1304 100644
--- a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/ApiFilterStore.java
+++ b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/ApiFilterStore.java
@@ -23,18 +23,17 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.NodeList;
-
-import org.eclipse.pde.api.tools.internal.problems.ApiProblemFactory;
-import org.eclipse.pde.api.tools.internal.problems.ApiProblemFilter;
-import org.eclipse.pde.api.tools.internal.provisional.ApiPlugin;
-import org.eclipse.pde.api.tools.internal.provisional.IApiFilterStore;
-import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem;
-import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblemFilter;
-import org.eclipse.pde.api.tools.internal.util.Util;
-
+import org.eclipse.core.resources.IFile;
+import org.eclipse.core.resources.IFolder;
+import org.eclipse.core.resources.IProject;
+import org.eclipse.core.resources.IResource;
+import org.eclipse.core.resources.IResourceChangeEvent;
+import org.eclipse.core.resources.IResourceChangeListener;
+import org.eclipse.core.resources.IResourceDelta;
+import org.eclipse.core.resources.IncrementalProjectBuilder;
+import org.eclipse.core.resources.ProjectScope;
+import org.eclipse.core.resources.ResourcesPlugin;
+import org.eclipse.core.resources.WorkspaceJob;
 import org.eclipse.core.runtime.Assert;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IPath;
@@ -47,47 +46,21 @@ import org.eclipse.core.runtime.SubMonitor;
 import org.eclipse.core.runtime.jobs.Job;
 import org.eclipse.core.runtime.preferences.IScopeContext;
 import org.eclipse.core.runtime.preferences.InstanceScope;
-
-import org.eclipse.core.resources.IFile;
-import org.eclipse.core.resources.IFolder;
-import org.eclipse.core.resources.IProject;
-import org.eclipse.core.resources.IResource;
-import org.eclipse.core.resources.IResourceChangeEvent;
-import org.eclipse.core.resources.IResourceChangeListener;
-import org.eclipse.core.resources.IResourceDelta;
-import org.eclipse.core.resources.IncrementalProjectBuilder;
-import org.eclipse.core.resources.ProjectScope;
-import org.eclipse.core.resources.ResourcesPlugin;
-import org.eclipse.core.resources.WorkspaceJob;
-
 import org.eclipse.jdt.core.IJavaProject;
+import org.eclipse.pde.api.tools.internal.problems.ApiProblemFilter;
+import org.eclipse.pde.api.tools.internal.provisional.ApiPlugin;
+import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem;
+import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblemFilter;
+import org.eclipse.pde.api.tools.internal.util.Util;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 
 /**
  * Base implementation of a filter store for API components
  * 
  * @since 1.0.0
  */
-public class ApiFilterStore implements IApiFilterStore, IResourceChangeListener {
-	
-	/**
-	 * Constant representing the name of the .settings folder
-	 */
-	private static final String SETTINGS_FOLDER = ".settings"; //$NON-NLS-1$
-	public static final String GLOBAL = "!global!"; //$NON-NLS-1$
-	public static final int CURRENT_STORE_VERSION = 2;
-
-	/**
-	 * Represents no filters
-	 */
-	private static IApiProblemFilter[] NO_FILTERS = new IApiProblemFilter[0];
-	
-	/**
-	 * The mapping of filters for this store.
-	 * <pre>
-	 * HashMap<IResource, HashSet<IApiProblemFilter>>
-	 * </pre>
-	 */
-	private HashMap fFilterMap = null;
+public class ApiFilterStore extends FilterStore implements IResourceChangeListener {
 	
 	/**
 	 * Map used to collect unused {@link IApiProblemFilter}s
@@ -154,8 +127,9 @@ public class ApiFilterStore implements IApiFilterStore, IResourceChangeListener
 					}
 					String lineDelimiter= getLineDelimiterPreference(file);
 					String lineSeparator= System.getProperty("line.separator"); //$NON-NLS-1$
-					if (lineDelimiter != null && !lineDelimiter.equals(lineSeparator))
+					if (lineDelimiter != null && !lineDelimiter.equals(lineSeparator)) {
 						xml= xml.replaceAll(lineSeparator, lineDelimiter);
+					}
 					InputStream xstream = Util.getInputStreamFromString(xml);
 					if(xstream == null) {
 						return Status.CANCEL_STATUS;
@@ -255,7 +229,8 @@ public class ApiFilterStore implements IApiFilterStore, IResourceChangeListener
 			return;
 		}
 		initializeApiFilters();
-		internalAddFilters(problems, null, true);
+		internalAddFilters(problems, null);
+		persistApiFilters();
 	}
 
 	/* (non-Javadoc)
@@ -265,7 +240,7 @@ public class ApiFilterStore implements IApiFilterStore, IResourceChangeListener
 		initializeApiFilters();
 		Map pTypeNames = (Map) fFilterMap.get(resource);
 		if(pTypeNames == null) {
-			return NO_FILTERS;
+			return FilterStore.NO_FILTERS;
 		}
 		List allFilters = new ArrayList();
 		for (Iterator iterator = pTypeNames.values().iterator(); iterator.hasNext(); ) {
@@ -525,11 +500,10 @@ public class ApiFilterStore implements IApiFilterStore, IResourceChangeListener
 		return Util.serializeDocument(document);
 	}
 
-	/**
-	 * Initializes the backing filter map for this store from the .api_filters file. Does nothing if the filter store has already been
-	 * initialized.
+	/* (non-Javadoc)
+	 * @see org.eclipse.pde.api.tools.internal.FilterStore#initializeApiFilters()
 	 */
-	private synchronized void initializeApiFilters() {
+	protected synchronized void initializeApiFilters() {
 		if(fFilterMap != null) {
 			return;
 		}
@@ -545,13 +519,12 @@ public class ApiFilterStore implements IApiFilterStore, IResourceChangeListener
 			}
 			return;
 		}
-		String xml = null;
 		InputStream contents = null;
 		try {
 			IFile filterFile = (IFile)file;
 			if (filterFile.exists()) {
 				contents = filterFile.getContents();
-				xml = new String(Util.getInputStreamAsCharArray(contents, -1, IApiCoreConstants.UTF_8));
+				readFilterFile(contents);
 			}
 		}
 		catch(CoreException e) {
@@ -569,101 +542,15 @@ public class ApiFilterStore implements IApiFilterStore, IResourceChangeListener
 				}
 			}
 		}
-		if(xml == null) {
-			return;
-		}
-		Element root = null;
-		try {
-			root = Util.parseDocument(xml);
-		}
-		catch(CoreException ce) {
-			ApiPlugin.log(ce);
-		}
-		if (root == null) {
-			return;
-		}
-		if (!root.getNodeName().equals(IApiXmlConstants.ELEMENT_COMPONENT)) {
-			return;
-		}
-		String component = root.getAttribute(IApiXmlConstants.ATTR_ID);
-		if(component.length() == 0) {
-			return;
-		}
-		String versionValue = root.getAttribute(IApiXmlConstants.ATTR_VERSION);
-		int currentVersion = Integer.parseInt(IApiXmlConstants.API_FILTER_STORE_CURRENT_VERSION);
-		int version = 0;
-		if(versionValue.length() != 0) {
-			try {
-				version = Integer.parseInt(versionValue);
-			} catch (NumberFormatException e) {
-				// ignore
-			}
-		}
-		if (version != currentVersion) {
-			// we discard all filters since there is no way to retrieve the type name
-			fNeedsSaving = true;
-			persistApiFilters();
-			return;
-		}
-		NodeList resources = root.getElementsByTagName(IApiXmlConstants.ELEMENT_RESOURCE);
-		ArrayList newfilters = new ArrayList();
-		ArrayList comments = new ArrayList();
-		for(int i = 0; i < resources.getLength(); i++) {
-			Element element = (Element) resources.item(i);
-			String path = element.getAttribute(IApiXmlConstants.ATTR_PATH);
-			if(path.length() == 0) {
-				continue;
-			}
-			String typeName = element.getAttribute(IApiXmlConstants.ATTR_TYPE);
-			if (typeName.length() == 0) {
-				typeName = null;
-			}
-			IProject project = (IProject) ResourcesPlugin.getWorkspace().getRoot().findMember(component);
-			if(project == null) {
-				continue;
-			}
-			IResource resource = project.findMember(new Path(path));
-			if(resource == null) {
-				continue;
-			}
-			NodeList filters = element.getElementsByTagName(IApiXmlConstants.ELEMENT_FILTER);
-			for(int j = 0; j < filters.getLength(); j++) {
-				element = (Element) filters.item(j);
-				int id = loadIntegerAttribute(element, IApiXmlConstants.ATTR_ID);
-				if(id <= 0) {
-					continue;
-				}
-				String[] messageargs = null;
-				NodeList elements = element.getElementsByTagName(IApiXmlConstants.ELEMENT_PROBLEM_MESSAGE_ARGUMENTS);
-				if (elements.getLength() != 1) continue;
-				Element messageArguments = (Element) elements.item(0);
-				NodeList arguments = messageArguments.getElementsByTagName(IApiXmlConstants.ELEMENT_PROBLEM_MESSAGE_ARGUMENT);
-				int length = arguments.getLength();
-				messageargs = new String[length];
-				for (int k = 0; k < length; k++) {
-					Element messageArgument = (Element) arguments.item(k);
-					messageargs[k] = messageArgument.getAttribute(IApiXmlConstants.ATTR_VALUE);
-				}
-				String comment = element.getAttribute(IApiXmlConstants.ATTR_COMMENT);
-				comments.add((comment.length() < 1 ? null : comment));
-				newfilters.add(ApiProblemFactory.newApiProblem(resource.getProjectRelativePath().toPortableString(),
-						typeName,
-						messageargs, null, null, -1, -1, -1, id));
-			}
-		}
-		internalAddFilters((IApiProblem[]) newfilters.toArray(new IApiProblem[newfilters.size()]), 
-				(String[]) comments.toArray(new String[comments.size()]), 
-				false);
-		newfilters.clear();
+		//need to reset the flag during initialization if we are not going to persist
+		//the filters, see https://bugs.eclipse.org/bugs/show_bug.cgi?id=309635
+		fNeedsSaving = false;
 	}
 	
-	/**
-	 * Internal use method that allows auto-persisting of the filter file to be turned on or off
-	 * @param problems the problems to add the the store
-	 * @param comments the comments associated with each problem
-	 * @param persist if the filters should be auto-persisted after they are added
+	/* (non-Javadoc)
+	 * @see org.eclipse.pde.api.tools.internal.FilterStore#internalAddFilters(org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem[], java.lang.String[])
 	 */
-	private synchronized void internalAddFilters(IApiProblem[] problems, String[] comments, boolean persist) {
+	protected synchronized void internalAddFilters(IApiProblem[] problems, String[] comments) {
 		Set filters = null;
 		for(int i = 0; i < problems.length; i++) {
 			IApiProblem problem = problems[i];
@@ -695,14 +582,6 @@ public class ApiFilterStore implements IApiFilterStore, IResourceChangeListener
 			}
 			fNeedsSaving |= filters.add(filter);
 		}
-		if(persist) {
-			persistApiFilters();
-		}
-		else {
-			//need to reset the flag during initialization if we are not going to persist
-			//the filters, see https://bugs.eclipse.org/bugs/show_bug.cgi?id=309635
-			fNeedsSaving = false;
-		}
 	}
 	
 	/**
@@ -715,32 +594,14 @@ public class ApiFilterStore implements IApiFilterStore, IResourceChangeListener
 	}
 	
 	/**
-	 * Loads the specified integer attribute from the given xml element
-	 * @param element
-	 * @param name
-	 * @return
-	 */
-	private static int loadIntegerAttribute(Element element, String name) {
-		String value = element.getAttribute(name);
-		if(value.length() == 0) {
-			return -1;
-		}
-		try {
-			int number = Integer.parseInt(value);
-			return number;
-		}
-		catch(NumberFormatException nfe) {}
-		return -1;
-	}
-	/**
 	 * @return the {@link IPath} to the filters file
 	 */
 	IPath getFilterFilePath(boolean includeproject) {
 		if(includeproject) {
 			IPath path = fProject.getPath();
-			return path.append(SETTINGS_FOLDER).append(IApiCoreConstants.API_FILTERS_XML_NAME);
+			return path.append(FilterStore.SETTINGS_FOLDER).append(IApiCoreConstants.API_FILTERS_XML_NAME);
 		}
-		return new Path(SETTINGS_FOLDER).append(IApiCoreConstants.API_FILTERS_XML_NAME);
+		return new Path(FilterStore.SETTINGS_FOLDER).append(IApiCoreConstants.API_FILTERS_XML_NAME);
 	}
 
 	static String getLineDelimiterPreference(IFile file) {
@@ -841,11 +702,11 @@ public class ApiFilterStore implements IApiFilterStore, IResourceChangeListener
 			}
 			int size = unused.size();
 			if (size == 0) {
-				return NO_FILTERS;
+				return FilterStore.NO_FILTERS;
 			}
 			return (IApiProblemFilter[]) unused.toArray(new IApiProblemFilter[size]);
 		}
-		return NO_FILTERS;
+		return FilterStore.NO_FILTERS;
 	}
 	
 	/**
diff --git a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/CoreMessages.java b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/CoreMessages.java
index d6ce2b6aba..176aafd7e7 100644
--- a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/CoreMessages.java
+++ b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/CoreMessages.java
@@ -23,6 +23,7 @@ public class CoreMessages extends NLS {
 	public static String ApiBaseline_4;
 	public static String ApiBaseline_5;
 	public static String ApiBaseline_6;
+	public static String FilterStore_0;
 	public static String ProjectComponent_could_not_locate_model;
 	static {
 		// initialize resource bundle
diff --git a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/FilterStore.java b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/FilterStore.java
new file mode 100644
index 0000000000..20d65e9794
--- /dev/null
+++ b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/FilterStore.java
@@ -0,0 +1,420 @@
+/*******************************************************************************
+ * Copyright (c) 2012 IBM Corporation and others.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *     IBM Corporation - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.pde.api.tools.internal;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.eclipse.core.resources.IResource;
+import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.Path;
+import org.eclipse.pde.api.tools.internal.model.BundleComponent;
+import org.eclipse.pde.api.tools.internal.problems.ApiProblemFactory;
+import org.eclipse.pde.api.tools.internal.problems.ApiProblemFilter;
+import org.eclipse.pde.api.tools.internal.provisional.ApiPlugin;
+import org.eclipse.pde.api.tools.internal.provisional.IApiFilterStore;
+import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem;
+import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblemFilter;
+import org.eclipse.pde.api.tools.internal.util.Util;
+import org.w3c.dom.Element;
+import org.w3c.dom.NodeList;
+
+/**
+ * A generic {@link IApiFilterStore} that does not depend on workspace resources
+ * to filter {@link IApiProblem}s.
+ * <br>
+ * This filter store can have filters added and removed from it, but those changes 
+ * are not saved.
+ */
+public class FilterStore implements IApiFilterStore {
+
+	public static final String GLOBAL = "!global!"; //$NON-NLS-1$
+	/**
+	 * Represents no filters
+	 */
+	public static IApiProblemFilter[] NO_FILTERS = new IApiProblemFilter[0];
+	/**
+	 * The current version of this filter store file format
+	 */
+	public static final int CURRENT_STORE_VERSION = 2;
+	/**
+	 * Constant representing the name of the .settings folder
+	 */
+	static final String SETTINGS_FOLDER = ".settings"; //$NON-NLS-1$
+	/**
+	 * The mapping of filters for this store.
+	 */
+	protected HashMap fFilterMap = null;
+	/**
+	 * The bundle component backing this store
+	 */
+	private BundleComponent fComponent = null;
+
+	/**
+	 * Constructor
+	 */
+	public FilterStore() {}
+	
+	/**
+	 * Constructor
+	 * @param component
+	 */
+	public FilterStore(BundleComponent component) {
+		fComponent = component;
+		initializeApiFilters();
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.eclipse.pde.api.tools.internal.provisional.IApiFilterStore#addFilters(org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblemFilter[])
+	 */
+	public void addFilters(IApiProblemFilter[] filters) {
+		if(filters != null && filters.length > 0) {
+			initializeApiFilters();
+			for (int i = 0; i < filters.length; i++) {
+				fFilterMap.put(filters[i].getComponentId(), filters[i]);
+			}
+		}
+	}
+
+	/* (non-Javadoc)
+	 * @see org.eclipse.pde.api.tools.internal.provisional.IApiFilterStore#addFiltersFor(org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem[])
+	 */
+	public void addFiltersFor(IApiProblem[] problems) {
+		if(problems != null && problems.length > 0) {
+			initializeApiFilters();
+			internalAddFilters(problems, null);
+		}
+	}
+
+	/* (non-Javadoc)
+	 * @see org.eclipse.pde.api.tools.internal.provisional.IApiFilterStore#getFilters(org.eclipse.core.resources.IResource)
+	 */
+	public IApiProblemFilter[] getFilters(IResource resource) {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.eclipse.pde.api.tools.internal.provisional.IApiFilterStore#getResources()
+	 */
+	public IResource[] getResources() {
+		return null;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.eclipse.pde.api.tools.internal.provisional.IApiFilterStore#removeFilters(org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblemFilter[])
+	 */
+	public boolean removeFilters(IApiProblemFilter[] filters) {
+		if(filters != null && filters.length > 0) {
+			initializeApiFilters();
+			boolean removed = true;
+			for(int i = 0; i < filters.length; i++) {
+				removed &= (fFilterMap.remove(filters[i].getComponentId()) != null);
+			}
+			return removed;
+		}
+		return false;
+	}
+
+	/**
+	 * Loads the filters from the .api_filters file
+	 */
+	protected synchronized void initializeApiFilters() {
+		if(fFilterMap == null) {
+			fFilterMap = new HashMap(5);
+			ZipFile jarFile = null;
+			InputStream filterstream = null;
+			File loc = new File(fComponent.getLocation());
+			String extension = new Path(loc.getName()).getFileExtension();
+			try {
+				if (extension != null && extension.equals("jar") && loc.isFile()) { //$NON-NLS-1$
+					jarFile = new ZipFile(loc, ZipFile.OPEN_READ);
+					ZipEntry filterfile = jarFile.getEntry(IApiCoreConstants.API_FILTERS_XML_NAME);
+					if (filterfile != null) {
+						filterstream = jarFile.getInputStream(filterfile);
+					}
+				} else {
+					File file = new File(loc, SETTINGS_FOLDER+File.separator+IApiCoreConstants.API_FILTERS_XML_NAME);
+					if (file.exists()) {
+						filterstream = new FileInputStream(file);
+					}
+				}
+				if (filterstream == null) {
+					return;
+				}
+				readFilterFile(filterstream);
+				
+			} catch (IOException e) {
+				ApiPlugin.log(e);
+			} finally {
+				fComponent.closingZipFileAndStream(filterstream, jarFile);
+			}
+		}
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.eclipse.pde.api.tools.internal.provisional.IApiFilterStore#isFiltered(org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem)
+	 */
+	public boolean isFiltered(IApiProblem problem) {
+		if (fFilterMap == null || fFilterMap.isEmpty()) {
+			return false;
+		}
+		String typeName = problem.getTypeName();
+		if (typeName == null || typeName.length() == 0) {
+			typeName = GLOBAL;
+		}
+		Set filters = (Set) fFilterMap.get(typeName);
+		if (filters == null) {
+			return false;
+		}
+		for (Iterator iterator = filters.iterator(); iterator.hasNext();) {
+			IApiProblemFilter filter = (IApiProblemFilter) iterator.next();
+			if (problemsMatch(filter.getUnderlyingProblem(), problem)) {
+				return true;
+			}
+		}
+		return false;
+	}
+	
+	/**
+	 * Returns <code>true</code> if the attributes of the problems match, <code>false</code> otherwise
+	 * 
+	 * @param filterProblem the problem from the filter store
+	 * @param problem the problem from the builder
+	 * @return <code>true</code> if the problems match, <code>false</code> otherwise
+	 */
+	protected boolean problemsMatch(IApiProblem filterProblem, IApiProblem problem) {
+		if (problem.getId() == filterProblem.getId()) {
+			// check arguments
+//			String problemPath = problem.getResourcePath();
+//			String filterProblemPath = filterProblem.getResourcePath();
+//			if (problemPath == null) {
+//				if (filterProblemPath != null) {
+//					return false;
+//				}
+//			} else if (filterProblemPath == null) {
+//				return false;
+//			} else if (!new Path(problemPath).equals(new Path(filterProblemPath))) {
+//				return false;
+//			}
+			String problemTypeName = problem.getTypeName();
+			String filterProblemTypeName = filterProblem.getTypeName();
+			if (problemTypeName == null) {
+				if (filterProblemTypeName != null) {
+					return false;
+				}
+			} else if (filterProblemTypeName == null) {
+				return false;
+			} else if (!problemTypeName.equals(filterProblemTypeName)) {
+				return false;
+			}
+			return argumentsEquals(problem.getMessageArguments(), filterProblem.getMessageArguments());
+		}
+		return false;
+	}
+	
+	/**
+	 * Returns if the arrays of message arguments are equal. 
+	 * <br>
+	 * The arrays are considered equal iff:
+	 * <ul>
+	 * <li>both are <code>null</code></li>
+	 * <li>both are the same length</li>
+	 * <li>both have equal elements at equal positions in the array</li>
+	 * </ul>
+	 * @param problemMessageArguments
+	 * @param filterProblemMessageArguments
+	 * @return <code>true</code> if the arrays are equal, <code>false</code> otherwise
+	 */
+	private boolean argumentsEquals(String[] problemMessageArguments, String[] filterProblemMessageArguments) {
+		// filter problems message arguments are always simple name
+		// problem message arguments are fully qualified name outside the IDE
+		int length = problemMessageArguments.length;
+		if (length == filterProblemMessageArguments.length) {
+			for (int i = 0; i < length; i++) {
+				String problemMessageArgument = problemMessageArguments[i];
+				String filterProblemMessageArgument = filterProblemMessageArguments[i];
+				if (problemMessageArgument.equals(filterProblemMessageArgument)) {
+					continue;
+				}
+				int index = problemMessageArgument.lastIndexOf('.');
+				int filterProblemIndex = filterProblemMessageArgument.lastIndexOf('.');
+				if (index == -1) {
+					if (filterProblemIndex == -1) {
+						return false; // simple names should match
+					}
+					if (filterProblemMessageArgument.substring(filterProblemIndex + 1).equals(problemMessageArgument)) {
+						continue;
+					} else {
+						return false;
+					}
+				} else if (filterProblemIndex != -1) {
+					return false; // fully qualified name should match
+				} else {
+					if (problemMessageArgument.substring(index + 1).equals(filterProblemMessageArgument)) {
+						continue;
+					} else {
+						return false;
+					}
+				}
+			}
+			return true;
+		}
+		return false;
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.eclipse.pde.api.tools.internal.provisional.IApiFilterStore#dispose()
+	 */
+	public void dispose() {
+		if(fFilterMap != null) {
+			fFilterMap.clear();
+			fFilterMap = null;
+		}
+	}
+	
+	/**
+	 * Reads the API problem filter file and calls back to {@link #addFilters(IApiProblemFilter[])} 
+	 * to store the filters.
+	 * <br>
+	 * This method will not close the given input stream when done reading it.
+	 * 
+	 * @param contents the {@link InputStream} for the contents of the filter file, <code>null</code> is not allowed.
+	 * @throws IOException if the stream cannot be read or fails
+	 */
+	protected void readFilterFile(InputStream contents) throws IOException {
+		if(contents == null) {
+			throw new IOException(CoreMessages.FilterStore_0);
+		}
+		String xml = new String(Util.getInputStreamAsCharArray(contents, -1, IApiCoreConstants.UTF_8));
+		Element root = null;
+		try {
+			root = Util.parseDocument(xml);
+		}
+		catch(CoreException ce) {
+			ApiPlugin.log(ce);
+		}
+		if (root == null) {
+			return;
+		}
+		if (!root.getNodeName().equals(IApiXmlConstants.ELEMENT_COMPONENT)) {
+			return;
+		}
+		String component = root.getAttribute(IApiXmlConstants.ATTR_ID);
+		if(component.length() == 0) {
+			return;
+		}
+		String versionValue = root.getAttribute(IApiXmlConstants.ATTR_VERSION);
+		int currentVersion = Integer.parseInt(IApiXmlConstants.API_FILTER_STORE_CURRENT_VERSION);
+		int version = 0;
+		if(versionValue.length() != 0) {
+			try {
+				version = Integer.parseInt(versionValue);
+			} catch (NumberFormatException e) {
+				// ignore
+			}
+		}
+		if (version != currentVersion) {
+			return;
+		}
+		NodeList resources = root.getElementsByTagName(IApiXmlConstants.ELEMENT_RESOURCE);
+		ArrayList newfilters = new ArrayList();
+		ArrayList comments = new ArrayList();
+		for(int i = 0; i < resources.getLength(); i++) {
+			Element element = (Element) resources.item(i);
+			String typeName = element.getAttribute(IApiXmlConstants.ATTR_TYPE);
+			if (typeName.length() == 0) {
+				// if there is no type attribute, an empty string is returned
+				typeName = null;
+			}
+			String path = element.getAttribute(IApiXmlConstants.ATTR_PATH);
+			NodeList filters = element.getElementsByTagName(IApiXmlConstants.ELEMENT_FILTER);
+			for(int j = 0; j < filters.getLength(); j++) {
+				element = (Element) filters.item(j);
+				int id = loadIntegerAttribute(element, IApiXmlConstants.ATTR_ID);
+				if(id <= 0) {
+					continue;
+				}
+				String[] messageargs = null;
+				NodeList elements = element.getElementsByTagName(IApiXmlConstants.ELEMENT_PROBLEM_MESSAGE_ARGUMENTS);
+				if (elements.getLength() != 1) continue;
+				Element messageArguments = (Element) elements.item(0);
+				NodeList arguments = messageArguments.getElementsByTagName(IApiXmlConstants.ELEMENT_PROBLEM_MESSAGE_ARGUMENT);
+				int length = arguments.getLength();
+				messageargs = new String[length];
+				String comment = element.getAttribute(IApiXmlConstants.ATTR_COMMENT);
+				comments.add((comment.length() < 1 ? null : comment));
+				for (int k = 0; k < length; k++) {
+					Element messageArgument = (Element) arguments.item(k);
+					messageargs[k] = messageArgument.getAttribute(IApiXmlConstants.ATTR_VALUE);
+				}
+				newfilters.add(ApiProblemFactory.newApiProblem(path, typeName, messageargs, null, null, -1, -1, -1, id));
+			}
+		}
+		internalAddFilters(
+				(IApiProblem[]) newfilters.toArray(new IApiProblem[newfilters.size()]),
+				(String[]) comments.toArray(new String[comments.size()]));
+		newfilters.clear();
+	}
+	
+	/**
+	 * Internal use method that allows auto-persisting of the filter file to be turned on or off
+	 * @param problems the problems to add the the store
+	 * @param persist if the filters should be auto-persisted after they are added
+	 */
+	protected void internalAddFilters(IApiProblem[] problems, String[] comments) {
+		if(problems == null) {
+			return;
+		}
+		for(int i = 0; i < problems.length; i++) {
+			IApiProblem problem = problems[i];
+			IApiProblemFilter filter = new ApiProblemFilter(fComponent.getSymbolicName(), problem, comments[i]);
+			String typeName = problem.getTypeName();
+			if (typeName == null) {
+				typeName = GLOBAL;
+			}
+			Set filters = (Set) fFilterMap.get(typeName);
+			if(filters == null) {
+				filters = new HashSet();
+				fFilterMap.put(typeName, filters);
+			}
+			filters.add(filter);
+		}
+	}
+	
+	/**
+	 * Loads the specified integer attribute from the given XML element
+	 * @param element the XML element
+	 * @param name the name of the attribute
+	 * @return the specified value in XML or -1
+	 */
+	protected int loadIntegerAttribute(Element element, String name) {
+		String value = element.getAttribute(name);
+		if(value.length() == 0) {
+			return -1;
+		}
+		try {
+			int number = Integer.parseInt(value);
+			return number;
+		}
+		catch(NumberFormatException nfe) {}
+		return -1;
+	}
+
+}
diff --git a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/IApiXmlConstants.java b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/IApiXmlConstants.java
index 0e7b931116..bc8bb9acbe 100644
--- a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/IApiXmlConstants.java
+++ b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/IApiXmlConstants.java
@@ -25,7 +25,7 @@ public interface IApiXmlConstants {
 	/**
 	 * Constant representing the current version for API filter store files
 	 */
-	public static final String API_FILTER_STORE_CURRENT_VERSION = Integer.toString(ApiFilterStore.CURRENT_STORE_VERSION);
+	public static final String API_FILTER_STORE_CURRENT_VERSION = Integer.toString(FilterStore.CURRENT_STORE_VERSION);
 	/**
 	 * Constant representing the current version for API profile files
 	 */
diff --git a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/coremessages.properties b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/coremessages.properties
index 8053c0ef8a..8cd2a78e64 100644
--- a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/coremessages.properties
+++ b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/coremessages.properties
@@ -15,4 +15,5 @@ ApiBaseline_2=Error occurred while binding execution environment
 ApiBaseline_4=Baseline has bundles requiring unavailable execution environments
 ApiBaseline_5={0} is unavailable
 ApiBaseline_6=Baseline not bound - there are no installed VMs compatible with the required execution environments
+FilterStore_0=Cannot read API problem filters from a null stream
 ProjectComponent_could_not_locate_model=Could not locate the plugin model base for project: {0}
diff --git a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/model/BundleComponent.java b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/model/BundleComponent.java
index a1525a39d0..c47ceac4bb 100644
--- a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/model/BundleComponent.java
+++ b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/model/BundleComponent.java
@@ -28,7 +28,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.jar.JarFile;
-import java.util.jar.Manifest;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipFile;
 
@@ -55,6 +54,7 @@ import org.eclipse.pde.api.tools.internal.ApiDescription;
 import org.eclipse.pde.api.tools.internal.ApiDescriptionProcessor;
 import org.eclipse.pde.api.tools.internal.BundleVersionRange;
 import org.eclipse.pde.api.tools.internal.CompositeApiDescription;
+import org.eclipse.pde.api.tools.internal.FilterStore;
 import org.eclipse.pde.api.tools.internal.IApiCoreConstants;
 import org.eclipse.pde.api.tools.internal.RequiredComponentDescription;
 import org.eclipse.pde.api.tools.internal.provisional.ApiPlugin;
@@ -529,8 +529,7 @@ public class BundleComponent extends Component {
 	 * @see org.eclipse.pde.api.tools.internal.AbstractApiComponent#createApiFilterStore()
 	 */
 	protected IApiFilterStore createApiFilterStore() throws CoreException {
-		//always return a new empty store since we do not support filtering from bundles
-		return null;
+		return new FilterStore(this);
 	}
 	
 	/**
@@ -814,41 +813,8 @@ public class BundleComponent extends Component {
 		}
 		return null;
 	}
-	
-	/**
-	 * Reads and returns this bunlde's manifest in a Manifest object.
-	 * The bundle may be in a jar or in a directory at the specified location.
-	 * 
-	 * @param bundleLocation root location of the bundle
-	 * @return manifest or <code>null</code> if not present
-	 * @throws IOException if unable to parse
-	 */
-	protected Manifest readManifest(File bundleLocation) throws IOException {
-		ZipFile jarFile = null;
-		InputStream manifestStream = null;
-		try {
-			String extension = new Path(bundleLocation.getName()).getFileExtension();
-			if (extension != null && extension.equals("jar") && bundleLocation.isFile()) { //$NON-NLS-1$
-				jarFile = new ZipFile(bundleLocation, ZipFile.OPEN_READ);
-				ZipEntry manifestEntry = jarFile.getEntry(JarFile.MANIFEST_NAME);
-				if (manifestEntry != null) {
-					manifestStream = jarFile.getInputStream(manifestEntry);
-				}
-			} else {
-				File file = new File(bundleLocation, JarFile.MANIFEST_NAME);
-				if (file.exists())
-					manifestStream = new FileInputStream(file);
-			}
-			if (manifestStream == null) {
-				return null;
-			}
-			return new Manifest(manifestStream);
-		} finally {
-			closingZipFileAndStream(manifestStream, jarFile);
-		}
-	}
 
-	void closingZipFileAndStream(InputStream stream, ZipFile jarFile) {
+	public void closingZipFileAndStream(InputStream stream, ZipFile jarFile) {
 		try {
 			if (stream != null) {
 				stream.close();
diff --git a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/search/UseSearchRequestor.java b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/search/UseSearchRequestor.java
index 967c17a3c5..68de9d03c4 100644
--- a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/search/UseSearchRequestor.java
+++ b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/search/UseSearchRequestor.java
@@ -19,6 +19,7 @@ import org.eclipse.pde.api.tools.internal.builder.Reference;
 import org.eclipse.pde.api.tools.internal.builder.ReferenceAnalyzer;
 import org.eclipse.pde.api.tools.internal.provisional.ApiPlugin;
 import org.eclipse.pde.api.tools.internal.provisional.IApiAnnotations;
+import org.eclipse.pde.api.tools.internal.provisional.IApiFilterStore;
 import org.eclipse.pde.api.tools.internal.provisional.VisibilityModifiers;
 import org.eclipse.pde.api.tools.internal.provisional.builder.IApiProblemDetector;
 import org.eclipse.pde.api.tools.internal.provisional.builder.IReference;
@@ -29,6 +30,7 @@ import org.eclipse.pde.api.tools.internal.provisional.model.IApiMember;
 import org.eclipse.pde.api.tools.internal.provisional.model.IApiScope;
 import org.eclipse.pde.api.tools.internal.provisional.model.IApiType;
 import org.eclipse.pde.api.tools.internal.provisional.model.IApiTypeContainer;
+import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem;
 import org.eclipse.pde.api.tools.internal.provisional.search.IApiSearchRequestor;
 
 /**
@@ -47,6 +49,18 @@ public class UseSearchRequestor implements IApiSearchRequestor {
 	private Set fComponentIds = null;
 
 	/**
+	 * The current {@link IApiFilterStore} from the current {@link IApiComponent} context we are visiting
+	 */
+	private IApiFilterStore currentStore = null;
+	
+	/**
+	 * An {@link IApiFilterStore} that was set from an external source
+	 * 
+	 * @see #setGlobalFilterStore
+	 */
+	private IApiFilterStore globalStore = null;
+	
+	/**
 	 * The mask to use while searching
 	 */
 	private int fSearchMask = 0;
@@ -94,12 +108,14 @@ public class UseSearchRequestor implements IApiSearchRequestor {
 				if(includesIllegalUse()) {
 					fAnalyzer.buildProblemDetectors(component, ProblemDetectorBuilder.K_USE, null);
 				}
+				currentStore = component.getFilterStore();
 				return true;
 			}
 		}
 		catch(CoreException ce) {
 			//do nothing, return false
 		}
+		currentStore = null;
 		return false;
 	}
 	
@@ -195,7 +211,19 @@ public class UseSearchRequestor implements IApiSearchRequestor {
 				Reference ref = (Reference) reference;
 				ref.setFlags(IReference.F_ILLEGAL);
 				try {
-					ref.addProblems(((AbstractProblemDetector)detectors[i]).createProblem(reference));
+					IApiProblem pb = ((AbstractProblemDetector)detectors[i]).createProblem(reference);
+					if(!isFiltered(pb)) {
+						ref.addProblems(pb);
+					} else {
+						
+						
+						// TODO CWindatt - Remove tracing
+						System.out.println("332772 - Problem filtered");
+						
+						
+						
+						
+					}
 				} catch (CoreException e) {
 					ApiPlugin.log(e);
 				}
@@ -205,6 +233,16 @@ public class UseSearchRequestor implements IApiSearchRequestor {
 		return false;
 	}
 	
+	/**
+	 * Returns if the given problem is filtered
+	 * @param problem
+	 * @return <code>true</code> is filtered, false otherwise
+	 */
+	boolean isFiltered(IApiProblem problem) throws CoreException {
+		return (currentStore != null && currentStore.isFiltered(problem)) || 
+				(globalStore != null && globalStore.isFiltered(problem));
+	}
+	
 	/* (non-Javadoc)
 	 * @see org.eclipse.pde.api.tools.internal.provisional.search.IApiSearchRequestor#getReferenceKinds()
 	 */
@@ -260,4 +298,12 @@ public class UseSearchRequestor implements IApiSearchRequestor {
 	public void setJarPatterns(String[] patterns) {
 		jarPatterns = patterns;
 	}
+	
+	/**
+	 * Allows a global {@link IApiFilterStore} to be used to filter all references found during the scan
+	 * @param store the store to set or <code>null</code> to remove the store
+	 */
+	public void setGlobalFilterStore(IApiFilterStore store) {
+		globalStore = store;
+	}
 }
diff --git a/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/APIToolsAnalysisTask.java b/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/APIToolsAnalysisTask.java
index ef4a5ab74c..7b3e81edb7 100644
--- a/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/APIToolsAnalysisTask.java
+++ b/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/APIToolsAnalysisTask.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2008, 2011 IBM Corporation and others.
+ * Copyright (c) 2008, 2012 IBM Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
@@ -14,7 +14,6 @@ import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
-import java.io.InputStream;
 import java.io.PrintWriter;
 import java.io.StringWriter;
 import java.util.ArrayList;
@@ -29,18 +28,14 @@ import java.util.Properties;
 import java.util.Set;
 
 import org.apache.tools.ant.BuildException;
-import org.eclipse.core.resources.IResource;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.NullProgressMonitor;
-import org.eclipse.core.runtime.Path;
 import org.eclipse.osgi.util.NLS;
-import org.eclipse.pde.api.tools.internal.IApiCoreConstants;
 import org.eclipse.pde.api.tools.internal.IApiXmlConstants;
 import org.eclipse.pde.api.tools.internal.builder.BaseApiAnalyzer;
 import org.eclipse.pde.api.tools.internal.builder.BuildContext;
 import org.eclipse.pde.api.tools.internal.model.StubApiComponent;
 import org.eclipse.pde.api.tools.internal.problems.ApiProblemFactory;
-import org.eclipse.pde.api.tools.internal.problems.ApiProblemFilter;
 import org.eclipse.pde.api.tools.internal.provisional.ApiPlugin;
 import org.eclipse.pde.api.tools.internal.provisional.IApiFilterStore;
 import org.eclipse.pde.api.tools.internal.provisional.IApiMarkerConstants;
@@ -48,305 +43,17 @@ import org.eclipse.pde.api.tools.internal.provisional.comparator.IDelta;
 import org.eclipse.pde.api.tools.internal.provisional.model.IApiBaseline;
 import org.eclipse.pde.api.tools.internal.provisional.model.IApiComponent;
 import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem;
-import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblemFilter;
 import org.eclipse.pde.api.tools.internal.util.FilteredElements;
 import org.eclipse.pde.api.tools.internal.util.Util;
 import org.w3c.dom.DOMException;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
-import org.w3c.dom.NodeList;
 
 /**
  * Ant task to run the API tool verification during Eclipse build.
  */
 public class APIToolsAnalysisTask extends CommonUtilsTask {
-	/**
-	 * This filter store is only used to filter problem using existing filters.
-	 * It doesn't add or remove any filters.
-	 */
-	private static class AntFilterStore implements IApiFilterStore {
-		private static final String GLOBAL = "!global!"; //$NON-NLS-1$
-		private static int loadIntegerAttribute(Element element, String name) {
-			String value = element.getAttribute(name);
-			if(value.length() == 0) {
-				return -1;
-			}
-			try {
-				int number = Integer.parseInt(value);
-				return number;
-			}
-			catch(NumberFormatException nfe) {}
-			return -1;
-		}
-		private boolean debug;
-
-		private Map fFilterMap;
-
-		public AntFilterStore(boolean debug, String filtersRoot, String componentID) {
-			this.initialize(filtersRoot, componentID);
-		}
-
-		public void addFiltersFor(IApiProblem[] problems) {
-			// do nothing
-		}
-
-		public void addFilters(IApiProblemFilter[] filters) {
-			// do nothing
-		}
-
-		private boolean argumentsEquals(String[] problemMessageArguments,
-				String[] filterProblemMessageArguments) {
-			// filter problems message arguments are always simple name
-			// problem message arguments are fully qualified name outside the IDE
-			int length = problemMessageArguments.length;
-			if (length == filterProblemMessageArguments.length) {
-				for (int i = 0; i < length; i++) {
-					String problemMessageArgument = problemMessageArguments[i];
-					String filterProblemMessageArgument = filterProblemMessageArguments[i];
-					if (problemMessageArgument.equals(filterProblemMessageArgument)) {
-						continue;
-					}
-					int index = problemMessageArgument.lastIndexOf('.');
-					int filterProblemIndex = filterProblemMessageArgument.lastIndexOf('.');
-					if (index == -1) {
-						if (filterProblemIndex == -1) {
-							return false; // simple names should match
-						}
-						if (filterProblemMessageArgument.substring(filterProblemIndex + 1).equals(problemMessageArgument)) {
-							continue;
-						} else {
-							return false;
-						}
-					} else if (filterProblemIndex != -1) {
-						return false; // fully qualified name should match
-					} else {
-						if (problemMessageArgument.substring(index + 1).equals(filterProblemMessageArgument)) {
-							continue;
-						} else {
-							return false;
-						}
-					}
-				}
-				return true;
-			}
-			return false;
-		}
-
-		public void dispose() {
-			// do nothing
-		}
-
-		public IApiProblemFilter[] getFilters(IResource resource) {
-			return null;
-		}
-
-		public IResource[] getResources() {
-			return null;
-		}
-
-		/**
-		 * Initialize the filter store using the given component id
-		 */
-		private void initialize(String filtersRoot, String componentID) {
-			if(fFilterMap != null) {
-				return;
-			}
-			if(this.debug) {
-				System.out.println("null filter map, creating a new one"); //$NON-NLS-1$
-			}
-			fFilterMap = new HashMap(5);
-			String xml = null;
-			InputStream contents = null;
-			try {
-				File filterFileParent = new File(filtersRoot, componentID);
-				if (!filterFileParent.exists()) {
-					return;
-				}
-				contents = new BufferedInputStream(new FileInputStream(new File(filterFileParent, IApiCoreConstants.API_FILTERS_XML_NAME)));
-				xml = new String(Util.getInputStreamAsCharArray(contents, -1, IApiCoreConstants.UTF_8));
-			}
-			catch(IOException ioe) {}
-			finally {
-				if (contents != null) {
-					try {
-						contents.close();
-					} catch(IOException e) {
-						// ignore
-					}
-				}
-			}
-			if(xml == null) {
-				return;
-			}
-			Element root = null;
-			try {
-				root = Util.parseDocument(xml);
-			}
-			catch(CoreException ce) {
-				ApiPlugin.log(ce);
-			}
-			if (root == null) {
-				return;
-			}
-			if (!root.getNodeName().equals(IApiXmlConstants.ELEMENT_COMPONENT)) {
-				return;
-			}
-			String component = root.getAttribute(IApiXmlConstants.ATTR_ID);
-			if(component.length() == 0) {
-				return;
-			}
-			String versionValue = root.getAttribute(IApiXmlConstants.ATTR_VERSION);
-			int version = 0;
-			if(versionValue.length() != 0) {
-				try {
-					version = Integer.parseInt(versionValue);
-				} catch (NumberFormatException e) {
-					// ignore
-				}
-			}
-			if (version < 2) {
-				// we discard all filters since there is no way to retrieve the type name
-				return;
-			}
-			NodeList resources = root.getElementsByTagName(IApiXmlConstants.ELEMENT_RESOURCE);
-			ArrayList newfilters = new ArrayList();
-			ArrayList comments = new ArrayList();
-			for(int i = 0; i < resources.getLength(); i++) {
-				Element element = (Element) resources.item(i);
-				String typeName = element.getAttribute(IApiXmlConstants.ATTR_TYPE);
-				if (typeName.length() == 0) {
-					// if there is no type attribute, an empty string is returned
-					typeName = null;
-				}
-				String path = element.getAttribute(IApiXmlConstants.ATTR_PATH);
-				NodeList filters = element.getElementsByTagName(IApiXmlConstants.ELEMENT_FILTER);
-				for(int j = 0; j < filters.getLength(); j++) {
-					element = (Element) filters.item(j);
-					int id = loadIntegerAttribute(element, IApiXmlConstants.ATTR_ID);
-					if(id <= 0) {
-						continue;
-					}
-					String[] messageargs = null;
-					NodeList elements = element.getElementsByTagName(IApiXmlConstants.ELEMENT_PROBLEM_MESSAGE_ARGUMENTS);
-					if (elements.getLength() != 1) continue;
-					Element messageArguments = (Element) elements.item(0);
-					NodeList arguments = messageArguments.getElementsByTagName(IApiXmlConstants.ELEMENT_PROBLEM_MESSAGE_ARGUMENT);
-					int length = arguments.getLength();
-					messageargs = new String[length];
-					String comment = element.getAttribute(IApiXmlConstants.ATTR_COMMENT);
-					comments.add((comment.length() < 1 ? null : comment));
-					for (int k = 0; k < length; k++) {
-						Element messageArgument = (Element) arguments.item(k);
-						messageargs[k] = messageArgument.getAttribute(IApiXmlConstants.ATTR_VALUE);
-					}
-					newfilters.add(ApiProblemFactory.newApiProblem(path, typeName, messageargs, null, null, -1, -1, -1, id));
-				}
-			}
-			internalAddFilters(componentID, (IApiProblem[]) newfilters.toArray(new IApiProblem[newfilters.size()]),
-					(String[]) comments.toArray(new String[comments.size()]));
-			newfilters.clear();
-		}
-
-		/**
-		 * Internal use method that allows auto-persisting of the filter file to be turned on or off
-		 * @param problems the problems to add the the store
-		 * @param persist if the filters should be auto-persisted after they are added
-		 */
-		private void internalAddFilters(String componentID, IApiProblem[] problems, String[] comments) {
-			if(problems == null) {
-				if(this.debug) {
-					System.out.println("null problems array not addding filters"); //$NON-NLS-1$
-				}
-				return;
-			}
-			for(int i = 0; i < problems.length; i++) {
-				IApiProblem problem = problems[i];
-				IApiProblemFilter filter = new ApiProblemFilter(componentID, problem, comments[i]);
-				String typeName = problem.getTypeName();
-				if (typeName == null) {
-					typeName = GLOBAL;
-				}
-				Set filters = (Set) fFilterMap.get(typeName);
-				if(filters == null) {
-					filters = new HashSet();
-					fFilterMap.put(typeName, filters);
-				}
-				filters.add(filter);
-			}
-		}
-
-		public boolean isFiltered(IApiProblem problem) {
-			if (this.fFilterMap == null || this.fFilterMap.isEmpty()) return false;
-			String typeName = problem.getTypeName();
-			if (typeName == null || typeName.length() == 0) {
-				typeName = GLOBAL;
-			}
-			Set filters = (Set) this.fFilterMap.get(typeName);
-			if (filters == null) {
-				return false;
-			}
-			for (Iterator iterator = filters.iterator(); iterator.hasNext();) {
-				IApiProblemFilter filter = (IApiProblemFilter) iterator.next();
-				if (problem.getCategory() == IApiProblem.CATEGORY_USAGE) {
-					// write our own matching implementation
-					return matchUsageProblem(filter.getUnderlyingProblem(), problem);
-				} else if (matchFilters(filter.getUnderlyingProblem(), problem)) {
-					return true;
-				}
-			}
-			return false;
-		}
-
-		private boolean matchFilters(IApiProblem filterProblem, IApiProblem problem) {
-			if (problem.getId() == filterProblem.getId() && argumentsEquals(problem.getMessageArguments(), filterProblem.getMessageArguments())) {
-				String typeName = problem.getTypeName();
-				String filteredProblemTypeName = filterProblem.getTypeName();
-				if (typeName == null) {
-					if (filteredProblemTypeName != null) {
-						return false;
-					}
-					return true;
-				} else if (filteredProblemTypeName == null) {
-					return false;
-				}
-				return typeName.equals(filteredProblemTypeName);
-			}
-			return false;
-		}
-
-		private boolean matchUsageProblem(IApiProblem filterProblem, IApiProblem problem) {
-			if (problem.getId() == filterProblem.getId()) {
-				// check arguments
-				String problemPath = problem.getResourcePath();
-				String filterProblemPath = filterProblem.getResourcePath();
-				if (problemPath == null) {
-					if (filterProblemPath != null) {
-						return false;
-					}
-				} else if (filterProblemPath == null) {
-					return false;
-				} else if (!new Path(problemPath).equals(new Path(filterProblemPath))) {
-					return false;
-				}
-				String problemTypeName = problem.getTypeName();
-				String filterProblemTypeName = filterProblem.getTypeName();
-				if (problemTypeName == null) {
-					if (filterProblemTypeName != null) {
-						return false;
-					}
-				} else if (filterProblemTypeName == null) {
-					return false;
-				} else if (!problemTypeName.equals(filterProblemTypeName)) {
-					return false;
-				}
-				return argumentsEquals(problem.getMessageArguments(), filterProblem.getMessageArguments());
-			}
-			return false;
-		}
-		public boolean removeFilters(IApiProblemFilter[] filters) {
-			return false;
-		}
-	}
+	
 	private static class Summary {
 		List apiBundleVersionProblems = new ArrayList();
 		List apiCompatibilityProblems = new ArrayList();
diff --git a/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/AntFilterStore.java b/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/AntFilterStore.java
new file mode 100644
index 0000000000..a4c5e328ab
--- /dev/null
+++ b/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/AntFilterStore.java
@@ -0,0 +1,104 @@
+/*******************************************************************************
+ * Copyright (c) 2012 IBM Corporation and others.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *     IBM Corporation - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.pde.api.tools.internal.tasks;
+
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.eclipse.pde.api.tools.internal.FilterStore;
+import org.eclipse.pde.api.tools.internal.IApiCoreConstants;
+import org.eclipse.pde.api.tools.internal.problems.ApiProblemFilter;
+import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem;
+import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblemFilter;
+
+/**
+ * This filter store is only used to filter problem using existing filters.
+ * It doesn't add or remove any filters.
+ */
+public class AntFilterStore extends FilterStore {
+
+	private boolean debug;
+	String fComponentId = null;
+	String fFiltersRoot = null;
+	
+	/**
+	 * Constructor
+	 * @param debug
+	 * @param filtersRoot
+	 * @param componentID
+	 */
+	public AntFilterStore(boolean debug, String filtersRoot, String componentID) {
+		fComponentId = componentID;
+		fFiltersRoot = filtersRoot;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.eclipse.pde.api.tools.internal.FilterStore#initializeApiFilters()
+	 */
+	protected synchronized void initializeApiFilters() {
+		if(fFilterMap != null) {
+			return;
+		}
+		if(this.debug) {
+			System.out.println("null filter map, creating a new one"); //$NON-NLS-1$
+		}
+		fFilterMap = new HashMap(5);
+		InputStream contents = null;
+		try {
+			File filterFileParent = new File(fFiltersRoot, fComponentId);
+			if (!filterFileParent.exists()) {
+				return;
+			}
+			contents = new BufferedInputStream(new FileInputStream(new File(filterFileParent, IApiCoreConstants.API_FILTERS_XML_NAME)));
+			readFilterFile(contents);
+		}
+		catch(IOException ioe) {
+		}
+		finally {
+			if (contents != null) {
+				try {
+					contents.close();
+				} catch(IOException e) {
+					// ignore
+				}
+			}
+		}
+	}
+	
+	/* (non-Javadoc)
+	 * @see org.eclipse.pde.api.tools.internal.FilterStore#internalAddFilters(org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem[], java.lang.String[])
+	 */
+	protected void internalAddFilters(IApiProblem[] problems, String[] comments) {
+		if(problems == null) {
+			return;
+		}
+		for(int i = 0; i < problems.length; i++) {
+			IApiProblem problem = problems[i];
+			IApiProblemFilter filter = new ApiProblemFilter(fComponentId, problem, comments[i]);
+			String typeName = problem.getTypeName();
+			if (typeName == null) {
+				typeName = GLOBAL;
+			}
+			Set filters = (Set) fFilterMap.get(typeName);
+			if(filters == null) {
+				filters = new HashSet();
+				fFilterMap.put(typeName, filters);
+			}
+			filters.add(filter);
+		}
+	}
+}
\ No newline at end of file
diff --git a/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/ApiUseTask.java b/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/ApiUseTask.java
index aa958be7b7..92266f98a9 100644
--- a/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/ApiUseTask.java
+++ b/apitools/org.eclipse.pde.api.tools/src_ant/org/eclipse/pde/api/tools/internal/tasks/ApiUseTask.java
@@ -25,6 +25,7 @@ import org.eclipse.core.runtime.CoreException;
 import org.eclipse.osgi.service.resolver.ResolverError;
 import org.eclipse.osgi.util.NLS;
 import org.eclipse.pde.api.tools.internal.provisional.ApiPlugin;
+import org.eclipse.pde.api.tools.internal.provisional.IApiFilterStore;
 import org.eclipse.pde.api.tools.internal.provisional.model.IApiBaseline;
 import org.eclipse.pde.api.tools.internal.provisional.model.IApiComponent;
 import org.eclipse.pde.api.tools.internal.provisional.model.IApiElement;
@@ -97,6 +98,10 @@ public final class ApiUseTask extends CommonUtilsTask {
 	 * </pre>
 	 */
 	private String[] archivePatterns = null;
+	/**
+	 * Absolute file paths to the filter files to use
+	 */
+	private String[] filterPaths = null;
 	
 	/**
 	 * List of elements excluded from the scope
@@ -238,6 +243,14 @@ public final class ApiUseTask extends CommonUtilsTask {
 	}
 	
 	/**
+	 * Sets the paths of the filter files to use
+	 * @param paths
+	 */
+	public void setFilterPaths(String paths) {
+		filterPaths = parsePatterns(paths);
+	}
+	
+	/**
 	 * @see org.eclipse.pde.api.tools.internal.tasks.UseTask#assertParameters()
 	 */
 	protected void assertParameters() throws BuildException {
@@ -298,6 +311,7 @@ public final class ApiUseTask extends CommonUtilsTask {
 					(IApiElement[]) scope.toArray(new IApiElement[scope.size()]), 
 					getSearchFlags());
 			requestor.setJarPatterns(archivePatterns);
+			requestor.setGlobalFilterStore(getFilterStore(ids));
 			// override API descriptions as required
 			if (apiPatterns != null || internalPatterns != null) {
 				// modify API descriptions
@@ -461,6 +475,18 @@ public final class ApiUseTask extends CommonUtilsTask {
 	}
 	
 	/**
+	 * Create a global filter store from a group of filter files
+	 * 
+	 * @return the new {@link IApiFilterStore} or <code>null</code>
+	 */
+	protected IApiFilterStore getFilterStore(Set ids) {
+		if(filterPaths != null && !ids.isEmpty()) {
+			//TODO we need to create the filter store
+		}
+		return null;
+	}
+	
+	/**
 	 * Cleans the report location specified by the parameter {@link CommonUtilsTask#reportLocation}
 	 */
 	protected void cleanReportLocation() {