3 import jalview.datamodel.*;
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8 public abstract class AlignFile extends FileParse {
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21 public AlignFile(String inStr) {
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23 System.out.println("is this ever called??");
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26 }catch(Exception ex){}
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30 * Constructor which parses the data from a file of some specified type.
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31 * @param inFile Filename to read from.
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32 * @param type What type of file to read from (File, URL)
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34 public AlignFile(String inFile, String type) throws IOException {
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44 * Return the seqs Vector
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46 public Vector getSeqs() {
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51 * Return the Sequences in the seqs Vector as an array of Sequences
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53 public SequenceI [] getSeqsAsArray() {
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54 SequenceI [] s = new SequenceI[seqs.size()];
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55 for (int i=0;i < seqs.size();i++) {
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56 s[i] = (SequenceI)seqs.elementAt(i);
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63 * Initialise objects to store sequence data in.
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65 protected void initData() {
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66 seqs = new Vector();
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67 headers = new Vector();
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70 protected void setSeqs(SequenceI [] s) {
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71 seqs = new Vector();
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72 for (int i=0; i<s.length; i++) {
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73 seqs.addElement(s[i]);
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77 // Checks whether sequence is valid aa characters
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78 protected boolean isValidProteinSequence(String sequence)
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80 for (int i = 0; i < sequence.length(); i++)
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81 if (!jalview.schemes.ResidueProperties.aaHash.containsKey(String.valueOf(sequence.charAt(i))))
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89 * This method must be implemented to parse the contents of the file.
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91 public abstract void parse() throws IOException;
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95 * Print out in alignment file format the Sequences in the seqs Vector.
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97 public abstract String print();
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