gentoo-overlay/sci-biology/amap/files/amap-2.2-includes.patch

Fixes build with gcc 4.3 and 4.6

http://bugs.gentoo.org/217921
http://bugs.gentoo.org/360517

--- amap-align/align/Amap.cc
+++ amap-align/align/Amap.cc
@@ -12,6 +12,8 @@
 #include "ProbabilisticModel.h"
 #include "EvolutionaryTree.h"
 #include "SparseMatrix.h"
+#include <limits>
+#include <climits>
 #include <string>
 #include <sstream>
 #include <iomanip>
@@ -23,6 +25,7 @@
 #include <cstdlib>
 #include <cerrno>
 #include <iomanip>
+#include <cstring>
 
 string parametersInputFilename = "";
 string parametersOutputFilename = "no training";
--- amap-align/align/MultiSequenceDag.h
+++ amap-align/align/MultiSequenceDag.h
@@ -13,6 +13,7 @@
 #include <map>
 #include <queue>
 #include <iostream>
+#include <limits>
 #include "MultiSequence.h"
 #include "SparseMatrix.h"
 
--- amap-align/align/SafeVector.h.org	2011-03-26 11:50:11.935069583 +0100
+++ amap-align/align/SafeVector.h	2011-03-26 11:50:21.112553151 +0100
@@ -9,6 +9,7 @@
 #define SAFEVECTOR_H
 
 #include <cassert>
+#include <cstddef>
 #include <vector>
 
 /////////////////////////////////////////////////////////////////