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Copy pathAFPFromFasta.java
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66 lines (61 loc) · 4.59 KB
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/**
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on 2013-05-28
* Created by Douglas Myers-Turnbull
*
* @since 3.0.6
*/
package demo;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.model.AfpChainWriter;
import org.biojava.nbio.structure.align.util.AFPChainScorer;
import org.biojava.nbio.structure.align.xml.AFPChainXMLConverter;
import org.biojava.nbio.structure.io.FastaAFPChainConverter;
import org.biojava.nbio.structure.io.FastaStructureParser;
import java.io.IOException;
/**
* Demo displaying a structural alignment from a FASTA file using {@link FastaAFPChainConverter}.
* See {@link DemoAlignmentFromFasta} Also demonstrates the display of {@link StructureAlignment StructureAlignments} from FASTA sequences, but does so using the more general
* {@link FastaStructureParser}
* @author dmyerstu
*/
public class AFPFromFasta {
public static void main(String[] args) throws Exception {
Structure structure1 = StructureTools.getStructure("1w0p");
Structure structure2 = StructureTools.getStructure("1w0p");
String first = "alfdynatgdtefdspakqgwmqdntnngsgvltnadgmpawlvqgiggraqwtyslstnqhaqassfgwrmttemkvlsggmitnyyangtqrvlpiisldssgnlvvefegqtgrtvlatgtaateyhkfelvflpgsnpsasfyfdgklirdniqptaskQNMIVWGNGSSntdgvaayrdikfei------------------------------------------------------------------------------------------------------------------QGDVIf------------RGPDRIPSIVASsvTPGVVTAFAEKRVGGgdpgalsntNDIITRTSRDGGITWDTELNLTEQinvsdeFDFSDPRPIYDPs---SNTVLVSYARWPtdaaqngdrikpwmpNGIFYSVYDVASgnWQAPIDVTdqvkersfqiagwggselyrrntslnsqqdwqsnakirivdgaanqiqvadgsrkyvvtlsidesgglvanlngvsapiilqsehakvhsfhdyelqysalnhtttlfvdgqqittwagevsqenniqfgnadaqidgrlhvqkivltqqghnlvefdafylaqqtpevekdleklgwtkiktgntmslygNASVNPGpgHGITLtrqqnisgsqNGRLIYPAIVLdrfFLNVMSIYSDDGgsnwq-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGSTLpipfrwksssileTLEPSEADMVELQN--GDLLLTARLDFNQivngvny--SPRQQFLSKDGGITWSLLEANNANvfsnistgTVDASITRFEqsdgSHFLLFTNPQGnpagTNgr------------QNLGLWFSFDEG--VTWKGPIQ--LVNGasaysdiyqldsenaivivetdnsnmrilrmpitllkqklt";
String second = "--------------------------------------------------------------------------------------------kirivdgaanqiqvadgsrkyvvtlsidesgglvanlngvsapiilqsehakvhsfhdyelqysalnhtttLFVDGQQITTWagevsqenniqfgnadaqidgrlhvqkivltqqghnlvefdafylaqqtpevekdleklgwtkiktgntmslygnasvnpgpghgitltrqqnisgsqngrliypaivldrfflnvmsiysddggsnwqTGSTLpipfrwksssileTLEPSEADMVEL--QNGDLLLTARLDFNQivngvny--SPRQQFLSKDGGITWSLLEANNANvfsnisTGTVDASITRFEqsdgSHFLLFTNPQGNpagtngr--------QNLGLWFSFDEG--VTWKGPIQlv---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NGASAYS--DIYQLd---------SENAIVIVETD---NSNMRILRMPITllkqkltalfdynatgdtefdspakqgwmqdntnngsgvltnadgmpawlvqgiggraqwtyslstnqhaqassfgwrmttemkvlsggmitnyyangtqrvlpiisldssgnlvvefegqtgrtvlatgtaateyhkfelvflpgsnpsasfyfdgklirdniqptaskqnmivwgngssntdgvaayrdikfeiQGDVIf------------RGPDRIPSIVASSVtpGVVTAFAEKRVGGgdpgalsntNDIITRTSRDGGITWDTELNLTEQinvsdefdFSDPRPIYDPs---SNTVLVSYARW----PTdaaqngdrikpwmpNGIFYSVYDVASgnWQAPIDVTdqVKERsfqiagwggselyrrntslnsqqdwqsna------------";
AFPChain afpChain = FastaAFPChainConverter.cpFastaToAfpChain(first, second, structure1, -393);
Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
Atom[] ca2 = StructureTools.getAtomCAArray(structure2);
String xml = AFPChainXMLConverter.toXML(afpChain);
System.out.println(xml);
double tmScore = AFPChainScorer.getTMScore(afpChain, ca1, ca2);
afpChain.setTMScore(tmScore);
System.out.println(AfpChainWriter.toScoresList(afpChain));
StructureAlignmentDisplay.display(afpChain, ca1, ca2);
}
}