debian/changelog

-prottest (3.4.2+dfsg-3) UNRELEASED; urgency=medium
+prottest (3.4.2+dfsg-3) unstable; urgency=medium
 
   * debhelper 11
   * Point Vcs fields to salsa.debian.org
   * Standards-Version: 4.1.5
+  * alter-sequence-statement has changed paths - thanks for the patch
+    to adapt this to Markus Koschany <apo@debian.org>
+  * Do not parse d/changelog
 
- -- Andreas Tille <tille@debian.org>  Wed, 11 Jul 2018 22:22:42 +0200
+ -- Andreas Tille <tille@debian.org>  Fri, 13 Jul 2018 13:49:49 +0200
 
 prottest (3.4.2+dfsg-2) unstable; urgency=medium
 

debian/patches/alter-import.patch

+From: Markus Koschany <apo@debian.org>
+Date: Fri, 13 Jul 2018 13:05:25 +0200
+Subject: alter import
+
+---
+ .../es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java     | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+--- a/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java
++++ b/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java
+@@ -17,9 +17,9 @@ Foundation, Inc., 59 Temple Place, Suite
+ */
+ package es.uvigo.darwin.prottest.util.fileio;
+ 
+-import converter.Converter;
+-import converter.DefaultFactory;
+-import converter.Factory;
++import es.uvigo.ei.sing.alter.converter.Converter;
++import es.uvigo.ei.sing.alter.converter.DefaultFactory;
++import es.uvigo.ei.sing.alter.converter.Factory;
+ import java.io.IOException;
+ import java.io.PrintWriter;
+ import java.io.PushbackReader;
+@@ -44,7 +44,7 @@ import pal.tree.Tree;
+ import pal.tree.TreeParseException;
+ 
+ // TODO: Auto-generated Javadoc
+-import parser.ParseException;
++import es.uvigo.ei.sing.alter.parser.ParseException;
+ /**
+  * The Class AlignmentReader.
+  */

debian/patches/series

 use_debian_packaged_phyml.patch
 build.patch
+alter-import.patch

debian/rules

 #!/usr/bin/make -f
 
-DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+include /usr/share/dpkg/default.mk
 
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
@@ -12,9 +12,9 @@ JAVA_HOME=/usr/lib/jvm/default-java
 
 override_dh_fixperms:
 	dh_fixperms
-	chmod -x debian/$(DEBPKGNAME)/etc/$(DEBPKGNAME)/*
-	find debian/$(DEBPKGNAME)/usr/share/doc/$(DEBPKGNAME)/examples -type f -exec chmod -x \{\} \;
-	find debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/models -type f -exec chmod -x \{\} \;
+	chmod -x debian/$(DEB_SOURCE)/etc/$(DEB_SOURCE)/*
+	find debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples -type f -exec chmod -x \{\} \;
+	find debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)/models -type f -exec chmod -x \{\} \;
 
 override_dh_installchangelogs:
 	dh_installchangelogs src/main/resources/CHANGELOG