From: cmzmasek <cmzmasek@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Mon, 10 Dec 2012 01:37:48 +0000 (+0000)
Subject: not needed
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b4feb429a0026b7946c480debd9f4cf54b9ee6cf;p=jalview.git

not needed
---

diff --git a/forester/java/src/org/forester/sdi/RIOn.java b/forester/java/src/org/forester/sdi/RIOn.java
deleted file mode 100644
index 058e10f..0000000
--- a/forester/java/src/org/forester/sdi/RIOn.java
+++ /dev/null
@@ -1,132 +0,0 @@
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 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
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
-
-package org.forester.sdi;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Event;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.util.GeneralTable;
-
-public class RIOn {
-
-    private final static boolean  ROOT_BY_MINIMIZING_MAPPING_COST = false;
-    private final static boolean  ROOT_BY_MINIMIZING_SUM_OF_DUPS  = true;
-    private final static boolean  ROOT_BY_MINIMIZING_TREE_HEIGHT  = true;
-    GeneralTable<String, Integer> _orthologs                      = null;
-    GeneralTable<String, Integer> _paralogs                       = null;
-    GeneralTable<String, Integer> _super_orthologs                = null;
-    GeneralTable<String, Integer> _ultra_paralogs                 = null;
-
-    private void doInferOrthologs( final Phylogeny gene_tree, final Phylogeny species_tree ) throws SDIException {
-        final SDIR sdiunrooted = new SDIR();
-        final Phylogeny assigned_tree = sdiunrooted.infer( gene_tree,
-                                                           species_tree,
-                                                           ROOT_BY_MINIMIZING_MAPPING_COST,
-                                                           ROOT_BY_MINIMIZING_SUM_OF_DUPS,
-                                                           ROOT_BY_MINIMIZING_TREE_HEIGHT,
-                                                           true,
-                                                           1 )[ 0 ];
-        final List<PhylogenyNode> external_nodes = new ArrayList<PhylogenyNode>();
-        for( final PhylogenyNodeIterator iterator = assigned_tree.iteratorExternalForward(); iterator.hasNext(); ) {
-            external_nodes.add( iterator.next() );
-        }
-        final PhylogenyMethods methods = PhylogenyMethods.getInstance();
-        for( int i = 0; i < external_nodes.size(); ++i ) {
-            for( int j = 0; j < external_nodes.size(); ++j ) {
-                if ( i != j ) {
-                    final PhylogenyNode node_i = external_nodes.get( i );
-                    final PhylogenyNode node_j = external_nodes.get( j );
-                    final PhylogenyNode lca = PhylogenyMethods.calculateLCA( node_i, node_j );
-                    final Event event = lca.getNodeData().getEvent();
-                    final String node_i_name = node_i.getNodeData().getSequence().getName();
-                    final String node_j_name = node_j.getNodeData().getSequence().getName();
-                    if ( event.isDuplication() ) {
-                        increaseCounter( getOrthologs(), node_i_name, node_j_name );
-                    }
-                    else {
-                        increaseCounter( getParalogs(), node_i_name, node_j_name );
-                    }
-                }
-            }
-        }
-    }
-
-    public GeneralTable<String, Integer> getOrthologs() {
-        return _orthologs;
-    }
-
-    public GeneralTable<String, Integer> getParalogs() {
-        return _paralogs;
-    }
-
-    public GeneralTable<String, Integer> getSuperOrthologs() {
-        return _super_orthologs;
-    }
-
-    public GeneralTable<String, Integer> getUltraParalogs() {
-        return _ultra_paralogs;
-    }
-
-    private void increaseCounter( final GeneralTable<String, Integer> table,
-                                  final String node_i_name,
-                                  final String node_j_name ) {
-        final Integer value = table.getValue( node_i_name, node_j_name );
-        if ( value == null ) {
-            table.setValue( node_i_name, node_j_name, 1 );
-        }
-        else {
-            table.setValue( node_i_name, node_j_name, value.intValue() + 1 );
-        }
-    }
-
-    private void init() {
-        _orthologs = new GeneralTable<String, Integer>();
-        _paralogs = new GeneralTable<String, Integer>();
-        _super_orthologs = new GeneralTable<String, Integer>();
-        _ultra_paralogs = new GeneralTable<String, Integer>();
-    }
-
-    private void setOrthologs( final GeneralTable<String, Integer> orthologs ) {
-        _orthologs = orthologs;
-    }
-
-    private void setParalogs( final GeneralTable<String, Integer> paralogs ) {
-        _paralogs = paralogs;
-    }
-
-    private void setSuperOrthologs( final GeneralTable<String, Integer> super_orthologs ) {
-        _super_orthologs = super_orthologs;
-    }
-
-    private void setUltraParalogs( final GeneralTable<String, Integer> ultra_paralogs ) {
-        _ultra_paralogs = ultra_paralogs;
-    }
-}