1 package jalview.analysis;
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3 import jalview.jbgui.*;
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4 import jalview.datamodel.*;
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6 import jalview.analysis.*;
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9 import java.applet.Applet;
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14 public class AAFrequency {
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16 // Takes in a vector of sequences and column start and column end
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17 // and returns a vector of size (end-start+1). Each element of the
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18 // vector contains a hashtable with the keys being residues and
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19 // the values being the count of each residue in that column.
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20 // This class is used extensively in calculating alignment colourschemes
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21 // that depend on the amount of conservation in each alignment column.
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24 public static Vector calculate(Vector sequences,int start,int end) {
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26 Vector result = new Vector();
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28 for (int i = start;i <= end; i++)
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31 Hashtable residueHash = new Hashtable();
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33 String maxResidue = "-";
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35 for (int j=0; j < sequences.size(); j++)
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38 if (sequences.elementAt(j) instanceof Sequence)
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40 Sequence s = (Sequence)sequences.elementAt(j);
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42 if (s.getSequence().length() > i)
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45 String res = s.getSequence().charAt(i)+"";
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47 if (!jalview.util.Comparison.isGap(res.charAt(0)))
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50 res = "-"; // we always use this for gaps in the property vectors
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52 if (residueHash.containsKey(res))
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55 int count = ((Integer)residueHash.get(res)).intValue() ;
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58 if (!jalview.util.Comparison.isGap(res.charAt(0)) && count >= maxCount)
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63 else if(maxResidue.indexOf(res)==-1)
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69 residueHash.put(res,new Integer(count));
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72 residueHash.put(res,new Integer(1));
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78 if (residueHash.containsKey("-"))
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80 int count = ((Integer)residueHash.get("-")).intValue() ;
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82 residueHash.put("-",new Integer(count));
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85 residueHash.put("-",new Integer(1));
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91 residueHash.put("maxCount",new Integer(maxCount));
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93 System.out.println("asasa "+maxCount);
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94 residueHash.put("maxResidue", maxResidue);
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95 residueHash.put("size", new Integer(sequences.size()));
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96 residueHash.put("nongap", new Integer(nongap));
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97 result.addElement(residueHash);
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103 public static Vector calculatePID(SequenceI refseq,Vector sequences,int window,int start,int end) {
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105 Vector result = new Vector();
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107 boolean init = true;
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110 Vector prev = null;
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112 for (int i = start;i <= end; i++) {
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113 Vector values = new Vector();
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115 result.addElement(values);
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117 // If start < window/2 then set value to zero.
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119 if (i< window/2 || i >= refseq.getSequence().length()-window/2) {
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120 for (int j = 0; j < sequences.size(); j++) {
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121 values.addElement(new Integer(0));
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123 } else if (init == true) {
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126 int winstart = i-window/2;
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127 int winend = i+window/2;
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129 if (window%2 != 0) {
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133 for (int j = 0; j < sequences.size(); j++) {
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134 values.addElement(new Integer(0));
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137 for (int k = winstart; k <= winend; k++) {
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138 String refchar = refseq.getSequence().substring(k,k+1);
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139 if (jalview.util.Comparison.isGap(refchar.charAt(0)))
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142 for (int j = 0; j < sequences.size(); j++) {
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144 Sequence s = (Sequence)sequences.elementAt(j);
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146 if (s.getSequence().length() > k) {
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148 String res = s.getSequence().substring(k,k+1); // no gapchar test needed
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150 if (res.equals(refchar)) {
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151 int val = ((Integer)values.elementAt(j)).intValue();
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153 values.setElementAt(new Integer(val),j);
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163 int winstart = i-window/2;
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164 int winend = i+window/2;
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166 if (window%2 != 0) {
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169 // We need to take the previous set of values
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170 // subtract the pid at winstart-1
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171 // and add the pid at winend;
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173 String pre_refchar = refseq.getSequence().substring(winstart-1,winstart);
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174 String pos_refchar = "-";
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176 if (refseq.getSequence().length() > winend) {
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177 pos_refchar = refseq.getSequence().substring(winend,winend+1);
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180 for (int j = 0; j < sequences.size(); j++) {
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181 // First copy the pid value from i-1
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183 int val = ((Integer)prev.elementAt(j)).intValue();
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185 Sequence s = (Sequence)sequences.elementAt(j);
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187 String pre_char = s.getSequence().substring(winstart-1,winstart);
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189 String pos_char = "-";
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191 if (s.getSequence().length() > winend) {
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192 pos_char = s.getSequence().substring(winend,winend+1);
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195 // Now substract 1 if the chars at winstart-1 match
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197 if (jalview.util.Comparison.isGap(pre_refchar.charAt(0)) == false
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198 && pre_char.equals(pre_refchar)) {
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202 if (jalview.util.Comparison.isGap(pos_refchar.charAt(0)) == false
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203 && pos_char.equals(pos_refchar)) {
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207 values.addElement(new Integer(val));
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218 public static Hashtable findBlocks(Vector seqs, int start, int end,Vector exc) {
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220 // start and end are in real (not relative coords);
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222 // The coords in the hashtable that is returned are in relative coords
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223 // i.e. start from 0
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225 Hashtable blocks = new Hashtable();
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227 boolean prev = false;
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230 for (int i = start; i <= end ; i++) {
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231 SequenceI seq = (SequenceI)seqs.elementAt(0);
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233 char c = seq.getCharAt(i);
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235 boolean found = true;
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239 while (j < seqs.size() && found == true) {
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241 SequenceI jseq = (SequenceI)seqs.elementAt(j);
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243 if (!exc.contains(jseq)) {
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245 char cc = jseq.getCharAt(i);
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255 if (prev == false && found == true) {
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257 } else if (prev == true && found == false && bstart != -1) {
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259 int blockstart = bstart-start;
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260 int blocklen = i-bstart;
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262 //System.out.println("Start len " + blockstart + " " + blocklen);
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264 for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
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265 blocks.put(new Integer(jj),new Integer(blocklen));
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273 if (bstart != -1) {
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275 int blockstart = bstart-start;
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276 int blocklen = end-bstart;
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278 // System.out.println("Start len " + blockstart + " " + blocklen);
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280 for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
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281 blocks.put(new Integer(blockstart),new Integer(blocklen));
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290 public static Hashtable findKmerCount(SequenceI seq, int start, int end,int window, int step,Vector kmers) {
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292 int tmpstart = start;
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293 Hashtable vals = new Hashtable();
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295 while (tmpstart <= end) {
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297 String tmpstr = seq.getSequence().substring(tmpstart-window/2,tmpstart+window/2);
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301 //System.out.println("Str " + tmpstr);
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303 for (int ii = 0; ii < kmers.size(); ii++) {
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304 String kmer = ((SequenceI)kmers.elementAt(ii)).getSequence();
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308 while (tmpstr.indexOf(kmer,i) != -1) {
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309 i = tmpstr.indexOf(kmer,i);
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316 vals.put(new Integer(tmpstart),new Integer(count));
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322 public static Hashtable findBlockStarts(Vector seqs, int start, int end,Vector exc) {
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324 // start and end are in real (not relative coords);
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326 // The coords in the hashtable that is returned are in relative coords
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327 // i.e. start from 0
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329 Hashtable blocks = new Hashtable();
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331 boolean prev = false;
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334 for (int i = start; i <= end ; i++) {
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335 SequenceI seq = (SequenceI)seqs.elementAt(0);
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337 char c = seq.getCharAt(i);
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339 boolean found = true;
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343 while (j < seqs.size() && found == true) {
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345 SequenceI jseq = (SequenceI)seqs.elementAt(j);
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347 if (!exc.contains(jseq)) {
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349 char cc = jseq.getCharAt(i);
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359 if (prev == false && found == true) {
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361 } else if (prev == true && found == false && bstart != -1) {
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363 int blockstart = bstart-start;
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364 int blocklen = i-bstart;
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366 // System.out.println("Start len " + blockstart + " " + blocklen);
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368 //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
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369 blocks.put(new Integer(blockstart),new Integer(blocklen));
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377 if (bstart != -1) {
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379 int blockstart = bstart-start;
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380 int blocklen = end-bstart;
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382 // System.out.println("Start len " + blockstart + " " + blocklen);
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384 //for (int jj = blockstart; jj < blockstart + blocklen;jj++) {
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385 blocks.put(new Integer(blockstart),new Integer(blocklen));
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