X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=2fcc593ccd718e1d13caf7e92080ba66451527b7;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=db549a4c99b28c6b992b508e367869b32b481138;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index db549a4..2fcc593 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -1,33 +1,30 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.analysis; -import jalview.datamodel.SequenceI; - -import jalview.schemes.*; - -import jalview.util.*; +import java.util.*; import java.awt.*; -import java.util.*; - +import jalview.datamodel.*; +import jalview.schemes.*; +import jalview.util.*; /** * @@ -37,841 +34,853 @@ import java.util.*; */ public class AlignSeq { - public static final String PEP = "pep"; - public static final String DNA = "dna"; - /** DOCUMENT ME!! */ - public static java.util.Hashtable dnaHash = new java.util.Hashtable(); - - static - { - dnaHash.put("C", new Integer(0)); - dnaHash.put("T", new Integer(1)); - dnaHash.put("A", new Integer(2)); - dnaHash.put("G", new Integer(3)); - dnaHash.put("-", new Integer(4)); - } - - static String[] dna = { "C", "T", "A", "G", "-" }; - static String[] pep = - { - "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", - "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" - }; - int[][] score; - int[][] E; - int[][] F; - int[][] traceback; - int[] seq1; - int[] seq2; - SequenceI s1; - SequenceI s2; - public String s1str; - public String s2str; - int maxi; - int maxj; - int[] aseq1; - int[] aseq2; - public String astr1=""; - public String astr2=""; - - /** DOCUMENT ME!! */ - public int seq1start; - - /** DOCUMENT ME!! */ - public int seq1end; - - /** DOCUMENT ME!! */ - public int seq2start; - - /** DOCUMENT ME!! */ - public int seq2end; - int count; - - /** DOCUMENT ME!! */ - public int maxscore; - float pid; - int prev = 0; - int gapOpen = 120; - int gapExtend = 20; - int[][] lookup = ResidueProperties.getBLOSUM62(); - String[] intToStr = pep; - int defInt = 23; - StringBuffer output = new StringBuffer(); - String type; - - /** - * Creates a new AlignSeq object. - * - * @param s1 DOCUMENT ME! - * @param s2 DOCUMENT ME! - * @param type DOCUMENT ME! - */ - public AlignSeq(SequenceI s1, SequenceI s2, String type) - { - SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), type); - } - - /** - * Creates a new AlignSeq object. - * - * @param s1 DOCUMENT ME! - * @param s2 DOCUMENT ME! - * @param type DOCUMENT ME! - */ - public AlignSeq(SequenceI s1, - String string1, - SequenceI s2, - String string2, - String type) + public static final String PEP = "pep"; + public static final String DNA = "dna"; + /** DOCUMENT ME!! */ + public static java.util.Hashtable dnaHash = new java.util.Hashtable(); + + static + { + dnaHash.put("C", new Integer(0)); + dnaHash.put("T", new Integer(1)); + dnaHash.put("A", new Integer(2)); + dnaHash.put("G", new Integer(3)); + dnaHash.put("-", new Integer(4)); + } + + static String[] dna = + { + "C", "T", "A", "G", "-"}; + static String[] pep = + { + "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", + "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" + }; + int[][] score; + int[][] E; + int[][] F; + int[][] traceback; + int[] seq1; + int[] seq2; + SequenceI s1; + SequenceI s2; + public String s1str; + public String s2str; + int maxi; + int maxj; + int[] aseq1; + int[] aseq2; + public String astr1 = ""; + public String astr2 = ""; + + /** DOCUMENT ME!! */ + public int seq1start; + + /** DOCUMENT ME!! */ + public int seq1end; + + /** DOCUMENT ME!! */ + public int seq2start; + + /** DOCUMENT ME!! */ + public int seq2end; + int count; + + /** DOCUMENT ME!! */ + public int maxscore; + float pid; + int prev = 0; + int gapOpen = 120; + int gapExtend = 20; + int[][] lookup = ResidueProperties.getBLOSUM62(); + String[] intToStr = pep; + int defInt = 23; + StringBuffer output = new StringBuffer(); + String type; + + /** + * Creates a new AlignSeq object. + * + * @param s1 DOCUMENT ME! + * @param s2 DOCUMENT ME! + * @param type DOCUMENT ME! + */ + public AlignSeq(SequenceI s1, SequenceI s2, String type) + { + SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), type); + } + + /** + * Creates a new AlignSeq object. + * + * @param s1 DOCUMENT ME! + * @param s2 DOCUMENT ME! + * @param type DOCUMENT ME! + */ + public AlignSeq(SequenceI s1, + String string1, + SequenceI s2, + String string2, + String type) + { + SeqInit(s1, string1, s2, string2, type); + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getMaxScore() + { + return maxscore; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getSeq2Start() + { + return seq2start; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getSeq2End() + { + return seq2end; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getSeq1Start() + { + return seq1start; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int getSeq1End() + { + return seq1end; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getOutput() + { + return output.toString(); + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getAStr1() + { + return astr1; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getAStr2() + { + return astr2; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int[] getASeq1() + { + return aseq1; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int[] getASeq2() + { + return aseq2; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public SequenceI getS1() + { + return s1; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public SequenceI getS2() + { + return s2; + } + + /** + * DOCUMENT ME! + * + * @param s1 DOCUMENT ME! + * @param string1 - string to align for sequence1 + * @param s2 sequence 2 + * @param string2 - string to align for sequence2 + * @param type DNA or PEPTIDE + */ + public void SeqInit(SequenceI s1, + String string1, + SequenceI s2, + String string2, + String type) + { + this.s1 = s1; + this.s2 = s2; + setDefaultParams(type); + SeqInit(string1, string2); + } + + public void SeqInit(SequenceI s1, + String string1, + SequenceI s2, + String string2, + ScoreMatrix scoreMatrix) + { + this.s1 = s1; + this.s2 = s2; + setType(scoreMatrix.isDNA() ? AlignSeq.DNA : AlignSeq.PEP); + lookup = scoreMatrix.getMatrix(); + } + + /** + * construct score matrix for string1 and string2 (after removing any existing gaps + * @param string1 + * @param string2 + */ + private void SeqInit(String string1, String string2) + { + s1str = extractGaps(jalview.util.Comparison.GapChars, string1); + s2str = extractGaps(jalview.util.Comparison.GapChars, string2); + + if (s1str.length() == 0 || s2str.length() == 0) { - SeqInit(s1, string1, s2, string2, type); + output.append("ALL GAPS: " + + (s1str.length() == 0 ? s1.getName() : " ") + + (s2str.length() == 0 ? s2.getName() : "")); + return; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getMaxScore() + //System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory()); + seq1 = new int[s1str.length()]; + + //System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory()); + seq2 = new int[s2str.length()]; + + //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory()); + score = new int[s1str.length()][s2str.length()]; + + //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory()); + E = new int[s1str.length()][s2str.length()]; + + //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory()); + F = new int[s1str.length()][s2str.length()]; + traceback = new int[s1str.length()][s2str.length()]; + + //System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory()); + seq1 = stringToInt(s1str, type); + + //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory()); + seq2 = stringToInt(s2str, type); + + //System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory()); + // long tstart = System.currentTimeMillis(); + // calcScoreMatrix(); + //long tend = System.currentTimeMillis(); + //System.out.println("Time take to calculate score matrix = " + (tend-tstart) + " ms"); + // printScoreMatrix(score); + //System.out.println(); + //printScoreMatrix(traceback); + //System.out.println(); + // printScoreMatrix(E); + //System.out.println(); + ///printScoreMatrix(F); + //System.out.println(); + // tstart = System.currentTimeMillis(); + //traceAlignment(); + //tend = System.currentTimeMillis(); + //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms"); + } + + private void setDefaultParams(String type) + { + setType(type); + + if (type.equals(AlignSeq.PEP)) { - return maxscore; + lookup = ResidueProperties.getDefaultPeptideMatrix(); } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getSeq2Start() + else if (type.equals(AlignSeq.DNA)) { - return seq2start; + lookup = ResidueProperties.getDefaultDnaMatrix(); } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getSeq2End() + private void setType(String type2) + { + this.type = type2; + if (type.equals(AlignSeq.PEP)) { - return seq2end; + intToStr = pep; + defInt = 23; } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getSeq1Start() + else if (type.equals(AlignSeq.DNA)) { - return seq1start; + intToStr = dna; + defInt = 4; } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getSeq1End() + else { - return seq1end; + output.append("Wrong type = dna or pep only"); + throw new Error("Unknown Type " + type2 + + " - dna or pep are the only allowed values."); } + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getOutput() - { - return output.toString(); - } + /** + * DOCUMENT ME! + */ + public void traceAlignment() + { + // Find the maximum score along the rhs or bottom row + int max = -9999; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getAStr1() + for (int i = 0; i < seq1.length; i++) { - return astr1; + if (score[i][seq2.length - 1] > max) + { + max = score[i][seq2.length - 1]; + maxi = i; + maxj = seq2.length - 1; + } } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getAStr2() + for (int j = 0; j < seq2.length; j++) { - return astr2; + if (score[seq1.length - 1][j] > max) + { + max = score[seq1.length - 1][j]; + maxi = seq1.length - 1; + maxj = j; + } } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int[] getASeq1() - { - return aseq1; - } + // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]); + int i = maxi; + int j = maxj; + int trace; + maxscore = score[i][j] / 10; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int[] getASeq2() - { - return aseq2; - } + seq1end = maxi + 1; + seq2end = maxj + 1; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SequenceI getS1() - { - return s1; - } + aseq1 = new int[seq1.length + seq2.length]; + aseq2 = new int[seq1.length + seq2.length]; - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SequenceI getS2() - { - return s2; - } + count = (seq1.length + seq2.length) - 1; - /** - * DOCUMENT ME! - * - * @param s1 DOCUMENT ME! - * @param string1 - string to align for sequence1 - * @param s2 sequence 2 - * @param string2 - string to align for sequence2 - * @param type DNA or PEPTIDE - */ - public void SeqInit(SequenceI s1, - String string1, - SequenceI s2, - String string2, - String type) + while ( (i > 0) && (j > 0)) { - this.s1 = s1; - this.s2 = s2; - setDefaultParams(type); - SeqInit(string1,string2); - } - public void SeqInit(SequenceI s1, - String string1, - SequenceI s2, - String string2, - ScoreMatrix scoreMatrix) { - this.s1=s1; - this.s2=s2; - setType(scoreMatrix.isDNA() ? AlignSeq.DNA : AlignSeq.PEP); - lookup=scoreMatrix.getMatrix(); - } - /** - * construct score matrix for string1 and string2 (after removing any existing gaps - * @param string1 - * @param string2 - */ - private void SeqInit(String string1, String string2) { - s1str = extractGaps(jalview.util.Comparison.GapChars, string1); - s2str = extractGaps(jalview.util.Comparison.GapChars, string2); - - if(s1str.length()==0 || s2str.length()==0) + if ( (aseq1[count] != defInt) && (i >= 0)) { - output.append("ALL GAPS: " + - (s1str.length()==0?s1.getName():" ") - +(s2str.length()==0?s2.getName():"")); - return; + aseq1[count] = seq1[i]; + astr1 = intToStr[seq1[i]] + astr1; } - //System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory()); - seq1 = new int[s1str.length()]; - - //System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory()); - seq2 = new int[s2str.length()]; - - //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory()); - score = new int[s1str.length()][s2str.length()]; - - //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory()); - E = new int[s1str.length()][s2str.length()]; - - //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory()); - F = new int[s1str.length()][s2str.length()]; - traceback = new int[s1str.length()][s2str.length()]; - - //System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory()); - seq1 = stringToInt(s1str, type); - - //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory()); - seq2 = stringToInt(s2str, type); - - //System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory()); - // long tstart = System.currentTimeMillis(); - // calcScoreMatrix(); - //long tend = System.currentTimeMillis(); - //System.out.println("Time take to calculate score matrix = " + (tend-tstart) + " ms"); - // printScoreMatrix(score); - //System.out.println(); - //printScoreMatrix(traceback); - //System.out.println(); - // printScoreMatrix(E); - //System.out.println(); - ///printScoreMatrix(F); - //System.out.println(); - // tstart = System.currentTimeMillis(); - //traceAlignment(); - //tend = System.currentTimeMillis(); - //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms"); - } + if ( (aseq2[count] != defInt) && (j > 0)) + { + aseq2[count] = seq2[j]; + astr2 = intToStr[seq2[j]] + astr2; + } - private void setDefaultParams(String type) { - setType(type); - - if (type.equals(AlignSeq.PEP)) - { - lookup = ResidueProperties.getDefaultPeptideMatrix(); - } - else if (type.equals(AlignSeq.DNA)) - { - lookup = ResidueProperties.getDefaultDnaMatrix(); - } - } + trace = findTrace(i, j); - private void setType(String type2) { - this.type = type2; - if (type.equals(AlignSeq.PEP)) + if (trace == 0) { - intToStr = pep; - defInt = 23; + i--; + j--; } - else if (type.equals(AlignSeq.DNA)) + else if (trace == 1) { - intToStr = dna; - defInt = 4; + j--; + aseq1[count] = defInt; + astr1 = "-" + astr1.substring(1); } - else + else if (trace == -1) { - output.append("Wrong type = dna or pep only"); - throw new Error("Unknown Type "+type2+" - dna or pep are the only allowed values."); + i--; + aseq2[count] = defInt; + astr2 = "-" + astr2.substring(1); } - } - /** - * DOCUMENT ME! - */ - public void traceAlignment() - { - // Find the maximum score along the rhs or bottom row - int max = -9999; + count--; + } - for (int i = 0; i < seq1.length; i++) - { - if (score[i][seq2.length - 1] > max) - { - max = score[i][seq2.length - 1]; - maxi = i; - maxj = seq2.length - 1; - } - } + seq1start = i + 1; + seq2start = j + 1; - for (int j = 0; j < seq2.length; j++) - { - if (score[seq1.length - 1][j] > max) - { - max = score[seq1.length - 1][j]; - maxi = seq1.length - 1; - maxj = j; - } - } + if (aseq1[count] != defInt) + { + aseq1[count] = seq1[i]; + astr1 = intToStr[seq1[i]] + astr1; + } - // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]); - int i = maxi; - int j = maxj; - int trace; - maxscore = score[i][j] / 10; + if (aseq2[count] != defInt) + { + aseq2[count] = seq2[j]; + astr2 = intToStr[seq2[j]] + astr2; + } + } - seq1end = maxi + 1; - seq2end = maxj + 1; + /** + * DOCUMENT ME! + */ + public void printAlignment(java.io.PrintStream os) + { + // Find the biggest id length for formatting purposes + int maxid = s1.getName().length(); - aseq1 = new int[seq1.length + seq2.length]; - aseq2 = new int[seq1.length + seq2.length]; + if (s2.getName().length() > maxid) + { + maxid = s2.getName().length(); + } - count = (seq1.length + seq2.length) - 1; + int len = 72 - maxid - 1; + int nochunks = ( (aseq1.length - count) / len) + 1; + pid = 0; + + output.append("Score = " + score[maxi][maxj] + "\n"); + output.append("Length of alignment = " + (aseq1.length - count) + "\n"); + output.append("Sequence "); + output.append(new Format("%" + maxid + "s").form(s1.getName())); + output.append(" : " + s1.getStart() + " - " + s1.getEnd() + + " (Sequence length = " + + s1str.length() + ")\n"); + output.append("Sequence "); + output.append(new Format("%" + maxid + "s").form(s2.getName())); + output.append(" : " + s2.getStart() + " - " + s2.getEnd() + + " (Sequence length = " + + s2str.length() + ")\n\n"); + + for (int j = 0; j < nochunks; j++) + { + // Print the first aligned sequence + output.append(new Format("%" + (maxid) + "s").form(s1.getName()) + " "); - while ((i > 0) && (j > 0)) + for (int i = 0; i < len; i++) + { + if ( (count + i + (j * len)) < aseq1.length) { - if ((aseq1[count] != defInt) && (i >= 0)) - { - aseq1[count] = seq1[i]; - astr1 = intToStr[seq1[i]] + astr1; - } - - if ((aseq2[count] != defInt) && (j > 0)) - { - aseq2[count] = seq2[j]; - astr2 = intToStr[seq2[j]] + astr2; - } + output.append(new Format("%s").form(intToStr[aseq1[count + i + + (j * len)]])); + } + } - trace = findTrace(i, j); + output.append("\n"); + output.append(new Format("%" + (maxid) + "s").form(" ") + " "); - if (trace == 0) - { - i--; - j--; - } - else if (trace == 1) + // Print out the matching chars + for (int i = 0; i < len; i++) + { + if ( (count + i + (j * len)) < aseq1.length) + { + if (intToStr[aseq1[count + i + (j * len)]].equals( + intToStr[aseq2[count + i + (j * len)]]) && + !intToStr[aseq1[count + i + (j * len)]].equals("-")) + { + pid++; + output.append("|"); + } + else if (type.equals("pep")) + { + if (ResidueProperties.getPAM250( + intToStr[aseq1[count + i + (j * len)]], + intToStr[aseq2[count + i + (j * len)]]) > 0) { - j--; - aseq1[count] = defInt; - astr1 = "-" + astr1.substring(1); + output.append("."); } - else if (trace == -1) + else { - i--; - aseq2[count] = defInt; - astr2 = "-" + astr2.substring(1); + output.append(" "); } - - count--; + } + else + { + output.append(" "); + } } + } - seq1start = i + 1; - seq2start = j + 1; + // Now print the second aligned sequence + output = output.append("\n"); + output = output.append(new Format("%" + (maxid) + "s").form(s2.getName()) + + " "); - if (aseq1[count] != defInt) + for (int i = 0; i < len; i++) + { + if ( (count + i + (j * len)) < aseq1.length) { - aseq1[count] = seq1[i]; - astr1 = intToStr[seq1[i]] + astr1; + output.append(new Format("%s").form(intToStr[aseq2[count + i + + (j * len)]])); } + } - if (aseq2[count] != defInt) - { - aseq2[count] = seq2[j]; - astr2 = intToStr[seq2[j]] + astr2; - } + output = output.append("\n\n"); } - /** - * DOCUMENT ME! - */ - public void printAlignment(java.io.PrintStream os) + pid = pid / (float) (aseq1.length - count) * 100; + output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid)); + + try + { + os.print(output.toString()); + } + catch (Exception ex) + {} + } + + /** + * DOCUMENT ME! + * + * @param mat DOCUMENT ME! + */ + public void printScoreMatrix(int[][] mat) + { + int n = seq1.length; + int m = seq2.length; + + for (int i = 0; i < n; i++) { - // Find the biggest id length for formatting purposes - int maxid = s1.getName().length(); + // Print the top sequence + if (i == 0) + { + Format.print(System.out, "%8s", s2str.substring(0, 1)); - if (s2.getName().length() > maxid) + for (int jj = 1; jj < m; jj++) { - maxid = s2.getName().length(); + Format.print(System.out, "%5s", s2str.substring(jj, jj + 1)); } - int len = 72 - maxid - 1; - int nochunks = ((aseq1.length - count) / len) + 1; - pid = 0; - - output.append("Score = " + score[maxi][maxj] + "\n"); - output.append("Length of alignment = " + (aseq1.length - count) + "\n"); - output.append("Sequence "); - output.append(new Format("%" + maxid + "s").form(s1.getName())); - output.append(" : " + s1.getStart() + " - " + s1.getEnd() + " (Sequence length = " + - s1str.length() + ")\n"); - output .append("Sequence "); - output.append(new Format("%" + maxid + "s").form(s2.getName())); - output.append(" : " + s2.getStart() + " - " + s2.getEnd() + " (Sequence length = " + - s2str.length() + ")\n\n"); - - for (int j = 0; j < nochunks; j++) - { - // Print the first aligned sequence - output.append(new Format("%" + (maxid) + "s").form(s1.getName()) + " "); - - for (int i = 0; i < len; i++) - { - if ((count + i + (j * len)) < aseq1.length) - { - output.append(new Format("%s").form(intToStr[aseq1[count + i + - (j * len)]])); - } - } - - output.append("\n"); - output.append(new Format("%" + (maxid) + "s").form(" ") + " "); - - // Print out the matching chars - for (int i = 0; i < len; i++) - { - if ((count + i + (j * len)) < aseq1.length) - { - if (intToStr[aseq1[count + i + (j * len)]].equals( - intToStr[aseq2[count + i + (j * len)]]) && - !intToStr[aseq1[count + i + (j * len)]].equals("-")) - { - pid++; - output.append("|"); - } - else if (type.equals("pep")) - { - if (ResidueProperties.getPAM250( - intToStr[aseq1[count + i + (j * len)]], - intToStr[aseq2[count + i + (j * len)]]) > 0) - { - output.append("."); - } - else - { - output.append(" "); - } - } - else - { - output.append(" "); - } - } - } - - // Now print the second aligned sequence - output = output.append("\n"); - output = output.append(new Format("%" + (maxid) + "s").form(s2.getName()) + " "); - - for (int i = 0; i < len; i++) - { - if ((count + i + (j * len)) < aseq1.length) - { - output .append(new Format("%s").form(intToStr[aseq2[count + i + - (j * len)]])); - } - } + System.out.println(); + } - output = output .append("\n\n"); + for (int j = 0; j < m; j++) + { + if (j == 0) + { + Format.print(System.out, "%3s", s1str.substring(i, i + 1)); } - pid = pid / (float) (aseq1.length - count) * 100; - output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid)); + Format.print(System.out, "%3d ", mat[i][j] / 10); + } - try{ - os.print(output.toString()); - }catch(Exception ex){} + System.out.println(); } - - /** - * DOCUMENT ME! - * - * @param mat DOCUMENT ME! - */ - public void printScoreMatrix(int[][] mat) + } + + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + * @param j DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int findTrace(int i, int j) + { + int t = 0; + int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10); + + if (F[i][j] > max) { - int n = seq1.length; - int m = seq2.length; - - for (int i = 0; i < n; i++) - { - // Print the top sequence - if (i == 0) - { - Format.print(System.out, "%8s", s2str.substring(0, 1)); + max = F[i][j]; + t = -1; + } + else if (F[i][j] == max) + { + if (prev == -1) + { + max = F[i][j]; + t = -1; + } + } - for (int jj = 1; jj < m; jj++) - { - Format.print(System.out, "%5s", s2str.substring(jj, jj + 1)); - } + if (E[i][j] >= max) + { + max = E[i][j]; + t = 1; + } + else if (E[i][j] == max) + { + if (prev == 1) + { + max = E[i][j]; + t = 1; + } + } - System.out.println(); - } + prev = t; - for (int j = 0; j < m; j++) - { - if (j == 0) - { - Format.print(System.out, "%3s", s1str.substring(i, i + 1)); - } + return t; + } - Format.print(System.out, "%3d ", mat[i][j] / 10); - } + /** + * DOCUMENT ME! + */ + public void calcScoreMatrix() + { + int n = seq1.length; + int m = seq2.length; - System.out.println(); - } - } + // top left hand element + score[0][0] = lookup[seq1[0]][seq2[0]] * 10; + E[0][0] = -gapExtend; + F[0][0] = 0; - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param j DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int findTrace(int i, int j) + // Calculate the top row first + for (int j = 1; j < m; j++) { - int t = 0; - int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10); + // What should these values be? 0 maybe + E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend); + F[0][j] = -gapExtend; - if (F[i][j] > max) - { - max = F[i][j]; - t = -1; - } - else if (F[i][j] == max) - { - if (prev == -1) - { - max = F[i][j]; - t = -1; - } - } + score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen, + -gapExtend); - if (E[i][j] >= max) - { - max = E[i][j]; - t = 1; - } - else if (E[i][j] == max) - { - if (prev == 1) - { - max = E[i][j]; - t = 1; - } - } + traceback[0][j] = 1; + } - prev = t; + // Now do the left hand column + for (int i = 1; i < n; i++) + { + E[i][0] = -gapOpen; + F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend); - return t; + score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]); + traceback[i][0] = -1; } - /** - * DOCUMENT ME! - */ - public void calcScoreMatrix() + // Now do all the other rows + for (int i = 1; i < n; i++) + { + for (int j = 1; j < m; j++) + { + E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] - + gapExtend); + F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] - + gapExtend); + + score[i][j] = max(score[i - 1][j - 1] + + (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]); + traceback[i][j] = findTrace(i, j); + } + } + } + + /** + * DOCUMENT ME! + * + * @param gapChar DOCUMENT ME! + * @param seq DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static String extractGaps(String gapChar, String seq) + { + StringTokenizer str = new StringTokenizer(seq, gapChar); + StringBuffer newString = new StringBuffer(); + + while (str.hasMoreTokens()) { - int n = seq1.length; - int m = seq2.length; + newString.append(str.nextToken()); + } - // top left hand element - score[0][0] = lookup[seq1[0]][seq2[0]] * 10; - E[0][0] = -gapExtend; - F[0][0] = 0; + return newString.toString(); + } + + /** + * DOCUMENT ME! + * + * @param i1 DOCUMENT ME! + * @param i2 DOCUMENT ME! + * @param i3 DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int max(int i1, int i2, int i3) + { + int max = i1; + + if (i2 > i1) + { + max = i2; + } - // Calculate the top row first - for (int j = 1; j < m; j++) - { - // What should these values be? 0 maybe - E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend); - F[0][j] = -gapExtend; + if (i3 > max) + { + max = i3; + } - score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen, - -gapExtend); + return max; + } + + /** + * DOCUMENT ME! + * + * @param i1 DOCUMENT ME! + * @param i2 DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int max(int i1, int i2) + { + int max = i1; + + if (i2 > i1) + { + max = i2; + } - traceback[0][j] = 1; - } + return max; + } + + /** + * DOCUMENT ME! + * + * @param s DOCUMENT ME! + * @param type DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int[] stringToInt(String s, String type) + { + int[] seq1 = new int[s.length()]; + + for (int i = 0; i < s.length(); i++) + { + // String ss = s.substring(i, i + 1).toUpperCase(); + char c = s.charAt(i); + if ('a' <= c && c <= 'z') + { + // TO UPPERCASE !!! + c -= ('a' - 'A'); + } - // Now do the left hand column - for (int i = 1; i < n; i++) + try + { + if (type.equals("pep")) { - E[i][0] = -gapOpen; - F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend); - - score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]); - traceback[i][0] = -1; + seq1[i] = ResidueProperties.aaIndex[c]; } - - // Now do all the other rows - for (int i = 1; i < n; i++) + else if (type.equals("dna")) { - for (int j = 1; j < m; j++) - { - E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] - - gapExtend); - F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] - - gapExtend); - - score[i][j] = max(score[i - 1][j - 1] + - (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]); - traceback[i][j] = findTrace(i, j); - } + seq1[i] = ResidueProperties.nucleotideIndex[c]; } - } - - - /** - * DOCUMENT ME! - * - * @param gapChar DOCUMENT ME! - * @param seq DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static String extractGaps(String gapChar, String seq) - { - StringTokenizer str = new StringTokenizer(seq, gapChar); - StringBuffer newString = new StringBuffer(); - - while (str.hasMoreTokens()) + if (seq1[i] > 23) { - newString.append( str.nextToken() ); + seq1[i] = 23; } - - return newString.toString(); - } - - /** - * DOCUMENT ME! - * - * @param i1 DOCUMENT ME! - * @param i2 DOCUMENT ME! - * @param i3 DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int max(int i1, int i2, int i3) - { - int max = i1; - - if (i2 > i1) + } + catch (Exception e) + { + if (type.equals("dna")) { - max = i2; + seq1[i] = 4; } - - if (i3 > max) + else { - max = i3; + seq1[i] = 23; } - - return max; + } } - /** - * DOCUMENT ME! - * - * @param i1 DOCUMENT ME! - * @param i2 DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int max(int i1, int i2) + return seq1; + } + + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + * @param mat DOCUMENT ME! + * @param n DOCUMENT ME! + * @param m DOCUMENT ME! + * @param psize DOCUMENT ME! + */ + public static void displayMatrix(Graphics g, int[][] mat, int n, int m, + int psize) + { + int max = -1000; + int min = 1000; + + for (int i = 0; i < n; i++) { - int max = i1; - - if (i2 > i1) + for (int j = 0; j < m; j++) + { + if (mat[i][j] >= max) { - max = i2; + max = mat[i][j]; } - return max; - } - - /** - * DOCUMENT ME! - * - * @param s DOCUMENT ME! - * @param type DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int[] stringToInt(String s, String type) - { - int[] seq1 = new int[s.length()]; - - for (int i = 0; i < s.length(); i++) + if (mat[i][j] <= min) { - // String ss = s.substring(i, i + 1).toUpperCase(); - char c = s.charAt(i); - if ('a' <= c && c <= 'z') - { - // TO UPPERCASE !!! - c -= ('a' - 'A'); - } - - - try - { - if (type.equals("pep")) - { - seq1[i] = ResidueProperties.aaIndex[c]; - } - else if (type.equals("dna")) - { - seq1[i] = ResidueProperties.nucleotideIndex[c]; - } - - if (seq1[i] > 23) - { - seq1[i] = 23; - } - } - catch (Exception e) - { - if (type.equals("dna")) - { - seq1[i] = 4; - } - else - { - seq1[i] = 23; - } - } + min = mat[i][j]; } - - return seq1; + } } - /** - * DOCUMENT ME! - * - * @param g DOCUMENT ME! - * @param mat DOCUMENT ME! - * @param n DOCUMENT ME! - * @param m DOCUMENT ME! - * @param psize DOCUMENT ME! - */ - public static void displayMatrix(Graphics g, int[][] mat, int n, int m, - int psize) - { - int max = -1000; - int min = 1000; + System.out.println(max + " " + min); - for (int i = 0; i < n; i++) - { - for (int j = 0; j < m; j++) - { - if (mat[i][j] >= max) - { - max = mat[i][j]; - } - - if (mat[i][j] <= min) - { - min = mat[i][j]; - } - } - } - - System.out.println(max + " " + min); - - for (int i = 0; i < n; i++) - { - for (int j = 0; j < m; j++) - { - int x = psize * i; - int y = psize * j; + for (int i = 0; i < n; i++) + { + for (int j = 0; j < m; j++) + { + int x = psize * i; + int y = psize * j; - // System.out.println(mat[i][j]); - float score = (float) (mat[i][j] - min) / (float) (max - min); - g.setColor(new Color(score, 0, 0)); - g.fillRect(x, y, psize, psize); + // System.out.println(mat[i][j]); + float score = (float) (mat[i][j] - min) / (float) (max - min); + g.setColor(new Color(score, 0, 0)); + g.fillRect(x, y, psize, psize); - // System.out.println(x + " " + y + " " + score); - } - } + // System.out.println(x + " " + y + " " + score); + } } + } }