Merge branch 'develop' into features/JAL-1705_ensembl

[jalview.git] / src / jalview / json / binding / biojson / v1 / AlignmentPojo.java

diff --git a/src/jalview/json/binding/biojson/v1/AlignmentPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
new file mode 100644 (file)
index 0000000..575b697
--- /dev/null
+++ b/src/jalview/json/binding/biojson/v1/AlignmentPojo.java
@@ -0,0 +1,158 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.json.binding.biojson.v1;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import com.github.reinert.jjschema.Attributes;
+
+@Attributes(
+  title = "BioJSON",
+  description = "A specification for the representation and exchange of bioinformatics data")
+public class AlignmentPojo
+{
+  @Attributes(
+    required = true,
+    description = "Serial version identifier for <b>BioJSON</b> schema")
+  private String svid = "1.0";
+
+  @Attributes(
+    required = true,
+    minItems = 1,
+    description = "An array of Sequences which makes up the Alignment")
+  private List<SequencePojo> seqs = new ArrayList<SequencePojo>();
+
+  @Attributes(
+    required = false,
+    minItems = 0,
+    exclusiveMaximum = true,
+    description = "Alignment annotations stores symbols and graphs usually rendered </br>"
+            + "below the alignment and often reflect properties of the alignment </br>as a whole.")
+  private List<AlignmentAnnotationPojo> alignAnnotation = new ArrayList<AlignmentAnnotationPojo>();
+
+  @Attributes(
+    required = false,
+    minItems = 0,
+    description = "A sequence group is a rectangular region of an alignment <br>bounded by startRes and endRes positions in the alignment <br>coordinate system for a set of sequences")
+  private List<SequenceGrpPojo> seqGroups = new ArrayList<SequenceGrpPojo>();
+
+  @Attributes(
+    required = false,
+    minItems = 0,
+    description = "Sequence features are properties of the individual sequences, <br>they do not change with the alignment, but are shown mapped<br> on to specific residues within the alignment")
+  private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
+
+  @Attributes(
+    required = false,
+    enums = { "None", "User Defined", "Clustal", "Zappo", "Taylor",
+        "Nucleotide", "Pyrimidine", "Purine", "Turn", "Helix", "Strand",
+        "Buried", "Hydro", "T-Coffee Scores", "RNA Interaction type",
+        "Blosum62", "RNA Helices", "% Identity" },
+    description = "The <a href=\"#colourScheme\">Colour Scheme</a> applied to the alignment")
+  private String colourScheme;
+
+  @Attributes(
+    required = true,
+    maxItems = 0,
+    description = "AppSettings stores key=value pairs of custom application specific <br>"
+            + "settings (i.e visualisation settings, etc) for different applications<br>"
+            + "that consume or generate BioJSON")
+  Map<String, Object> appSettings = new HashMap<String, Object>();
+
+  public AlignmentPojo()
+  {
+  }
+
+  public List<SequencePojo> getSeqs()
+  {
+    return seqs;
+  }
+
+  public void setSeqs(ArrayList<SequencePojo> seqs)
+  {
+    this.seqs = seqs;
+  }
+
+  public Map<String, Object> getAppSettings()
+  {
+    return appSettings;
+  }
+
+  public void setAppSettings(Map<String, Object> appSettings)
+  {
+    this.appSettings = appSettings;
+  }
+
+  public List<AlignmentAnnotationPojo> getAlignAnnotation()
+  {
+    return alignAnnotation;
+  }
+
+  public void setAlignAnnotation(
+          List<AlignmentAnnotationPojo> alignAnnotation)
+  {
+    this.alignAnnotation = alignAnnotation;
+  }
+
+  public List<SequenceGrpPojo> getSeqGroups()
+  {
+    return seqGroups;
+  }
+
+  public void setSeqGroups(List<SequenceGrpPojo> seqGroups)
+  {
+    this.seqGroups = seqGroups;
+  }
+
+  public List<SequenceFeaturesPojo> getSeqFeatures()
+  {
+    return seqFeatures;
+  }
+
+  public void setSeqFeatures(List<SequenceFeaturesPojo> seqFeatures)
+  {
+    this.seqFeatures = seqFeatures;
+  }
+
+  public String getSvid()
+  {
+    return svid;
+  }
+
+  public void setGlobalColorScheme(String globalColorScheme)
+  {
+    this.appSettings.put("globalColorScheme", globalColorScheme);
+  }
+
+  public String getColourScheme()
+  {
+    return colourScheme;
+  }
+
+  public void setColourScheme(String colourScheme)
+  {
+    this.colourScheme = colourScheme;
+  }
+
+}