X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fdecorator.java;h=a7dd6ee28ca237ee9a42f0702f95b200020a140f;hb=0b39293d1577083551ba528d0ac7afcacbf69dde;hp=54458a3dcbb00f7c7c1181885721f24b6625b09c;hpb=adbb9fb1f03f2de7b7738d433a52a9e69ddcf5bc;p=jalview.git

diff --git a/forester/java/src/org/forester/application/decorator.java b/forester/java/src/org/forester/application/decorator.java
index 54458a3..a7dd6ee 100644
--- a/forester/java/src/org/forester/application/decorator.java
+++ b/forester/java/src/org/forester/application/decorator.java
@@ -45,7 +45,7 @@ import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.data.Identifier;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.sequence.Sequence;
+import org.forester.sequence.MolecularSequence;
 import org.forester.tools.PhylogenyDecorator;
 import org.forester.tools.PhylogenyDecorator.FIELD;
 import org.forester.util.BasicTable;
@@ -249,7 +249,7 @@ public final class decorator {
                 }
                 else {
                     ForesterUtil.fatalError( decorator.PRG_NAME, "unknown value for \"" + decorator.FIELD_OPTION
-                            + "\" option: \"" + field_str + "\"" );
+                                             + "\" option: \"" + field_str + "\"" );
                 }
             }
         }
@@ -271,7 +271,7 @@ public final class decorator {
         }
         catch ( final Exception e ) {
             ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read phylgenies from [" + phylogenies_infile
-                    + "] [" + e.getMessage() + "]" );
+                                     + "] [" + e.getMessage() + "]" );
         }
         Map<String, String> map = null;
         if ( !advanced_table ) {
@@ -326,7 +326,7 @@ public final class decorator {
             if ( ( phylogenies.length > 1 )
                     && ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id ) ) ) {
                 ForesterUtil.fatalError( decorator.PRG_NAME,
-                                         "attempt to set same name or id on more than one phylogeny" );
+                        "attempt to set same name or id on more than one phylogeny" );
             }
             if ( !ForesterUtil.isEmpty( tree_name ) ) {
                 phylogenies[ 0 ].setName( tree_name );
@@ -399,7 +399,7 @@ public final class decorator {
     }
 
     private static Map<String, String> readFastaFileIntoMap( final File mapping_infile, final boolean verbose ) {
-        List<Sequence> seqs = null;
+        List<MolecularSequence> seqs = null;
         try {
             seqs = FastaParser.parse( new FileInputStream( mapping_infile ) );
         }
@@ -409,17 +409,17 @@ public final class decorator {
         }
         if ( ForesterUtil.isEmpty( seqs ) ) {
             ForesterUtil.fatalError( decorator.PRG_NAME, "fasta-file [" + mapping_infile
-                    + "] is devoid of fasta-formatted sequences" );
+                                     + "] is devoid of fasta-formatted sequences" );
         }
         final Map<String, String> map = new HashMap<String, String>();
-        for( final Sequence seq : seqs ) {
+        for( final MolecularSequence seq : seqs ) {
             if ( ForesterUtil.isEmpty( seq.getIdentifier() ) ) {
                 ForesterUtil.fatalError( decorator.PRG_NAME, "fasta-file [" + mapping_infile
-                        + "] contains sequence with empty identifier" );
+                                         + "] contains sequence with empty identifier" );
             }
             if ( map.containsKey( seq.getIdentifier() ) ) {
                 ForesterUtil.fatalError( decorator.PRG_NAME, "sequence identifier [" + seq.getIdentifier()
-                        + "] is not unique" );
+                                         + "] is not unique" );
             }
             if ( seq.getLength() < 1 ) {
                 ForesterUtil.fatalError( decorator.PRG_NAME, "sequence [" + seq.getIdentifier() + "] is empty" );
@@ -450,11 +450,11 @@ public final class decorator {
         System.out.println();
         System.out.println( " -f=<c> : field to be replaced: " + NODE_NAME_FIELD + " : node name" );
         System.out.println( "                                " + SEQUENCE_ANNOTATION_DESC
-                + " : sequence annotation description" );
+                            + " : sequence annotation description" );
         System.out.println( "                                " + DS_FILED + " : domain structure" );
         System.out.println( "                                " + TAXONOMY_CODE_FIELD + " : taxonomy code" );
         System.out.println( "                                " + TAXONOMY_SCIENTIFIC_NAME_FIELD
-                + ": taxonomy scientific name" );
+                            + ": taxonomy scientific name" );
         System.out.println( "                                " + SEQUENCE_NAME_FIELD + " : sequence name" );
         System.out.println( "                                " + MOL_SEQ + " : molecular sequence" );
         System.out.println( " -k=<n> : key column in mapping table (0 based)," );
@@ -462,13 +462,13 @@ public final class decorator {
         System.out.println( " -v=<n> : value column in mapping table (0 based)," );
         System.out.println( "          data which with to decorate - default is 1" );
         System.out.println( " -" + EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION
-                + "    : to extract bracketed scientific names, e.g. [Nematostella vectensis]" );
+                            + "    : to extract bracketed scientific names, e.g. [Nematostella vectensis]" );
         System.out.println( " -" + EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION
-                + "    : to extract bracketed taxonomic codes, e.g. [NEMVE]" );
+                            + "    : to extract bracketed taxonomic codes, e.g. [NEMVE]" );
         System.out.println( " -s=<c> : column separator in mapping file, default is tab" );
         System.out.println( " -c     : cut name after first space (only for -f=n)" );
         System.out.println( " -" + decorator.TRIM_AFTER_TILDE_OPTION
-                + "     : trim node name to be replaced after tilde" );
+                            + "     : trim node name to be replaced after tilde" );
         System.out.println( " -" + decorator.MIDPOINT_ROOT_OPTION + "    : to midpoint-root the tree" );
         System.out.println( " -" + decorator.ORDER_TREE_OPTION + "    : to order tree branches" );
         System.out.println( " -" + decorator.VERBOSE_OPTION + "    : verbose" );