1 package jalview.datamodel;
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3 import jalview.analysis.*;
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4 import jalview.util.*;
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7 /** Data structure to hold and manipulate a multiple sequence alignment
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9 public class Alignment implements AlignmentI
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12 protected Vector sequences;
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13 protected Vector groups = new Vector();
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14 public Hashtable[] cons;
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15 protected char gapCharacter = '-';
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17 /** Make an alignment from an array of Sequences.
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21 public Alignment(SequenceI[] seqs) {
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22 sequences = new Vector();
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24 for (int i=0; i < seqs.length; i++)
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25 sequences.addElement(seqs[i]);
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30 public Vector getSequences() {
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34 public SequenceI getSequenceAt(int i) {
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35 if (i < sequences.size()) {
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36 return (SequenceI)sequences.elementAt(i);
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42 /** Adds a sequence to the alignment. Recalculates maxLength and size.
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43 * Should put the new sequence in a sequence group!!!
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47 public void addSequence(SequenceI snew) {
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48 sequences.addElement(snew);
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50 ((SequenceGroup)groups.lastElement()).addSequence(snew);
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53 public void addSequence(SequenceI[] seq) {
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54 for (int i=0; i < seq.length; i++) {
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55 addSequence(seq[i]);
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59 /** Adds a sequence to the alignment. Recalculates maxLength and size.
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60 * Should put the new sequence in a sequence group!!!
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64 public void setSequenceAt(int i,SequenceI snew) {
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65 SequenceI oldseq = getSequenceAt(i);
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66 deleteSequence(oldseq);
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68 sequences.setElementAt(snew,i);
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70 ((SequenceGroup)groups.lastElement()).addSequence(snew);
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73 public Vector getGroups() {
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77 /** Sorts the sequences by sequence group size - largest to smallest.
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80 public void sortGroups() {
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81 float[] arr = new float [groups.size()];
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82 Object[] s = new Object[groups.size()];
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84 for (int i=0; i < groups.size(); i++) {
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85 arr[i] = ((SequenceGroup)groups.elementAt(i)).sequences.size();
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86 s[i] = groups.elementAt(i);
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89 QuickSort.sort(arr,s);
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91 Vector newg = new Vector(groups.size());
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93 for (int i=groups.size()-1; i >= 0; i--) {
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94 newg.addElement(s[i]);
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100 /** Takes out columns consisting entirely of gaps (-,.," ")
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102 public void removeGaps()
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106 int iSize = getWidth();
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107 for (int i=0; i < iSize; i++)
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109 boolean delete = true;
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110 for (int j=0; j < getHeight(); j++)
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112 current = getSequenceAt(j);
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113 if (current.getLength() > i)
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115 /* MC Should move this to a method somewhere */
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116 if (current.getCharAt(i)!='-' && current.getCharAt(i)!='.' && current.getCharAt(i)!=' ')
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124 deleteColumns(i,i);
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133 /** Returns an array of Sequences containing columns
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134 * start to end (inclusive) only.
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136 * @param start start column to fetch
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137 * @param end end column to fetch
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138 * @return Array of Sequences, ready to put into a new Alignment
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140 public SequenceI[] getColumns(int start, int end) {
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141 return getColumns(0,getHeight()-1,start,end);
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144 /** Removes a range of columns (start to end inclusive).
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146 * @param start Start column in the alignment
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147 * @param end End column in the alignment
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149 public void deleteColumns(int start, int end) {
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150 deleteColumns(0,getHeight()-1,start,end);
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153 public void deleteColumns(int seq1, int seq2, int start, int end) {
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155 for (int i=0; i <= (end-start); i++) {
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156 for (int j=seq1; j <= seq2; j++) {
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157 getSequenceAt(j).deleteCharAt(start);
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162 public void insertColumns(SequenceI[] seqs, int pos) {
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163 if (seqs.length == getHeight()) {
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164 for (int i=0; i < getHeight();i++) {
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165 String tmp = new String(getSequenceAt(i).getSequence());
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166 getSequenceAt(i).setSequence(tmp.substring(0,pos) + seqs[i].getSequence() + tmp.substring(pos));
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172 public SequenceI[] getColumns(int seq1, int seq2, int start, int end) {
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173 SequenceI[] seqs = new Sequence[(seq2-seq1)+1];
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174 for (int i=seq1; i<= seq2; i++ ) {
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175 seqs[i] = new Sequence(getSequenceAt(i).getName(),
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176 getSequenceAt(i).getSequence().substring(start,end),
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177 getSequenceAt(i).findPosition(start),
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178 getSequenceAt(i).findPosition(end));
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183 public void trimLeft(int i) {
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184 for (int j = 0;j< getHeight();j++) {
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186 SequenceI s = getSequenceAt(j);
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187 int newstart = s.findPosition(i);
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189 s.setStart(newstart);
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190 s.setSequence(s.getSequence().substring(i));
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195 public void trimRight(int i) {
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196 for (int j = 0;j< getHeight();j++) {
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197 SequenceI s = getSequenceAt(j);
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198 int newend = s.findPosition(i);
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201 s.setSequence(s.getSequence().substring(0,i+1));
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205 public void deleteSequence(SequenceI s)
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207 for (int i=0; i < getHeight(); i++)
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208 if (getSequenceAt(i) == s)
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212 public void deleteSequence(int i)
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214 sequences.removeElementAt(i);
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218 public Vector removeRedundancy(float threshold, Vector sel) {
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219 Vector del = new Vector();
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221 for (int i=1; i < sel.size(); i++) {
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222 for (int j = 0; j < i; j++) {
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223 // Only do the comparison if either have not been deleted
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224 if (!del.contains((SequenceI)sel.elementAt(i)) ||
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225 !del.contains((SequenceI)sel.elementAt(j))) {
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227 float pid = Comparison.compare((SequenceI)sel.elementAt(j),
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228 (SequenceI)sel.elementAt(i));
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230 if (pid >= threshold) {
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231 // Delete the shortest one
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232 if (((SequenceI)sel.elementAt(j)).getSequence().length() >
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233 ((SequenceI)sel.elementAt(i)).getSequence().length()) {
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234 del.addElement(sel.elementAt(i));
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235 System.out.println("Deleting sequence " + ((SequenceI)sel.elementAt(i)).getName());
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237 del.addElement(sel.elementAt(i));
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238 System.out.println("Deleting sequence " + ((SequenceI)sel.elementAt(i)).getName());
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245 // Now delete the sequences
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246 for (int i=0; i < del.size(); i++) {
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247 System.out.println("Deleting sequence " + ((SequenceI)del.elementAt(i)).getName());
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248 deleteSequence((SequenceI)del.elementAt(i));
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254 public void sortByPID(SequenceI s) {
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256 float scores[] = new float[getHeight()];
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257 SequenceI seqs[] = new SequenceI[getHeight()];
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259 for (int i = 0; i < getHeight(); i++) {
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260 scores[i] = Comparison.compare(getSequenceAt(i),s);
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261 seqs[i] = getSequenceAt(i);
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264 QuickSort.sort(scores,0,scores.length-1,seqs);
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268 if (getHeight()%2 == 0) {
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269 len = getHeight()/2;
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271 len = (getHeight()+1)/2;
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274 for (int i = 0; i < len; i++) {
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275 SequenceI tmp = seqs[i];
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276 sequences.setElementAt(seqs[getHeight()-i-1],i);
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277 sequences.setElementAt(tmp,getHeight()-i-1);
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281 public void sortByID() {
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282 String ids[] = new String[getHeight()];
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283 SequenceI seqs[] = new SequenceI[getHeight()];
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285 for (int i = 0; i < getHeight(); i++) {
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286 ids[i] = getSequenceAt(i).getName();
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287 seqs[i] = getSequenceAt(i);
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290 QuickSort.sort(ids,seqs);
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294 if (getHeight()%2 == 0) {
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295 len = getHeight()/2;
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297 len = (getHeight()+1)/2;
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298 System.out.println("Sort len is odd = " + len);
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300 for (int i = 0; i < len; i++) {
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301 System.out.println("Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName());
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302 SequenceI tmp = seqs[i];
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303 sequences.setElementAt(seqs[getHeight()-i-1],i);
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304 sequences.setElementAt(tmp,getHeight()-i-1);
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309 public SequenceGroup findGroup(int i) {
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310 return findGroup(getSequenceAt(i));
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314 public SequenceGroup findGroup(SequenceI s) {
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315 for (int i = 0; i < this.groups.size();i++)
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317 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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318 if (sg.sequences.contains(s))
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326 public void addToGroup(SequenceGroup g, SequenceI s) {
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327 if (!(g.sequences.contains(s))) {
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328 g.sequences.addElement(s);
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332 public void removeFromGroup(SequenceGroup g,SequenceI s) {
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333 if (g != null && g.sequences != null) {
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334 if (g.sequences.contains(s)) {
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335 g.sequences.removeElement(s);
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336 if (g.sequences.size() == 0) {
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337 groups.removeElement(g);
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344 public void addGroup(SequenceGroup sg) {
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345 if(!groups.contains(sg))
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346 groups.addElement(sg);
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350 public SequenceGroup addGroup() {
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351 SequenceGroup sg = new SequenceGroup();
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352 groups.addElement(sg);
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357 public void deleteGroup(SequenceGroup g) {
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358 if (groups.contains(g)) {
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359 groups.removeElement(g);
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364 public SequenceI findName(String name) {
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366 while (i < sequences.size()) {
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367 SequenceI s = getSequenceAt(i);
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368 if (s.getName().equals(name))
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377 public SequenceI findbyDisplayId(String name) {
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379 while (i < sequences.size()) {
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380 SequenceI s = getSequenceAt(i);
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381 if (s.getDisplayId().equals(name))
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390 public int findIndex(SequenceI s) {
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392 while (i < sequences.size()) {
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393 if (s == getSequenceAt(i)) {
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401 public int getHeight() {
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402 return sequences.size();
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406 public int getWidth()
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408 int maxLength = -1;
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409 for (int i = 0; i < sequences.size(); i++)
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411 if (getSequenceAt(i).getLength() > maxLength)
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412 maxLength = getSequenceAt(i).getLength();
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419 public int getMaxIdLength() {
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423 while (i < sequences.size()) {
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424 SequenceI seq = getSequenceAt(i);
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425 String tmp = seq.getName() + "/" + seq.getStart() + "-" + seq.getEnd();
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427 if (tmp.length() > max) {
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428 max = tmp.length();
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436 public void setGapCharacter(char gc)
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438 char old = getGapCharacter();
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440 for (int i=0; i < sequences.size(); i++)
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442 Sequence seq = (Sequence)sequences.elementAt(i);
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443 seq.sequence = seq.sequence.replace(old, gc);
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447 public char getGapCharacter() {
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448 return gapCharacter;
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451 public Vector getAAFrequency()
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453 return AAFrequency.calculate(sequences, 0, getWidth());
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