JAL-1641 cherry-picked changes into develop compatible branch

[jalview.git] / src / jalview / json / binding / v1 / JalviewSettingsPojo.java

diff --git a/src/jalview/json/binding/v1/BioJsAlignmentPojo.java b/src/jalview/json/binding/v1/JalviewSettingsPojo.java
similarity index 75%
rename from src/jalview/json/binding/v1/BioJsAlignmentPojo.java
rename to src/jalview/json/binding/v1/JalviewSettingsPojo.java
index 8e8747f..3cc8824 100644 (file)
--- a/src/jalview/json/binding/v1/BioJsAlignmentPojo.java
+++ b/src/jalview/json/binding/v1/JalviewSettingsPojo.java
@@ -14,34 +14,28 @@ import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.ZappoColourScheme;
 
-import java.util.ArrayList;
-
-public class BioJsAlignmentPojo
+public class JalviewSettingsPojo
 {
   private String globalColorScheme = "none";
 
   private String jalviewVersion;
 
   private String webStartUrl;
-  private ArrayList<BioJsSeqPojo> seqs = new ArrayList<BioJsSeqPojo>();
 
-  public BioJsAlignmentPojo()
-  {
+  private boolean showSeqFeatures;
 
-  }
-  public ArrayList<BioJsSeqPojo> getSeqs()
-  {
-    return seqs;
-  }
+  private boolean wrapModeEnabled;
 
-  public void setSeqs(ArrayList<BioJsSeqPojo> seqs)
+  public JalviewSettingsPojo()
   {
-    this.seqs = seqs;
+
   }
+
   public String getGlobalColorScheme()
   {
     return globalColorScheme;
   }
+
   public void setGlobalColorScheme(String globalColorScheme)
   {
     for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
@@ -53,22 +47,8 @@ public class BioJsAlignmentPojo
         break;
       }
     }
-
-    // JALVIEW colors not in biojs
-    // Blosum62
-    // T-Coffee Scores (almost same with Blosom62
-    // RNA Interaction type - no color applied
-    // RNA Helices - missing
-
-    // BIOJS Colour not in jalview
-    // schemes.push name: "Lesk", id: "lesk"
-    // schemes.push name: "Cinema", id: "cinema"
-    // schemes.push name: "MAE", id: "mae"
-    // schemes.push name: "Clustal2", id: "clustal2"
-
   }
 
-
   public String getJalviewVersion()
   {
     return jalviewVersion;
@@ -89,13 +69,33 @@ public class BioJsAlignmentPojo
     this.webStartUrl = webStartUrl;
   }
 
+  public boolean isShowSeqFeatures()
+  {
+    return showSeqFeatures;
+  }
+
+  public void setShowSeqFeatures(boolean showSeqFeatures)
+  {
+    this.showSeqFeatures = showSeqFeatures;
+  }
+
+  public boolean isWrapModeEnabled()
+  {
+    return wrapModeEnabled;
+  }
+
+  public void setWrapModeEnabled(boolean wrapModeEnabled)
+  {
+    this.wrapModeEnabled = wrapModeEnabled;
+  }
+
   public enum JalviewBioJsColorSchemeMapper
   {
     USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
             null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
-            "zappo", new ZappoColourScheme()), TAYLOR(
-            "Taylor", "taylor", new TaylorColourScheme()), NUCLEOTIDE(
-            "Nucleotide", "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
+            "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
+            new TaylorColourScheme()), NUCLEOTIDE("Nucleotide",
+            "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
             "Purine/Pyrimidine", "purine",
             new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
             "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
@@ -105,16 +105,15 @@ public class BioJsAlignmentPojo
             "Hydrophobic", "hydro", new HydrophobicColourScheme()),
 
     // The color types below are not yet supported by BioJs MSA viewer
-    T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores",
- null), RNA_INT_TYPE(
+    T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
             "RNA Interaction type", "RNA Interaction type",
             new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
             "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
             "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
-            "% Identity", "pid",
-            new PIDColourScheme());
+            "% Identity", "pid", new PIDColourScheme());
 
     private String jalviewName;
+
     private String bioJsName;
 
     private ColourSchemeI jvColourScheme;