java-callgraph

diff --git a/README.md b/README.md
index e68b300..48a1727 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,8 @@ A suite of programs for generating static and dynamic call graphs in Java.
    prints a table of caller-caller relationships.
 * javacg-dynamic: Runs as a [Java agent](http://download.oracle.com/javase/6/docs/api/index.html?java/lang/instrument/package-summary.html) and instruments
   the methods of a user-defined set of classes in order to track their invocations.
-  At JVM exit, prints a table of caller-callee relationships.
+  At JVM exit, prints a table of caller-callee relationships, along with a number
+  of calls
 
 #### Compile
 
@@ -19,6 +20,48 @@ mvn install
 
 This will produce a `target` directory with two executable jars:
 
+- `javacg-0.1-SNAPSHOT-static.jar`: This includes the static call graph
+generator
+- `javacg-0.1-SNAPSHOT-dycg-agent.jar`: This includes the dynamic call
+graph generator
+
+#### Run
+
+##### Static
+
+<code>
+java -jar javacg-0.1-SNAPSHOT-static.jar lib1.jar lib2.jar...
+</code>
+
+##### Dynamic
+
+`javacg-dynamic` uses the
+[javassist](http://www.csg.is.titech.ac.jp/~chiba/javassist/) to insert probes
+at method entry and exit points. To be able to analyze a class `javassist` must
+resolve all dependent classes at instrumentation time.  To do so, it reads
+classes from the JVM's boot classloader. However the JVM sets the boot
+classpath to use Java's default classpath implementation (`rt.jar` on
+Win/Linux, `classes.jar` on the Mac).  The boot classpath can be extended using
+the `-Xbootclasspath` option, which works the same as the traditional
+`-classpath` option. It is advisable for `javacg-dynamic` to work as expected,
+to set the boot classpath to the same, or an appropriate subset, entries as the
+normal application classpath.
+
+Moreover, since instrumenting all methods will produce huge callgraphs which
+are not necessarily helpful (e.g. it will include Java's default classpath
+entries), `javacg-dynamic` includes support for restricting the set of classes
+to be implemented through include and exclude statements. The options are
+appended to the `-javaagent` switch and has the following format
+
+<code>-javaagent:javacg-dycg-agent.jar="incl=mylib.*,mylib2.*,java.nio.*;excl=java.nio.charset.*"</code>
+
+The example above will instrument all classes under the the `mylib`, `mylib2` and
+`java.nio` namespaces, except those that fall under the `java.nio.charset` namespace.
+
+<code>
+java -Xbootclasspath::/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/classes.jar:mylib.jar -javaagent:javacg-0.1-SNAPSHOT-dycg-agent.jar="incl=mylib.*;" -classpath mylib.jar mylib.Mainclass 
+</code>
+
 #### Examples
 
 The following examples instrument the 
@@ -28,26 +71,53 @@ libraries. To build the boot class path required for the javacg-dyn program,
 extract the `dacapo.jar` to a directory: all the required libraries can be found
 in the `jar` directory.
 
+Running the batik Dacapo benchmark:
+
 <code>
-java 
-    -Xbootclasspath:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/classes.jar:jar/batik-all.jar:jar/xml-apis-ext.jar 
-    -javaagent:target/javacg-0.1-SNAPSHOT-dycg-agent.jar="incl=org.apache.batik.*,org.w3c.*;" 
-    -jar dacapo-9.12-bach.jar batik -s small
+java -Xbootclasspath:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/classes.jar:jar/batik-all.jar:jar/xml-apis-ext.jar -javaagent:target/javacg-0.1-SNAPSHOT-dycg-agent.jar="incl=org.apache.batik.*,org.w3c.*;" -jar dacapo-9.12-bach.jar batik -s small |tail -n 10
+
+[...]
+org.apache.batik.dom.AbstractParentNode:appendChild org.apache.batik.dom.AbstractParentNode:fireDOMNodeInsertedEvent 6270
+org.apache.batik.dom.AbstractParentNode:fireDOMNodeInsertedEvent org.apache.batik.dom.AbstractDocument:getEventsEnabled 6280
+org.apache.batik.dom.AbstractParentNode:checkAndRemove org.apache.batik.dom.AbstractNode:getOwnerDocument 6280
+org.apache.batik.dom.util.DoublyIndexedTable:put org.apache.batik.dom.util.DoublyIndexedTable$Entry:DoublyIndexedTable$Entry 6682
+org.apache.batik.dom.util.DoublyIndexedTable:put org.apache.batik.dom.util.DoublyIndexedTable:hashCode 6693
+org.apache.batik.dom.AbstractElement:invalidateElementsByTagName org.apache.batik.dom.AbstractElement:getNodeType 7198
+org.apache.batik.dom.AbstractElement:invalidateElementsByTagName org.apache.batik.dom.AbstractDocument:getElementsByTagName 14396
+org.apache.batik.dom.AbstractElement:invalidateElementsByTagName org.apache.batik.dom.AbstractDocument:getElementsByTagNameNS 28792
+
 </code>
 
+Running the lucene Dacapo benchmark:
+
 <code>
-java -Xbootclasspath:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/classes.jar:jar/lucene-core-2.4.jar:jar/luindex.jar -javaagent:target/javacg-0.1-SNAPSHOT-dycg-agent.jar="incl=org.apache.lucene.*;" -jar dacapo-9.12-bach.jar luindex  -s small
+java -Xbootclasspath:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/classes.jar:jar/lucene-core-2.4.jar:jar/luindex.jar -javaagent:target/javacg-0.1-SNAPSHOT-dycg-agent.jar="incl=org.apache.lucene.*;" -jar dacapo-9.12-bach.jar luindex -s small |tail -n 10
+
+[...]
+org.apache.lucene.analysis.Token:setTermBuffer org.apache.lucene.analysis.Token:growTermBuffer 43449
+org.apache.lucene.analysis.CharArraySet:getSlot org.apache.lucene.analysis.CharArraySet:getHashCode 43472
+org.apache.lucene.analysis.CharArraySet:getSlot org.apache.lucene.analysis.CharArraySet:equals 46107
+org.apache.lucene.index.FreqProxTermsWriter:appendPostings org.apache.lucene.store.IndexOutput:writeVInt 46507
+org.apache.lucene.store.IndexInput:readVInt org.apache.lucene.index.ByteSliceReader:readByte 63927
+org.apache.lucene.index.TermsHashPerField:writeVInt org.apache.lucene.index.TermsHashPerField:writeByte 63927
+org.apache.lucene.store.IndexOutput:writeVInt org.apache.lucene.store.BufferedIndexOutput:writeByte 94239
+org.apache.lucene.index.TermsHashPerField:quickSort org.apache.lucene.index.TermsHashPerField:comparePostings 107343
+org.apache.lucene.analysis.Token:termBuffer org.apache.lucene.analysis.Token:initTermBuffer 162115
+org.apache.lucene.analysis.Token:termLength org.apache.lucene.analysis.Token:initTermBuffer 205554
+
 </code>
 
+
+
 #### Known Restrictions
 
 * The static call graph generator does not account for methods invoked via
   reflection.
-  
+
 #### Author
 
 Georgios Gousios <gousiosg@gmail.com>
 
 #### License
 
-2-clause BSD
+[2-clause BSD](http://www.opensource.org/licenses/bsd-license.php)