in progress

[jalview.git] / forester / java / src / org / forester / application / msa_compactor.java

diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java
index 9ed5e20..bf04e12 100644 (file)
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -9,27 +9,30 @@ import java.util.List;
 import org.forester.io.parsers.FastaParser;
 import org.forester.io.parsers.GeneralMsaParser;
 import org.forester.msa.Msa;
+import org.forester.msa.MsaInferrer;
 import org.forester.msa.Msa.MSA_FORMAT;
-import org.forester.msa.MsaCompactor;
 import org.forester.msa.MsaMethods;
+import org.forester.msa_compactor.MsaCompactor;
 import org.forester.util.CommandLineArguments;
 import org.forester.util.ForesterUtil;
 
 public class msa_compactor {
 
-    final static private String HELP_OPTION_1                 = "help";
-    final static private String HELP_OPTION_2                 = "h";
-    final static private String REMOVE_WORST_OFFENDERS_OPTION = "w";
-    final static private String AV_GAPINESS_OPTION            = "a";
-    final static private String STEP_OPTION                   = "s";
-    final static private String LENGTH_OPTION                 = "l";
-    final static private String REALIGN_OPTION                = "r";
-    final static private String PRG_NAME                      = "msa_compactor";
-    final static private String PRG_DESC                      = "multiple sequnce aligment compactor";
-    final static private String PRG_VERSION                   = "0.01";
-    final static private String PRG_DATE                      = "140221";
-    final static private String E_MAIL                        = "phylosoft@gmail.com";
-    final static private String WWW                           = "https://sites.google.com/site/cmzmasek/home/software/forester";
+    final static private String HELP_OPTION_1                          = "help";
+    final static private String HELP_OPTION_2                          = "h";
+    final static private String REMOVE_WORST_OFFENDERS_OPTION          = "w";
+    final static private String AV_GAPINESS_OPTION                     = "a";
+    final static private String STEP_OPTION                            = "s";
+    final static private String LENGTH_OPTION                          = "l";
+    final static private String REALIGN_OPTION                         = "r";
+    final static private String PATH_TO_MAFFT_OPTION                   = "mafft";
+    final static private String DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION = "nn";
+    final static private String PRG_NAME                               = "msa_compactor";
+    final static private String PRG_DESC                               = "multiple sequnce aligment compactor";
+    final static private String PRG_VERSION                            = "0.01";
+    final static private String PRG_DATE                               = "140314";
+    final static private String E_MAIL                                 = "phylosoft@gmail.com";
+    final static private String WWW                                    = "https://sites.google.com/site/cmzmasek/home/software/forester";
 
     public static void main( final String args[] ) {
         try {
@@ -45,12 +48,16 @@ public class msa_compactor {
             int length = -1;
             int step = 1;
             boolean realign = false;
+            boolean norm = true;
+            String path_to_mafft = null;
             final List<String> allowed_options = new ArrayList<String>();
             allowed_options.add( REMOVE_WORST_OFFENDERS_OPTION );
             allowed_options.add( AV_GAPINESS_OPTION );
             allowed_options.add( LENGTH_OPTION );
             allowed_options.add( REALIGN_OPTION );
+            allowed_options.add( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION );
             allowed_options.add( STEP_OPTION );
+            allowed_options.add( PATH_TO_MAFFT_OPTION );
             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
             if ( dissallowed_options.length() > 0 ) {
                 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
@@ -70,6 +77,15 @@ public class msa_compactor {
             if ( cla.isOptionSet( REALIGN_OPTION ) ) {
                 realign = true;
             }
+            if ( cla.isOptionSet( PATH_TO_MAFFT_OPTION ) ) {
+                if ( !realign ) {
+                    ForesterUtil.fatalError( PRG_NAME, "no need to indicate path to MAFFT without realigning" );
+                }
+                path_to_mafft = cla.getOptionValueAsCleanString( PATH_TO_MAFFT_OPTION );
+            }
+            if ( cla.isOptionSet( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION ) ) {
+                norm = false;
+            }
             //            else if ( cla.isOptionSet( STEP_OPTION ) && cla.isOptionSet( WINDOW_OPTION ) ) {
             //                step = cla.getOptionValueAsInt( STEP_OPTION );
             //                window = cla.getOptionValueAsInt( WINDOW_OPTION );
@@ -86,9 +102,27 @@ public class msa_compactor {
             else {
                 msa = GeneralMsaParser.parse( is );
             }
+            
+            if ( realign ) {
+                if ( ForesterUtil.isEmpty( path_to_mafft ) ) {
+                    path_to_mafft = MsaCompactor.guessPathToMafft();
+                }
+                if ( !ForesterUtil.isEmpty( path_to_mafft ) && MsaInferrer.isInstalled( path_to_mafft ) ) {
+                    ForesterUtil.programMessage( PRG_NAME, "using MAFFT at \"" + path_to_mafft + "\""  );
+                }
+                else {
+                    if ( ForesterUtil.isEmpty( path_to_mafft ) ) {
+                        ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable found, use -\"" + PATH_TO_MAFFT_OPTION + "=<path to MAFFT>\" option" );
+                    }
+                    else {
+                        ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable at \""  + path_to_mafft + "\""  );
+                    }
+                }
+            }
+            
             MsaCompactor mc = null;
             if ( worst_remove > 0 ) {
-                mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign );
+                mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign, norm );
             }
             else if ( av > 0 ) {
                 mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, out, 50 );
@@ -116,13 +150,23 @@ public class msa_compactor {
                                               E_MAIL,
                                               WWW,
                                               ForesterUtil.getForesterLibraryInformation() );
+        final String path_to_mafft = MsaCompactor.guessPathToMafft();
+        String mafft_comment;
+        if ( !ForesterUtil.isEmpty( path_to_mafft ) ) {
+            mafft_comment = " (" + path_to_mafft + ")";
+        }
+        else {
+            mafft_comment = " (no path to MAFFT found, use -\"" + PATH_TO_MAFFT_OPTION + "=<path to MAFFT>\" option";
+        }
+        
         System.out.println( "Usage:" );
         System.out.println();
         System.out.println( PRG_NAME + " <options> <msa input file>" );
         System.out.println();
         System.out.println( " options: " );
         System.out.println();
-        System.out.println( "   -" + REMOVE_WORST_OFFENDERS_OPTION + "=<integer>: step size (msa columns)" );
+        System.out.println( "   -" + REMOVE_WORST_OFFENDERS_OPTION + "=<integer>  number of sequences to remove" );
+        System.out.println( "   -" + REALIGN_OPTION + " to realign using MAFFT" + mafft_comment );
         System.out.println();
         System.out.println();
         System.out.println();