javadoc fix

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7387 8f7bc0f5-282e-0410-95e3-8d296e9bb460
various tests for trac 734
e.g.
SELECT ?A ?B
WHERE {
    ?A rdf:type  / rdfs:subClassOf * <os:ClassA> ;
       rdf:value ?B .
    ?B rdf:type  / rdfs:subClassOf * <os:ClassB>
}
and
SELECT  (<os:0> as ?A)
WHERE {
     <eg:a> <eg:b> ? <eg:a>
}

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7388 8f7bc0f5-282e-0410-95e3-8d296e9bb460
I've added a simple InferenceChangeLogReporter. This class may be used to obtain the actual inferences computed during a transaction.  

I modified the change log listener test suite to also test this this new listener.

The present implementation uses a LinkedHashMap to store the ISPOs for the inferences.  This should be scalable up to millions of inferences.  If very large inferences will be drawn, then we could substitute an HTree index for the LinkedHashMap. The existing NativeDistinctFilter already does exactly this and simply replace the hard coded use of the LinkedHashSet for improved scaling.  In this case, the native memory associated with the HTree needs to be released, e.g., through an ICloseable protocol on the change listener.

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7389 8f7bc0f5-282e-0410-95e3-8d296e9bb460
Fix for trac734 - problem is to do with allowing legal paths when both ends are bound. Including tests in suite.

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7390 8f7bc0f5-282e-0410-95e3-8d296e9bb460
Amend compareBytes to handle null arguments

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7391 8f7bc0f5-282e-0410-95e3-8d296e9bb460
Change DumpLogDigests to provide entries for logs that are not found to simplify comparisons between services with different available log files.
And register protection with the HALogNexus to avoid file removal while digests are being computed.

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7392 8f7bc0f5-282e-0410-95e3-8d296e9bb460
Refactored the GASRunner into a base class and derived a BigdataGASRunner and a SAILGASRunner from it.  

Initial performance with the memory sail does not look very good. About 1/2 of the throughput that we observe with bigdata.  I am going to try this on a machine with more RAM and see how that helps.

See #629 (Graph mining API)

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7393 8f7bc0f5-282e-0410-95e3-8d296e9bb460
modified to allow runs against the SAIL or bigdata backends.


git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7394 8f7bc0f5-282e-0410-95e3-8d296e9bb460
Javadoc on AccessPath.MAX_FULLY_BUFFERED_READ_LIMIT

See #606

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7395 8f7bc0f5-282e-0410-95e3-8d296e9bb460
Fix for #741 (ctc-stiterators module must be independent, Apache 2 license).

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7396 8f7bc0f5-282e-0410-95e3-8d296e9bb460
Created a bigdata-commons module. This module is currently empty.  We should move some of the common classes into here and then remove them from the other modules.  The main classes that are getting duplicated are DaemonThreadFactory and CAT. However, we could actually move much more into this commons package.  

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7397 8f7bc0f5-282e-0410-95e3-8d296e9bb460
Decoupled the Apache2 module for the GAS Engine.  I had to duplicate two classes (DeamonThreadFactory and Sesame2BigdataIterator).

There is currently a problem running ant for the bigdata-gas module under eclipse.  In part, this may have to do with the path to the smallGraph.ttl file but it also appears to be confounded with the JDK6/JDK7 external executable configurations in exclipse.

See #629 (Graph mining API)

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7398 8f7bc0f5-282e-0410-95e3-8d296e9bb460
removed unmappable character for UTF8

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7399 8f7bc0f5-282e-0410-95e3-8d296e9bb460
Change test teardown to better ensure a clean tidy of the test directories - removing HALog files, snapshots and journals.
This will be more important as we extend service kill tests which previously would have resulted in potentially large numbers of files remaining.

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7400 8f7bc0f5-282e-0410-95e3-8d296e9bb460
Amend HALogNexus to add an accessor increment pattern to guard against file removal - initially used by DumpLogDigest.
And amend DumpLogDigest to access all joined services to determine the union of the range of halogs to test.

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7401 8f7bc0f5-282e-0410-95e3-8d296e9bb460
Added a very simple graph model for GAS graph mining.  It uses a collection of vertices and linked hash sets for the in-edges, out-edges, and property values.  This passes the basic "TestGather".  I have written an extension to load data into this. It is ready for testing against a larger data set.  The purpose is to replace the memory sail, which is way to slow when loading the data, and provide a basis for understanding the overhead associated with graph traversal versus object decoding as a pre-cursor to an exploration of column-wise indexing for graph mining.

See #629 (Graph Mining API)

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7402 8f7bc0f5-282e-0410-95e3-8d296e9bb460
organized import

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7403 8f7bc0f5-282e-0410-95e3-8d296e9bb460
added code to skip hidden files

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7404 8f7bc0f5-282e-0410-95e3-8d296e9bb460
again, skipping hidden files.

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7405 8f7bc0f5-282e-0410-95e3-8d296e9bb460
was attemping to load directories as files....

git-svn-id: https://bigdata.svn.sourceforge.net/svnroot/bigdata/branches/BIGDATA_RELEASE_1_3_0@7406 8f7bc0f5-282e-0410-95e3-8d296e9bb460