From: cmzmasek <chris.zma@outlook.com>
Date: Fri, 21 Jul 2017 22:54:29 +0000 (-0700)
Subject: first prototype
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c0c53d86b63599b080b7c42d80332ad9683b92d6;p=jalview.git

first prototype
---

diff --git a/forester/java/src/org/forester/application/cladinator.java b/forester/java/src/org/forester/application/cladinator.java
index 13143b0..d482f7a 100644
--- a/forester/java/src/org/forester/application/cladinator.java
+++ b/forester/java/src/org/forester/application/cladinator.java
@@ -96,9 +96,9 @@ public final class cladinator {
             final Result res = Analysis.execute( p, query );
             System.out.println();
             System.out.println( "Result:" );
-            System.out.println( "Greatest common prefix a       : " + res.getGreatestCommonPrefix() );
-            System.out.println( "Greatest common prefix a (up)  : " + res.getGreatestCommonPrefixUp() );
-            System.out.println( "Greatest common prefix b (down): " + res.getGreatestCommonPrefixDown() );
+            System.out.println( "Greatest common prefix     : " + res.getGreatestCommonPrefix() );
+            System.out.println( "Greatest common prefix up  : " + res.getGreatestCommonPrefixUp() );
+            System.out.println( "Greatest common prefix down: " + res.getGreatestCommonPrefixDown() );
             final double lec_ratio = ( 100.0 * res.getLeastEncompassingCladeSize() ) / res.getTreeSize();
             System.out.println( "Least Encompassing Clade has " + res.getLeastEncompassingCladeSize()
                     + " external nodes (" + df2.format( lec_ratio ) + "% of a total of " + res.getTreeSize() + ")" );
diff --git a/forester/java/src/org/forester/clade_analysis/Analysis.java b/forester/java/src/org/forester/clade_analysis/Analysis.java
index a154b12..bddd518 100644
--- a/forester/java/src/org/forester/clade_analysis/Analysis.java
+++ b/forester/java/src/org/forester/clade_analysis/Analysis.java
@@ -28,7 +28,7 @@
 // * More tests (including multiple children per node), especially on edge cases
 // * Utilize relevant support values for warnings
 // * Better system for "clade label creation" (e.g. 1.3.4 + 1.3.6 -> 1.3), use
-//   specific separator (eg . | _ )
+// specific separator (eg . | _ )
 
 package org.forester.clade_analysis;
 
@@ -89,22 +89,22 @@ public final class Analysis {
     }
 
     private final static String analyzeSiblings( final PhylogenyNode child, final PhylogenyNode parent ) {
-        final int qnode_p_index = child.getChildNodeIndex();
-        final List<String> qnode_ext_nodes_names_a = new ArrayList<>();
+        final int child_index = child.getChildNodeIndex();
+        final List<String> ext_nodes_names = new ArrayList<>();
         final List<PhylogenyNode> descs = parent.getDescendants();
         for( int i = 0; i < descs.size(); ++i ) {
-            if ( i != qnode_p_index ) {
+            if ( i != child_index ) {
                 final PhylogenyNode d = descs.get( i );
                 for( final PhylogenyNode n : d.getAllExternalDescendants() ) {
                     final String name = n.getName();
                     if ( ForesterUtil.isEmptyTrimmed( name ) ) {
                         throw new IllegalArgumentException( "external node(s) with empty names found" );
                     }
-                    qnode_ext_nodes_names_a.add( name.trim() );
+                    ext_nodes_names.add( name.trim() );
                 }
             }
         }
-        final String greatest_common_prefix_a = ForesterUtil.greatestCommonPrefix( qnode_ext_nodes_names_a );
-        return greatest_common_prefix_a;
+        final String greatest_common_prefix = ForesterUtil.greatestCommonPrefix( ext_nodes_names );
+        return greatest_common_prefix;
     }
 }