only include headers by names relative to project base path

diff --git a/alg/module.mk b/alg/module.mk
index 438fd8bf6398146e36d20ab96d2c26a4c0563d89..338fd4b434f1fe3783ba1c1caafb017454e7f9ce 100644 (file)
--- a/alg/module.mk
+++ b/alg/module.mk
@@ -12,7 +12,7 @@ SOURCES.cxx := flp.cxx \
 MUSSA_ALG_SRC := $(addprefix $(CURDIR), $(SOURCES.cxx))
 
 SRC += $(MUSSA_ALG_SRC)
-CXXFLAGS += -I$(CURDIR)
+CXXFLAGS += 
 
 MUSSA_ALG_LIB := $(CURDIR)libmussa$(LIBEXT)
 LIBDIRS += -L$(CURDIR)

diff --git a/gui/ConnView.hh b/gui/ConnView.hh
index fafc55c2c40b2116c66c3ae205047e5a93241b2b..91a30f09971b0db9522aa41863b38e60192d12e3 100644 (file)
--- a/gui/ConnView.hh
+++ b/gui/ConnView.hh
@@ -14,12 +14,12 @@
 #include <string>
 #include <vector>
 
-#include "sequence.hh"
+#include "alg/sequence.hh"
+#include "alg/nway_paths.hh"
 #include "SeqView.hh"
 #include "SeqWindow.hh"
 #include "MotifWindow.hh"
 #include "AnnotWindow.hh" // aparently for annot_color
-#include "alg/nway_paths.hh"
 
 #include <FL/Fl_Box.H>
 

diff --git a/gui/MotifWindow.hh b/gui/MotifWindow.hh
index 5c16594768f4deff1523f64b10e16aa1b4041e5b..ac1e60a3dd8c41b782cd47f35387cbf70a597cc7 100644 (file)
--- a/gui/MotifWindow.hh
+++ b/gui/MotifWindow.hh
@@ -19,7 +19,7 @@
 #include <FL/Fl_Input.H>
 #include <FL/Fl_Pack.H>
 
-#include "mussa_class.hh"
+#include "alg/mussa_class.hh"
 
 struct motif
 {

diff --git a/gui/SeqTextWindow.cxx b/gui/SeqTextWindow.cxx
index c9b84c5b68cb52459b715af4f48a7ed090f7002c..614a065e5b638bee20500f6fb2091e96de3e97d5 100644 (file)
--- a/gui/SeqTextWindow.cxx
+++ b/gui/SeqTextWindow.cxx
@@ -8,7 +8,7 @@
 // file for more information, or contact Tristan directly.
 
 
-#include "SeqTextWindow.hh"
+#include "gui/SeqTextWindow.hh"
 
 #include <iostream>
 using namespace std;

diff --git a/gui/SeqTextWindow.hh b/gui/SeqTextWindow.hh
index d4b6d7e4e91d852396691979fdb41a80a118fc45..810879c39b601dca5187f09fb6c19c8ff598e18e 100644 (file)
--- a/gui/SeqTextWindow.hh
+++ b/gui/SeqTextWindow.hh
@@ -19,7 +19,7 @@
 #include <FL/Fl_Multiline_Output.H>
 #include <FL/Fl_Window.H>
 
-#include "sequence.hh"
+#include "alg/sequence.hh"
 
 class SeqTextWindow : public Fl_Window
 { 

diff --git a/gui/SubAnalysisWindow.hh b/gui/SubAnalysisWindow.hh
index a459df39bfd277219f67909f131496c6a947bd74..d0fb150015894e5984d8af23057f30cc97737c71 100644 (file)
--- a/gui/SubAnalysisWindow.hh
+++ b/gui/SubAnalysisWindow.hh
@@ -18,7 +18,7 @@
 #include <FL/Fl_File_Chooser.H>
 #include <FL/Fl_Scroll.H>
 
-#include "mussa_class.hh"
+#include "alg/mussa_class.hh"
 #include "SeqTextWindow.hh"
 
 class SubAnalysisWindow : public Fl_Window

diff --git a/gui/module.mk b/gui/module.mk
index b289102a9109efce5239e2b1117dd620b78af8ce..01d046fa166e38c1c1f347b73f4f024d5e98d4bd 100644 (file)
--- a/gui/module.mk
+++ b/gui/module.mk
@@ -13,7 +13,7 @@ SOURCES.cxx := AnnotWindow.cxx \
 MUSSA_FLTK_SRC := $(addprefix $(CURDIR), $(SOURCES.cxx))
 
 SRC += $(MUSSA_FLTK_SRC)
-CXXFLAGS += -I$(CURDIR)
+CXXFLAGS += 
 
 MUSSA_FLTK_LIB := $(CURDIR)libmussa_fltk$(LIBEXT)
 LIBDIRS += -L$(CURDIR)

diff --git a/test/module.mk b/test/module.mk
index 42cca85c71dceeb05f55c55f316cc0ca8226e451..5fb4ede6d9d8cfd2e06b42bb0774626222e39257 100644 (file)
--- a/test/module.mk
+++ b/test/module.mk
@@ -9,7 +9,7 @@ SOURCES.cxx := test_main.cxx \
 TESTSRC := $(addprefix $(CURDIR), $(SOURCES.cxx))
 
 SRC += $(TESTSRC)
-CXXFLAGS += -I$(CURDIR)
+CXXFLAGS += 
 
 TEST := $(BASEDIR)/unittests$(BINEXT) 
 TARGETBINS += $(TEST)

diff --git a/test/test_flp.cxx b/test/test_flp.cxx
index 826123a3af4a8ddfd55bb70260b0c3d8e7857349..aa18f76d95047063f89fad78e8000d937652b932 100644 (file)
--- a/test/test_flp.cxx
+++ b/test/test_flp.cxx
@@ -1,9 +1,11 @@
+#include <iostream>
+#include <list>
+
 #include <boost/test/auto_unit_test.hpp>
 #include <boost/filesystem/operations.hpp>
 #include <boost/filesystem/path.hpp>
 
-#include "alg/flp.hh"
-#include "alg/sequence.hh"
+#include "flp.hh"
 #include <iostream>
 #include <list>
 

diff --git a/test/test_nway.cxx b/test/test_nway.cxx
index efd78891ca78777db6bdfb067e6950034de5c82f..aa6295bfc94236926fec0e82f2fbf4254bb44e66 100644 (file)
--- a/test/test_nway.cxx
+++ b/test/test_nway.cxx
@@ -1,5 +1,13 @@
 #include <boost/test/auto_unit_test.hpp>
 
+#include <string>
+
+#include "alg/mussa_class.hh"
+#include "alg/nway_paths.hh"
+#include "alg/sequence.hh"
+
+using namespace std;
+
 BOOST_AUTO_TEST_CASE( nway_test )
 {
 }