X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fbiojava%2Fdasobert%2Fdas%2FAlignmentParameters.java;fp=src%2Forg%2Fbiojava%2Fdasobert%2Fdas%2FAlignmentParameters.java;h=0000000000000000000000000000000000000000;hb=e4dca3706ab423352c26ac100f3ca5a3e7c3d2c4;hp=faf692460792cae0aa2608bb1aacbd60b6eeb441;hpb=07e8245f6f0fc4d96b67bc2e87db167436266d16;p=jalview.git

diff --git a/src/org/biojava/dasobert/das/AlignmentParameters.java b/src/org/biojava/dasobert/das/AlignmentParameters.java
deleted file mode 100755
index faf6924..0000000
--- a/src/org/biojava/dasobert/das/AlignmentParameters.java
+++ /dev/null
@@ -1,154 +0,0 @@
-/*
- *                  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;
-    }
-    
-    
-    
-
-}