1 package jalview.datamodel;
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3 import jalview.schemes.*;
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4 import jalview.analysis.*;
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5 import jalview.datamodel.*;
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6 import java.util.Vector;
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8 public class SequenceGroup
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11 Conservation conserve;
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13 boolean displayBoxes;
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14 boolean displayText;
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16 boolean aaFrequencyValid = false;
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17 public Vector sequences = new Vector();
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19 public ColourSchemeI cs;
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23 public SequenceGroup()
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25 groupName = "Group";
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26 this.displayBoxes = true;
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27 this.displayText = true;
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28 this.colourText = false;
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32 public SequenceGroup(String groupName, ColourSchemeI scheme,
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33 boolean displayBoxes, boolean displayText,
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39 this.groupName = groupName;
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40 this.displayBoxes = displayBoxes;
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41 this.displayText = displayText;
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42 this.colourText = colourText;
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48 public String getName()
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53 public void setName(String name)
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58 public Conservation getConservation()
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63 public void setConservation(Conservation c)
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68 public void addSequence(SequenceI s)
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70 if(!sequences.contains(s))
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71 sequences.addElement(s);
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74 public void addOrRemove(SequenceI s)
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76 if(sequences.contains(s))
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82 public void deleteSequence(SequenceI s)
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84 sequences.removeElement(s);
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88 public int getStartRes()
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93 public int getEndRes()
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98 public void setStartRes(int i)
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103 public void setEndRes(int i)
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108 public int getSize()
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110 return sequences.size();
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113 public SequenceI getSequenceAt(int i)
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115 return (SequenceI) sequences.elementAt(i);
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118 public void setColourText(boolean state)
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120 colourText = state;
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123 public boolean getColourText()
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128 public void setDisplayText(boolean state)
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130 displayText = state;
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133 public boolean getDisplayText()
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135 return displayText;
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138 public void setDisplayBoxes(boolean state)
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140 displayBoxes = state;
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143 public boolean getDisplayBoxes()
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145 return displayBoxes;
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148 public Vector getAAFrequency()
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150 if (aaFrequency == null || aaFrequencyValid == false)
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152 aaFrequency = AAFrequency.calculate(sequences, 0, getWidth());
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153 aaFrequencyValid = true;
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155 return aaFrequency;
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158 public int getWidth()
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160 System.out.println("it is called");
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161 // MC This needs to get reset when characters are inserted and deleted
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162 for (int i = 0; i < sequences.size(); i++)
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164 SequenceI seq = (SequenceI) sequences.elementAt(i);
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165 if (seq.getLength() > width)
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166 width = seq.getLength();
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