/**
* 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);
}
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);
}