sync with trunk. add inchi support to java wrapper.

Code/JavaWrappers/CMakeLists.txt

@@ -18,6 +18,9 @@ if(WIN32)
 	MolAlign
 	Alignment
 	RDGeometryLib RDGeneral )
+        if(RDK_BUILDING_INCHI_SUPPORT)
+          set(RDKit_Wrapper_Libs RDInchiLib Inchi ${RDKit_Wrapper_Libs})
+        endif(RDK_BUILDING_INCHI_SUPPORT)
 else()
 	set(RDKit_Wrapper_Libs 
         FileParsers_static SmilesParse_static
@@ -29,6 +32,11 @@ else()
 	MolAlign_static
 	Alignment_static
 	RDGeometryLib_static RDGeneral_static )
+        if(RDK_BUILDING_INCHI_SUPPORT)
+          set(RDKit_Wrapper_Libs RDInchiLib_static Inchi_static ${RDKit_Wrapper_Libs})
+        endif(RDK_BUILDING_INCHI_SUPPORT)
+
+
 endif()
 
 add_subdirectory(gmwrapper)

Code/JavaWrappers/Depict.h

@@ -96,6 +96,7 @@ namespace {
     for(unsigned int i=0;i<slen;++i){
       label+=(char)*pos++;
     }
+    int orient=*pos++;
     int width=fontSz*label.length();
     int height=fontSz;
     sstr<<"<svg:g transform='translate("<<xp<<","<<yp<<")'><svg:rect ";

Code/JavaWrappers/Inchi.i

@@ -0,0 +1,38 @@
+/* 
+* $Id: AddHs.i 122 2011-01-18 07:22:46Z bill.smith $
+*
+*  Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
+*  All rights reserved.
+* 
+* Redistribution and use in source and binary forms, with or without
+* modification, are permitted provided that the following conditions are
+* met: 
+*
+*     * Redistributions of source code must retain the above copyright 
+*       notice, this list of conditions and the following disclaimer.
+*     * Redistributions in binary form must reproduce the above
+*       copyright notice, this list of conditions and the following 
+*       disclaimer in the documentation and/or other materials provided 
+*       with the distribution.
+*     * Neither the name of Novartis Institutes for BioMedical Research Inc. 
+*       nor the names of its contributors may be used to endorse or promote 
+*       products derived from this software without specific prior written permission.
+*
+* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+%{
+#include <INCHI-API/inchi.h>
+%}
+%include <INCHI-API/inchi.h>
+

Code/JavaWrappers/gmwrapper/GraphMolJava.i

@@ -249,4 +249,6 @@ typedef unsigned long long int	uintmax_t;
 }
 
 %include "../Descriptors.i"
-
+#ifdef BUILD_INCHI_SUPPORT
+%include "../Inchi.i"
+#endif