X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=65fd1100b8e8a7f2cdc33f1d1a90f80aaa3076bf;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=e77a0d3025771df08ea09b60b5a37b23ab2f73d2;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index e77a0d3..65fd110 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,543 +1,1133 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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.schemes.*;
-import jalview.datamodel.SequenceI;
-import jalview.util.*;
-import jalview.io.*;
-
-import java.util.*;
-import java.io.*;
-import java.awt.*;
-
-public class AlignSeq {
-
- int[][] score;
- int[][] E;
- int[][] F;
- int[][] traceback;
-
- int[] seq1;
- int[] seq2;
-
- SequenceI s1;
- SequenceI s2;
-
- String s1str;
- String s2str;
-
- int maxi;
- int maxj;
-
- int[] aseq1;
- int[] aseq2;
-
- String astr1 = "";
- String astr2 = "";
-
- public int seq1start;
- public int seq1end;
- public int seq2start;
- public int seq2end;
-
- int count;
-
- public int maxscore;
- float pid;
- int prev = 0;
-
- 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 gapOpen = 120;
- int gapExtend = 20;
-
- int lookup[][] = ResidueProperties.getBLOSUM62();
- String intToStr[] = pep;
- int defInt = 23;
-
- String output = "";
-
- String type;
- Runtime rt;
- public AlignSeq() {}
-
- public AlignSeq(SequenceI s1, SequenceI s2,String type) {
- rt = Runtime.getRuntime();
- SeqInit(s1,s2,type);
- }
-
- public int getMaxScore() {
- return maxscore;
- }
-
- public int getSeq2Start() {
- return seq2start;
- }
-
- public int getSeq2End() {
- return seq2end;
- }
-
- public int getSeq1Start() {
- return seq1start;
- }
-
- public int getSeq1End() {
- return seq1end;
- }
-
- public String getOutput() {
- return output;
- }
-
- public String getAStr1() {
- return astr1;
- }
- public String getAStr2() {
- return astr2;
- }
- public int [] getASeq1() {
- return aseq1;
- }
- public int [] getASeq2() {
- return aseq2;
- }
- public SequenceI getS1() {
- return s1;
- }
- public SequenceI getS2() {
- return s2;
- }
-
- public void SeqInit(SequenceI s1, SequenceI s2,String type) {
- s1str = extractGaps(".",s1.getSequence());
- s2str = extractGaps(".",s2.getSequence());
- s1str = extractGaps("-",s1str);
- s2str = extractGaps("-",s2str);
- s1str = extractGaps(" ",s1str);
- s2str = extractGaps(" ",s2str);
-
- this.s1 = s1;
- this.s2 = s2;
-
- this.type = type;
-
- if (type.equals("pep")) {
- lookup = ResidueProperties.getBLOSUM62();
- intToStr = pep;
- defInt = 23;
- } else if (type.equals("dna")) {
- lookup = ResidueProperties.getDNA();
- intToStr = dna;
- defInt = 4;
- } else {
- output = output + ("Wrong type = dna or pep only");
- System.exit(0);
- }
-
-
- //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");
- }
-
- public void traceAlignment() {
-
- // Find the maximum score along the rhs or bottom row
- int max = -9999;
- 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;
- }
- }
- 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;
- }
- }
-
- // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
-
- int i = maxi;
- int j = maxj;
- int trace;
- maxscore = score[i][j] / 10;
-
- seq1end = maxi+1;
- seq2end = maxj+1;
-
- aseq1 = new int[seq1.length + seq2.length];
- aseq2 = new int[seq1.length + seq2.length];
-
- count = seq1.length + seq2.length - 1;
-
- while (i>0 && j >0) {
-
- 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;
- }
- trace = findTrace(i,j);
- if (trace == 0) {
- i--;
- j--;
-
- } else if (trace == 1) {
- j--;
- aseq1[count] = defInt;
- astr1 = "-" + astr1.substring(1);
- } else if (trace == -1) {
- i--;
- aseq2[count] = defInt;
- astr2 = "-" + astr2.substring(1);
- }
- count--;
- }
-
- seq1start = i+1;
- seq2start = j+1;
-
- if (aseq1[count] != defInt) {
- aseq1[count] = seq1[i];
- astr1 = intToStr[seq1[i]] + astr1;
- }
-
- if (aseq2[count] != defInt) {
- aseq2[count] = seq2[j];
- astr2 = intToStr[seq2[j]] + astr2;
- }
- }
-
- public void printAlignment() {
- // Find the biggest id length for formatting purposes
- int maxid = s1.getName().length();
-
- if (s2.getName().length() > maxid) {
- maxid = s2.getName().length();
- }
-
- int len = 72 - maxid - 1;
- int nochunks = ((aseq1.length - count) / len) + 1;
- pid = 0;
- int overlap = 0;
-
- output = output + ("Score = " + score[maxi][maxj] + "\n");
- output = output + ("Length of alignment = " + (aseq1.length-count) + "\n");
- output = output + ("Sequence ");
- output = output + (new Format("%" + maxid + "s").form(s1.getName()));
- output = output + (" : " + seq1start + " - " + seq1end + " (Sequence length = " + s1str.length() + ")\n");
- output = output + ("Sequence ");
- output = output + (new Format("%" + maxid + "s").form(s2.getName()));
- output = output + (" : " + seq2start + " - " + seq2end + " (Sequence length = " + s2str.length() + ")\n\n");
-
- for (int j = 0; j < nochunks; j++) {
- // Print the first aligned sequence
- output = output + (new Format("%" + (maxid) + "s").form(s1.getName()) + " ");
- for (int i = 0; i < len ; i++) {
-
- if ((count + i + j*len) < aseq1.length) {
- output = output + (new Format("%s").form(intToStr[aseq1[count + i + j*len]]));
- }
- }
-
- output = output + ("\n");
- output = output + (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 = output + ("|");
- } else if (type.equals("pep")) {
- if (ResidueProperties.getPAM250(intToStr[aseq1[count+i+j*len]],intToStr[aseq2[count+i+j*len]]) > 0) {
- output = output + (".");
- } else {
- output = output + (" ");
- }
- } else {
- output = output + (" ");
- }
-
- }
- }
- // Now print the second aligned sequence
- output = output + ("\n");
- output = output + (new Format("%" + (maxid) + "s").form(s2.getName()) + " " );
- for (int i = 0; i < len ; i++) {
- if ((count + i + j*len) < aseq1.length) {
- output = output + (new Format("%s").form(intToStr[aseq2[count + i + j*len]]));
- }
- }
- output = output + ("\n\n");
- }
- pid = pid/(float)(aseq1.length-count)*100;
- output = output + (new Format("Percentage ID = %2.2f\n\n").form(pid));
-
- }
-
- public void printScoreMatrix(int[][] mat) {
- 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));
- for (int jj = 1;jj < m; jj++) {
- Format.print(System.out,"%5s",s2str.substring(jj,jj+1));
- }
- System.out.println();
- }
-
- for (int j = 0;j < m; j++) {
- if (j == 0) {
- Format.print(System.out,"%3s",s1str.substring(i,i+1));
- }
- Format.print(System.out,"%3d ",mat[i][j]/10);
- }
- System.out.println();
- }
- }
-
- 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) {
- max = F[i][j];
- t = -1;
- } else if (F[i][j] == max) {
- if (prev == -1) {
- max = F[i][j];
- t = -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;
- }
- }
- prev = t;
- return t;
- }
-
- public void calcScoreMatrix() {
-
-
- int n = seq1.length;
- int m = seq2.length;
-
-
- // top left hand element
- score[0][0] = lookup[seq1[0]][seq2[0]] * 10;
- E[0][0] = -gapExtend;
- F[0][0] = 0;
-
- // 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;
-
- score[0][j] = max( lookup[seq1[0]][seq2[j]] * 10 ,-gapOpen,-gapExtend);
-
- traceback[0][j] = 1;
- }
-
- // 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);
-
- score[i][0] = max( lookup[seq1[i]][seq2[0]] * 10 ,E[i][0],F[i][0]);
- traceback[i][0] = -1;
- }
-
- // 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);
- }
- }
-
- }
- public static String extractChars(String chars, String seq) {
- String out = seq;
- for (int i=0; i < chars.length(); i++) {
- String gap = chars.substring(i,i+1);
- out = extractGaps(gap,out);
- }
- return out;
- }
- public static String extractGaps(String gapChar, String seq) {
- StringTokenizer str = new StringTokenizer(seq,gapChar);
- String newString = "";
-
- while (str.hasMoreTokens()) {
- newString = newString + str.nextToken();
- }
- return newString;
- }
-
-
- public int max(int i1, int i2, int i3) {
- int max = i1;
- if (i2 > i1) {
- max = i2;
- }
- if (i3 > max) {
- max = i3;
- }
- return max;
- }
-
- public int max(int i1, int i2) {
- int max = i1;
- if (i2 > i1) {
- max = i2;
- }
- return max;
- }
-
- 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();
- try {
- if (type.equals("pep")) {
- seq1[i] = ((Integer)ResidueProperties.aaHash.get(ss)).intValue();
- } else if (type.equals("dna")) {
- seq1[i] = ((Integer)dnaHash.get(ss)).intValue();
- }
- if (seq1[i] > 23) {
- seq1[i] = 23;
- }
- } catch (Exception e) {
- if (type.equals("dna")) {
- seq1[i] = 4;
- } else {
- seq1[i] = 23;
- }
- }
- }
- return seq1;
- }
-
- 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++) {
- 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;
- // 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);
- }
-
- }
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import java.util.Locale;
+
+import jalview.analysis.scoremodels.PIDModel;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+import jalview.util.Format;
+import jalview.util.MapList;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.StringTokenizer;
+
+/**
+ *
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignSeq
+{
+ private static final int MAX_NAME_LENGTH = 30;
+
+ private static final int GAP_OPEN_COST = 120;
+
+ private static final int GAP_EXTEND_COST = 20;
+
+ private static final int GAP_INDEX = -1;
+
+ public static final String PEP = "pep";
+
+ public static final String DNA = "dna";
+
+ private static final String NEWLINE = System.lineSeparator();
+
+ float[][] score;
+
+ float[][] E;
+
+ float[][] F;
+
+ int[][] traceback; // todo is this actually used?
+
+ 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;
+
+ public int seq2end;
+
+ int count;
+
+ public float maxscore;
+
+ int prev = 0;
+
+ StringBuffer output = new StringBuffer();
+
+ String type; // AlignSeq.PEP or AlignSeq.DNA
+
+ private ScoreMatrix scoreMatrix;
+
+ /**
+ * Creates a new AlignSeq object.
+ *
+ * @param s1
+ * first sequence for alignment
+ * @param s2
+ * second sequence for alignment
+ * @param type
+ * molecule type, either AlignSeq.PEP or AlignSeq.DNA
+ */
+ 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.toUpperCase(Locale.ROOT), s2,
+ string2.toUpperCase(Locale.ROOT), type);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public float 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;
+ }
+
+ /**
+ *
+ * @return aligned instance of Seq 1
+ */
+ public SequenceI getAlignedSeq1()
+ {
+ SequenceI alSeq1 = new Sequence(s1.getName(), getAStr1());
+ alSeq1.setStart(s1.getStart() + getSeq1Start() - 1);
+ alSeq1.setEnd(s1.getStart() + getSeq1End() - 1);
+ alSeq1.setDatasetSequence(
+ s1.getDatasetSequence() == null ? s1 : s1.getDatasetSequence());
+ return alSeq1;
+ }
+
+ /**
+ *
+ * @return aligned instance of Seq 2
+ */
+ public SequenceI getAlignedSeq2()
+ {
+ SequenceI alSeq2 = new Sequence(s2.getName(), getAStr2());
+ alSeq2.setStart(s2.getStart() + getSeq2Start() - 1);
+ alSeq2.setEnd(s2.getStart() + getSeq2End() - 1);
+ alSeq2.setDatasetSequence(
+ s2.getDatasetSequence() == null ? s2 : s2.getDatasetSequence());
+ return alSeq2;
+ }
+
+ /**
+ * Construct score matrix for sequences with standard DNA or PEPTIDE matrix
+ *
+ * @param s1
+ * - sequence 1
+ * @param string1
+ * - string to use for s1
+ * @param s2
+ * - sequence 2
+ * @param string2
+ * - string to use for s2
+ * @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);
+ }
+
+ /**
+ * 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)
+ {
+ output.append(
+ "ALL GAPS: " + (s1str.length() == 0 ? s1.getName() : " ")
+ + (s2str.length() == 0 ? s2.getName() : ""));
+ return;
+ }
+
+ score = new float[s1str.length()][s2str.length()];
+
+ E = new float[s1str.length()][s2str.length()];
+
+ F = new float[s1str.length()][s2str.length()];
+ traceback = new int[s1str.length()][s2str.length()];
+
+ seq1 = indexEncode(s1str);
+
+ seq2 = indexEncode(s2str);
+ }
+
+ private void setDefaultParams(String moleculeType)
+ {
+ if (!PEP.equals(moleculeType) && !DNA.equals(moleculeType))
+ {
+ output.append("Wrong type = dna or pep only");
+ throw new Error(MessageManager
+ .formatMessage("error.unknown_type_dna_or_pep", new String[]
+ { moleculeType }));
+ }
+
+ type = moleculeType;
+ scoreMatrix = ScoreModels.getInstance()
+ .getDefaultModel(PEP.equals(type));
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void traceAlignment()
+ {
+ // Find the maximum score along the rhs or bottom row
+ float max = -Float.MAX_VALUE;
+
+ 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;
+ }
+ }
+
+ 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;
+ }
+ }
+
+ int i = maxi;
+ int j = maxj;
+ int trace;
+ maxscore = score[i][j] / 10f;
+
+ seq1end = maxi + 1;
+ seq2end = maxj + 1;
+
+ aseq1 = new int[seq1.length + seq2.length];
+ aseq2 = new int[seq1.length + seq2.length];
+
+ StringBuilder sb1 = new StringBuilder(aseq1.length);
+ StringBuilder sb2 = new StringBuilder(aseq2.length);
+
+ count = (seq1.length + seq2.length) - 1;
+
+ while (i > 0 && j > 0)
+ {
+ aseq1[count] = seq1[i];
+ sb1.append(s1str.charAt(i));
+ aseq2[count] = seq2[j];
+ sb2.append(s2str.charAt(j));
+
+ trace = findTrace(i, j);
+
+ if (trace == 0)
+ {
+ i--;
+ j--;
+ }
+ else if (trace == 1)
+ {
+ j--;
+ aseq1[count] = GAP_INDEX;
+ sb1.replace(sb1.length() - 1, sb1.length(), "-");
+ }
+ else if (trace == -1)
+ {
+ i--;
+ aseq2[count] = GAP_INDEX;
+ sb2.replace(sb2.length() - 1, sb2.length(), "-");
+ }
+
+ count--;
+ }
+
+ seq1start = i + 1;
+ seq2start = j + 1;
+
+ if (aseq1[count] != GAP_INDEX)
+ {
+ aseq1[count] = seq1[i];
+ sb1.append(s1str.charAt(i));
+ }
+
+ if (aseq2[count] != GAP_INDEX)
+ {
+ aseq2[count] = seq2[j];
+ sb2.append(s2str.charAt(j));
+ }
+
+ /*
+ * we built the character strings backwards, so now
+ * reverse them to convert to sequence strings
+ */
+ astr1 = sb1.reverse().toString();
+ astr2 = sb2.reverse().toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void printAlignment(PrintStream os)
+ {
+ // TODO: Use original sequence characters rather than re-translated
+ // characters in output
+ // Find the biggest id length for formatting purposes
+ String s1id = getAlignedSeq1().getDisplayId(true);
+ String s2id = getAlignedSeq2().getDisplayId(true);
+ int nameLength = Math.max(s1id.length(), s2id.length());
+ if (nameLength > MAX_NAME_LENGTH)
+ {
+ int truncateBy = nameLength - MAX_NAME_LENGTH;
+ nameLength = MAX_NAME_LENGTH;
+ // JAL-527 - truncate the sequence ids
+ if (s1id.length() > nameLength)
+ {
+ int slashPos = s1id.lastIndexOf('/');
+ s1id = s1id.substring(0, slashPos - truncateBy)
+ + s1id.substring(slashPos);
+ }
+ if (s2id.length() > nameLength)
+ {
+ int slashPos = s2id.lastIndexOf('/');
+ s2id = s2id.substring(0, slashPos - truncateBy)
+ + s2id.substring(slashPos);
+ }
+ }
+ int len = 72 - nameLength - 1;
+ int nochunks = ((aseq1.length - count) / len)
+ + ((aseq1.length - count) % len > 0 ? 1 : 0);
+ float pid = 0f;
+
+ output.append("Score = ").append(score[maxi][maxj]).append(NEWLINE);
+ output.append("Length of alignment = ")
+ .append(String.valueOf(aseq1.length - count)).append(NEWLINE);
+ output.append("Sequence ");
+ Format nameFormat = new Format("%" + nameLength + "s");
+ output.append(nameFormat.form(s1id));
+ output.append(" (Sequence length = ")
+ .append(String.valueOf(s1str.length())).append(")")
+ .append(NEWLINE);
+ output.append("Sequence ");
+ output.append(nameFormat.form(s2id));
+ output.append(" (Sequence length = ")
+ .append(String.valueOf(s2str.length())).append(")")
+ .append(NEWLINE).append(NEWLINE);
+
+ ScoreMatrix pam250 = ScoreModels.getInstance().getPam250();
+
+ for (int j = 0; j < nochunks; j++)
+ {
+ // Print the first aligned sequence
+ output.append(nameFormat.form(s1id)).append(" ");
+
+ for (int i = 0; i < len; i++)
+ {
+ if ((i + (j * len)) < astr1.length())
+ {
+ output.append(astr1.charAt(i + (j * len)));
+ }
+ }
+
+ output.append(NEWLINE);
+ output.append(nameFormat.form(" ")).append(" ");
+
+ /*
+ * Print out the match symbols:
+ * | for exact match (ignoring case)
+ * . if PAM250 score is positive
+ * else a space
+ */
+ for (int i = 0; i < len; i++)
+ {
+ if ((i + (j * len)) < astr1.length())
+ {
+ char c1 = astr1.charAt(i + (j * len));
+ char c2 = astr2.charAt(i + (j * len));
+ boolean sameChar = Comparison.isSameResidue(c1, c2, false);
+ if (sameChar && !Comparison.isGap(c1))
+ {
+ pid++;
+ output.append("|");
+ }
+ else if (PEP.equals(type))
+ {
+ if (pam250.getPairwiseScore(c1, c2) > 0)
+ {
+ output.append(".");
+ }
+ else
+ {
+ output.append(" ");
+ }
+ }
+ else
+ {
+ output.append(" ");
+ }
+ }
+ }
+
+ // Now print the second aligned sequence
+ output = output.append(NEWLINE);
+ output = output.append(nameFormat.form(s2id)).append(" ");
+
+ for (int i = 0; i < len; i++)
+ {
+ if ((i + (j * len)) < astr2.length())
+ {
+ output.append(astr2.charAt(i + (j * len)));
+ }
+ }
+
+ output.append(NEWLINE).append(NEWLINE);
+ }
+
+ pid = pid / (aseq1.length - count) * 100;
+ output.append(new Format("Percentage ID = %3.2f\n").form(pid));
+ output.append(NEWLINE);
+ try
+ {
+ os.print(output.toString());
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int findTrace(int i, int j)
+ {
+ int t = 0;
+ float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
+ s2str.charAt(j));
+ float max = score[i - 1][j - 1] + (pairwiseScore * 10);
+
+ 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;
+ }
+ }
+
+ 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;
+ }
+ }
+
+ prev = t;
+
+ return t;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void calcScoreMatrix()
+ {
+ int n = seq1.length;
+ int m = seq2.length;
+
+ // top left hand element
+ score[0][0] = scoreMatrix.getPairwiseScore(s1str.charAt(0),
+ s2str.charAt(0)) * 10;
+ E[0][0] = -GAP_EXTEND_COST;
+ F[0][0] = 0;
+
+ // 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] - GAP_OPEN_COST,
+ E[0][j - 1] - GAP_EXTEND_COST);
+ F[0][j] = -GAP_EXTEND_COST;
+
+ float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0),
+ s2str.charAt(j));
+ score[0][j] = max(pairwiseScore * 10, -GAP_OPEN_COST,
+ -GAP_EXTEND_COST);
+
+ traceback[0][j] = 1;
+ }
+
+ // Now do the left hand column
+ for (int i = 1; i < n; i++)
+ {
+ E[i][0] = -GAP_OPEN_COST;
+ F[i][0] = max(score[i - 1][0] - GAP_OPEN_COST,
+ F[i - 1][0] - GAP_EXTEND_COST);
+
+ float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
+ s2str.charAt(0));
+ score[i][0] = max(pairwiseScore * 10, E[i][0], F[i][0]);
+ traceback[i][0] = -1;
+ }
+
+ // 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] - GAP_OPEN_COST,
+ E[i][j - 1] - GAP_EXTEND_COST);
+ F[i][j] = max(score[i - 1][j] - GAP_OPEN_COST,
+ F[i - 1][j] - GAP_EXTEND_COST);
+
+ float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
+ s2str.charAt(j));
+ score[i][j] = max(score[i - 1][j - 1] + (pairwiseScore * 10),
+ E[i][j], F[i][j]);
+ traceback[i][j] = findTrace(i, j);
+ }
+ }
+ }
+
+ /**
+ * Returns the given sequence with all of the given gap characters removed.
+ *
+ * @param gapChars
+ * a string of characters to be treated as gaps
+ * @param seq
+ * the input sequence
+ *
+ * @return
+ */
+ public static String extractGaps(String gapChars, String seq)
+ {
+ if (gapChars == null || seq == null)
+ {
+ return null;
+ }
+ StringTokenizer str = new StringTokenizer(seq, gapChars);
+ StringBuilder newString = new StringBuilder(seq.length());
+
+ while (str.hasMoreTokens())
+ {
+ newString.append(str.nextToken());
+ }
+
+ return newString.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f1
+ * DOCUMENT ME!
+ * @param f2
+ * DOCUMENT ME!
+ * @param f3
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private static float max(float f1, float f2, float f3)
+ {
+ float max = f1;
+
+ if (f2 > f1)
+ {
+ max = f2;
+ }
+
+ if (f3 > max)
+ {
+ max = f3;
+ }
+
+ return max;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f1
+ * DOCUMENT ME!
+ * @param f2
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private static float max(float f1, float f2)
+ {
+ float max = f1;
+
+ if (f2 > f1)
+ {
+ max = f2;
+ }
+
+ return max;
+ }
+
+ /**
+ * Converts the character string to an array of integers which are the
+ * corresponding indices to the characters in the score matrix
+ *
+ * @param s
+ *
+ * @return
+ */
+ int[] indexEncode(String s)
+ {
+ int[] encoded = new int[s.length()];
+
+ for (int i = 0; i < s.length(); i++)
+ {
+ char c = s.charAt(i);
+ encoded[i] = scoreMatrix.getMatrixIndex(c);
+ }
+
+ return encoded;
+ }
+
+ /**
+ * 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)
+ {
+ // TODO method doesn't seem to be referenced anywhere delete??
+ int max = -1000;
+ int min = 1000;
+
+ 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;
+
+ // 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);
+ }
+ }
+ }
+
+ /**
+ * Compute a globally optimal needleman and wunsch alignment between two
+ * sequences
+ *
+ * @param s1
+ * @param s2
+ * @param type
+ * AlignSeq.DNA or AlignSeq.PEP
+ */
+ public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
+ String type)
+ {
+ AlignSeq as = new AlignSeq(s1, s2, type);
+
+ as.calcScoreMatrix();
+ as.traceAlignment();
+ return as;
+ }
+
+ /**
+ *
+ * @return mapping from positions in S1 to corresponding positions in S2
+ */
+ public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch)
+ {
+ ArrayList as1 = new ArrayList(),
+ as2 = new ArrayList();
+ int pdbpos = s2.getStart() + getSeq2Start() - 2;
+ int alignpos = s1.getStart() + getSeq1Start() - 2;
+ int lp2 = pdbpos - 3, lp1 = alignpos - 3;
+ boolean lastmatch = false;
+ // and now trace the alignment onto the atom set.
+ for (int i = 0; i < astr1.length(); i++)
+ {
+ char c1 = astr1.charAt(i), c2 = astr2.charAt(i);
+ if (c1 != '-')
+ {
+ alignpos++;
+ }
+
+ if (c2 != '-')
+ {
+ pdbpos++;
+ }
+
+ if (allowmismatch || c1 == c2)
+ {
+ // extend mapping interval
+ if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
+ {
+ as1.add(Integer.valueOf(alignpos));
+ as2.add(Integer.valueOf(pdbpos));
+ }
+ lastmatch = true;
+ lp1 = alignpos;
+ lp2 = pdbpos;
+ }
+ else
+ {
+ // extend mapping interval
+ if (lastmatch)
+ {
+ as1.add(Integer.valueOf(lp1));
+ as2.add(Integer.valueOf(lp2));
+ }
+ lastmatch = false;
+ }
+ }
+ // construct range pairs
+
+ int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)],
+ mapseq2 = new int[as2.size() + (lastmatch ? 1 : 0)];
+ int i = 0;
+ for (Integer ip : as1)
+ {
+ mapseq1[i++] = ip;
+ }
+ ;
+ i = 0;
+ for (Integer ip : as2)
+ {
+ mapseq2[i++] = ip;
+ }
+ ;
+ if (lastmatch)
+ {
+ mapseq1[mapseq1.length - 1] = alignpos;
+ mapseq2[mapseq2.length - 1] = pdbpos;
+ }
+ MapList map = new MapList(mapseq1, mapseq2, 1, 1);
+
+ jalview.datamodel.Mapping mapping = new Mapping(map);
+ mapping.setTo(s2);
+ return mapping;
+ }
+
+ /**
+ * matches ochains against al and populates seqs with the best match between
+ * each ochain and the set in al
+ *
+ * @param ochains
+ * @param al
+ * @param dnaOrProtein
+ * @param removeOldAnnots
+ * when true, old annotation is cleared before new annotation
+ * transferred
+ * @return List originals, List replacement,
+ * List alignment between each>
+ */
+ public static List> replaceMatchingSeqsWith(
+ List seqs, List annotations,
+ List ochains, AlignmentI al, String dnaOrProtein,
+ boolean removeOldAnnots)
+ {
+ List orig = new ArrayList(),
+ repl = new ArrayList();
+ List aligs = new ArrayList();
+ if (al != null && al.getHeight() > 0)
+ {
+ ArrayList matches = new ArrayList();
+ ArrayList aligns = new ArrayList();
+
+ for (SequenceI sq : ochains)
+ {
+ SequenceI bestm = null;
+ AlignSeq bestaseq = null;
+ float bestscore = 0;
+ for (SequenceI msq : al.getSequences())
+ {
+ AlignSeq aseq = doGlobalNWAlignment(msq, sq, dnaOrProtein);
+ if (bestm == null || aseq.getMaxScore() > bestscore)
+ {
+ bestscore = aseq.getMaxScore();
+ bestaseq = aseq;
+ bestm = msq;
+ }
+ }
+ // System.out.println("Best Score for " + (matches.size() + 1) + " :"
+ // + bestscore);
+ matches.add(bestm);
+ aligns.add(bestaseq);
+ al.deleteSequence(bestm);
+ }
+ for (int p = 0, pSize = seqs.size(); p < pSize; p++)
+ {
+ SequenceI sq, sp = seqs.get(p);
+ int q;
+ if ((q = ochains.indexOf(sp)) > -1)
+ {
+ seqs.set(p, sq = matches.get(q));
+ orig.add(sp);
+ repl.add(sq);
+ sq.setName(sp.getName());
+ sq.setDescription(sp.getDescription());
+ Mapping sp2sq;
+ sq.transferAnnotation(sp,
+ sp2sq = aligns.get(q).getMappingFromS1(false));
+ aligs.add(aligns.get(q));
+ int inspos = -1;
+ for (int ap = 0; ap < annotations.size();)
+ {
+ if (annotations.get(ap).sequenceRef == sp)
+ {
+ if (inspos == -1)
+ {
+ inspos = ap;
+ }
+ if (removeOldAnnots)
+ {
+ annotations.remove(ap);
+ }
+ else
+ {
+ AlignmentAnnotation alan = annotations.remove(ap);
+ alan.liftOver(sq, sp2sq);
+ alan.setSequenceRef(sq);
+ sq.addAlignmentAnnotation(alan);
+ }
+ }
+ else
+ {
+ ap++;
+ }
+ }
+ if (sq.getAnnotation() != null && sq.getAnnotation().length > 0)
+ {
+ annotations.addAll(inspos == -1 ? annotations.size() : inspos,
+ Arrays.asList(sq.getAnnotation()));
+ }
+ }
+ }
+ }
+ return Arrays.asList(orig, repl, aligs);
+ }
+
+ /**
+ * compute the PID vector used by the redundancy filter.
+ *
+ * @param originalSequences
+ * - sequences in alignment that are to filtered
+ * @param omitHidden
+ * - null or strings to be analysed (typically, visible portion of
+ * each sequence in alignment)
+ * @param start
+ * - first column in window for calculation
+ * @param end
+ * - last column in window for calculation
+ * @param ungapped
+ * - if true then use ungapped sequence to compute PID
+ * @return vector containing maximum PID for i-th sequence and any sequences
+ * longer than that seuqence
+ */
+ public static float[] computeRedundancyMatrix(
+ SequenceI[] originalSequences, String[] omitHidden, int start,
+ int end, boolean ungapped)
+ {
+ int height = originalSequences.length;
+ float[] redundancy = new float[height];
+ int[] lngth = new int[height];
+ for (int i = 0; i < height; i++)
+ {
+ redundancy[i] = 0f;
+ lngth[i] = -1;
+ }
+
+ // long start = System.currentTimeMillis();
+
+ SimilarityParams pidParams = new SimilarityParams(true, true, true,
+ true);
+ float pid;
+ String seqi, seqj;
+ for (int i = 0; i < height; i++)
+ {
+
+ for (int j = 0; j < i; j++)
+ {
+ if (i == j)
+ {
+ continue;
+ }
+
+ if (omitHidden == null)
+ {
+ seqi = originalSequences[i].getSequenceAsString(start, end);
+ seqj = originalSequences[j].getSequenceAsString(start, end);
+ }
+ else
+ {
+ seqi = omitHidden[i];
+ seqj = omitHidden[j];
+ }
+ if (lngth[i] == -1)
+ {
+ String ug = AlignSeq.extractGaps(Comparison.GapChars, seqi);
+ lngth[i] = ug.length();
+ if (ungapped)
+ {
+ seqi = ug;
+ }
+ }
+ if (lngth[j] == -1)
+ {
+ String ug = AlignSeq.extractGaps(Comparison.GapChars, seqj);
+ lngth[j] = ug.length();
+ if (ungapped)
+ {
+ seqj = ug;
+ }
+ }
+ pid = (float) PIDModel.computePID(seqi, seqj, pidParams);
+
+ // use real sequence length rather than string length
+ if (lngth[j] < lngth[i])
+ {
+ redundancy[j] = Math.max(pid, redundancy[j]);
+ }
+ else
+ {
+ redundancy[i] = Math.max(pid, redundancy[i]);
+ }
+
+ }
+ }
+ return redundancy;
+ }
+}