src/org/biojava/dasobert/das/AlignmentParameters.java

   1 /*
   2  *                  BioJava development code
   3  *
   4  * This code may be freely distributed and modified under the
   5  * terms of the GNU Lesser General Public Licence.  This should
   6  * be distributed with the code.  If you do not have a copy,
   7  * see:
   8  *
   9  *      http://www.gnu.org/copyleft/lesser.html
  10  *
  11  * Copyright for this code is held jointly by the individual
  12  * authors.  These should be listed in @author doc comments.
  13  *
  14  * For more information on the BioJava project and its aims,
  15  * or to join the biojava-l mailing list, visit the home page
  16  * at:
  17  *
  18  *      http://www.biojava.org/
  19  *
  20  * Created on Dec 10, 2005
  21  *
  22  */
  23 package org.biojava.dasobert.das;
  24
  25 import org.biojava.dasobert.dasregistry.Das1Source;
  26 import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
  27
  28 /** a class that stores the arguments that can be sent to the AlignmentThread class
  29  *
  30  * @author Andreas Prlic
  31  *
  32  */
  33 public class AlignmentParameters {
  34
  35     String query;
  36     String subject;
  37     String queryPDBChainId;
  38     String subjectPDBChainId;
  39
  40
  41     DasCoordinateSystem queryCoordinateSystem;
  42     DasCoordinateSystem subjectCoordinateSystem;
  43     Das1Source[] dasSources;
  44
  45
  46     public static String DEFAULT_PDBCOORDSYS     = "PDBresnum,Protein Structure";
  47     public static String DEFAULT_UNIPROTCOORDSYS = "UniProt,Protein Sequence";
  48     public static String DEFAULT_ENSPCOORDSYS    = "Ensembl,Protein Sequence";
  49
  50
  51     public AlignmentParameters() {
  52         super();
  53         dasSources = new SpiceDasSource[0];
  54
  55     }
  56
  57     public DasCoordinateSystem getDefaultPDBCoordSys(){
  58         return DasCoordinateSystem.fromString(DEFAULT_PDBCOORDSYS);
  59     }
  60     public DasCoordinateSystem getDefaultUniProtCoordSys(){
  61         return DasCoordinateSystem.fromString(DEFAULT_UNIPROTCOORDSYS);
  62     }
  63     public DasCoordinateSystem getDefaultEnspCoordSys(){
  64         return DasCoordinateSystem.fromString(DEFAULT_ENSPCOORDSYS);
  65     }
  66
  67
  68     public Das1Source[] getDasSources() {
  69         return dasSources;
  70     }
  71
  72
  73
  74     public void setDasSources(SpiceDasSource[] dasSources) {
  75         this.dasSources = dasSources;
  76     }
  77
  78
  79
  80     public String getQuery() {
  81         return query;
  82     }
  83
  84
  85
  86     public void setQuery(String query) {
  87         this.query = query;
  88     }
  89
  90
  91
  92     public DasCoordinateSystem getQueryCoordinateSystem() {
  93         return queryCoordinateSystem;
  94     }
  95
  96
  97
  98     public void setQueryCoordinateSystem(DasCoordinateSystem queryCoordinateSystem) {
  99         this.queryCoordinateSystem = queryCoordinateSystem;
 100     }
 101
 102
 103
 104     public String getQueryPDBChainId() {
 105         return queryPDBChainId;
 106     }
 107
 108
 109
 110     public void setQueryPDBChainId(String queryPDBChainId) {
 111         this.queryPDBChainId = queryPDBChainId;
 112     }
 113
 114
 115
 116     public String getSubject() {
 117         return subject;
 118     }
 119
 120
 121
 122     public void setSubject(String subject) {
 123         this.subject = subject;
 124     }
 125
 126
 127
 128     public DasCoordinateSystem getSubjectCoordinateSystem() {
 129         return subjectCoordinateSystem;
 130     }
 131
 132
 133
 134     public void setSubjectCoordinateSystem(
 135             DasCoordinateSystem subjectCoordinateSystem) {
 136         this.subjectCoordinateSystem = subjectCoordinateSystem;
 137     }
 138
 139
 140
 141     public String getSubjectPDBChainId() {
 142         return subjectPDBChainId;
 143     }
 144
 145
 146
 147     public void setSubjectPDBChainId(String subjectPDBChainId) {
 148         this.subjectPDBChainId = subjectPDBChainId;
 149     }
 150
 151
 152
 153
 154 }