- Clustal("Clustal")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new ClustalxColourScheme(coll, null);
- }
- },
- Blosum62("Blosum62")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new Blosum62ColourScheme();
- }
- },
- PID("% Identity")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new PIDColourScheme();
- }
- },
- Zappo("Zappo")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new ZappoColourScheme();
- }
- },
- Taylor("Taylor")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new TaylorColourScheme();
- }
- },
- Hydrophobic("Hydrophobic")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new HydrophobicColourScheme();
- }
- },
- Helix("Helix Propensity")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new HelixColourScheme();
- }
- },
- Strand("Strand Propensity")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new StrandColourScheme();
- }
- },
- Turn("Turn Propensity")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new TurnColourScheme();
- }
- },
- Buried("Buried Index")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new BuriedColourScheme();
- }
- },
- Nucleotide("Nucleotide")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new NucleotideColourScheme();
- }
- },
- PurinePyrimidine("Purine/Pyrimidine")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new PurinePyrimidineColourScheme();
- }
- },
- TCoffee("T-Coffee Scores")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new TCoffeeColourScheme(coll);
- }
- },
- RNAHelices("RNA Helices")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new RNAHelicesColour(coll);
- }
- },
- // RNAInteraction("RNA Interaction type")
- // {
- // @Override
- // public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- // {
- // return new RNAInteractionColourScheme();
- // }
- // },
- UserDefined("User Defined")
- {
- @Override
- public ColourSchemeI getColourScheme(AnnotatedCollectionI coll)
- {
- return new UserColourScheme("white");
- }
- };
-
- static Map<String, JalviewColourScheme> names = new HashMap<String, JalviewColourScheme>();
+ /*
+ * the order of declaration is the default order in which
+ * items are added to Colour menus
+ */
+ Clustal("Clustal", ClustalxColourScheme.class),
+ Blosum62("Blosum62", Blosum62ColourScheme.class),
+ PID("% Identity", PIDColourScheme.class),
+ Zappo("Zappo", ZappoColourScheme.class),
+ Taylor("Taylor", TaylorColourScheme.class),
+ Hydrophobic("Hydrophobic", HydrophobicColourScheme.class),
+ Helix("Helix Propensity", HelixColourScheme.class),
+ Strand("Strand Propensity", StrandColourScheme.class),
+ Turn("Turn Propensity", TurnColourScheme.class),
+ Buried("Buried Index", BuriedColourScheme.class),
+ Nucleotide("Nucleotide", NucleotideColourScheme.class),
+ PurinePyrimidine("Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
+ RNAHelices("RNA Helices", RNAHelicesColour.class),
+ TCoffee("T-Coffee Scores", TCoffeeColourScheme.class),
+ IdColour("Sequence ID", IdColourScheme.class),
+ HMMERU("HMMER-Uniprot", HmmerGlobalBackground.class),
+ HMMERA("HMMER-Alignment", HmmerLocalBackground.class),
+ HMMMatchScore("HMM Match Score", HMMMatchScoreColourScheme.class);
+ // RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)