/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/
package jalview.io;

import jalview.datamodel.*;

import jalview.gui.*;

import jalview.io.*;

import java.io.*;

import java.util.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class SequenceFeatureFetcher implements Runnable
{
    AlignmentI align;
    AlignmentPanel ap;
    ArrayList unknownSequences;
    CutAndPasteTransfer output = new CutAndPasteTransfer();
    StringBuffer sbuffer = new StringBuffer();

    /**
     * Creates a new SequenceFeatureFetcher object.
     *
     * @param align DOCUMENT ME!
     * @param ap DOCUMENT ME!
     */
    public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)
    {
        unknownSequences = new ArrayList();
        this.align = align;
        this.ap = ap;

        Thread thread = new Thread(this);
        thread.start();
    }

    /**
     * DOCUMENT ME!
     */
    public void run()
    {
        RandomAccessFile out = null;

        try
        {
            String cache = System.getProperty("user.home") +
                "/.jalview.uniprot.xml";

            File test = new File(cache);

            if (!test.exists())
            {
                out = new RandomAccessFile(cache, "rw");
                out.writeBytes("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
                out.writeBytes("<UNIPROT_CACHE>\n");
            }
            else
            {
                out = new RandomAccessFile(cache, "rw");

                // open exisiting cache and remove </UNIPROT_CACHE> from the end
                long lastLine = 0;
                String data;

                while ((data = out.readLine()) != null)
                {
                    if (data.indexOf("</entry>") > -1)
                    {
                        lastLine = out.getFilePointer();
                    }
                }

                out.seek(lastLine);
            }

            int seqIndex = 0;
            Vector sequences = align.getSequences();

            while (seqIndex < sequences.size())
            {
                ArrayList ids = new ArrayList();

                for (int i = 0; (seqIndex < sequences.size()) && (i < 50);
                        seqIndex++, i++)
                {
                    SequenceI sequence = (SequenceI) sequences.get(seqIndex);
                    ids.add(sequence.getName());
                }

                tryLocalCacheFirst(ids, align);

                if (ids.size() > 0)
                {
                    StringBuffer remainingIds = new StringBuffer("uniprot:");

                    for (int i = 0; i < ids.size(); i++)
                        remainingIds.append(ids.get(i) + ";");

                    EBIFetchClient ebi = new EBIFetchClient();
                    String[] result = ebi.fetchData(remainingIds.toString(),
                            "xml", null);

                    if (result != null)
                    {
                        ReadUniprotFile(result, out, align);
                    }
                }
            }

            if (out != null)
            {
                out.writeBytes("</UNIPROT_CACHE>\n");
                out.close();
            }
        }
        catch (Exception ex)
        {
            ex.printStackTrace();
        }

        findMissingIds(align);

        if (sbuffer.length() > 0)
        {
            output.setText(
                "Your sequences have been matched to Uniprot. Some of the ids have been\n" +
                "altered, most likely the start/end residue will have been updated.\n" +
                "Save your alignment to maintain the updated id.\n\n" +
                sbuffer.toString());
            Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
        }

        if (unknownSequences.size() > 0)
        {
            //ignore for now!!!!!!!!!!
            //  WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);
        }

        jalview.gui.PaintRefresher.Refresh(null, align);
    }

    /**
     * DOCUMENT ME!
     *
     * @param result DOCUMENT ME!
     * @param out DOCUMENT ME!
     * @param align DOCUMENT ME!
     */
    void ReadUniprotFile(String[] result, RandomAccessFile out, AlignmentI align)
    {
        SequenceI sequence = null;
        Vector features = null;
        String type;
        String description;
        String status;
        String start;
        String end;
        String pdb = null;

        for (int r = 0; r < result.length; r++)
        {
            if ((sequence == null) && (result[r].indexOf("<name>") > -1))
            {
                long filePointer = 0;

                if (out != null)
                {
                    try
                    {
                        filePointer = out.getFilePointer();
                        out.writeBytes("<entry>\n");
                    }
                    catch (Exception ex)
                    {
                    }
                }

                String seqName = parseElement(result[r], "<name>", out);
                sequence = align.findName(seqName);

                if (sequence == null)
                {
                    sequence = align.findName(seqName.substring(0,
                                seqName.indexOf('_')));

                    if (sequence != null)
                    {
                        sbuffer.append("changing " + sequence.getName() +
                            " to " + seqName + "\n");
                        sequence.setName(seqName);
                    }
                }

                if (sequence == null)
                {
                    sbuffer.append("UNIPROT updated suggestion is " +
                        result[r] + "\n");
                    sequence = align.findName(result[r]);

                    // this entry has been suggested by ebi.
                    // doesn't match id in alignment file
                    try
                    {
                        out.setLength(filePointer);
                    }
                    catch (Exception ex)
                    {
                    }

                    // now skip to next entry
                    while (result[r].indexOf("</entry>") == -1)
                        r++;
                }

                features = new Vector();
                type = "";
                start = "0";
                end = "0";
                description = "";
                status = "";
                pdb = "";
            }

            if (sequence == null)
            {
                continue;
            }

            if (result[r].indexOf("<property type=\"pdb accession\"") > -1)
            {
                pdb = parseValue(result[r], "value=", out);
                sequence.setPDBId(pdb);
            }

            if (result[r].indexOf("feature type") > -1)
            {
                type = parseValue(result[r], "type=", out);
                description = parseValue(result[r], "description=", null);
                status = parseValue(result[r], "status=", null);

                while (result[r].indexOf("position") == -1)
                {
                    r++; //<location>
                }

                // r++;
                if (result[r].indexOf("begin") > -1)
                {
                    start = parseValue(result[r], "position=", out);
                    end = parseValue(result[++r], "position=", out);
                }
                else
                {
                    start = parseValue(result[r], "position=", out);
                    end = parseValue(result[r], "position=", null);
                }

                int sstart = Integer.parseInt(start);
                int eend = Integer.parseInt(end);

                if (out != null)
                {
                    try
                    {
                        out.writeBytes("</feature>\n");
                    }
                    catch (Exception ex)
                    {
                    }
                }

                SequenceFeature sf = new SequenceFeature(type, sstart, eend,
                        description, status);
                features.add(sf);
            }

            if (result[r].indexOf("<sequence") > -1)
            {
                StringBuffer seqString = new StringBuffer();

                if (out != null)
                {
                    try
                    {
                        out.writeBytes(result[r] + "\n");
                    }
                    catch (Exception ex)
                    {
                    }
                }

                while (result[++r].indexOf("</sequence>") == -1)
                {
                    seqString.append(result[r]);

                    if (out != null)
                    {
                        try
                        {
                            out.writeBytes(result[r] + "\n");
                        }
                        catch (Exception ex)
                        {
                        }
                    }
                }

                if (out != null)
                {
                    try
                    {
                        out.writeBytes(result[r] + "\n");
                    }
                    catch (Exception ex)
                    {
                    }
                }

                StringBuffer nonGapped = new StringBuffer();

                for (int i = 0; i < sequence.getSequence().length(); i++)
                {
                    if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))
                    {
                        nonGapped.append(sequence.getCharAt(i));
                    }
                }

                int absStart = seqString.toString().indexOf(nonGapped.toString());

                if (absStart == -1)
                {
                    unknownSequences.add(sequence.getName());
                    features = null;
                    sbuffer.append(sequence.getName() +
                        " SEQUENCE NOT %100 MATCH \n");

                    continue;
                }

                int absEnd = absStart + nonGapped.toString().length();
                absStart += 1;

                if ((absStart != sequence.getStart()) ||
                        (absEnd != sequence.getEnd()))
                {
                    sbuffer.append("Updated: " + sequence.getName() + " " +
                        sequence.getStart() + "/" + sequence.getEnd() +
                        "  to  " + absStart + "/" + absEnd + "\n");
                }

                sequence.setStart(absStart);
                sequence.setEnd(absEnd);
            }

            if (result[r].indexOf("</entry>") > -1)
            {
                if (features != null)
                {
                    sequence.setSequenceFeatures(features);
                }

                features = null;
                sequence = null;

                if (out != null)
                {
                    try
                    {
                        out.writeBytes("</entry>\n");
                    }
                    catch (Exception ex)
                    {
                    }
                }
            }
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param align DOCUMENT ME!
     */
    void findMissingIds(AlignmentI align)
    {
        String data;
        ArrayList cachedIds = new ArrayList();

        try
        {
            BufferedReader in = new BufferedReader(new FileReader(
                        jalview.bin.Cache.getProperty("UNIPROT_CACHE")));

            while ((data = in.readLine()) != null)
            {
                if (data.indexOf("name") > -1)
                {
                    String name = parseElement(data, "<name>", null);
                    cachedIds.add(name);
                }
            }
        }
        catch (Exception ex)
        {
            ex.printStackTrace();
        }

        for (int i = 0; i < align.getHeight(); i++)
            if (!cachedIds.contains(align.getSequenceAt(i).getName()))
            {
                unknownSequences.add(align.getSequenceAt(i).getName());
            }
    }

    /**
     * DOCUMENT ME!
     *
     * @param ids DOCUMENT ME!
     * @param align DOCUMENT ME!
     */
    void tryLocalCacheFirst(ArrayList ids, AlignmentI align)
    {
        ArrayList cacheData = new ArrayList();

        try
        {
            BufferedReader in = new BufferedReader(new FileReader(
                        jalview.bin.Cache.getProperty("UNIPROT_CACHE")));

            // read through cache file, if the cache has sequences we're looking for
            // add the lines to a new String array, Readthis new array and
            // make sure we remove the ids from the list to retrieve from EBI
            String data;

            while ((data = in.readLine()) != null)
            {
                if (data.indexOf("name") > -1)
                {
                    String name = parseElement(data, "<name>", null);

                    if (ids.contains(name))
                    {
                        cacheData.add("<entry>");
                        cacheData.add(data);

                        while (data.indexOf("</entry>") == -1)
                        {
                            data = in.readLine();
                            cacheData.add(data);
                        }

                        cacheData.add(data);

                        ids.remove(name);
                    }
                }
            }
        }
        catch (Exception ex)
        {
            ex.printStackTrace();
        }

        String[] localData = new String[cacheData.size()];
        cacheData.toArray(localData);

        if ((localData != null) && (localData.length > 0))
        {
            ReadUniprotFile(localData, null, align);
        }
    }

    /**
     * DOCUMENT ME!
     *
     * @param line DOCUMENT ME!
     * @param tag DOCUMENT ME!
     * @param out DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    String parseValue(String line, String tag, RandomAccessFile out)
    {
        if (out != null)
        {
            try
            {
                out.writeBytes(line + "\n");
            }
            catch (Exception ex)
            {
            }
        }

        int index = line.indexOf(tag) + tag.length() + 1;

        if (index == tag.length())
        {
            return "";
        }

        return line.substring(index, line.indexOf("\"", index + 1));
    }

    /**
     * DOCUMENT ME!
     *
     * @param line DOCUMENT ME!
     * @param tag DOCUMENT ME!
     * @param out DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    String parseElement(String line, String tag, RandomAccessFile out)
    {
        if (out != null)
        {
            try
            {
                out.writeBytes(line + "\n");
            }
            catch (Exception ex)
            {
            }
        }

        int index = line.indexOf(tag) + tag.length();

        return line.substring(index, line.indexOf("</"));
    }
}