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 ArrayList superGroup = new ArrayList();
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15 protected char gapCharacter = '-';
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16 public AlignmentAnnotation [] annotations;
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17 public Conservation conservation;
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19 public boolean featuresAdded = false;
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21 /** Make an alignment from an array of Sequences.
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25 public Alignment(SequenceI[] seqs) {
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26 sequences = new Vector();
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28 for (int i=0; i < seqs.length; i++)
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29 sequences.addElement(seqs[i]);
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34 public Vector getSequences() {
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38 public SequenceI getSequenceAt(int i) {
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39 if (i < sequences.size()) {
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40 return (SequenceI)sequences.elementAt(i);
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46 /** Adds a sequence to the alignment. Recalculates maxLength and size.
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50 public void addSequence(SequenceI snew) {
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51 sequences.addElement(snew);
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54 public void addSequence(SequenceI[] seq) {
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55 for (int i=0; i < seq.length; i++) {
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56 addSequence(seq[i]);
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60 /** Adds a sequence to the alignment. Recalculates maxLength and size.
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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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71 public Vector getGroups() {
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75 /** Sorts the sequences by sequence group size - largest to smallest.
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78 public void sortGroups() {
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79 float[] arr = new float [groups.size()];
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80 Object[] s = new Object[groups.size()];
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82 for (int i=0; i < groups.size(); i++) {
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83 arr[i] = ((SequenceGroup)groups.elementAt(i)).sequences.size();
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84 s[i] = groups.elementAt(i);
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87 QuickSort.sort(arr,s);
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89 Vector newg = new Vector(groups.size());
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91 for (int i=groups.size()-1; i >= 0; i--) {
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92 newg.addElement(s[i]);
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98 /** Takes out columns consisting entirely of gaps (-,.," ")
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100 public void removeGaps()
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104 int iSize = getWidth();
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105 for (int i=0; i < iSize; i++)
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107 boolean delete = true;
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108 for (int j=0; j < getHeight(); j++)
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110 current = getSequenceAt(j);
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111 if (current.getLength() > i)
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113 /* MC Should move this to a method somewhere */
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114 if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))
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122 deleteColumns(i,i);
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131 /** Returns an array of Sequences containing columns
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132 * start to end (inclusive) only.
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134 * @param start start column to fetch
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135 * @param end end column to fetch
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136 * @return Array of Sequences, ready to put into a new Alignment
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138 public SequenceI[] getColumns(int start, int end) {
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139 return getColumns(0,getHeight()-1,start,end);
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142 /** Removes a range of columns (start to end inclusive).
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144 * @param start Start column in the alignment
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145 * @param end End column in the alignment
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147 public void deleteColumns(int start, int end) {
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148 deleteColumns(0,getHeight()-1,start,end);
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151 public void deleteColumns(int seq1, int seq2, int start, int end) {
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153 for (int i=0; i <= (end-start); i++) {
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154 for (int j=seq1; j <= seq2; j++) {
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155 getSequenceAt(j).deleteCharAt(start);
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160 public void insertColumns(SequenceI[] seqs, int pos) {
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161 if (seqs.length == getHeight()) {
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162 for (int i=0; i < getHeight();i++) {
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163 String tmp = new String(getSequenceAt(i).getSequence());
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164 getSequenceAt(i).setSequence(tmp.substring(0,pos) + seqs[i].getSequence() + tmp.substring(pos));
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170 public SequenceI[] getColumns(int seq1, int seq2, int start, int end) {
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171 SequenceI[] seqs = new Sequence[(seq2-seq1)+1];
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172 for (int i=seq1; i<= seq2; i++ ) {
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173 seqs[i] = new Sequence(getSequenceAt(i).getName(),
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174 getSequenceAt(i).getSequence().substring(start,end),
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175 getSequenceAt(i).findPosition(start),
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176 getSequenceAt(i).findPosition(end));
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181 public void trimLeft(int i) {
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182 for (int j = 0;j< getHeight();j++) {
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184 SequenceI s = getSequenceAt(j);
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185 int newstart = s.findPosition(i);
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187 s.setStart(newstart);
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188 s.setSequence(s.getSequence().substring(i));
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193 public void trimRight(int i) {
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194 for (int j = 0;j< getHeight();j++) {
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195 SequenceI s = getSequenceAt(j);
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196 int newend = s.findPosition(i);
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199 s.setSequence(s.getSequence().substring(0,i+1));
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203 public void deleteSequence(SequenceI s)
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205 for (int i=0; i < getHeight(); i++)
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206 if (getSequenceAt(i) == s)
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210 public void deleteSequence(int i)
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212 sequences.removeElementAt(i);
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216 public Vector removeRedundancy(float threshold, Vector sel) {
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217 Vector del = new Vector();
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219 for (int i = 1; i < sel.size(); i++)
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221 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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228 float pid = Comparison.compare( (SequenceI) sel.elementAt(j),
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229 (SequenceI) sel.elementAt(i));
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231 if (pid >= threshold)
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233 // Delete the shortest one
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234 if ( ( (SequenceI) sel.elementAt(j)).getSequence().length() >
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235 ( (SequenceI) sel.elementAt(i)).getSequence().length())
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236 del.addElement(sel.elementAt(i));
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238 del.addElement(sel.elementAt(i));
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244 // Now delete the sequences
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245 for (int i=0; i < del.size(); i++)
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246 deleteSequence((SequenceI)del.elementAt(i));
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251 public void sortByPID(SequenceI s) {
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253 float scores[] = new float[getHeight()];
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254 SequenceI seqs[] = new SequenceI[getHeight()];
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256 for (int i = 0; i < getHeight(); i++) {
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257 scores[i] = Comparison.compare(getSequenceAt(i),s);
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258 seqs[i] = getSequenceAt(i);
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261 QuickSort.sort(scores,0,scores.length-1,seqs);
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265 if (getHeight()%2 == 0) {
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266 len = getHeight()/2;
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268 len = (getHeight()+1)/2;
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271 for (int i = 0; i < len; i++) {
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272 SequenceI tmp = seqs[i];
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273 sequences.setElementAt(seqs[getHeight()-i-1],i);
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274 sequences.setElementAt(tmp,getHeight()-i-1);
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278 public void sortByID() {
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279 String ids[] = new String[getHeight()];
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280 SequenceI seqs[] = new SequenceI[getHeight()];
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282 for (int i = 0; i < getHeight(); i++) {
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283 ids[i] = getSequenceAt(i).getName();
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284 seqs[i] = getSequenceAt(i);
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287 QuickSort.sort(ids,seqs);
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291 if (getHeight()%2 == 0) {
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292 len = getHeight()/2;
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294 len = (getHeight()+1)/2;
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295 System.out.println("Sort len is odd = " + len);
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297 for (int i = 0; i < len; i++) {
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298 System.out.println("Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName());
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299 SequenceI tmp = seqs[i];
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300 sequences.setElementAt(seqs[getHeight()-i-1],i);
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301 sequences.setElementAt(tmp,getHeight()-i-1);
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306 public SequenceGroup findGroup(int i) {
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307 return findGroup(getSequenceAt(i));
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311 public SequenceGroup findGroup(SequenceI s) {
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312 for (int i = 0; i < this.groups.size();i++)
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314 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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315 if (sg.sequences.contains(s))
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322 public SequenceGroup [] findAllGroups(SequenceI s)
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325 ArrayList temp = new ArrayList();
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327 for (int i = 0; i < this.groups.size();i++)
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329 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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331 if (sg.sequences.contains(s))
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335 SequenceGroup [] ret = new SequenceGroup[temp.size()];
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336 temp.toArray( ret );
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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.add(sg);
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364 public void removeSuperGroup(SuperGroup sg)
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366 superGroup.remove(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.get(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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389 superGroup.clear();
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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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484 char old = getGapCharacter();
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486 for (int i=0; i < sequences.size(); i++)
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488 Sequence seq = (Sequence)sequences.elementAt(i);
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489 seq.sequence = seq.sequence.replace(old, 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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