001/**
002 * Copyright (C) 2010-2015 The Roslin Institute <contact andy.law@roslin.ed.ac.uk>
003 *
004 * This file is part of JEnsembl: a Java API to Ensembl data sources developed by the
005 * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of
006 * Veterinary Studies, University of Edinburgh.
007 *
008 * Project hosted at: http://jensembl.sourceforge.net
009 *
010 * This is free software: you can redistribute it and/or modify
011 * it under the terms of the GNU General Public License (version 3) as published by
012 * the Free Software Foundation.
013 *
014 * This software is distributed in the hope that it will be useful,
015 * but WITHOUT ANY WARRANTY; without even the implied warranty of
016 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
017 * GNU General Public License for more details.
018 *
019 * You should have received a copy of the GNU General Public License
020 * in this software distribution. If not, see: http://opensource.org/licenses/gpl-3.0.html
021 */
022package uk.ac.roslin.ensembl.demo;
023
024import uk.ac.roslin.ensembl.config.DBConnection.DataSource;
025import uk.ac.roslin.ensembl.dao.database.DBRegistry;
026import uk.ac.roslin.ensembl.dao.database.DBSpecies;
027import uk.ac.roslin.ensembl.datasourceaware.DAXRef;
028import uk.ac.roslin.ensembl.datasourceaware.core.DAGene;
029import uk.ac.roslin.ensembl.datasourceaware.core.DATranscript;
030import uk.ac.roslin.ensembl.datasourceaware.core.DATranslation;
031
032public class XRefs {
033
034    public static void main(String[] args) throws Exception {
035        
036        DBRegistry eReg = DBRegistry.createRegistryForDataSource(DataSource.ENSEMBLDB);
037        DBSpecies sp = eReg.getSpeciesByAlias("human");
038        
039        DAGene g = sp.getGeneByStableID("ENSG00000006128");
040        int count = 0;
041        System.out.println(g.getStableID() + " " + g.getDisplayName());
042        for (DAXRef x : g.getAllXRefs()) {
043
044            System.out.println("XREF " + ++count
045                    + " : " + x.getPrimaryAccession());
046
047            System.out.println("\tDBHashID: " + x.getHashID());
048            System.out.println("\tDBName: " + x.getDBDisplayName());
049            System.out.println("\tDescription: " + x.getDescription());
050            System.out.println("\tDisplayID: " + x.getDisplayID());
051            System.out.println("\tInfo: " + x.getInfo());
052            System.out.println("\tInfoType: " + x.getInfoType());
053            System.out.println("\tPrimaryAccession: " + x.getPrimaryAccession());
054            System.out.println("\tVersion: " + x.getVersion());
055        }
056        System.out.println("");
057        for (DAXRef x : g.getVegaXRefs()) {
058
059            System.out.println("Vega XREF " + ++count
060                    + " : " + x.getPrimaryAccession());
061
062            System.out.println("\tDBHashID: " + x.getHashID());
063            System.out.println("\tDBName: " + x.getDBDisplayName());
064            System.out.println("\tDescription: " + x.getDescription());
065            System.out.println("\tDisplayID: " + x.getDisplayID());
066            System.out.println("\tInfo: " + x.getInfo());
067            System.out.println("\tInfoType: " + x.getInfoType());
068            System.out.println("\tPrimaryAccession: " + x.getPrimaryAccession());
069            System.out.println("\tVersion: " + x.getVersion());
070        }
071        System.out.println("");
072
073        DAXRef dx = g.getDisplayXRef();
074        System.out.println("Display XREF " + ++count
075                + " : " + dx.getPrimaryAccession());
076
077        System.out.println("\tDBHashID: " + dx.getHashID());
078        System.out.println("\tDBName: " + dx.getDBDisplayName());
079        System.out.println("\tDescription: " + dx.getDescription());
080        System.out.println("\tDisplayID: " + dx.getDisplayID());
081        System.out.println("\tInfo: " + dx.getInfo());
082        System.out.println("\tInfoType: " + dx.getInfoType());
083        System.out.println("\tPrimaryAccession: " + dx.getPrimaryAccession());
084        System.out.println("\tVersion: " + dx.getVersion());
085
086        System.out.println("");
087        System.out.println("");
088        System.out.println("");
089        
090        
091        DATranscript t = sp.getTranscriptByStableID("ENST00000319273");
092         count = 0;
093        System.out.println(t.getStableID() + " " + t.getDisplayName());
094        for (DAXRef x : t.getAllXRefs()) {
095
096            System.out.println("XREF " + ++count
097                    + " : " + x.getPrimaryAccession());
098
099            System.out.println("\tDBHashID: " + x.getHashID());
100            System.out.println("\tDBName: " + x.getDBDisplayName());
101            System.out.println("\tDescription: " + x.getDescription());
102            System.out.println("\tDisplayID: " + x.getDisplayID());
103            System.out.println("\tInfo: " + x.getInfo());
104            System.out.println("\tInfoType: " + x.getInfoType());
105            System.out.println("\tPrimaryAccession: " + x.getPrimaryAccession());
106            System.out.println("\tVersion: " + x.getVersion());
107        }
108        System.out.println("");
109        for (DAXRef x : t.getVegaXRefs()) {
110
111            System.out.println("Vega XREF " + ++count
112                    + " : " + x.getPrimaryAccession());
113
114            System.out.println("\tDBHashID: " + x.getHashID());
115            System.out.println("\tDBName: " + x.getDBDisplayName());
116            System.out.println("\tDescription: " + x.getDescription());
117            System.out.println("\tDisplayID: " + x.getDisplayID());
118            System.out.println("\tInfo: " + x.getInfo());
119            System.out.println("\tInfoType: " + x.getInfoType());
120            System.out.println("\tPrimaryAccession: " + x.getPrimaryAccession());
121            System.out.println("\tVersion: " + x.getVersion());
122        }
123        System.out.println("");
124        for (DAXRef x : t.getCCDSXRefs()) {
125
126            System.out.println("CCDS XREF " + ++count
127                    + " : " + x.getPrimaryAccession());
128
129            System.out.println("\tDBHashID: " + x.getHashID());
130            System.out.println("\tDBName: " + x.getDBDisplayName());
131            System.out.println("\tDescription: " + x.getDescription());
132            System.out.println("\tDisplayID: " + x.getDisplayID());
133            System.out.println("\tInfo: " + x.getInfo());
134            System.out.println("\tInfoType: " + x.getInfoType());
135            System.out.println("\tPrimaryAccession: " + x.getPrimaryAccession());
136            System.out.println("\tVersion: " + x.getVersion());
137        }
138        System.out.println("");
139
140        DAXRef dxr = t.getDisplayXRef();
141        System.out.println("Display XREF " + ++count
142                + " : " + dxr.getPrimaryAccession());
143
144        System.out.println("\tDBHashID: " + dxr.getHashID());
145        System.out.println("\tDBName: " + dxr.getDBDisplayName());
146        System.out.println("\tDescription: " + dxr.getDescription());
147        System.out.println("\tDisplayID: " + dxr.getDisplayID());
148        System.out.println("\tInfo: " + dxr.getInfo());
149        System.out.println("\tInfoType: " + dxr.getInfoType());
150        System.out.println("\tPrimaryAccession: " + dxr.getPrimaryAccession());
151        System.out.println("\tVersion: " + dxr.getVersion());
152
153        System.out.println("");
154        System.out.println("");
155        System.out.println("");
156        
157        DATranslation tr = sp.getTranslationByStableID("ENSP00000321106");
158         count = 0;
159        System.out.println(tr.getStableID() );
160        for (DAXRef x : tr.getAllXRefs()) {
161
162            System.out.println("XREF " + ++count
163                    + " : " + x.getPrimaryAccession());
164
165            System.out.println("\tDBHashID: " + x.getHashID());
166            System.out.println("\tDBName: " + x.getDBDisplayName());
167            System.out.println("\tDescription: " + x.getDescription());
168            System.out.println("\tDisplayID: " + x.getDisplayID());
169            System.out.println("\tInfo: " + x.getInfo());
170            System.out.println("\tInfoType: " + x.getInfoType());
171            System.out.println("\tPrimaryAccession: " + x.getPrimaryAccession());
172            System.out.println("\tVersion: " + x.getVersion());
173            if (x.getEvidence()!=null ) {
174                System.out.println("\tEvidence: " + x.getEvidence());
175            }
176        }
177        System.out.println("");
178        for (DAXRef x : tr.getVegaXRefs()) {
179
180            System.out.println("Vega XREF " + ++count
181                    + " : " + x.getPrimaryAccession());
182
183            System.out.println("\tDBHashID: " + x.getHashID());
184            System.out.println("\tDBName: " + x.getDBDisplayName());
185            System.out.println("\tDescription: " + x.getDescription());
186            System.out.println("\tDisplayID: " + x.getDisplayID());
187            System.out.println("\tInfo: " + x.getInfo());
188            System.out.println("\tInfoType: " + x.getInfoType());
189            System.out.println("\tPrimaryAccession: " + x.getPrimaryAccession());
190            System.out.println("\tVersion: " + x.getVersion());
191        }
192        System.out.println("");
193
194       
195
196
197
198    }
199}