From 0bbf7742023f862d29f1266c5a172b4cb99b7939 Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 23 Apr 2014 23:18:33 +0000
Subject: [PATCH] inprogress

---
 .../java/src/org/forester/application/msa_compactor.java |   14 +++++++-------
 .../{MsaCompactor2.java => MsaCompactor.java}            |    4 ++--
 2 files changed, 9 insertions(+), 9 deletions(-)
 rename forester/java/src/org/forester/msa_compactor/{MsaCompactor2.java => MsaCompactor.java} (99%)

diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java
index 556fba7..8e71f5e 100644
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -36,7 +36,7 @@ import org.forester.msa.Msa.MSA_FORMAT;
 import org.forester.msa.MsaInferrer;
 import org.forester.msa.MsaMethods;
 import org.forester.msa_compactor.Chart;
-import org.forester.msa_compactor.MsaCompactor2;
+import org.forester.msa_compactor.MsaCompactor;
 import org.forester.msa_compactor.MsaProperties;
 import org.forester.util.CommandLineArguments;
 import org.forester.util.DescriptiveStatistics;
@@ -205,7 +205,7 @@ public class msa_compactor {
             }
             if ( realign ) {
                 if ( ForesterUtil.isEmpty( path_to_mafft ) ) {
-                    path_to_mafft = MsaCompactor2.guessPathToMafft();
+                    path_to_mafft = MsaCompactor.guessPathToMafft();
                 }
                 checkPathToMafft( path_to_mafft );
                 if ( cla.isOptionSet( MAFFT_OPTIONS ) ) {
@@ -269,7 +269,7 @@ public class msa_compactor {
             //
             //
             if ( worst_remove > 0 ) {
-                final MsaCompactor2 mc = new MsaCompactor2( msa );
+                final MsaCompactor mc = new MsaCompactor( msa );
                 mc.setRealign( realign );
                 if ( realign ) {
                     mc.setPathToMafft( path_to_mafft );
@@ -280,7 +280,7 @@ public class msa_compactor {
                 mc.removeWorstOffenders( worst_remove, true );
             }
             else if ( av_gap > 0 ) {
-                final MsaCompactor2 mc = new MsaCompactor2( msa );
+                final MsaCompactor mc = new MsaCompactor( msa );
                 mc.setRealign( realign );
                 if ( realign ) {
                     mc.setPathToMafft( path_to_mafft );
@@ -292,7 +292,7 @@ public class msa_compactor {
             }
             else if ( length > 0 ) {
                 // TODO if < shortest seq -> error
-                final MsaCompactor2 mc = new MsaCompactor2( msa );
+                final MsaCompactor mc = new MsaCompactor( msa );
                 mc.setRealign( realign );
                 if ( realign ) {
                     mc.setPathToMafft( path_to_mafft );
@@ -305,7 +305,7 @@ public class msa_compactor {
             else {
                 //MsaCompactor.chart( msa, step, realign, norm, path_to_mafft );
                 final int initial_number_of_seqs = msa.getNumberOfSequences();
-                final MsaCompactor2 mc = new MsaCompactor2( msa );
+                final MsaCompactor mc = new MsaCompactor( msa );
                 mc.setRealign( realign );
                 if ( realign ) {
                     mc.setPathToMafft( path_to_mafft );
@@ -346,7 +346,7 @@ public class msa_compactor {
                                               E_MAIL,
                                               WWW,
                                               ForesterUtil.getForesterLibraryInformation() );
-        final String path_to_mafft = MsaCompactor2.guessPathToMafft();
+        final String path_to_mafft = MsaCompactor.guessPathToMafft();
         String mafft_comment;
         if ( !ForesterUtil.isEmpty( path_to_mafft ) ) {
             mafft_comment = " (using " + path_to_mafft + ")";
diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor2.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
similarity index 99%
rename from forester/java/src/org/forester/msa_compactor/MsaCompactor2.java
rename to forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index 5fd5242..b8332bb 100644
--- a/forester/java/src/org/forester/msa_compactor/MsaCompactor2.java
+++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@ -54,7 +54,7 @@ import org.forester.sequence.Sequence;
 import org.forester.tools.ConfidenceAssessor;
 import org.forester.util.ForesterUtil;
 
-public class MsaCompactor2 {
+public class MsaCompactor {
 
     final private static NumberFormat NF_3                      = new DecimalFormat( "#.###" );
     final private static NumberFormat NF_4                      = new DecimalFormat( "#.####" );
@@ -80,7 +80,7 @@ public class MsaCompactor2 {
         NF_3.setRoundingMode( RoundingMode.HALF_UP );
     }
 
-    public MsaCompactor2( final DeleteableMsa msa ) {
+    public MsaCompactor( final DeleteableMsa msa ) {
         _msa = msa;
         _removed_seq_ids = new TreeSet<String>();
     }
-- 
1.7.10.2