in progress

[jalview.git] / forester / java / src / org / forester / msa / BasicMsa.java

diff --git a/forester/java/src/org/forester/msa/BasicMsa.java b/forester/java/src/org/forester/msa/BasicMsa.java
index 1fdef10..7d90c3c 100644 (file)
--- a/forester/java/src/org/forester/msa/BasicMsa.java
+++ b/forester/java/src/org/forester/msa/BasicMsa.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.msa;
 
@@ -32,6 +32,8 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
+import org.forester.io.writers.SequenceWriter;
+import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
 import org.forester.sequence.BasicSequence;
 import org.forester.sequence.Sequence;
 import org.forester.sequence.Sequence.TYPE;
@@ -69,8 +71,8 @@ public class BasicMsa implements Msa {
 
     private int determineMaxIdLength() {
         int max = 0;
-        for( int row = 0; row < _data.length; ++row ) {
-            final int l = _identifiers[ row ].toString().length();
+        for( int row = 0; row < getNumberOfSequences(); ++row ) {
+            final int l = getIdentifier(row).length();
             if ( l > max ) {
                 max = l;
             }
@@ -110,17 +112,22 @@ public class BasicMsa implements Msa {
 
     @Override
     public Sequence getSequence( final int row ) {
-        return new BasicSequence( getIdentifier( row ), _data[ row ], getType() );
+        return new BasicSequence( getIdentifier( row ),  getSequenceAsArray( row ), getType() );
     }
 
     @Override
     public StringBuffer getSequenceAsString( final int row ) {
-        final StringBuffer sb = new StringBuffer( _data[ 0 ].length );
-        for( int col = 0; col < _data[ 0 ].length; ++col ) {
+        final StringBuffer sb = new StringBuffer(getLength() );
+        for( int col = 0; col < getLength(); ++col ) {
             sb.append( getResidueAt( row, col ) );
         }
         return sb;
     }
+    
+    @Override
+    public char[] getSequenceAsArray( final int row ) {
+        return  _data[ row ];
+    }
 
     @Override
     public TYPE getType() {
@@ -141,9 +148,9 @@ public class BasicMsa implements Msa {
     public String toString() {
         final int max = determineMaxIdLength() + 1;
         final StringBuffer sb = new StringBuffer();
-        for( int row = 0; row < _data.length; ++row ) {
-            sb.append( ForesterUtil.pad( _identifiers[ row ].toString(), max, ' ', false ) );
-            for( int col = 0; col < _data[ 0 ].length; ++col ) {
+        for( int row = 0; row < getNumberOfSequences(); ++row ) {
+            sb.append( ForesterUtil.pad( getIdentifier( row ).toString(), max, ' ', false ) );
+            for( int col = 0; col < getLength(); ++col ) {
                 sb.append( getResidueAt( row, col ) );
             }
             sb.append( ForesterUtil.LINE_SEPARATOR );
@@ -152,11 +159,28 @@ public class BasicMsa implements Msa {
     }
 
     @Override
-    public void write( final Writer w ) throws IOException {
+    public void write( final Writer w, final MSA_FORMAT format ) throws IOException {
+        switch ( format ) {
+            case PHYLIP:
+                writeToPhylip( w );
+                break;
+            case FASTA:
+                writeToFasta( w );
+                break;
+            default:
+                throw new RuntimeException( "unknown format " + format );
+        }
+    }
+
+    private void writeToFasta( final Writer w ) throws IOException {
+        SequenceWriter.writeSeqs( asSequenceList(), w, SEQ_FORMAT.FASTA, 100 );
+    }
+
+    private void writeToPhylip( final Writer w ) throws IOException {
         final int max = determineMaxIdLength() + 1;
-        for( int row = 0; row < _data.length; ++row ) {
-            w.write( ForesterUtil.pad( _identifiers[ row ].toString(), max, ' ', false ).toString() );
-            for( int col = 0; col < _data[ 0 ].length; ++col ) {
+        for( int row = 0; row < getNumberOfSequences(); ++row ) {
+            w.write( ForesterUtil.pad( getIdentifier( row ), max, ' ', false ).toString() );
+            for( int col = 0; col < getLength(); ++col ) {
                 w.write( getResidueAt( row, col ) );
             }
             w.write( ForesterUtil.LINE_SEPARATOR );
@@ -172,11 +196,27 @@ public class BasicMsa implements Msa {
         final BasicMsa msa = new BasicMsa( seqs.size(), length, seqs.get( 0 ).getType() );
         for( int row = 0; row < seqs.size(); ++row ) {
             final Sequence seq = seqs.get( row );
+            //
+            //            int x = length - seq.getLength();
+            //            if ( x > 0 ) {
+            //                String a = "";
+            //                for( int i = 0; i < x; i++ ) {
+            //                    a += "-";
+            //                }
+            //                seq = BasicSequence.createAaSequence( seq.getIdentifier(), seq.getMolecularSequenceAsString() + a );
+            //            }
+            //            else {
+            //                seq = BasicSequence.createAaSequence( seq.getIdentifier(), seq.getMolecularSequenceAsString()
+            //                        .substring( 0, length ) );
+            //            }
+            //
             if ( seq.getLength() != length ) {
-                throw new IllegalArgumentException( "illegal attempt to build msa from sequences of unequal length" );
+                throw new IllegalArgumentException( "illegal attempt to build msa from sequences of unequal length ["
+                        + seq.getIdentifier() + "]" );
             }
             if ( seq.getType() != msa.getType() ) {
-                throw new IllegalArgumentException( "illegal attempt to build msa from sequences of different type" );
+                throw new IllegalArgumentException( "illegal attempt to build msa from sequences of different type ["
+                        + seq.getIdentifier() + "]" );
             }
             if ( ids.contains( seq.getIdentifier() ) ) {
                 throw new IllegalArgumentException( "illegal attempt to create msa with non-unique identifiers ["
@@ -199,4 +239,9 @@ public class BasicMsa implements Msa {
         }
         return column;
     }
+
+    @Override
+    public boolean isGapAt( final int row, final int col ) {
+        return getResidueAt( row, col ) == Sequence.GAP;
+    }
 }