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
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;
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(
"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;