Documentation updates and first configuration changes:

  - Added @deprecated tags to the old bindings, with test pointing to their replacement.
  - Added a note in the header of the new bindings suggesting to keep the classes synchronized with GeoAPI (if possible).
  - Edited the README file for the new bindings, but did not yet edited the example.
  - Added the new files to the list of files declared in Makefile.in, and ran automake to regenerate Makefile.am.
  - Edited build.xml to generate the header file of PJ.h instead than Projections.h.


git-svn-id: http://svn.osgeo.org/metacrs/proj/trunk@2092 4e78687f-474d-0410-85f9-8d5e500ac6b2

13 files changed, 290 insertions, 202 deletions

diff --git a/jniwrap/README b/jniwrap/README
index ce0c212e..0c5818e8 100644
--- a/jniwrap/README
+++ b/jniwrap/README
@@ -1,81 +1,92 @@
    -------------------- J P R O J . 4 --------------------
 
-This is the first release of a JNI wrap of the main proj4 functions.
+This is the second release of JNI wrappers for the main proj4 functions.
 
 PLEASE read the following information.
 
-For more information regarding JPROJ4 please contact me through the 
-web page at:
+The first release of JNI wrappers were created by:
 
-		http://www.hydrologis.com
+                http://www.hydrologis.com
+
+For more information regarding the current release please see the web page at:
+
+                http://www.geoapi.org/geoapi-proj4/
 
    ---------------------------------------------------
 
 
-What is JPROJ4:
+What is "Proj.4 wrapper":
 -------------
 
-JPROJ is a small library of java classes that wrap a few proj functions by 
-using the java native interface. 
+"Proj.4 wrapper" is a small library of Java classes that wrap a few Proj.4 functions by
+using the Java Native Interface (JNI).
 
 
 Compilation:
 -------------
 
-To complile the native part, configure has to be run like this:
-CFLAGS=-Iinclude2 ./configure --with-jni=include1
+To compile the native part, configure has to be run in the proj directory like this:
+
+    CFLAGS=-Iinclude2 ./configure --with-jni=include1
+
 where
-include1 = folder in which the header file jni.h resides (usually $JAVA_HOME/include)
-include2 = folder in which the header file jni_md.h resides (usually $JAVA_HOME/include/linux or whatever)
+
+    include1 = folder in which the header file jni.h resides (usually $JAVA_HOME/include)
+    include2 = folder in which the header file jni_md.h resides (usually $JAVA_HOME/include/linux or whatever)
+
+On MacOS, those two folders are /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home/include/
 
 
-The java part is compiled by running ant inside the "jniwrap" folder. 
+The java part is compiled by running ant inside the "jniwrap" folder.
 This will compile the classes and archive them in a jar library.
-It applies to Linux, Macos and Windows (and virtually to every system 
+It applies to Linux, Macos and Windows (and virtually to every system
 supporting java).
 
 
 Requirements:
 -------------
 
-Beyond the ones already put by proj, you need:
-- j2sdk, the java standard development kit
-- ant, to run the build
-- doxygen for the documentation generation
+Beyond the ones already put by Proj.4, you need:
+- JSE 1.5+, the Java standard development kit version 1.5 or above
+- Ant, to run the build
+- Doxygen for the documentation generation
 
 
 Documentation:
 --------------
 
 The documentation is held inside the code and can be retrieved by running
-doxygen inside the folder jniwrap. This will create the html format 
+doxygen inside the folder jniwrap. This will create the HTML format
 documentation inside of jniwrap/docs
 
-The standard way to achive this is to use an ant target: 
-ant do_make_help
+The standard way to achive this is to use an Ant target:
+
+    ant do_make_help
 
 
 License:
 --------
 
-GPL
+GPL for the first release
+Proj.4 license for the second release.
 
 
 Authors:
 --------
 
 Andrea Antonello (andrea.antonello@hydrologis.com)
+Martin Desruisseaux (martin.desruisseaux@geomatys.fr)
 
 
 Usage & a fast example:
 -----------------------
 
 The jproj.jar is all is needed to implement proj support in java applications.
-The whole job is done by the proj4, so there are just a couple of functions that 
+The whole job is done by the proj4, so there are just a couple of functions that
 be used.
 
 The best way is to see everything through an example.
-In the following example we read projection informations and data from a file 
+In the following example we read projection informations and data from a file
 and then transform the data and query the information.
 
 ________________________________________________________________________________
@@ -87,13 +98,13 @@ rows: 1
 46        11    194.0
 
 
-This contains info about a source and destination projection, the number of data 
+This contains info about a source and destination projection, the number of data
 triplets and then the data (in this case just one point)
 
 
 ________________________________________________________________________________
 Step two:
-create a test code. Simply copy the following into a file called Main.java. The 
+create a test code. Simply copy the following into a file called Main.java. The
 code is commented to see what we are doing:
 
 
@@ -145,10 +156,10 @@ public class Main
       }
     }
     // with what you see above, the header was read
-    
+
     // now I can define the number of rows of data triplets
     int rows = new Integer((String) mapHeader.get("rows")).intValue();
-    
+
     double[][] testCoord = new double[rows][2];
     double[] testValues = new double[rows];
     System.out.println("Source coordinates and values:");
@@ -182,7 +193,7 @@ public class Main
     Proj4 testProjection = new Proj4((String) mapHeader.get("srcProj"),
         (String) mapHeader.get("destProj"));
 
-    // the instantiation of the proj4 object instantiated also the projection 
+    // the instantiation of the proj4 object instantiated also the projection
     // objects for source and destination projection
     // therefore we can already print the projection infos:
     testProjection.printSrcProjInfo();
@@ -190,10 +201,10 @@ public class Main
 
     // and transform, passing as parameter the created dataset:
     testProjection.transform(dataTP, 1, 1);
-    
+
     // if we need the parameters as Hashmap for a later use:
     LinkedHashMap testMap = testProjection.getSrcProjInfo();
-    
+
     // and let us print them to screen to see them
     System.out.println();
     System.out.println("Proj as a Hashmap");
diff --git a/jniwrap/build.xml b/jniwrap/build.xml
index 8f181dd8..3032a52f 100644
--- a/jniwrap/build.xml
+++ b/jniwrap/build.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <project name="jproj" default="compile" basedir=".">
-   
+
    <!-- ******************************************* -->
    <!--     set the variables                       -->
    <!-- ******************************************* -->
@@ -14,7 +14,7 @@
    <target name="compile" depends="start, do_javac, jar_it">
         <echo>Compilation finished...</echo>
    </target>
-   
+
    <!-- ******************************************* -->
    <!--     create some begin stuff                 -->
    <!-- ******************************************* -->
@@ -25,7 +25,7 @@
         <mkdir dir="${build}"/>
         <mkdir dir="${libs}"/>
    </target>
-      
+
    <!-- ******************************************* -->
    <!--     execute javac compilation               -->
    <!-- ******************************************* -->
@@ -34,21 +34,21 @@
        <javac srcdir="${src}" destdir="${build}" debug="on">
        </javac>
    </target>
-    
-	
+
+
 
    <!-- ******************************************* -->
    <!--     execute javah for JNI headers           -->
    <!-- ******************************************* -->
-   <!-- needed if something if new native methods are added  -->
-	   <!-- ******************************************* -->
+   <!-- needed if new native methods are added      -->
+   <!-- ******************************************* -->
    <target name="do_javah" depends="do_javac">
        <echo>Creating jni headers...</echo>
        <exec dir="${build}" executable="javah" os="Linux">
-          <arg line="-jni -d ../native org.proj4.Projections"/>
+          <arg line="-jni -d ../native org.proj4.PJ"/>
        </exec>
    </target>
-   
+
    <!-- ******************************************* -->
    <!--     do the C part compilation through make  -->
    <!-- ******************************************* -->
@@ -58,11 +58,11 @@
           <arg line=""/>
        </exec>
    </target>
-   
+
    <!-- ******************************************* -->
    <!-- create binary package distribution with ant -->
    <!-- ******************************************* -->
-   
+
    <!-- this is not working properly by now -->
    <target name="jar_it">
      <delete file="${libs}/jproj.jar"/>
@@ -73,7 +73,7 @@
       </jar>
        <delete dir="${build}"/>
    </target>
-   
+
    <!-- ****************************************************** -->
    <!--     execute doxygen help file and source file creation -->
    <!-- ****************************************************** -->
diff --git a/jniwrap/org/proj4/LatLong.java b/jniwrap/org/proj4/LatLong.java
index 221a986f..94093837 100644
--- a/jniwrap/org/proj4/LatLong.java
+++ b/jniwrap/org/proj4/LatLong.java
@@ -14,33 +14,39 @@
  REVISION:  ---
  =====================================================================================*/
 
-/* 
- This library is free software; you can redistribute it and/or 
- modify it under the terms of the GNU Library General Public 
- License as published by the Free Software Foundation; either 
- version 2 of the License, or (at your option) any later version. 
+/*
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
 
- This library is distributed in the hope that it will be useful, 
- but WITHOUT ANY WARRANTY; without even the implied warranty of 
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU 
- Library General Public License for more details. 
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Library General Public License for more details.
 
- You should have received a copy of the GNU Library General Public 
- License along with this library; if not, write to the Free 
- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 
- USA 
+ You should have received a copy of the GNU Library General Public
+ License along with this library; if not, write to the Free
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307
+ USA
 
- 1. Redistributions of source code must retain the above copyright   
- notice, this list of conditions and the following disclaimer.   
- 2. 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.   
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. 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.
  */
 package org.proj4;
 
 /**
  * class representing a latitude longitude projection
+ *
+ * @deprecated Replaced by {@link PJ}, which doesn't need special subclass for this case.
+ * The conversion of angular values, if needed, is performed directly in the {@link PJ}
+ * native code, because the native code can more easily exploit the information provided
+ * by Proj.4 about the CRS type.
  */
+@Deprecated
 public class LatLong extends Projections
 {
 
diff --git a/jniwrap/org/proj4/Makefile.am b/jniwrap/org/proj4/Makefile.am
index 67ed8779..71429aef 100644
--- a/jniwrap/org/proj4/Makefile.am
+++ b/jniwrap/org/proj4/Makefile.am
@@ -1,4 +1,5 @@
-EXTRA_DIST = LatLong.java Others.java Proj4Factory.java Proj4.java \
+EXTRA_DIST = PJ.java PJException.java package-info.java \
+		LatLong.java Others.java Proj4Factory.java Proj4.java \
 		ProjectionData.java Projections.java
 
 
diff --git a/jniwrap/org/proj4/Makefile.in b/jniwrap/org/proj4/Makefile.in
index a59b9980..08214d60 100644
--- a/jniwrap/org/proj4/Makefile.in
+++ b/jniwrap/org/proj4/Makefile.in
@@ -162,7 +162,8 @@ target_alias = @target_alias@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-EXTRA_DIST = LatLong.java Others.java Proj4Factory.java Proj4.java \
+EXTRA_DIST = PJ.java PJException.java package-info.java \
+		LatLong.java Others.java Proj4Factory.java Proj4.java \
 		ProjectionData.java Projections.java
 
 all: all-am
diff --git a/jniwrap/org/proj4/Others.java b/jniwrap/org/proj4/Others.java
index fe9d841a..d87a9ab1 100644
--- a/jniwrap/org/proj4/Others.java
+++ b/jniwrap/org/proj4/Others.java
@@ -14,34 +14,40 @@
  REVISION:  ---
  =====================================================================================*/
 
-/* 
- This library is free software; you can redistribute it and/or 
- modify it under the terms of the GNU Library General Public 
- License as published by the Free Software Foundation; either 
- version 2 of the License, or (at your option) any later version. 
+/*
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
 
- This library is distributed in the hope that it will be useful, 
- but WITHOUT ANY WARRANTY; without even the implied warranty of 
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU 
- Library General Public License for more details. 
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Library General Public License for more details.
 
- You should have received a copy of the GNU Library General Public 
- License along with this library; if not, write to the Free 
- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 
- USA 
+ You should have received a copy of the GNU Library General Public
+ License along with this library; if not, write to the Free
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307
+ USA
 
- 1. Redistributions of source code must retain the above copyright   
- notice, this list of conditions and the following disclaimer.   
- 2. 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.   
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. 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.
  */
 package org.proj4;
 
 /**
- * class representing a generic projection, i.e. with no particular 
+ * class representing a generic projection, i.e. with no particular
  * preprocessing needs.
+ *
+ * @deprecated Replaced by {@link PJ}, which doesn't need special subclass for this case.
+ * The conversion of angular values, if needed, is performed directly in the {@link PJ}
+ * native code, because the native code can more easily exploit the information provided
+ * by Proj.4 about the CRS type.
  */
+@Deprecated
 public class Others extends Projections
 {
 
diff --git a/jniwrap/org/proj4/PJ.java b/jniwrap/org/proj4/PJ.java
index 21bf7a5a..b1b30c20 100644
--- a/jniwrap/org/proj4/PJ.java
+++ b/jniwrap/org/proj4/PJ.java
@@ -25,7 +25,11 @@
  * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  * DEALINGS IN THE SOFTWARE.
- *****************************************************************************/
+ *****************************************************************************
+ * This file is a copy of a file developed in the GeoAPI "Proj.4 binding"
+ * module (http://www.geoapi.org/geoapi-proj4/index.html). If this file is
+ * modified, please consider synchronizing the changes with GeoAPI.
+ */
 package org.proj4;
 
 
diff --git a/jniwrap/org/proj4/PJException.java b/jniwrap/org/proj4/PJException.java
index 68897703..ed0dba98 100644
--- a/jniwrap/org/proj4/PJException.java
+++ b/jniwrap/org/proj4/PJException.java
@@ -25,7 +25,11 @@
  * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  * DEALINGS IN THE SOFTWARE.
- *****************************************************************************/
+ *****************************************************************************
+ * This file is a copy of a file developed in the GeoAPI "Proj.4 binding"
+ * module (http://www.geoapi.org/geoapi-proj4/index.html). If this file is
+ * modified, please consider synchronizing the changes with GeoAPI.
+ */
 package org.proj4;
 
 
diff --git a/jniwrap/org/proj4/Proj4.java b/jniwrap/org/proj4/Proj4.java
index 5873c661..d2fe8b72 100644
--- a/jniwrap/org/proj4/Proj4.java
+++ b/jniwrap/org/proj4/Proj4.java
@@ -2,7 +2,7 @@
 
  FILE:  Proj4.java
 
- DESCRIPTION:  
+ DESCRIPTION:
 
  NOTES:  ---
  AUTHOR:          Antonello Andrea
@@ -14,34 +14,34 @@
  REVISION:  ---
  =====================================================================================*/
 
-/* 
- This library is free software; you can redistribute it and/or 
- modify it under the terms of the GNU Library General Public 
- License as published by the Free Software Foundation; either 
- version 2 of the License, or (at your option) any later version. 
-
- This library is distributed in the hope that it will be useful, 
- but WITHOUT ANY WARRANTY; without even the implied warranty of 
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU 
- Library General Public License for more details. 
-
- You should have received a copy of the GNU Library General Public 
- License along with this library; if not, write to the Free 
- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 
- USA 
-
- 1. Redistributions of source code must retain the above copyright   
- notice, this list of conditions and the following disclaimer.   
- 2. 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.   
+/*
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Library General Public License for more details.
+
+ You should have received a copy of the GNU Library General Public
+ License along with this library; if not, write to the Free
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307
+ USA
+
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. 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.
  */
 package org.proj4;
 
 import java.util.LinkedHashMap;
 
 /**
- * This is the public 
+ * This is the public
  * test class to try the jproj api. Reads data from file.
  * The input file has three lines of header:<BR>
  * 1) source projection code or option <BR>
@@ -58,18 +58,20 @@ import java.util.LinkedHashMap;
  * destProj: +init=epsg:32632
  * rows: 2
  * ...datatriplets
- * 
+ *
+ * @deprecated Replaced by {@link PJ}. See package description for usage example.
  */
+@Deprecated
 public class Proj4 implements Proj4Factory
 {
   Projections srcProjection = null;
   Projections destProjection = null;
   Projections projection = null;
-  
+
   /**
    * constructor used to instatiate a single projection. This is used
    * if the goal is to simply get information about a projection definition
-   * 
+   *
    * @param proj the projection definition
    */
   public Proj4(String proj)
@@ -83,12 +85,12 @@ public class Proj4 implements Proj4Factory
       projection = new Others(proj);
     }
   }
-  
+
   /**
    * constructor used to instantiate the object for a further reproiection.
-   * From the definitions the source and destination projection are 
+   * From the definitions the source and destination projection are
    * created.
-   * 
+   *
    * @param srcProj
    * @param destProj
    */
@@ -115,7 +117,7 @@ public class Proj4 implements Proj4Factory
   /**
    * method to reproject a dataset from the source projection to the destination
    * projection as defined in the constructor
-   * 
+   *
    * @param dataTP the data set to reproject
    * @param point_count
    * @param point_offset
@@ -134,7 +136,7 @@ public class Proj4 implements Proj4Factory
           + dataTP.z[i]);
     }
   }
-  
+
   /**
    * @return the projection info as a hashmap
    */
@@ -150,7 +152,7 @@ public class Proj4 implements Proj4Factory
   {
     return srcProjection.mapProjInfo();
   }
-  
+
   /**
    * @return the destination projection info as a hashmap
    */
@@ -158,7 +160,7 @@ public class Proj4 implements Proj4Factory
   {
     return destProjection.mapProjInfo();
   }
-  
+
 
   /**
    * print the projection info to standard output
@@ -167,7 +169,7 @@ public class Proj4 implements Proj4Factory
   {
     projection.printProjInfo();
   }
-  
+
   /**
    * print the source projection info to standard output
    */
diff --git a/jniwrap/org/proj4/Proj4Factory.java b/jniwrap/org/proj4/Proj4Factory.java
index b480a97f..e9998a7b 100644
--- a/jniwrap/org/proj4/Proj4Factory.java
+++ b/jniwrap/org/proj4/Proj4Factory.java
@@ -2,7 +2,7 @@
 
   FILE:  Proj4Factory.java
 
-  DESCRIPTION:  
+  DESCRIPTION:
 
   NOTES:  ---
   AUTHOR:          Antonello Andrea
@@ -14,28 +14,28 @@
   REVISION:  ---
 =====================================================================================*/
 
-/* 
- This library is free software; you can redistribute it and/or 
- modify it under the terms of the GNU Library General Public 
- License as published by the Free Software Foundation; either 
- version 2 of the License, or (at your option) any later version. 
-
- This library is distributed in the hope that it will be useful, 
- but WITHOUT ANY WARRANTY; without even the implied warranty of 
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU 
- Library General Public License for more details. 
-
- You should have received a copy of the GNU Library General Public 
- License along with this library; if not, write to the Free 
- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 
- USA 
-
-1. Redistributions of source code must retain the above copyright   
-  notice, this list of conditions and the following disclaimer.   
-2. 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.   
-*/ 
+/*
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Library General Public License for more details.
+
+ You should have received a copy of the GNU Library General Public
+ License along with this library; if not, write to the Free
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307
+ USA
+
+1. Redistributions of source code must retain the above copyright
+  notice, this list of conditions and the following disclaimer.
+2. 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.
+*/
 
 package org.proj4;
 
@@ -43,23 +43,27 @@ import java.util.LinkedHashMap;
 
 
 
+/**
+ * @deprecated Replaced by {@link PJ}. See package description for usage example.
+ */
+@Deprecated
 public interface Proj4Factory
 {
   /**
    * method to reproject a dataset from the source projection to the destination
    * projection as defined in the constructor
-   * 
+   *
    * @param dataTP the data set to reproject
    * @param point_count
    * @param point_offset
    */
   public void transform(ProjectionData dataTP, long point_count, int point_offset);
-  
+
   /**
    * @return the projection info as a hashmap
    */
   public LinkedHashMap getProjInfo();
-  
+
   /**
    * @return the source projection info as a hashmap
    */
diff --git a/jniwrap/org/proj4/ProjectionData.java b/jniwrap/org/proj4/ProjectionData.java
index 95356d09..8ee72772 100644
--- a/jniwrap/org/proj4/ProjectionData.java
+++ b/jniwrap/org/proj4/ProjectionData.java
@@ -14,33 +14,39 @@
  REVISION:  ---
  =====================================================================================*/
 
-/* 
- This library is free software; you can redistribute it and/or 
- modify it under the terms of the GNU Library General Public 
- License as published by the Free Software Foundation; either 
- version 2 of the License, or (at your option) any later version. 
+/*
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
 
- This library is distributed in the hope that it will be useful, 
- but WITHOUT ANY WARRANTY; without even the implied warranty of 
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU 
- Library General Public License for more details. 
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Library General Public License for more details.
 
- You should have received a copy of the GNU Library General Public 
- License along with this library; if not, write to the Free 
- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 
- USA 
+ You should have received a copy of the GNU Library General Public
+ License along with this library; if not, write to the Free
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307
+ USA
 
- 1. Redistributions of source code must retain the above copyright   
- notice, this list of conditions and the following disclaimer.   
- 2. 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.   
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. 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.
  */
 package org.proj4;
 
 /**
  * class representing the dataset to be reprojected
+ *
+ * @deprecated The new {@link PJ} class uses a different layout for coordinate values.
+ * The new layout is the same than the one used by {@link java.awt.geom.AffineTransform}
+ * in Java2D: tuples of (<var>x</var>,<var>y</var>,&lt;<var>y</var>&gt;) coordinates in
+ * a single flat array.
  */
+@Deprecated
 public class ProjectionData
 {
 
@@ -52,7 +58,7 @@ public class ProjectionData
   public int rows = 0;
 
   /**
-   * object to hold the data to be transformed. This will be passed from 
+   * object to hold the data to be transformed. This will be passed from
    * the starting projection object to the destinantion projection passing through
    * the transformation.
    */
@@ -61,7 +67,7 @@ public class ProjectionData
     rows = _coord.length;
     x = new double[rows];
     y = new double[rows];
-    
+
     for (int i = 0; i < rows; i++)
     {
       x[i] = _coord[i][0];
diff --git a/jniwrap/org/proj4/Projections.java b/jniwrap/org/proj4/Projections.java
index 289da281..61892074 100644
--- a/jniwrap/org/proj4/Projections.java
+++ b/jniwrap/org/proj4/Projections.java
@@ -2,7 +2,7 @@
 
  FILE:  Projections.java
 
- DESCRIPTION:  
+ DESCRIPTION:
 
  NOTES:  ---
  AUTHOR:          Antonello Andrea
@@ -14,27 +14,27 @@
  REVISION:  ---
  =====================================================================================*/
 
-/* 
- This library is free software; you can redistribute it and/or 
- modify it under the terms of the GNU Library General Public 
- License as published by the Free Software Foundation; either 
- version 2 of the License, or (at your option) any later version. 
+/*
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
 
- This library is distributed in the hope that it will be useful, 
- but WITHOUT ANY WARRANTY; without even the implied warranty of 
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU 
- Library General Public License for more details. 
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Library General Public License for more details.
 
- You should have received a copy of the GNU Library General Public 
- License along with this library; if not, write to the Free 
- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 
- USA 
+ You should have received a copy of the GNU Library General Public
+ License along with this library; if not, write to the Free
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307
+ USA
 
- 1. Redistributions of source code must retain the above copyright   
- notice, this list of conditions and the following disclaimer.   
- 2. 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.   
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. 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.
  */
 package org.proj4;
 
@@ -42,7 +42,10 @@ import java.util.LinkedHashMap;
 
 /**
  * superclass of all the projections the main proj methods are held here
+ *
+ * @deprecated Replaced by {@link PJ}.
  */
+@Deprecated
 public abstract class Projections
 {
 
@@ -88,45 +91,58 @@ public abstract class Projections
   }
 
   /**
-   * get all the projection informations needed from the 
+   * get all the projection informations needed from the
    * projection code (reproduces pj_get_def() of the proj api)
-   * 
+   *
    * @param the  proj code or options
    * @return the info String
+   *
+   * @deprecated Replaced by {@link PJ#getDefinition()}.
    */
+  @Deprecated
   protected native String getProjInfo(String proj);
 
   /**
-   * get the ellipsoid parameters from the 
+   * get the ellipsoid parameters from the
    * projection code
-   * 
+   *
    * @param the  proj code or options
    * @return the info String
+   *
+   * @deprecated Replaced by {@link PJ#getSemiMajorAxis()}, {@link PJ#getSemiMinorAxis()},
+   *             {@link PJ#getEccentricitySquared()} and {@link PJ#getDefinition()}.
    */
+  @Deprecated
   protected native String getEllipsInfo(String proj);
 
   /**
    * native call to the reprojections routines of proj
-   * 
+   *
    * @param firstCoord array of x
    * @param secondCoord array of y
    * @param values array of z
    * @param srcCodeString source projection code or option
    * @param destCodeString destination projection code or option
-   * @param pointcount 
+   * @param pointcount
    * @param pointoffset
+   *
+   * @deprecated Replaced by {@link PJ#transform(PJ, int, double[], int, int)}.
    */
+  @Deprecated
   protected native void transform(double[] firstCoord, double[] secondCoord,
       double[] values, String srcCodeString, String destCodeString,
       long pointcount, int pointoffset);
 
   /**
    * public method to call the native getProjInfo
-   * 
-   * @return quoting the proj api:"Returns the PROJ.4 command string that 
-   * would produce this definition expanded as much as possible.  For 
+   *
+   * @return quoting the proj api:"Returns the PROJ.4 command string that
+   * would produce this definition expanded as much as possible.  For
    * instance, +init= calls and +datum= defintions would be expanded"
+   *
+   * @deprecated Replaced by {@link PJ#getDefinition()}.
    */
+  @Deprecated
   public String getProjInfo()
   {
     return getProjInfo(proj);
@@ -134,9 +150,13 @@ public abstract class Projections
 
   /**
    * public method to call the native getEllispdInfo
-   * 
+   *
    * @return the list of ellipsoid parameters
+   *
+   * @deprecated Replaced by {@link PJ#getSemiMajorAxis()}, {@link PJ#getSemiMinorAxis()},
+   *             {@link PJ#getEccentricitySquared()} and {@link PJ#getDefinition()}.
    */
+  @Deprecated
   public String getEllipseInfo()
   {
     return getEllipsInfo(proj);
@@ -144,7 +164,10 @@ public abstract class Projections
 
   /**
    * print to standard output the proj info in a nice format
+   *
+   * @deprecated Replaced by {@link PJ#toString()}.
    */
+  @Deprecated
   public void printProjInfo()
   {
     String projinfo = getProjInfo();
@@ -215,18 +238,22 @@ public abstract class Projections
    * if there is some operation to perform on the input data, this is
    * the right moment (ex. latlong from degree to radiant)
    * -> i.e. do whatever is needed
-   * 
+   *
    * @param dataTP
+   *
+   * @deprecated The conversion from degrees to radians is now performed directly by
+   *             {@link PJ#transform(PJ, int, double[], int, int)}.
    */
+  @Deprecated
   public abstract void prepareData(ProjectionData dataTP);
 
   /**
-   * do the transform. The srcProjection is passed to the destination proj and 
+   * do the transform. The srcProjection is passed to the destination proj and
    * the transformation takes place. Then the resulting transformed data
-   * are passed to the destProj, so that the destProj in case can take care of 
-   * final transformation of data (ex. if the destProj is latlong, the values 
+   * are passed to the destProj, so that the destProj in case can take care of
+   * final transformation of data (ex. if the destProj is latlong, the values
    * have to be set beck to degrees
-   * 
+   *
    * @param srcProj object holding the source projection
    * @param dataTP the data set
    * @param point_count
@@ -241,18 +268,26 @@ public abstract class Projections
 
   /**
    * this takes care that the reprojected data are in the correct format
-   * (ex. latlong has to be transformed back to radiant) 
-   * 
+   * (ex. latlong has to be transformed back to radiant)
+   *
    * @param dataTP the data set
+   *
+   * @deprecated The conversion from radians to degrees is now performed directly by
+   *             {@link PJ#transform(PJ, int, double[], int, int)}.
    */
+  @Deprecated
   public abstract void prepareTransformedData(ProjectionData dataTP);
 
   /**
    * transform latitude and longitude from degree to radiant format
-   * 
+   *
    * @param la
    * @param lo
+   *
+   * @deprecated The conversion from degrees to radians is now performed directly by
+   *             {@link PJ#transform(PJ, int, double[], int, int)}.
    */
+  @Deprecated
   protected void degreeToRadiant(double[] la, double[] lo)
   {
     for (int i = 0; i < la.length; i++)
@@ -264,10 +299,14 @@ public abstract class Projections
 
   /**
    * transform latitude and longitude from radiant to degree format
-   * 
+   *
    * @param la
    * @param lo
+   *
+   * @deprecated The conversion from radians to degrees is now performed directly by
+   *             {@link PJ#transform(PJ, int, double[], int, int)}.
    */
+  @Deprecated
   protected void radiantToDegree(double[] la, double[] lo)
   {
     for (int i = 0; i < la.length; i++)
diff --git a/jniwrap/org/proj4/package-info.java b/jniwrap/org/proj4/package-info.java
index 17a5767c..30e8ffe7 100644
--- a/jniwrap/org/proj4/package-info.java
+++ b/jniwrap/org/proj4/package-info.java
@@ -25,7 +25,11 @@
  * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  * DEALINGS IN THE SOFTWARE.
- *****************************************************************************/
+ *****************************************************************************
+ * This file is a copy of a file developed in the GeoAPI "Proj.4 binding"
+ * module (http://www.geoapi.org/geoapi-proj4/index.html). If this file is
+ * modified, please consider synchronizing the changes with GeoAPI.
+ */
 
 /**
  * Wrappers for the <a href="http://proj.osgeo.org/">Proj4</a> library. The {@link org.proj4.PJ}