inprogress

[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 765648f..fd035fe 100644 (file)
--- a/forester/java/src/org/forester/application/msa_compactor.java
+++ b/forester/java/src/org/forester/application/msa_compactor.java
@@ -9,7 +9,6 @@ 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.Msa.MSA_FORMAT;
 import org.forester.msa.MsaInferrer;
 import org.forester.msa_compactor.MsaCompactor;
 import org.forester.util.CommandLineArguments;
@@ -27,9 +26,9 @@ public class msa_compactor {
     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_DESC                               = "multiple sequence aligment compactor";
     final static private String PRG_VERSION                            = "0.01";
-    final static private String PRG_DATE                               = "140314";
+    final static private String PRG_DATE                               = "140316";
     final static private String E_MAIL                                 = "phylosoft@gmail.com";
     final static private String WWW                                    = "https://sites.google.com/site/cmzmasek/home/software/forester";
 
@@ -85,14 +84,6 @@ public class msa_compactor {
             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 );
-            //            }
-            //            else {
-            //                printHelp();
-            //                System.exit( 0 );
-            //            }
             if ( realign ) {
                 if ( ForesterUtil.isEmpty( path_to_mafft ) ) {
                     path_to_mafft = MsaCompactor.guessPathToMafft();
@@ -109,19 +100,19 @@ public class msa_compactor {
             }
             MsaCompactor mc = null;
             if ( worst_remove > 0 ) {
-                mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign, norm, path_to_mafft );
+                mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, step, realign, norm, path_to_mafft, out );
             }
             else if ( av > 0 ) {
-                mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, out, 50, path_to_mafft );
+                mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, norm, path_to_mafft, out );
             }
             else if ( length > 0 ) {
-                mc = MsaCompactor.reduceLength( msa, length, step, realign, path_to_mafft );
+                if ( length >= msa.getLength() ) {
+                    ForesterUtil.fatalError( PRG_NAME, "target MSA length (" + length
+                            + ") is greater than or equal to MSA original length (" + msa.getLength() + ")" );
+                }
+                // TODO if < shortest seq -> error
+                mc = MsaCompactor.reduceLength( msa, length, step, realign, norm, path_to_mafft, out );
             }
-            //System.out.println( MsaMethods.calcGapRatio( mc.getMsa() ) );
-            // for( final String id : mc.getRemovedSeqIds() ) {
-            //     System.out.println( id );
-            //}
-            mc.writeMsa( out, MSA_FORMAT.PHYLIP, ".aln" );
         }
         catch ( final Exception e ) {
             e.printStackTrace();
@@ -168,6 +159,9 @@ public class msa_compactor {
         System.out.println();
         System.out.println( "   -" + REMOVE_WORST_OFFENDERS_OPTION
                 + "=<integer>  number of worst offender sequences to remove" );
+        System.out.println( "   -" + LENGTH_OPTION + "=<integer>  target MSA length" );
+        System.out.println( "   -" + AV_GAPINESS_OPTION + "=<decimal>  target gap-ratio (0.0-1.0)" );
+        System.out.println( "   -" + STEP_OPTION + "=<integer>  step (for output and re-aligning)" );
         System.out.println( "   -" + REALIGN_OPTION + "            to realign using MAFFT" + mafft_comment );
         System.out.println();
         System.out.println();