/**
  * Prints out the XML representation of an AFPChain from a file containing exactly two FASTA
  * sequences.
  *
  * @param args A String array of fasta-file structure-1-name structure-2-name
  * @throws StructureException
  * @throws IOException
  */
 public static void main(String[] args) throws StructureException, IOException {
   if (args.length != 3) {
     System.err.println(
         "Usage: FastaAFPChainConverter fasta-file structure-1-name structure-2-name");
     return;
   }
   File fasta = new File(args[0]);
   Structure structure1 = StructureTools.getStructure(args[1]);
   Structure structure2 = StructureTools.getStructure(args[2]);
   if (structure1 == null)
     throw new IllegalArgumentException("No structure for " + args[1] + " was found");
   if (structure2 == null)
     throw new IllegalArgumentException("No structure for " + args[2] + " was found");
   AFPChain afpChain = fastaFileToAfpChain(fasta, structure1, structure2);
   String xml = AFPChainXMLConverter.toXML(afpChain);
   System.out.println(xml);
 }
示例#2
0
  public void testOldSecOutput() throws Exception {

    String fileName = "/ce_1fdo.A_2iv2.X.out";
    InputStream inStream = this.getClass().getResourceAsStream(fileName);
    assertNotNull("Could not find file " + fileName + " in resource path. Config error?", inStream);
    String xml = StringManipulationHelper.convertStreamToString(inStream);

    AtomCache cache = new AtomCache();
    String name1 = "1FDO.A";
    String name2 = "2IV2.X";
    Atom[] ca1 = cache.getAtoms(name1);
    Atom[] ca2 = cache.getAtoms(name2);

    assertEquals(715, ca1.length);
    assertEquals(697, ca2.length);

    AFPChain afpChainOrig = AFPChainXMLParser.fromXML(xml, ca1, ca2);

    assertNotNull("Could not get AfpChain object from flat file!", afpChainOrig);

    assertEquals(
        "Could not find alignment string for prot 1",
        "MKKVVTVCPYCASGCKINLVVDNGKIVRAEAAQGKTNQGTLCLKGYYGWDFINDTQILTPRLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGPDAIQTTGSSRGTGNETNYVMQKFARAVIGTNNVDCCARVUHGPSVA-----GLHQSVGNGAMSNAINEIDNTDLVFVFGYNPADSHPIVANHVINAKRNGAKIIVCDPRKIETARIADMHIALKNGSNIALLNAMGHVIIEENLYDKAFVASRTEGFEEYRKIVEGYTPESVEDITGVSASEIRQAARMYAQAKSAAILWGMGVTQFYQGVETVRSLTSLAMLTGNLGKPHAGVNPVRGQNNVQGACDMGALPDTYPGYQYVKDPANREKFAKAWGVESLPAHTGYRISELPHRAAHGEVRAAYIMGEDPLQTDAELSAVRKAFEDLELVIVQDIFMTKTASAADVILPSTSWGEHEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNTQEIWDELRHLCPDFYGATYEKMGELGFIQWPCRDTSDADQGTSYLFKEKFDTPNGLAQFFTCDWVAPIDKLTDEYPMVLSTVREVGHYSCRSMTGNCAALAALADEPGYAQINTEDAKRLGIEDEALVWVHSRKGKIITRAQVSDRPNKGAIYMTYQWWIGACNELVTENLSPITKTPEYKYCAVRVEPIADQRAAEQYVIDEYNKLKTRLREAALA",
        new String(afpChainOrig.getAlnseq1(), 0, afpChainOrig.getAlnLength()));
    assertEquals(
        "Could not find alignment string for prot 2",
        "MKKVVTVCPYCASGCKINLVVDNGKIVRAEAAQGKTNQGTLCLKGYYGWDFINDTQILTPRLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGPDAIQTTGSSRGTGNETNYVMQKFARAVIGTNNVDCCAR-----VUHGPSVAGLHQSVGNGAMSNAINEIDNTDLVFVFGYNPADSHPIVANHVINAKRNGAKIIVCDPRKIETARIADMHIALKNGSNIALLNAMGHVIIEENLYDKAFVASRTEGFEEYRKIVEGYTPESVEDITGVSASEIRQAARMYAQAKSAAILWGMGVTQFYQGVETVRSLTSLAMLTGNLGKPHAGVNPVRGQNNVQGACDMGALPDTYPGYQYVKDPANREKFAKAWGVESLPAHTGYRISELPHRAAHGEVRAAYIMGEDPLQTDAELSAVRKAFEDLELVIVQDIFMTKTASAADVILPSTSWGEHEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNTQEIWDELRHLCPDFYGATYEKMGELGFIQWPCRDTSDADQGTSYLFKEKFDTPNGLAQFFTCDWVAPIDKLTDEYPMVLSTVREVGHYSCRSMTGNCAALAALADEPGYAQINTEDAKRLGIEDEALVWVHSRKGKIITRAQVSDRPNKGAIYMTYQWW------------------PEYKYCAVRVEPIADQRAAEQYVIDEYNKLKTRLREAALA",
        new String(afpChainOrig.getAlnseq2(), 0, afpChainOrig.getAlnLength()));

    // calc time is hardware dependent.... overwrite...
    afpChainOrig.setCalculationTime(-1);

    assertEquals(
        "alnLength is wrong! (" + afpChainOrig.getAfpChainLen() + ")",
        720,
        afpChainOrig.getAlnLength());
    assertEquals(
        "gapLength is wrong! (" + afpChainOrig.getGapLen() + ")", 28, afpChainOrig.getGapLen());

    // identity should be 0.9569
    assertTrue(
        "alinment ID is < 0.95 ! (" + afpChainOrig.getIdentity() + ")",
        afpChainOrig.getIdentity() > 0.95);
    assertTrue(
        "alignment ID is > 0.96 ! (" + afpChainOrig.getIdentity() + ")",
        afpChainOrig.getIdentity() < 0.96);

    String xmlComp = AFPChainXMLConverter.toXML(afpChainOrig, ca1, ca2);

    FlipAFPChainTest t = new FlipAFPChainTest();
    t.printFirstMismatch(xml, xmlComp);
    StringManipulationTestsHelper.assertEqualsIgnoreEndline(xml, xmlComp);
    StructureAlignment ce = StructureAlignmentFactory.getAlgorithm(CeMain.algorithmName);

    AFPChain afpChainNew = ce.align(ca1, ca2);
    afpChainNew.setCalculationTime(-1);
    afpChainNew.setName1(name1);
    afpChainNew.setName2(name2);

    String xmlNew = AFPChainXMLConverter.toXML(afpChainNew, ca1, ca2);

    StringManipulationTestsHelper.assertEqualsIgnoreEndline(xml, xmlNew);
  }