five-column, tab-delimited table of feature locations and qualifiers

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8731 ee4ac58c-ac51-4696-9907-e4b3aa274f04

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

+/* GenbankTblOutputStream.java
+ *
+ * created: 2008
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2008  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 javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+
+import uk.ac.sanger.artemis.Entry;
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.util.FileDocument;
+import uk.ac.sanger.artemis.util.StringVector;
+
+
+/**
+ *  Handle writing tbl format:
+ *  http://www.ncbi.nlm.nih.gov/Sequin/table.html
+ */
+public class GenbankTblOutputStream
+{
+  
+  /**
+   * Write out an entry as tbl format.
+   * @param entry
+   * @param f
+   */
+  public static void writeEntryAsTbl(final Entry entry, final JFrame f)
+  {
+    final JFileChooser chooser = new JFileChooser();
+    chooser.setMultiSelectionEnabled(false);
+    int returnVal = chooser.showSaveDialog(f);
+    if(returnVal == JFileChooser.CANCEL_OPTION)
+      return;
+
+    final File fileSave = chooser.getSelectedFile();
+    if(fileSave.exists())
+    {
+      returnVal = JOptionPane.showConfirmDialog(f, 
+                          "File exists. Overwrite?", 
+                          "File Exists",
+                          JOptionPane.YES_NO_OPTION);
+      if(returnVal == JOptionPane.CANCEL_OPTION ||
+         returnVal == JOptionPane.NO_OPTION)
+        return;
+    }
+    
+    final FileDocument fileDocument = new FileDocument(fileSave);
+    try
+    {
+      final Writer writer = fileDocument.getWriter();
+      writer.write(">Feature "+entry.getName()+"\n");
+      
+      final FeatureVector features = entry.getAllFeatures();
+      final EntryInformation entry_information = entry.getEntryInformation ();
+      
+      int count = 0;
+      for(int i=0; i<features.size(); i++)
+      {
+        final Feature feature = features.elementAt(i);
+        if(feature.getKey().getKeyString().equals("source"))
+          continue;
+        if(count > 0)
+          writer.write("\n");
+        
+        count++;
+        writeRanges(feature, writer);
+        writeQualifiers(feature, entry_information, writer);
+      }
+      writer.close();
+    }
+    catch(IOException e1)
+    {
+      JOptionPane.showMessageDialog(f, e1.getMessage());
+    }
+  }
+  
+  /**
+   * Write out ranges and feature key
+   * @param feature
+   * @param writer
+   * @throws IOException
+   */
+  private static void writeRanges(final Feature feature, final Writer writer) 
+          throws IOException
+  {
+    final RangeVector ranges = feature.getLocation().getRanges();
+    if(!feature.isForwardFeature() && ranges.size() > 1)
+      ranges.reverse();
+    
+    Range r = (Range)ranges.elementAt(0);
+    if(feature.isForwardFeature())
+      writer.write(r.getStart()+"\t"+r.getEnd());
+    else
+      writer.write(r.getEnd()+"\t"+r.getStart());
+    
+    writer.write("\t"+feature.getKey().getKeyString());
+    
+    for(int j=1; j<ranges.size(); j++)
+    {
+      writer.write("\n");
+      r = (Range)ranges.elementAt(j);
+      if(feature.isForwardFeature())
+        writer.write(r.getStart()+"\t"+r.getEnd());
+      else
+        writer.write(r.getEnd()+"\t"+r.getStart());
+    }
+  }
+  
+  /**
+   * Write out qualifiers
+   * @param feature
+   * @param entry_information
+   * @param writer
+   * @throws IOException 
+   */
+  private static void writeQualifiers(final Feature feature, 
+                                      final EntryInformation entry_information,
+                                      final Writer writer) throws IOException
+  {
+    QualifierVector qualifiers = feature.getQualifiers();
+    for(int j=0; j<qualifiers.size(); j++)
+    {
+      Qualifier current_qualifier = (Qualifier) qualifiers.elementAt(j);
+
+      final QualifierInfo qualifier_info =
+        entry_information.getQualifierInfo (current_qualifier.getName ());
+
+      // this will contain one String for each /name=value pair
+      final StringVector qualifier_strings =
+        StreamQualifier.toStringVector (qualifier_info, current_qualifier);
+      
+      for(int k=0; k<qualifier_strings.size(); k++)
+      {
+        String qualifierStr = (String)qualifier_strings.get(k);
+        int index = qualifierStr.indexOf("=");
+        if(index < 1)
+          continue;
+        qualifierStr = qualifierStr.substring(index+1);
+        if(qualifierStr.startsWith("\""))
+          qualifierStr = qualifierStr.substring(1);
+        if(qualifierStr.endsWith("\""))
+          qualifierStr = qualifierStr.substring(0, qualifierStr.length()-1);
+        writer.write("\n\t\t\t"+current_qualifier.getName()+"\t"+
+            qualifierStr);
+      }
+    }
+  }
+}
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