From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 31 Mar 2015 02:24:34 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ee0d693a8a5a3e3fee98642886800ec3132773ce;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/application/table2fasta.java b/forester/java/src/org/forester/application/table2fasta.java
index 3735d2e..18b47f0 100644
--- a/forester/java/src/org/forester/application/table2fasta.java
+++ b/forester/java/src/org/forester/application/table2fasta.java
@@ -66,14 +66,21 @@ public final class table2fasta {
         final int position = Integer.parseInt( cla.getName( 0 ) );
         final File intable = cla.getFile( 1 );
         final File outfile = cla.getFile( 2 );
+        if ( outfile.exists() ) {
+            ForesterUtil.fatalError( PRG_NAME, outfile + " already exists" );
+        }
+        if ( !intable.exists() ) {
+            ForesterUtil.fatalError( PRG_NAME, intable + " does not exist" );
+        }
         BasicTable<String> t = null;
         try {
             t = BasicTableParser.parse( intable, '\t' );
         }
         catch ( final IOException e ) {
-            e.printStackTrace();
+            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
         }
         final List<MolecularSequence> seqs = new ArrayList<MolecularSequence>();
+        System.out.println( "Number of rows: " + t.getNumberOfRows() );
         for( int r = 0; r < t.getNumberOfRows(); ++r ) {
             String seq = null;
             final StringBuilder id = new StringBuilder();
@@ -81,19 +88,40 @@ public final class table2fasta {
                 if ( c == position ) {
                     seq = t.getValue( c, r );
                 }
-                else {
+                else if ( ( c == 0 ) || ( c == 1 ) ) {
                     id.append( t.getValue( c, r ) );
                     id.append( " " );
                 }
             }
-            final MolecularSequence s = BasicSequence.createDnaSequence( id.toString().trim(), seq );
-            seqs.add( s );
+            if ( id.length() < 2 ) {
+                ForesterUtil.fatalError( PRG_NAME, "row " + r + " id is empty" );
+            }
+            String id_str = id.toString().trim();
+            if ( id_str.startsWith( ">" ) ) {
+                id_str = id_str.substring( 1 );
+            }
+            if ( ForesterUtil.isEmpty( seq ) ) {
+                seq = t.getValue( position - 1, r );
+                if ( ForesterUtil.isEmpty( seq ) ) {
+                    ForesterUtil.fatalError( PRG_NAME, "row " + r + " seq is empty" );
+                }
+            }
+            MolecularSequence s = null;
+            try {
+                s = BasicSequence.createAaSequence( id_str, seq );
+            }
+            catch ( final Exception e ) {
+                ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+            }
+            if ( s != null ) {
+                seqs.add( s );
+            }
         }
         try {
-            SequenceWriter.writeSeqs( seqs, outfile, SEQ_FORMAT.FASTA, 6 );
+            SequenceWriter.writeSeqs( seqs, outfile, SEQ_FORMAT.FASTA, 60 );
         }
         catch ( final IOException e ) {
-            e.printStackTrace();
+            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
         }
     }
 
diff --git a/forester/java/src/org/forester/sequence/BasicSequence.java b/forester/java/src/org/forester/sequence/BasicSequence.java
index 42861fb..6d339ca 100644
--- a/forester/java/src/org/forester/sequence/BasicSequence.java
+++ b/forester/java/src/org/forester/sequence/BasicSequence.java
@@ -39,15 +39,19 @@ public class BasicSequence implements MolecularSequence {
      *
      */
     public BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
+        check( identifier, mol_sequence );
+        _mol_sequence = mol_sequence.toCharArray();
+        _identifier = identifier;
+        _type = type;
+    }
+
+    private static final void check( final String identifier, final String mol_sequence ) {
         if ( ForesterUtil.isEmpty( identifier ) ) {
             throw new IllegalArgumentException( "identifier of sequence cannot be empty" );
         }
         if ( ForesterUtil.isEmpty( mol_sequence ) ) {
             throw new IllegalArgumentException( "molecular sequence cannot be empty" );
         }
-        _mol_sequence = mol_sequence.toCharArray();
-        _identifier = identifier;
-        _type = type;
     }
 
     /**
@@ -144,16 +148,19 @@ public class BasicSequence implements MolecularSequence {
     }
 
     public static MolecularSequence createAaSequence( final String identifier, final String mol_sequence ) {
+        check( identifier, mol_sequence );
         return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
                                   .replaceAll( AA_REGEXP, Character.toString( UNSPECIFIED_AA ) ), TYPE.AA );
     }
 
     public static MolecularSequence createDnaSequence( final String identifier, final String mol_sequence ) {
+        check( identifier, mol_sequence );
         return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
                                   .replaceAll( DNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.DNA );
     }
 
     public static MolecularSequence createRnaSequence( final String identifier, final String mol_sequence ) {
+        check( identifier, mol_sequence );
         return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
                                   .replaceAll( RNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.RNA );
     }