1 package jalview.datamodel;
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6 public class Sequence implements SequenceI {
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7 protected String name;
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8 protected String sequence;
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11 protected String description;
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12 protected int charHeight;
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13 protected String displayId;
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14 protected Color color = Color.black;
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16 public Sequence(String name, String sequence, int start, int end)
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20 this.sequence = sequence;
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28 public Sequence(String name,String sequence) {
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29 this(name,sequence,1,sequence.length());
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31 public Sequence(SequenceI seq) {
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32 this(seq.getName(),seq.getSequence(),seq.getStart(),seq.getEnd());
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34 public String getDisplayId() {
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37 public void setDisplayId() {
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38 displayId = name + "/" + start + "-" + end;
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40 public void setName(String name) {
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44 public String getName() {
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47 public void setStart(int start) {
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51 public int getStart() {
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54 public void setEnd(int end) {
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58 public int getEnd() {
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61 public int getLength() {
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62 return this.sequence.length();
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64 public void setSequence(String seq) {
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65 this.sequence = seq;
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67 public String getSequence() {
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68 return this.sequence;
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70 public String getSequence(int start,int end) {
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71 return this.sequence.substring(start,end);
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74 public char getCharAt(int i) {
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75 if (i < sequence.length()) {
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76 return sequence.charAt(i);
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81 public void setDescription(String desc) {
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82 this.description = desc;
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84 public String getDescription() {
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85 return this.description;
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88 public int findIndex(int pos) {
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89 // returns the alignment position for a residue
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93 while (i< sequence.length() && j <= end && j <= pos) {
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95 String s = sequence.substring(i,i+1);
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97 if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
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102 if (j == end && j < pos) {
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110 public int findPosition(int i) {
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111 // Returns the sequence position for an alignment position
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116 String s = sequence.substring(j,j+1);
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118 if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
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125 public void deleteCharAt(int i)
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127 StringBuffer sbuffer = new StringBuffer(sequence);
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128 sbuffer.deleteCharAt(i);
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129 sequence = sbuffer.toString();
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132 public void insertCharAt(int i, char c)
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134 insertCharAt(i,c,true);
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137 public void insertCharAt(int i,char c,boolean chop) {
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139 String tmp = new String(sequence);
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141 if (i < sequence.length()) {
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142 sequence = tmp.substring(0,i) + String.valueOf(c) + tmp.substring(i);
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144 sequence = tmp + String.valueOf(c);
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149 public void setColor(Color c) {
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153 public Color getColor() {
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