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Re: Help needed to build prottest

Am 13.07.2018 um 11:02 schrieb Andreas Tille:
> Hmmm, not sure whether this is the same question.  I always have trouble
> to find out in what package the respective JAR can be found.  In the
> current case when browsing the alter.jar content the respective classes
> are just moved to a sbdirectory hierarchy:
>    es/uvigo/ei/sing/alter
> I wonder whether I simply have build alter-sequence-alignment wrongly
> or whether prottest needs to be adapted to the new location.

It turned out that the import statement must be adapted to the new
location. Patch is attached.


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(-)

diff --git a/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java b/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java
index 8d08537..dc12930 100644
--- 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 330, Boston, MA  02111-1307  USA
 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.

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