From 8571ac663cce8aade42941742402a8fe37c27ff4 Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Mon, 26 Nov 2012 21:07:49 +0000
Subject: [PATCH] cleanup

---
 .../java/src/org/forester/analysis/AncestralTaxonomyInference.java  |    2 +-
 forester/java/src/org/forester/archaeopteryx/AptxUtil.java          |    2 +-
 forester/java/src/org/forester/datastructures/IntMatrix.java        |    2 +-
 forester/java/src/org/forester/phylogeny/data/NodeData.java         |    2 +-
 forester/java/src/org/forester/phylogeny/data/Taxonomy.java         |    2 +-
 forester/java/src/org/forester/sdi/RIO.java                         |    3 ++-
 6 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
index 2fbdb92..5a6a32a 100644
--- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
+++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
@@ -65,7 +65,7 @@ public final class AncestralTaxonomyInference {
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getScientificName() )
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() )
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getTaxonomyCode() ) || !ForesterUtil
-                                .isEmpty( desc.getNodeData().getTaxonomy().getCommonName() ) ) ) {
+                            .isEmpty( desc.getNodeData().getTaxonomy().getCommonName() ) ) ) {
                 final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomy( desc.getNodeData()
                         .getTaxonomy(), null, null );
                 if ( ( up_tax == null ) && ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() ) ) {
diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index f10fabd..ab8bcf6 100644
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -328,7 +328,7 @@ public final class AptxUtil {
             if ( n.getNodeData().isHasTaxonomy()
                     && ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() )
                             || !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) || !ForesterUtil
-                                .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+                            .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
                 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() )
                         && n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) ) {
                     final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( n.getNodeData()
diff --git a/forester/java/src/org/forester/datastructures/IntMatrix.java b/forester/java/src/org/forester/datastructures/IntMatrix.java
index e8707b1..b8b915d 100644
--- a/forester/java/src/org/forester/datastructures/IntMatrix.java
+++ b/forester/java/src/org/forester/datastructures/IntMatrix.java
@@ -31,7 +31,7 @@ public final class IntMatrix {
     final public void set( final int x, final int y, final int value ) {
         _data[ x ][ y ] = value;
     }
-    
+
     final public void inreaseByOne( final int x, final int y ) {
         _data[ x ][ y ]++;
     }
diff --git a/forester/java/src/org/forester/phylogeny/data/NodeData.java b/forester/java/src/org/forester/phylogeny/data/NodeData.java
index e0d74a2..bc7e8b9 100644
--- a/forester/java/src/org/forester/phylogeny/data/NodeData.java
+++ b/forester/java/src/org/forester/phylogeny/data/NodeData.java
@@ -273,7 +273,7 @@ public class NodeData implements PhylogenyData {
         return ( getDate() != null )
                 && ( !ForesterUtil.isEmpty( getDate().getDesc() ) || !ForesterUtil.isNull( getDate().getMax() )
                         || !ForesterUtil.isNull( getDate().getMin() ) || !ForesterUtil.isNull( getDate().getValue() ) || !ForesterUtil
-                            .isEmpty( getDate().getUnit() ) );
+                        .isEmpty( getDate().getUnit() ) );
     }
 
     public boolean isHasDistribution() {
diff --git a/forester/java/src/org/forester/phylogeny/data/Taxonomy.java b/forester/java/src/org/forester/phylogeny/data/Taxonomy.java
index 1396cf8..544522b 100644
--- a/forester/java/src/org/forester/phylogeny/data/Taxonomy.java
+++ b/forester/java/src/org/forester/phylogeny/data/Taxonomy.java
@@ -251,7 +251,7 @@ public class Taxonomy implements PhylogenyData, MultipleUris, Comparable<Taxonom
                 && ForesterUtil.isEmpty( getCommonName() ) && ForesterUtil.isEmpty( getScientificName() )
                 && ForesterUtil.isEmpty( getRank() ) && ForesterUtil.isEmpty( _uris )
                 && ForesterUtil.isEmpty( getAuthority() ) && ForesterUtil.isEmpty( _synonyms ) && ForesterUtil
-                    .isEmpty( _lineage ) );
+                .isEmpty( _lineage ) );
     }
 
     /**
diff --git a/forester/java/src/org/forester/sdi/RIO.java b/forester/java/src/org/forester/sdi/RIO.java
index ff5e3e9..0258db7 100644
--- a/forester/java/src/org/forester/sdi/RIO.java
+++ b/forester/java/src/org/forester/sdi/RIO.java
@@ -111,7 +111,8 @@ public final class RIO {
             for( int x = 0; x < m.size(); ++x ) {
                 final PhylogenyNode nx = map.get( m.getLabel( x ) );
                 for( int y = 0; y < m.size(); ++y ) {
-                    if ( !PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( nx, map.get( m.getLabel( y ) ) ).isDuplication() ) {
+                    if ( !PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( nx, map.get( m.getLabel( y ) ) )
+                            .isDuplication() ) {
                         m.inreaseByOne( x, y );
                     }
                 }
-- 
1.7.10.2