JAL-653 JAL-1968 FeaturesFile now handles Jalview or GFF2 or GFF3

[jalview.git] / src / jalview / io / Gff3File.java

diff --git a/src/jalview/io/Gff3File.java b/src/jalview/io/Gff3File.java
deleted file mode 100644 (file)
index 248fa09..0000000
--- a/src/jalview/io/Gff3File.java
+++ /dev/null
@@ -1,174 +0,0 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- * 
- * This file is part of Jalview.
- * 
- * Jalview 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 3
- * of the License, or (at your option) any later version.
- *  
- * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.io;
-
-import jalview.api.AlignViewportI;
-import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-
-import java.io.IOException;
-import java.util.List;
-
-/**
- * A GFF3 File parsing wrapper for the tangled mess that is FeaturesFile.
- * 
- * This class implements the methods relied on by FileLoader/FormatAdapter in
- * order to allow them to load alignments directly from GFF2 and GFF3 files that
- * contain sequence data and alignment information.
- * 
- * Major issues:
- * 
- * 1. GFF3 files commonly include mappings between DNA, RNA and Protein - so
- * this class needs a dataset AlignmentI context to create alignment codon
- * mappings.
- * 
- * 2. A single GFF3 file can generate many distinct alignments. Support will be
- * needed to allow several AlignmentI instances to be generated from a single
- * file.
- * 
- * 
- * @author jprocter
- *
- */
-public class Gff3File extends FeaturesFile
-{
-
-  /**
-   * 
-   */
-  public Gff3File()
-  {
-    super();
-  }
-
-  /**
-   * @param source
-   * @throws IOException
-   */
-  public Gff3File(FileParse source) throws IOException
-  {
-    super(source);
-  }
-
-  /**
-   * @param inFile
-   * @param type
-   * @throws IOException
-   */
-  public Gff3File(String inFile, String type) throws IOException
-  {
-    super(inFile, type);
-  }
-
-  /**
-   * @param parseImmediately
-   * @param source
-   * @throws IOException
-   */
-  public Gff3File(boolean parseImmediately, FileParse source)
-          throws IOException
-  {
-    super(parseImmediately, source);
-  }
-
-  /**
-   * @param parseImmediately
-   * @param inFile
-   * @param type
-   * @throws IOException
-   */
-  public Gff3File(boolean parseImmediately, String inFile, String type)
-          throws IOException
-  {
-    super(parseImmediately, inFile, type);
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.io.FeaturesFile#print()
-   */
-  @Override
-  public String print()
-  {
-    // TODO GFF3 writer with sensible defaults for writing alignment data
-
-    // return super.printGFFFormat(seqs, visible);
-    return ("Not yet implemented.");
-  }
-
-  AlignmentI dataset;
-
-  List<AlignmentI> alignments;
-
-  @Override
-  public void parse()
-  {
-    AlignViewportI av = getViewport();
-    if (av != null)
-    {
-      if (av.getAlignment() != null)
-      {
-        dataset = av.getAlignment().getDataset();
-      }
-      if (dataset == null)
-      {
-        // working in the applet context ?
-        dataset = av.getAlignment();
-      }
-    }
-    else
-    {
-      dataset = new Alignment(new SequenceI[] {});
-    }
-
-    boolean parseResult = parse(dataset, null, null, false, true);
-    if (!parseResult)
-    {
-      // pass error up somehow
-    }
-    if (av != null)
-    {
-      // update viewport with the dataset data ?
-    }
-    else
-    {
-      setSeqs(dataset.getSequencesArray());
-    }
-
-  }
-
-  @Override
-  public void addProperties(AlignmentI al)
-  {
-    super.addProperties(al);
-    if (dataset.getCodonFrames() != null)
-    {
-      AlignmentI ds = (al.getDataset() == null) ? al : al.getDataset();
-      for (AlignedCodonFrame codons : dataset.getCodonFrames())
-      {
-        ds.addCodonFrame(codons);
-      }
-    }
-  }
-}