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 protected Vector superGroup = new Vector();
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15 protected char gapCharacter = '-';
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16 public AlignmentAnnotation [] annotations;
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18 public boolean featuresAdded = false;
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20 /** Make an alignment from an array of Sequences.
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24 public Alignment(SequenceI[] seqs) {
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25 sequences = new Vector();
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27 for (int i=0; i < seqs.length; i++)
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28 sequences.addElement(seqs[i]);
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33 public Vector getSequences() {
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37 public SequenceI getSequenceAt(int i) {
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38 if (i < sequences.size()) {
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39 return (SequenceI)sequences.elementAt(i);
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45 /** Adds a sequence to the alignment. Recalculates maxLength and size.
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49 public void addSequence(SequenceI snew) {
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50 sequences.addElement(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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63 public void setSequenceAt(int i,SequenceI snew) {
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64 SequenceI oldseq = getSequenceAt(i);
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65 deleteSequence(oldseq);
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67 sequences.setElementAt(snew,i);
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70 public Vector getGroups() {
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74 /** Sorts the sequences by sequence group size - largest to smallest.
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77 public void sortGroups() {
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78 float[] arr = new float [groups.size()];
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79 Object[] s = new Object[groups.size()];
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81 for (int i=0; i < groups.size(); i++) {
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82 arr[i] = ((SequenceGroup)groups.elementAt(i)).sequences.size();
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83 s[i] = groups.elementAt(i);
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86 QuickSort.sort(arr,s);
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88 Vector newg = new Vector(groups.size());
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90 for (int i=groups.size()-1; i >= 0; i--) {
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91 newg.addElement(s[i]);
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97 /** Takes out columns consisting entirely of gaps (-,.," ")
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99 public void removeGaps()
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103 int iSize = getWidth();
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104 for (int i=0; i < iSize; i++)
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106 boolean delete = true;
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107 for (int j=0; j < getHeight(); j++)
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109 current = getSequenceAt(j);
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110 if (current.getLength() > i)
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112 /* MC Should move this to a method somewhere */
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113 if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))
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121 deleteColumns(i,i);
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130 /** Returns an array of Sequences containing columns
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131 * start to end (inclusive) only.
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133 * @param start start column to fetch
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134 * @param end end column to fetch
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135 * @return Array of Sequences, ready to put into a new Alignment
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137 public SequenceI[] getColumns(int start, int end) {
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138 return getColumns(0,getHeight()-1,start,end);
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141 /** Removes a range of columns (start to end inclusive).
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143 * @param start Start column in the alignment
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144 * @param end End column in the alignment
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146 public void deleteColumns(int start, int end) {
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147 deleteColumns(0,getHeight()-1,start,end);
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150 public void deleteColumns(int seq1, int seq2, int start, int end) {
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152 for (int i=0; i <= (end-start); i++) {
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153 for (int j=seq1; j <= seq2; j++) {
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154 getSequenceAt(j).deleteCharAt(start);
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159 public void insertColumns(SequenceI[] seqs, int pos) {
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160 if (seqs.length == getHeight()) {
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161 for (int i=0; i < getHeight();i++) {
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162 String tmp = new String(getSequenceAt(i).getSequence());
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163 getSequenceAt(i).setSequence(tmp.substring(0,pos) + seqs[i].getSequence() + tmp.substring(pos));
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169 public SequenceI[] getColumns(int seq1, int seq2, int start, int end) {
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170 SequenceI[] seqs = new Sequence[(seq2-seq1)+1];
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171 for (int i=seq1; i<= seq2; i++ ) {
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172 seqs[i] = new Sequence(getSequenceAt(i).getName(),
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173 getSequenceAt(i).getSequence().substring(start,end),
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174 getSequenceAt(i).findPosition(start),
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175 getSequenceAt(i).findPosition(end));
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180 public void trimLeft(int i) {
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181 for (int j = 0;j< getHeight();j++) {
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183 SequenceI s = getSequenceAt(j);
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184 int newstart = s.findPosition(i);
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186 s.setStart(newstart);
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187 s.setSequence(s.getSequence().substring(i));
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192 public void trimRight(int i) {
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193 for (int j = 0;j< getHeight();j++) {
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194 SequenceI s = getSequenceAt(j);
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195 int newend = s.findPosition(i);
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198 s.setSequence(s.getSequence().substring(0,i+1));
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202 public void deleteSequence(SequenceI s)
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204 for (int i=0; i < getHeight(); i++)
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205 if (getSequenceAt(i) == s)
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209 public void deleteSequence(int i)
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211 sequences.removeElementAt(i);
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215 public Vector removeRedundancy(float threshold, Vector sel) {
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216 Vector del = new Vector();
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218 for (int i = 1; i < sel.size(); i++)
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220 for (int j = 0; j < i; j++)
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222 // Only do the comparison if either have not been deleted
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223 if (!del.contains( (SequenceI) sel.elementAt(i)) ||
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224 !del.contains( (SequenceI) sel.elementAt(j)))
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226 // use PID instead of Comparison (which is really not pleasant)
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227 float pid = Comparison.PID( (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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232 // Delete the shortest one
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233 if ( ( (SequenceI) sel.elementAt(j)).getSequence().length() >
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234 ( (SequenceI) sel.elementAt(i)).getSequence().length())
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235 del.addElement(sel.elementAt(i));
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237 del.addElement(sel.elementAt(i));
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243 // Now delete the sequences
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244 for (int i=0; i < del.size(); i++)
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245 deleteSequence((SequenceI)del.elementAt(i));
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250 public void sortByPID(SequenceI s) {
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252 float scores[] = new float[getHeight()];
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253 SequenceI seqs[] = new SequenceI[getHeight()];
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255 for (int i = 0; i < getHeight(); i++) {
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256 scores[i] = Comparison.compare(getSequenceAt(i),s);
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257 seqs[i] = getSequenceAt(i);
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260 QuickSort.sort(scores,0,scores.length-1,seqs);
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264 if (getHeight()%2 == 0) {
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265 len = getHeight()/2;
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267 len = (getHeight()+1)/2;
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270 for (int i = 0; i < len; i++) {
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271 SequenceI tmp = seqs[i];
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272 sequences.setElementAt(seqs[getHeight()-i-1],i);
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273 sequences.setElementAt(tmp,getHeight()-i-1);
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277 public void sortByID() {
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278 String ids[] = new String[getHeight()];
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279 SequenceI seqs[] = new SequenceI[getHeight()];
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281 for (int i = 0; i < getHeight(); i++) {
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282 ids[i] = getSequenceAt(i).getName();
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283 seqs[i] = getSequenceAt(i);
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286 QuickSort.sort(ids,seqs);
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290 if (getHeight()%2 == 0) {
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291 len = getHeight()/2;
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293 len = (getHeight()+1)/2;
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294 System.out.println("DEBUG:Sort len is odd = " + len); // log.
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296 for (int i = 0; i < len; i++) {
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297 System.out.println("DEBUG:Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName()); // log.
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298 SequenceI tmp = seqs[i];
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299 sequences.setElementAt(seqs[getHeight()-i-1],i);
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300 sequences.setElementAt(tmp,getHeight()-i-1);
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305 public SequenceGroup findGroup(int i) {
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306 return findGroup(getSequenceAt(i));
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310 public SequenceGroup findGroup(SequenceI s) {
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311 for (int i = 0; i < this.groups.size();i++)
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313 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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314 if (sg.sequences.contains(s))
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321 public SequenceGroup [] findAllGroups(SequenceI s)
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324 Vector temp = new Vector();
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326 for (int i = 0; i < this.groups.size();i++)
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328 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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330 if (sg.sequences.contains(s))
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331 temp.addElement(sg);
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334 SequenceGroup [] ret = new SequenceGroup[temp.size()];
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335 for(int i=0; i<temp.size(); i++)
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336 ret[i] = (SequenceGroup)temp.elementAt(i);
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342 public void addToGroup(SequenceGroup g, SequenceI s) {
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343 if (!(g.sequences.contains(s))) {
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344 g.sequences.addElement(s);
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348 public void removeFromGroup(SequenceGroup g,SequenceI s) {
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349 if (g != null && g.sequences != null) {
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350 if (g.sequences.contains(s)) {
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351 g.sequences.removeElement(s);
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352 if (g.sequences.size() == 0) {
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353 groups.removeElement(g);
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359 public void addSuperGroup(SuperGroup sg)
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361 superGroup.addElement(sg);
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364 public void removeSuperGroup(SuperGroup sg)
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366 superGroup.removeElement(sg);
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369 public SuperGroup getSuperGroup(SequenceGroup sg)
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371 for (int i = 0; i < this.superGroup.size(); i++)
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373 SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
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374 if (temp.sequenceGroups.contains(sg))
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381 public void addGroup(SequenceGroup sg) {
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382 if(!groups.contains(sg))
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383 groups.addElement(sg);
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386 public void deleteAllGroups()
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388 groups.removeAllElements();
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389 superGroup.removeAllElements();
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391 while (i < sequences.size()) {
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392 SequenceI s = getSequenceAt(i);
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393 s.setColor(java.awt.Color.white);
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401 public void deleteGroup(SequenceGroup g) {
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402 if (groups.contains(g)) {
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403 groups.removeElement(g);
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408 public SequenceI findName(String name) {
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410 while (i < sequences.size()) {
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411 SequenceI s = getSequenceAt(i);
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412 if (s.getName().equals(name))
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421 public SequenceI findbyDisplayId(String name) {
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423 while (i < sequences.size()) {
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424 SequenceI s = getSequenceAt(i);
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425 if (s.getDisplayId().equals(name))
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434 public int findIndex(SequenceI s)
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437 while (i < sequences.size())
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439 if (s == getSequenceAt(i))
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447 public int getHeight() {
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448 return sequences.size();
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452 public int getWidth()
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454 int maxLength = -1;
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455 for (int i = 0; i < sequences.size(); i++)
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457 if (getSequenceAt(i).getLength() > maxLength)
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458 maxLength = getSequenceAt(i).getLength();
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465 public int getMaxIdLength() {
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469 while (i < sequences.size()) {
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470 SequenceI seq = getSequenceAt(i);
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471 String tmp = seq.getName() + "/" + seq.getStart() + "-" + seq.getEnd();
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473 if (tmp.length() > max) {
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474 max = tmp.length();
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482 public void setGapCharacter(char gc)
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485 for (int i=0; i < sequences.size(); i++)
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487 Sequence seq = (Sequence)sequences.elementAt(i);
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488 seq.sequence = seq.sequence.replace('.', gc);
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489 seq.sequence = seq.sequence.replace('-', gc);
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493 public char getGapCharacter() {
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494 return gapCharacter;
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497 public Vector getAAFrequency()
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499 return AAFrequency.calculate(sequences, 0, getWidth());
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502 public boolean isAligned()
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504 int width = getWidth();
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505 for (int i = 0; i < sequences.size(); i++)
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506 if (getSequenceAt(i).getLength() != width)
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512 public void deleteAnnotation(AlignmentAnnotation aa)
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515 if(annotations!=null)
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516 aSize = annotations.length;
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518 AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize-1];
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521 for (int i = 0; i < aSize; i++)
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523 if(annotations[i]==aa)
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527 temp[tIndex] = annotations[i];
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531 annotations = temp;
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535 public void addAnnotation(AlignmentAnnotation aa)
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538 if(annotations!=null)
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539 aSize = annotations.length+1;
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541 AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize];
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544 for (i = 0; i < aSize-1; i++)
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545 temp[i] = annotations[i];
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549 annotations = temp;
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551 public AlignmentAnnotation[] getAlignmentAnnotation()
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553 return annotations;
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