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 August 13, 2010
21+ * Author: Mark Chapman
22+ */
23+
24+ package org .biojava3 .alignment .io ;
25+
26+ /**
27+ * Stores all the content parsed from the #=GC lines
28+ *
29+ * @since 3.0.5
30+ * @author Amr AL-Hossary
31+ * @author Marko Vaz
32+ *
33+ */
34+ class StockholmConsensusAnnotation {
35+ private String secondaryStructure ;
36+ private String sequenceConsensus ;
37+ private String surfaceAccessibility ;
38+ private String transMembrane ;
39+ private String posteriorProbability ;
40+ private String ligandBinding ;
41+ private String activeSite ;
42+ private String asPFamPredicted ;
43+ private String asSwissProt ;
44+ private String intron ; //TODO (?)
45+ private String referenceAnnotation ;
46+ private String modelMask ;
47+
48+ public String getSecondaryStructure () {
49+ return secondaryStructure ;
50+ }
51+
52+ public void setSecondaryStructure (String secondaryStructure ) {
53+ this .secondaryStructure = secondaryStructure ;
54+ }
55+
56+ public String getSequenceConsensus () {
57+ return sequenceConsensus ;
58+ }
59+
60+ public void setSequenceConsensus (String sequenceConsensus ) {
61+ this .sequenceConsensus = sequenceConsensus ;
62+ }
63+
64+ public String getSurfaceAccessibility () {
65+ return surfaceAccessibility ;
66+ }
67+
68+ public void setSurfaceAccessibility (String surfaceAccessibility ) {
69+ this .surfaceAccessibility = surfaceAccessibility ;
70+ }
71+
72+ public String getTransMembrane () {
73+ return transMembrane ;
74+ }
75+
76+ public void setTransMembrane (String transMembrane ) {
77+ this .transMembrane = transMembrane ;
78+ }
79+
80+ public String getPosteriorProbability () {
81+ return posteriorProbability ;
82+ }
83+
84+ public void setPosteriorProbability (String posteriorProbability ) {
85+ this .posteriorProbability = posteriorProbability ;
86+ }
87+
88+ public String getLigandBinding () {
89+ return ligandBinding ;
90+ }
91+
92+ public void setLigandBinding (String ligandBinding ) {
93+ this .ligandBinding = ligandBinding ;
94+ }
95+
96+ public String getActiveSite () {
97+ return activeSite ;
98+ }
99+
100+ public void setActiveSite (String activeSite ) {
101+ this .activeSite = activeSite ;
102+ }
103+
104+ public String getAsPFamPredicted () {
105+ return asPFamPredicted ;
106+ }
107+
108+ public void setAsPFamPredicted (String asPFamPredicted ) {
109+ this .asPFamPredicted = asPFamPredicted ;
110+ }
111+
112+ public String getAsSwissProt () {
113+ return asSwissProt ;
114+ }
115+
116+ public void setAsSwissProt (String asSwissProt ) {
117+ this .asSwissProt = asSwissProt ;
118+ }
119+
120+ public String getIntron () {
121+ return intron ;
122+ }
123+
124+ public void setIntron (String intron ) {
125+ this .intron = intron ;
126+ }
127+
128+ public String getReferenceAnnotation () {
129+ return referenceAnnotation ;
130+ }
131+
132+ public void setReferenceAnnotation (String referenceAnnotation ) {
133+ this .referenceAnnotation = referenceAnnotation ;
134+ }
135+
136+ public String getModelMask () {
137+ return modelMask ;
138+ }
139+
140+ public void setModelMask (String modelMask ) {
141+ this .modelMask = modelMask ;
142+ }
143+
144+ }
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