handle indexed fasta

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14748 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/io/IndexFastaStream.java

+/* 
+ * created: 2010
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2010  Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.io;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.Writer;
+import java.util.Iterator;
+
+import net.sf.picard.reference.FastaSequenceIndex;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.picard.reference.ReferenceSequence;
+
+import uk.ac.sanger.artemis.util.FileDocument;
+
+public class IndexFastaStream extends StreamSequence 
+{
+  private IndexedFastaSequenceFile indexSeqFile;
+  private FastaSequenceIndex fastaIndex;
+  private int len;
+  private String contig;
+  
+  public IndexFastaStream(Entry entry)
+  {
+    File fasta = ((FileDocument)((DocumentEntry)entry).getDocument()).getFile();
+    File fastaIndexFile = new File(fasta.getParentFile().getAbsolutePath(), fasta.getName()+".fai");
+    fastaIndex = new FastaSequenceIndex(fastaIndexFile);
+
+    indexSeqFile = new IndexedFastaSequenceFile(fasta, fastaIndex);
+    setContigByIndex(0);
+  }
+  
+  /**
+   * Test if the entry contains an indexed sequence
+   * @param entry
+   * @return
+   */
+  public static boolean isIndexed(Entry entry)
+  {
+    if( entry instanceof DocumentEntry && 
+        ((DocumentEntry)entry).getDocument() instanceof FileDocument)
+    {
+      File fasta = ((FileDocument)((DocumentEntry)entry).getDocument()).getFile();
+      File fastaIndexFile = new File(fasta.getParentFile().getAbsolutePath(), fasta.getName()+".fai");
+      if(fastaIndexFile.exists())
+        return true;
+    }
+    return false;
+  }
+  
+  public void setContigByIndex(int seqIndex) 
+  {
+    /*ReferenceSequence ref = getReferenceSequence(seqIndex);
+    len = ref.length();
+    contig = ref.getName();*/
+    
+    len = getLengthByIndex(seqIndex);
+    contig = getContigByIndex(seqIndex);
+  }
+
+  /**
+   *  Return a the given range of bases as a String.  Returns an empty
+   *  sequence if the end position is less than the start position.
+   *  @param start The start base of the range.
+   *  @param end The end base of the range.
+   **/
+  public String getSubSequence(int start, int end) 
+  {
+    return new String(indexSeqFile.getSubsequenceAt(contig, start, end).getBases()).toLowerCase();
+  }
+  
+  public char[] getCharSubSequence(int start, int end) 
+  {
+    return getSubSequence(start, end).toCharArray();
+  }
+  
+  private int getLengthByIndex(int seqIndex)
+  {
+    Iterator it = fastaIndex.iterator();
+    int i = 0;
+    while(it.hasNext())
+    {
+      Object obj = it.next();
+      if(i == seqIndex)
+      {
+        String size = obj.toString().split(";")[2].substring(5).trim();
+        return Integer.parseInt(size);
+      }
+      i++;
+    }
+    return -1;
+  }
+  
+  private String getContigByIndex(int seqIndex)
+  {
+    Iterator it = fastaIndex.iterator();
+    int i = 0;
+    while(it.hasNext())
+    {
+      Object obj = it.next();
+      if(i == seqIndex)
+        return obj.toString().split(";")[0].substring(6).trim();
+      i++;
+    }
+    return null;
+  }
+  
+  public ReferenceSequence getReferenceSequence(int seqIndex)
+  {
+    int i = 0;
+    ReferenceSequence ref;
+    indexSeqFile.reset();
+    while( (ref=indexSeqFile.nextSequence()) != null ) 
+    {  
+      if(i == seqIndex)
+        return ref;
+       i++;
+    }
+    return null;
+  }
+  
+
+  /**
+   *  Returns the length of the sequence in bases.
+   **/
+  public int length() 
+  {
+    return len;
+  }
+  
+  @Override
+  public StreamSequence copy()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public int getFormatType()
+  {
+    return StreamSequenceFactory.INDEXED_FASTA_FORMAT;
+  }
+
+  @Override
+  public void writeToStream(Writer writer) throws IOException
+  {
+    // TODO Auto-generated method stub
+  }
+  
+  public IndexedFastaSequenceFile getIndexSeqFile()
+  {
+    return indexSeqFile;
+  }
+  
+  public FastaSequenceIndex getFastaIndex()
+  {
+    return fastaIndex;
+  }
+}
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