1 package jalview.schemes;
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3 public class ColourSchemeProperty
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5 public static final int CLUSTAL = 0;
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6 public static final int BLOSUM = 1;
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7 public static final int PID = 2;
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8 public static final int ZAPPO = 3;
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9 public static final int HYDROPHOBIC=4;
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10 public static final int HELIX=5;
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11 public static final int STRAND=6;
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12 public static final int TURN = 7;
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13 public static final int BURIED = 8;
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14 public static final int NUCLEOTIDE = 9;
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15 public static final int USER_DEFINED = 10;
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16 public static final int NONE = 11;
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18 public static int getColourIndexFromName(String name)
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21 if(name.equalsIgnoreCase("Clustal"))
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23 else if(name.equalsIgnoreCase("Blosum62"))
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25 else if(name.equalsIgnoreCase("% Identity"))
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27 else if(name.equalsIgnoreCase("Zappo"))
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29 else if(name.equalsIgnoreCase("Hydrophobic"))
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31 else if(name.equalsIgnoreCase("Helix Propensity"))
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33 else if(name.equalsIgnoreCase("Strand Propensity"))
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35 else if(name.equalsIgnoreCase("Turn Propensity"))
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37 else if(name.equalsIgnoreCase("Buried Index"))
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39 else if(name.equalsIgnoreCase("Nucleotide"))
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41 else if(name.equalsIgnoreCase("User Defined"))
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47 public static String getColourName(int index)
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52 case CLUSTAL: ret = "Clustal"; break;
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53 case BLOSUM: ret = "Blosum62"; break;
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54 case PID: ret = "% Identity"; break;
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55 case ZAPPO: ret = "Zappo"; break;
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56 case HYDROPHOBIC: ret="Hydrophobic";break;
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57 case HELIX: ret="Helix Propensity";break;
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58 case STRAND: ret="Strand Propensity";break;
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59 case TURN: ret="Turn Propensity";break;
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60 case BURIED: ret="Buried Index";break;
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61 case NUCLEOTIDE:ret="Nucleotide"; break;
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62 case USER_DEFINED:ret="User Defined";break;
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63 default: ret = "None"; break;
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68 public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)
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70 return getColour(al, getColourIndexFromName(name));
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73 public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)
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75 ColourSchemeI cs = null;
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78 case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;
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79 case BLOSUM: cs = new Blosum62ColourScheme(); break;
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80 case PID: cs = new PIDColourScheme(); break;
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81 case ZAPPO: cs = new ZappoColourScheme(); break;
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82 case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;
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83 case HELIX: cs = new HelixColourScheme(); break;
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84 case STRAND: cs = new StrandColourScheme(); break;
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85 case TURN: cs = new TurnColourScheme(); break;
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86 case BURIED: cs = new BuriedColourScheme(); break;
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87 case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;
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89 // if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
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91 // cs = jalview.gui.UserDefinedColours.loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
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