1 package jalview.datamodel;
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3 import jalview.analysis.*;
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5 import java.util.StringTokenizer;
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9 public class Sequence implements SequenceI
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11 protected String name;
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12 protected String sequence;
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13 protected int start;
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15 protected String description;
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16 protected int charHeight;
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17 protected String displayId;
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18 protected Color color = Color.white;
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20 public int maxchain = -1;
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22 public int pdbstart;
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24 public int seqstart;
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26 public void setPDBfile(PDBfile pdb)
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32 for (int i=0; i < pdb.chains.size(); i++) {
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34 System.out.println("PDB sequence = " + ((PDBChain)pdb.chains.elementAt(i)).sequence);
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35 // Now lets compare the sequences to get
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36 // the start and end points.
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39 StringTokenizer str = new StringTokenizer(sequence, ".");
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40 String newString = "";
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42 while (str.hasMoreTokens()) {
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43 newString += str.nextToken();
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45 // Align the sequence to the pdb
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46 AlignSeq as = new AlignSeq(this,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");
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47 as.calcScoreMatrix();
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48 as.traceAlignment();
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49 as.printAlignment();
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51 System.out.println("Score = " + as.maxscore);
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52 if (as.maxscore > max) {
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53 System.out.println("New max score");
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57 pdbstart = as.seq2start;
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58 pdbend = as.seq2end;
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59 seqstart = as.seq1start - 1 ;
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60 seqend = as.seq1end -1;
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63 System.out.println("PDB start/end " + pdbstart + " " + pdbend);
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64 System.out.println("SEQ start/end " + seqstart + " " + seqend);
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68 public Sequence(String name, String sequence, int start, int end)
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72 this.sequence = sequence;
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80 public Sequence(String name,String sequence) {
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81 this(name,sequence,1,sequence.length());
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83 public Sequence(SequenceI seq) {
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84 this(seq.getName(),seq.getSequence(),seq.getStart(),seq.getEnd());
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86 public String getDisplayId() {
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89 public void setDisplayId() {
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90 displayId = name + "/" + start + "-" + end;
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92 public void setName(String name) {
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96 public String getName() {
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99 public void setStart(int start) {
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100 this.start = start;
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103 public int getStart() {
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106 public void setEnd(int end) {
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110 public int getEnd() {
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113 public int getLength() {
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114 return this.sequence.length();
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116 public void setSequence(String seq) {
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117 this.sequence = seq;
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119 public String getSequence() {
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120 return this.sequence;
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122 public String getSequence(int start,int end) {
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123 return this.sequence.substring(start,end);
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126 public char getCharAt(int i) {
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127 if (i < sequence.length()) {
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128 return sequence.charAt(i);
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133 public void setDescription(String desc) {
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134 this.description = desc;
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136 public String getDescription() {
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137 return this.description;
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140 public int findIndex(int pos) {
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141 // returns the alignment position for a residue
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145 while (i< sequence.length() && j <= end && j <= pos) {
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147 char c = sequence.charAt(i);
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149 if (!jalview.util.Comparison.isGap((c)))
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154 if (j == end && j < pos)
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161 public int findPosition(int i) {
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162 // Returns the sequence position for an alignment position
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168 char c = sequence.charAt(j);
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170 if (!jalview.util.Comparison.isGap((c)))
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177 public void deleteCharAt(int i)
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179 StringBuffer sbuffer = new StringBuffer(sequence);
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180 sbuffer.deleteCharAt(i);
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181 sequence = sbuffer.toString();
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184 public void insertCharAt(int i, char c)
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186 insertCharAt(i,c,true);
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189 public void insertCharAt(int i,char c,boolean chop) {
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191 String tmp = new String(sequence);
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193 if (i < sequence.length()) {
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194 sequence = tmp.substring(0,i) + String.valueOf(c) + tmp.substring(i);
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196 sequence = tmp + String.valueOf(c);
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201 public void setColor(Color c) {
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205 public Color getColor() {
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