3 import jalview.datamodel.*;
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4 import java.util.Vector;
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5 public class FormatAdapter
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8 public static Vector formats = new Vector();
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10 formats.addElement("FASTA");
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11 formats.addElement("MSF");
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12 formats.addElement("CLUSTAL");
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13 formats.addElement("BLC");
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14 formats.addElement("PIR");
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15 formats.addElement("PFAM");
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18 public static SequenceI[] readFile(String inFile, String type, String format)
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23 AlignFile afile = null;
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24 if (format.equals("FASTA"))
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25 afile = new FastaFile(inFile, type);
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26 else if (format.equals("MSF"))
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27 afile = new MSFfile(inFile, type);
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28 else if (format.equals("CLUSTAL"))
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29 afile = new ClustalFile(inFile, type);
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30 else if (format.equals("BLC"))
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31 afile = new BLCFile(inFile, type);
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32 else if (format.equals("PIR"))
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33 afile = new PIRFile(inFile, type);
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34 else if (format.equals("PFAM"))
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35 afile = new PfamFile(inFile, type);
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37 return afile.getSeqsAsArray();
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39 catch (Exception e) {
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40 System.err.println("Failed to read alignment using the '"+format+"' reader.");
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41 e.printStackTrace();
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48 public static String formatSequences(String format, Vector seqs)
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50 SequenceI [] s = new SequenceI[seqs.size()];
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52 for (int i = 0; i < seqs.size(); i++)
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53 s[i] = (SequenceI) seqs.elementAt(i);
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57 AlignFile afile = null;
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58 if (format.equals("FASTA"))
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59 afile = new FastaFile();
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60 else if (format.equals("MSF"))
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61 afile = new MSFfile();
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62 else if (format.equals("CLUSTAL"))
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63 afile = new ClustalFile();
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64 else if (format.equals("BLC"))
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65 afile = new BLCFile();
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66 else if (format.equals("PIR"))
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67 afile = new PIRFile();
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68 else if (format.equals("PFAM"))
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69 afile = new PfamFile();
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72 return afile.print();
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74 catch (Exception e) {
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75 System.err.println("Failed to write alignment as a '"+format+"' file\n");
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76 e.printStackTrace();
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