2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.analysis;
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21 import jalview.datamodel.SequenceI;
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23 import jalview.schemes.*;
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25 import jalview.util.*;
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36 * @version $Revision$
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38 public class AlignSeq
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40 /** DOCUMENT ME!! */
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41 public static java.util.Hashtable dnaHash = new java.util.Hashtable();
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45 dnaHash.put("C", new Integer(0));
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46 dnaHash.put("T", new Integer(1));
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47 dnaHash.put("A", new Integer(2));
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48 dnaHash.put("G", new Integer(3));
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49 dnaHash.put("-", new Integer(4));
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52 static String[] dna = { "C", "T", "A", "G", "-" };
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53 static String[] pep =
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55 "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
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56 "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-"
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72 public String astr1 = "";
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73 public String astr2 = "";
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75 /** DOCUMENT ME!! */
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76 public int seq1start;
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78 /** DOCUMENT ME!! */
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81 /** DOCUMENT ME!! */
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82 public int seq2start;
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84 /** DOCUMENT ME!! */
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88 /** DOCUMENT ME!! */
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89 public int maxscore;
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94 int[][] lookup = ResidueProperties.getBLOSUM62();
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95 String[] intToStr = pep;
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97 StringBuffer output = new StringBuffer();
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102 * Creates a new AlignSeq object.
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104 * @param s1 DOCUMENT ME!
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105 * @param s2 DOCUMENT ME!
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106 * @param type DOCUMENT ME!
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108 public AlignSeq(SequenceI s1, SequenceI s2, String type)
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110 rt = Runtime.getRuntime();
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111 SeqInit(s1, s1.getSequence(), s2, s2.getSequence(), type);
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115 * Creates a new AlignSeq object.
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117 * @param s1 DOCUMENT ME!
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118 * @param s2 DOCUMENT ME!
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119 * @param type DOCUMENT ME!
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121 public AlignSeq(SequenceI s1,
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127 rt = Runtime.getRuntime();
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128 SeqInit(s1, string1, s2, string2, type);
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134 * @return DOCUMENT ME!
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136 public int getMaxScore()
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144 * @return DOCUMENT ME!
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146 public int getSeq2Start()
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154 * @return DOCUMENT ME!
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156 public int getSeq2End()
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164 * @return DOCUMENT ME!
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166 public int getSeq1Start()
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174 * @return DOCUMENT ME!
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176 public int getSeq1End()
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184 * @return DOCUMENT ME!
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186 public String getOutput()
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188 return output.toString();
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194 * @return DOCUMENT ME!
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196 public String getAStr1()
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204 * @return DOCUMENT ME!
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206 public String getAStr2()
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214 * @return DOCUMENT ME!
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216 public int[] getASeq1()
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224 * @return DOCUMENT ME!
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226 public int[] getASeq2()
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234 * @return DOCUMENT ME!
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236 public SequenceI getS1()
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244 * @return DOCUMENT ME!
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246 public SequenceI getS2()
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254 * @param s1 DOCUMENT ME!
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255 * @param s2 DOCUMENT ME!
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256 * @param type DOCUMENT ME!
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258 public void SeqInit(SequenceI s1,
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264 s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
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265 s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
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272 if (type.equals("pep"))
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274 lookup = ResidueProperties.getBLOSUM62();
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278 else if (type.equals("dna"))
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280 lookup = ResidueProperties.getDNA();
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286 output.append("Wrong type = dna or pep only");
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290 //System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory());
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291 seq1 = new int[s1str.length()];
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293 //System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory());
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294 seq2 = new int[s2str.length()];
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296 //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
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297 score = new int[s1str.length()][s2str.length()];
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299 //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
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300 E = new int[s1str.length()][s2str.length()];
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302 //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());
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303 F = new int[s1str.length()][s2str.length()];
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304 traceback = new int[s1str.length()][s2str.length()];
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306 //System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());
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307 seq1 = stringToInt(s1str, type);
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309 //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());
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310 seq2 = stringToInt(s2str, type);
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312 //System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory());
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313 // long tstart = System.currentTimeMillis();
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314 // calcScoreMatrix();
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315 //long tend = System.currentTimeMillis();
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316 //System.out.println("Time take to calculate score matrix = " + (tend-tstart) + " ms");
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317 // printScoreMatrix(score);
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318 //System.out.println();
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319 //printScoreMatrix(traceback);
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320 //System.out.println();
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321 // printScoreMatrix(E);
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322 //System.out.println();
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323 ///printScoreMatrix(F);
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324 //System.out.println();
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325 // tstart = System.currentTimeMillis();
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326 //traceAlignment();
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327 //tend = System.currentTimeMillis();
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328 //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms");
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334 public void traceAlignment()
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336 // Find the maximum score along the rhs or bottom row
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339 for (int i = 0; i < seq1.length; i++)
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341 if (score[i][seq2.length - 1] > max)
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343 max = score[i][seq2.length - 1];
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345 maxj = seq2.length - 1;
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349 for (int j = 0; j < seq2.length; j++)
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351 if (score[seq1.length - 1][j] > max)
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353 max = score[seq1.length - 1][j];
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354 maxi = seq1.length - 1;
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359 // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
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363 maxscore = score[i][j] / 10;
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365 seq1end = maxi + 1;
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366 seq2end = maxj + 1;
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368 aseq1 = new int[seq1.length + seq2.length];
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369 aseq2 = new int[seq1.length + seq2.length];
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371 count = (seq1.length + seq2.length) - 1;
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373 while ((i > 0) && (j > 0))
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375 if ((aseq1[count] != defInt) && (i >= 0))
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377 aseq1[count] = seq1[i];
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378 astr1 = intToStr[seq1[i]] + astr1;
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381 if ((aseq2[count] != defInt) && (j > 0))
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383 aseq2[count] = seq2[j];
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384 astr2 = intToStr[seq2[j]] + astr2;
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387 trace = findTrace(i, j);
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394 else if (trace == 1)
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397 aseq1[count] = defInt;
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398 astr1 = "-" + astr1.substring(1);
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400 else if (trace == -1)
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403 aseq2[count] = defInt;
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404 astr2 = "-" + astr2.substring(1);
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413 if (aseq1[count] != defInt)
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415 aseq1[count] = seq1[i];
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416 astr1 = intToStr[seq1[i]] + astr1;
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419 if (aseq2[count] != defInt)
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421 aseq2[count] = seq2[j];
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422 astr2 = intToStr[seq2[j]] + astr2;
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429 public void printAlignment(java.io.PrintStream os)
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431 // Find the biggest id length for formatting purposes
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432 int maxid = s1.getName().length();
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434 if (s2.getName().length() > maxid)
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436 maxid = s2.getName().length();
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439 int len = 72 - maxid - 1;
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440 int nochunks = ((aseq1.length - count) / len) + 1;
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443 output.append("Score = " + score[maxi][maxj] + "\n");
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444 output.append("Length of alignment = " + (aseq1.length - count) + "\n");
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445 output.append("Sequence ");
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446 output.append(new Format("%" + maxid + "s").form(s1.getName()));
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447 output.append(" : " + s1.getStart() + " - " + s1.getEnd() + " (Sequence length = " +
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448 s1str.length() + ")\n");
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449 output .append("Sequence ");
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450 output.append(new Format("%" + maxid + "s").form(s2.getName()));
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451 output.append(" : " + s2.getStart() + " - " + s2.getEnd() + " (Sequence length = " +
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452 s2str.length() + ")\n\n");
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454 for (int j = 0; j < nochunks; j++)
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456 // Print the first aligned sequence
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457 output.append(new Format("%" + (maxid) + "s").form(s1.getName()) + " ");
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459 for (int i = 0; i < len; i++)
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461 if ((count + i + (j * len)) < aseq1.length)
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463 output.append(new Format("%s").form(intToStr[aseq1[count + i +
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468 output.append("\n");
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469 output.append(new Format("%" + (maxid) + "s").form(" ") + " ");
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471 // Print out the matching chars
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472 for (int i = 0; i < len; i++)
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474 if ((count + i + (j * len)) < aseq1.length)
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476 if (intToStr[aseq1[count + i + (j * len)]].equals(
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477 intToStr[aseq2[count + i + (j * len)]]) &&
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478 !intToStr[aseq1[count + i + (j * len)]].equals("-"))
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481 output.append("|");
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483 else if (type.equals("pep"))
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485 if (ResidueProperties.getPAM250(
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486 intToStr[aseq1[count + i + (j * len)]],
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487 intToStr[aseq2[count + i + (j * len)]]) > 0)
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489 output.append(".");
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493 output.append(" ");
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498 output.append(" ");
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503 // Now print the second aligned sequence
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504 output = output.append("\n");
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505 output = output.append(new Format("%" + (maxid) + "s").form(s2.getName()) + " ");
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507 for (int i = 0; i < len; i++)
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509 if ((count + i + (j * len)) < aseq1.length)
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511 output .append(new Format("%s").form(intToStr[aseq2[count + i +
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516 output = output .append("\n\n");
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519 pid = pid / (float) (aseq1.length - count) * 100;
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520 output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));
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523 os.print(output.toString());
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524 }catch(Exception ex){}
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530 * @param mat DOCUMENT ME!
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532 public void printScoreMatrix(int[][] mat)
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534 int n = seq1.length;
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535 int m = seq2.length;
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537 for (int i = 0; i < n; i++)
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539 // Print the top sequence
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542 Format.print(System.out, "%8s", s2str.substring(0, 1));
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544 for (int jj = 1; jj < m; jj++)
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546 Format.print(System.out, "%5s", s2str.substring(jj, jj + 1));
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549 System.out.println();
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552 for (int j = 0; j < m; j++)
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556 Format.print(System.out, "%3s", s1str.substring(i, i + 1));
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559 Format.print(System.out, "%3d ", mat[i][j] / 10);
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562 System.out.println();
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569 * @param i DOCUMENT ME!
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570 * @param j DOCUMENT ME!
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572 * @return DOCUMENT ME!
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574 public int findTrace(int i, int j)
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577 int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10);
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584 else if (F[i][j] == max)
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593 if (E[i][j] >= max)
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598 else if (E[i][j] == max)
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615 public void calcScoreMatrix()
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617 int n = seq1.length;
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618 int m = seq2.length;
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620 // top left hand element
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621 score[0][0] = lookup[seq1[0]][seq2[0]] * 10;
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622 E[0][0] = -gapExtend;
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625 // Calculate the top row first
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626 for (int j = 1; j < m; j++)
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628 // What should these values be? 0 maybe
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629 E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend);
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630 F[0][j] = -gapExtend;
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632 score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen,
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635 traceback[0][j] = 1;
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638 // Now do the left hand column
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639 for (int i = 1; i < n; i++)
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641 E[i][0] = -gapOpen;
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642 F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend);
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644 score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]);
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645 traceback[i][0] = -1;
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648 // Now do all the other rows
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649 for (int i = 1; i < n; i++)
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651 for (int j = 1; j < m; j++)
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653 E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] -
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655 F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] -
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658 score[i][j] = max(score[i - 1][j - 1] +
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659 (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]);
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660 traceback[i][j] = findTrace(i, j);
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670 * @param gapChar DOCUMENT ME!
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671 * @param seq DOCUMENT ME!
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673 * @return DOCUMENT ME!
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675 public static String extractGaps(String gapChar, String seq)
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677 StringTokenizer str = new StringTokenizer(seq, gapChar);
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678 StringBuffer newString = new StringBuffer();
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680 while (str.hasMoreTokens())
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682 newString.append( str.nextToken() );
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685 return newString.toString();
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691 * @param i1 DOCUMENT ME!
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692 * @param i2 DOCUMENT ME!
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693 * @param i3 DOCUMENT ME!
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695 * @return DOCUMENT ME!
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697 public int max(int i1, int i2, int i3)
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717 * @param i1 DOCUMENT ME!
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718 * @param i2 DOCUMENT ME!
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720 * @return DOCUMENT ME!
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722 public int max(int i1, int i2)
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737 * @param s DOCUMENT ME!
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738 * @param type DOCUMENT ME!
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740 * @return DOCUMENT ME!
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742 public int[] stringToInt(String s, String type)
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744 int[] seq1 = new int[s.length()];
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746 for (int i = 0; i < s.length(); i++)
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748 String ss = s.substring(i, i + 1).toUpperCase();
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752 if (type.equals("pep"))
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754 seq1[i] = ((Integer) ResidueProperties.aaHash.get(ss)).intValue();
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756 else if (type.equals("dna"))
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758 seq1[i] = ((Integer) dnaHash.get(ss)).intValue();
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766 catch (Exception e)
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768 if (type.equals("dna"))
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785 * @param g DOCUMENT ME!
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786 * @param mat DOCUMENT ME!
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787 * @param n DOCUMENT ME!
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788 * @param m DOCUMENT ME!
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789 * @param psize DOCUMENT ME!
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791 public static void displayMatrix(Graphics g, int[][] mat, int n, int m,
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797 for (int i = 0; i < n; i++)
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799 for (int j = 0; j < m; j++)
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801 if (mat[i][j] >= max)
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806 if (mat[i][j] <= min)
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813 System.out.println(max + " " + min);
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815 for (int i = 0; i < n; i++)
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817 for (int j = 0; j < m; j++)
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822 // System.out.println(mat[i][j]);
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823 float score = (float) (mat[i][j] - min) / (float) (max - min);
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824 g.setColor(new Color(score, 0, 0));
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825 g.fillRect(x, y, psize, psize);
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827 // System.out.println(x + " " + y + " " + score);
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