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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9 public class SequenceGroup
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12 Conservation conserve;
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14 boolean displayBoxes;
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15 boolean displayText;
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17 boolean aaFrequencyValid = false;
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18 public Vector sequences = new Vector();
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20 public ColourSchemeI cs;
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23 Color outlineColour = Color.black;
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25 public SequenceGroup()
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27 groupName = "Group";
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28 this.displayBoxes = true;
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29 this.displayText = true;
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30 this.colourText = false;
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34 public SequenceGroup(String groupName, ColourSchemeI scheme,
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35 boolean displayBoxes, boolean displayText,
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41 this.groupName = groupName;
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42 this.displayBoxes = displayBoxes;
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43 this.displayText = displayText;
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44 this.colourText = colourText;
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50 public String getName()
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55 public void setName(String name)
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60 public Conservation getConservation()
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65 public void setConservation(Conservation c)
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70 public void addSequence(SequenceI s)
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72 if(!sequences.contains(s))
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73 sequences.addElement(s);
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76 public void addOrRemove(SequenceI s)
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78 if(sequences.contains(s))
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84 public void deleteSequence(SequenceI s)
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86 sequences.removeElement(s);
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90 public int getStartRes()
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95 public int getEndRes()
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100 public void setStartRes(int i)
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105 public void setEndRes(int i)
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110 public int getSize()
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112 return sequences.size();
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115 public SequenceI getSequenceAt(int i)
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117 return (SequenceI) sequences.elementAt(i);
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120 public void setColourText(boolean state)
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122 colourText = state;
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125 public boolean getColourText()
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130 public void setDisplayText(boolean state)
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132 displayText = state;
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135 public boolean getDisplayText()
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137 return displayText;
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140 public void setDisplayBoxes(boolean state)
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142 displayBoxes = state;
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145 public boolean getDisplayBoxes()
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147 return displayBoxes;
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150 public Vector getAAFrequency()
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152 if (aaFrequency == null || aaFrequencyValid == false)
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154 aaFrequency = AAFrequency.calculate(sequences, 0, getWidth());
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155 aaFrequencyValid = true;
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157 return aaFrequency;
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160 public int getWidth()
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162 System.out.println("it is called");
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163 // MC This needs to get reset when characters are inserted and deleted
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164 for (int i = 0; i < sequences.size(); i++)
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166 SequenceI seq = (SequenceI) sequences.elementAt(i);
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167 if (seq.getLength() > width)
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168 width = seq.getLength();
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174 public void setOutlineColour(Color c)
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178 public Color getOutlineColour()
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180 return outlineColour;
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