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

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

diff --git a/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java b/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
new file mode 100644 (file)
index 0000000..2a4efe8
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+++ b/src/jalview/json/binding/biojson/v1/SequenceGrpPojo.java
@@ -0,0 +1,181 @@
+/*
+ * 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 com.github.reinert.jjschema.Attributes;
+
+public class SequenceGrpPojo
+{
+  @Attributes(
+    required = false,
+    description = "The <a href=\"#colourScheme\">Colour Scheme</a> applied to the Sequence Group")
+  private String colourScheme;
+
+  @Attributes(
+    required = true,
+    description = "The name assigned to the seqGroup")
+  private String groupName;
+
+  @Attributes(
+    required = false,
+    description = "Serial version identifier for the <b>seqGroup</b> object model")
+  private String description;
+
+  @Attributes(
+    required = false,
+    description = "Determines if the seqGroup border should be visible or not")
+  private boolean displayBoxes;
+
+  @Attributes(
+    required = false,
+    description = "Determines if the texts of the group is displayed or not")
+  private boolean displayText;
+
+  @Attributes(
+    required = false,
+    description = "Determines if the residues text for the group is coloured")
+  private boolean colourText;
+
+  @Attributes(
+    required = false,
+    description = "Boolean value indicating whether residues should only be shown <br/>that are different from current reference or consensus sequence")
+  private boolean showNonconserved;
+
+  @Attributes(
+    required = true,
+    description = "The index of the group’s first residue in the alignment space")
+  private int startRes;
+
+  @Attributes(
+    required = true,
+    description = "The index of the group’s last residue in the alignment space")
+  private int endRes;
+
+  @Attributes(
+    required = true,
+    minItems = 1,
+    uniqueItems = true,
+    description = "An array of the unique id's for the sequences belonging to the group")
+  private ArrayList<String> sequenceRefs = new ArrayList<String>();
+
+  public String getColourScheme()
+  {
+    return colourScheme;
+  }
+
+  public void setColourScheme(String colourScheme)
+  {
+    this.colourScheme = colourScheme;
+  }
+
+  public String getGroupName()
+  {
+    return groupName;
+  }
+
+  public void setGroupName(String groupName)
+  {
+    this.groupName = groupName;
+  }
+
+  public String getDescription()
+  {
+    return description;
+  }
+
+  public void setDescription(String description)
+  {
+    this.description = description;
+  }
+
+  public boolean isDisplayBoxes()
+  {
+    return displayBoxes;
+  }
+
+  public void setDisplayBoxes(boolean displayBoxes)
+  {
+    this.displayBoxes = displayBoxes;
+  }
+
+  public boolean isDisplayText()
+  {
+    return displayText;
+  }
+
+  public void setDisplayText(boolean displayText)
+  {
+    this.displayText = displayText;
+  }
+
+  public boolean isColourText()
+  {
+    return colourText;
+  }
+
+  public void setColourText(boolean colourText)
+  {
+    this.colourText = colourText;
+  }
+
+  public boolean isShowNonconserved()
+  {
+    return showNonconserved;
+  }
+
+  public void setShowNonconserved(boolean showNonconserved)
+  {
+    this.showNonconserved = showNonconserved;
+  }
+
+  public int getStartRes()
+  {
+    return startRes;
+  }
+
+  public void setStartRes(int startRes)
+  {
+    this.startRes = startRes;
+  }
+
+  public int getEndRes()
+  {
+    return endRes;
+  }
+
+  public void setEndRes(int endRes)
+  {
+    this.endRes = endRes;
+  }
+
+  public ArrayList<String> getSequenceRefs()
+  {
+    return sequenceRefs;
+  }
+
+  public void setSequenceRefs(ArrayList<String> sequenceRefs)
+  {
+    this.sequenceRefs = sequenceRefs;
+  }
+
+}