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 boolean featuresAdded = false;
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18 /** Make an alignment from an array of Sequences.
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22 public Alignment(SequenceI[] seqs) {
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23 sequences = new Vector();
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25 for (int i=0; i < seqs.length; i++)
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26 sequences.addElement(seqs[i]);
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31 public Vector getSequences() {
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35 public SequenceI getSequenceAt(int i) {
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36 if (i < sequences.size()) {
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37 return (SequenceI)sequences.elementAt(i);
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43 /** Adds a sequence to the alignment. Recalculates maxLength and size.
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47 public void addSequence(SequenceI snew) {
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48 sequences.addElement(snew);
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51 public void addSequence(SequenceI[] seq) {
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52 for (int i=0; i < seq.length; i++) {
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53 addSequence(seq[i]);
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57 /** Adds a sequence to the alignment. Recalculates maxLength and size.
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61 public void setSequenceAt(int i,SequenceI snew) {
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62 SequenceI oldseq = getSequenceAt(i);
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63 deleteSequence(oldseq);
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65 sequences.setElementAt(snew,i);
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68 public Vector getGroups() {
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72 /** Sorts the sequences by sequence group size - largest to smallest.
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75 public void sortGroups() {
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76 float[] arr = new float [groups.size()];
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77 Object[] s = new Object[groups.size()];
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79 for (int i=0; i < groups.size(); i++) {
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80 arr[i] = ((SequenceGroup)groups.elementAt(i)).sequences.size();
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81 s[i] = groups.elementAt(i);
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84 QuickSort.sort(arr,s);
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86 Vector newg = new Vector(groups.size());
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88 for (int i=groups.size()-1; i >= 0; i--) {
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89 newg.addElement(s[i]);
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95 /** Takes out columns consisting entirely of gaps (-,.," ")
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97 public void removeGaps()
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101 int iSize = getWidth();
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102 for (int i=0; i < iSize; i++)
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104 boolean delete = true;
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105 for (int j=0; j < getHeight(); j++)
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107 current = getSequenceAt(j);
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108 if (current.getLength() > i)
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110 /* MC Should move this to a method somewhere */
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111 if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))
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119 deleteColumns(i,i);
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128 /** Returns an array of Sequences containing columns
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129 * start to end (inclusive) only.
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131 * @param start start column to fetch
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132 * @param end end column to fetch
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133 * @return Array of Sequences, ready to put into a new Alignment
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135 public SequenceI[] getColumns(int start, int end) {
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136 return getColumns(0,getHeight()-1,start,end);
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139 /** Removes a range of columns (start to end inclusive).
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141 * @param start Start column in the alignment
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142 * @param end End column in the alignment
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144 public void deleteColumns(int start, int end) {
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145 deleteColumns(0,getHeight()-1,start,end);
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148 public void deleteColumns(int seq1, int seq2, int start, int end) {
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150 for (int i=0; i <= (end-start); i++) {
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151 for (int j=seq1; j <= seq2; j++) {
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152 getSequenceAt(j).deleteCharAt(start);
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157 public void insertColumns(SequenceI[] seqs, int pos) {
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158 if (seqs.length == getHeight()) {
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159 for (int i=0; i < getHeight();i++) {
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160 String tmp = new String(getSequenceAt(i).getSequence());
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161 getSequenceAt(i).setSequence(tmp.substring(0,pos) + seqs[i].getSequence() + tmp.substring(pos));
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167 public SequenceI[] getColumns(int seq1, int seq2, int start, int end) {
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168 SequenceI[] seqs = new Sequence[(seq2-seq1)+1];
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169 for (int i=seq1; i<= seq2; i++ ) {
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170 seqs[i] = new Sequence(getSequenceAt(i).getName(),
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171 getSequenceAt(i).getSequence().substring(start,end),
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172 getSequenceAt(i).findPosition(start),
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173 getSequenceAt(i).findPosition(end));
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178 public void trimLeft(int i) {
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179 for (int j = 0;j< getHeight();j++) {
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181 SequenceI s = getSequenceAt(j);
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182 int newstart = s.findPosition(i);
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184 s.setStart(newstart);
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185 s.setSequence(s.getSequence().substring(i));
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190 public void trimRight(int i) {
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191 for (int j = 0;j< getHeight();j++) {
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192 SequenceI s = getSequenceAt(j);
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193 int newend = s.findPosition(i);
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196 s.setSequence(s.getSequence().substring(0,i+1));
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200 public void deleteSequence(SequenceI s)
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202 for (int i=0; i < getHeight(); i++)
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203 if (getSequenceAt(i) == s)
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207 public void deleteSequence(int i)
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209 sequences.removeElementAt(i);
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213 public Vector removeRedundancy(float threshold, Vector sel) {
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214 Vector del = new Vector();
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216 for (int i = 1; i < sel.size(); i++)
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218 for (int j = 0; j < i; j++)
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220 // Only do the comparison if either have not been deleted
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221 if (!del.contains( (SequenceI) sel.elementAt(i)) ||
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222 !del.contains( (SequenceI) sel.elementAt(j)))
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225 float pid = Comparison.compare( (SequenceI) sel.elementAt(j),
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226 (SequenceI) sel.elementAt(i));
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228 if (pid >= threshold)
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230 // Delete the shortest one
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231 if ( ( (SequenceI) sel.elementAt(j)).getSequence().length() >
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232 ( (SequenceI) sel.elementAt(i)).getSequence().length())
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233 del.addElement(sel.elementAt(i));
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235 del.addElement(sel.elementAt(i));
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241 // Now delete the sequences
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242 for (int i=0; i < del.size(); i++)
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243 deleteSequence((SequenceI)del.elementAt(i));
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248 public void sortByPID(SequenceI s) {
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250 float scores[] = new float[getHeight()];
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251 SequenceI seqs[] = new SequenceI[getHeight()];
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253 for (int i = 0; i < getHeight(); i++) {
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254 scores[i] = Comparison.compare(getSequenceAt(i),s);
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255 seqs[i] = getSequenceAt(i);
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258 QuickSort.sort(scores,0,scores.length-1,seqs);
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262 if (getHeight()%2 == 0) {
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263 len = getHeight()/2;
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265 len = (getHeight()+1)/2;
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268 for (int i = 0; i < len; i++) {
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269 SequenceI tmp = seqs[i];
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270 sequences.setElementAt(seqs[getHeight()-i-1],i);
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271 sequences.setElementAt(tmp,getHeight()-i-1);
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275 public void sortByID() {
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276 String ids[] = new String[getHeight()];
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277 SequenceI seqs[] = new SequenceI[getHeight()];
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279 for (int i = 0; i < getHeight(); i++) {
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280 ids[i] = getSequenceAt(i).getName();
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281 seqs[i] = getSequenceAt(i);
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284 QuickSort.sort(ids,seqs);
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288 if (getHeight()%2 == 0) {
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289 len = getHeight()/2;
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291 len = (getHeight()+1)/2;
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292 System.out.println("Sort len is odd = " + len);
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294 for (int i = 0; i < len; i++) {
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295 System.out.println("Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName());
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296 SequenceI tmp = seqs[i];
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297 sequences.setElementAt(seqs[getHeight()-i-1],i);
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298 sequences.setElementAt(tmp,getHeight()-i-1);
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303 public SequenceGroup findGroup(int i) {
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304 return findGroup(getSequenceAt(i));
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308 public SequenceGroup findGroup(SequenceI s) {
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309 for (int i = 0; i < this.groups.size();i++)
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311 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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312 if (sg.sequences.contains(s))
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319 public SequenceGroup [] findAllGroups(SequenceI s)
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322 ArrayList temp = new ArrayList();
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324 for (int i = 0; i < this.groups.size();i++)
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326 SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
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328 if (sg.sequences.contains(s))
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332 SequenceGroup [] ret = new SequenceGroup[temp.size()];
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333 temp.toArray( ret );
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339 public void addToGroup(SequenceGroup g, SequenceI s) {
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340 if (!(g.sequences.contains(s))) {
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341 g.sequences.addElement(s);
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345 public void removeFromGroup(SequenceGroup g,SequenceI s) {
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346 if (g != null && g.sequences != null) {
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347 if (g.sequences.contains(s)) {
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348 g.sequences.removeElement(s);
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349 if (g.sequences.size() == 0) {
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350 groups.removeElement(g);
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356 public void addSuperGroup(SuperGroup sg)
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358 superGroup.add(sg);
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361 public void removeSuperGroup(SuperGroup sg)
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363 superGroup.remove(sg);
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366 public SuperGroup getSuperGroup(SequenceGroup sg)
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368 for (int i = 0; i < this.superGroup.size(); i++)
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370 SuperGroup temp = (SuperGroup) superGroup.get(i);
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371 if (temp.sequenceGroups.contains(sg))
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378 public void addGroup(SequenceGroup sg) {
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379 if(!groups.contains(sg))
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380 groups.addElement(sg);
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383 public void deleteAllGroups()
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386 superGroup.clear();
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388 while (i < sequences.size()) {
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389 SequenceI s = getSequenceAt(i);
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390 s.setColor(java.awt.Color.white);
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398 public void deleteGroup(SequenceGroup g) {
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399 if (groups.contains(g)) {
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400 groups.removeElement(g);
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405 public SequenceI findName(String name) {
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407 while (i < sequences.size()) {
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408 SequenceI s = getSequenceAt(i);
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409 if (s.getName().equals(name))
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418 public SequenceI findbyDisplayId(String name) {
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420 while (i < sequences.size()) {
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421 SequenceI s = getSequenceAt(i);
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422 if (s.getDisplayId().equals(name))
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431 public int findIndex(SequenceI s)
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434 while (i < sequences.size())
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436 if (s == getSequenceAt(i))
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444 public int getHeight() {
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445 return sequences.size();
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449 public int getWidth()
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451 int maxLength = -1;
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452 for (int i = 0; i < sequences.size(); i++)
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454 if (getSequenceAt(i).getLength() > maxLength)
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455 maxLength = getSequenceAt(i).getLength();
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462 public int getMaxIdLength() {
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466 while (i < sequences.size()) {
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467 SequenceI seq = getSequenceAt(i);
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468 String tmp = seq.getName() + "/" + seq.getStart() + "-" + seq.getEnd();
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470 if (tmp.length() > max) {
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471 max = tmp.length();
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479 public void setGapCharacter(char gc)
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481 char old = getGapCharacter();
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483 for (int i=0; i < sequences.size(); i++)
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485 Sequence seq = (Sequence)sequences.elementAt(i);
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486 seq.sequence = seq.sequence.replace(old, gc);
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490 public char getGapCharacter() {
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491 return gapCharacter;
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494 public Vector getAAFrequency()
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496 return AAFrequency.calculate(sequences, 0, getWidth());
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499 public boolean isAligned()
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501 int width = getWidth();
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502 for (int i = 0; i < sequences.size(); i++)
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503 if (getSequenceAt(i).getLength() != width)
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