+++ /dev/null
-/*
- * 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 Dec 10, 2005
- *
- */
-package org.biojava.dasobert.das;
-
-import org.biojava.dasobert.dasregistry.Das1Source;
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
-
-/** a class that stores the arguments that can be sent to the AlignmentThread class
- *
- * @author Andreas Prlic
- *
- */
-public class AlignmentParameters {
-
- String query;
- String subject;
- String queryPDBChainId;
- String subjectPDBChainId;
-
-
- DasCoordinateSystem queryCoordinateSystem;
- DasCoordinateSystem subjectCoordinateSystem;
- Das1Source[] dasSources;
-
-
- public static String DEFAULT_PDBCOORDSYS = "PDBresnum,Protein Structure";
- public static String DEFAULT_UNIPROTCOORDSYS = "UniProt,Protein Sequence";
- public static String DEFAULT_ENSPCOORDSYS = "Ensembl,Protein Sequence";
-
-
- public AlignmentParameters() {
- super();
- dasSources = new SpiceDasSource[0];
-
- }
-
- public DasCoordinateSystem getDefaultPDBCoordSys(){
- return DasCoordinateSystem.fromString(DEFAULT_PDBCOORDSYS);
- }
- public DasCoordinateSystem getDefaultUniProtCoordSys(){
- return DasCoordinateSystem.fromString(DEFAULT_UNIPROTCOORDSYS);
- }
- public DasCoordinateSystem getDefaultEnspCoordSys(){
- return DasCoordinateSystem.fromString(DEFAULT_ENSPCOORDSYS);
- }
-
-
- public Das1Source[] getDasSources() {
- return dasSources;
- }
-
-
-
- public void setDasSources(SpiceDasSource[] dasSources) {
- this.dasSources = dasSources;
- }
-
-
-
- public String getQuery() {
- return query;
- }
-
-
-
- public void setQuery(String query) {
- this.query = query;
- }
-
-
-
- public DasCoordinateSystem getQueryCoordinateSystem() {
- return queryCoordinateSystem;
- }
-
-
-
- public void setQueryCoordinateSystem(DasCoordinateSystem queryCoordinateSystem) {
- this.queryCoordinateSystem = queryCoordinateSystem;
- }
-
-
-
- public String getQueryPDBChainId() {
- return queryPDBChainId;
- }
-
-
-
- public void setQueryPDBChainId(String queryPDBChainId) {
- this.queryPDBChainId = queryPDBChainId;
- }
-
-
-
- public String getSubject() {
- return subject;
- }
-
-
-
- public void setSubject(String subject) {
- this.subject = subject;
- }
-
-
-
- public DasCoordinateSystem getSubjectCoordinateSystem() {
- return subjectCoordinateSystem;
- }
-
-
-
- public void setSubjectCoordinateSystem(
- DasCoordinateSystem subjectCoordinateSystem) {
- this.subjectCoordinateSystem = subjectCoordinateSystem;
- }
-
-
-
- public String getSubjectPDBChainId() {
- return subjectPDBChainId;
- }
-
-
-
- public void setSubjectPDBChainId(String subjectPDBChainId) {
- this.subjectPDBChainId = subjectPDBChainId;
- }
-
-
-
-
-}