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 boolean displayBoxes;
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12 boolean displayText;
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15 Conservation conserve;
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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 public SequenceGroup() {
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24 groupName = "Group";
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25 this.isSelected = false;
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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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29 this.display = true;
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30 cs = new ZappoColourScheme();
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33 public SequenceGroup( String groupName, ColourSchemeI scheme, boolean isSelected,
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34 boolean displayBoxes, boolean displayText,
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38 this.groupName = groupName;
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39 this.isSelected = isSelected;
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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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43 this.display = display;
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47 public String getName()
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52 public void setName(String name)
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56 public Conservation getConservation() {
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59 public void setConservation(Conservation c)
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62 public void addSequence(SequenceI s) {
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63 sequences.addElement(s);
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66 public void deleteSequence(SequenceI s) {
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67 sequences.removeElement(s);
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70 public void setColourText(boolean state) {
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73 public boolean getColourText() {
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77 public void setDisplayText(boolean state) {
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78 displayText = state;
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81 public boolean getDisplayText() {
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85 public void setDisplayBoxes(boolean state) {
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86 displayBoxes = state;
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89 public boolean getDisplayBoxes() {
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90 return displayBoxes;
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93 public int getSize() {
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94 return sequences.size();
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96 public SequenceI getSequenceAt(int i) {
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97 return (SequenceI)sequences.elementAt(i);
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100 public Vector getAAFrequency() {
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101 if (aaFrequency == null || aaFrequencyValid == false) {
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102 aaFrequency = AAFrequency.calculate(sequences,0,getWidth());
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103 aaFrequencyValid = true;
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105 return aaFrequency;
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108 public int getWidth()
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110 // MC This needs to get reset when characters are inserted and deleted
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111 for (int i = 0; i < sequences.size(); i++)
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113 SequenceI seq = (SequenceI) sequences.elementAt(i);
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114 if (seq.getLength() > width)
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115 width = seq.getLength();
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