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(ColourSchemeI cs)
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49 if(cs instanceof ConservationColourScheme)
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50 cs = ((ConservationColourScheme)cs).cs;
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54 if(cs instanceof ClustalxColourScheme)
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56 else if(cs instanceof Blosum62ColourScheme)
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58 else if(cs instanceof PIDColourScheme)
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60 else if(cs instanceof ZappoColourScheme)
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62 else if(cs instanceof HydrophobicColourScheme)
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63 index = HYDROPHOBIC;
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64 else if(cs instanceof HelixColourScheme)
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66 else if(cs instanceof StrandColourScheme)
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68 else if(cs instanceof TurnColourScheme)
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70 else if(cs instanceof BuriedColourScheme)
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72 else if(cs instanceof NucleotideColourScheme)
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74 else if(cs instanceof UserColourScheme)
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75 index = USER_DEFINED;
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77 return getColourName(index);
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80 public static String getColourName(int index)
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85 case CLUSTAL: ret = "Clustal"; break;
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86 case BLOSUM: ret = "Blosum62"; break;
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87 case PID: ret = "% Identity"; break;
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88 case ZAPPO: ret = "Zappo"; break;
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89 case HYDROPHOBIC: ret="Hydrophobic";break;
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90 case HELIX: ret="Helix Propensity";break;
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91 case STRAND: ret="Strand Propensity";break;
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92 case TURN: ret="Turn Propensity";break;
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93 case BURIED: ret="Buried Index";break;
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94 case NUCLEOTIDE:ret="Nucleotide"; break;
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95 case USER_DEFINED:ret="User Defined";break;
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96 default: ret = "None"; break;
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101 public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)
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103 return getColour(al, getColourIndexFromName(name));
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106 public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)
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108 ColourSchemeI cs = null;
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111 case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;
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112 case BLOSUM: cs = new Blosum62ColourScheme(); break;
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113 case PID: cs = new PIDColourScheme(); break;
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114 case ZAPPO: cs = new ZappoColourScheme(); break;
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115 case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;
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116 case HELIX: cs = new HelixColourScheme(); break;
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117 case STRAND: cs = new StrandColourScheme(); break;
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118 case TURN: cs = new TurnColourScheme(); break;
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119 case BURIED: cs = new BuriedColourScheme(); break;
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120 case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;
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121 case USER_DEFINED: cs = new UserColourScheme(null);
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