X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=96c9b72219d39dcc665f987e80374bc89c488feb;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=d0c5869e411a1644f104500335b4845ac8eb495c;hpb=6c4bc68ae8b1c5005e79661bb2d8246515cb787d;p=jalview.git
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index d0c5869..96c9b72 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,844 +1,1255 @@
-/*
-* 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
-*/
-package jalview.analysis;
-
-import jalview.datamodel.SequenceI;
-
-import jalview.schemes.*;
-
-import jalview.util.*;
-
-import java.awt.*;
-
-import java.util.*;
-
-
-/**
- *
- *
- * @author $author$
- * @version $Revision$
- */
-public class AlignSeq
-{
- /** 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 s2 DOCUMENT ME!
- * @param type DOCUMENT ME!
- */
- public void SeqInit(SequenceI s1,
- String string1,
- SequenceI s2,
- String string2,
- String type)
- {
-
- s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
- s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
-
- if(s1str.length()==0 || s2str.length()==0)
- {
- System.out.println("ALL GAPS: " +
- (s1str.length()==0?s1.getName():" ")
- +(s2str.length()==0?s2.getName():""));
- return;
- }
-
- 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.append("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");
- }
-
- /**
- * DOCUMENT ME!
- */
- 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;
- }
- }
-
- /**
- * DOCUMENT ME!
- */
- public void printAlignment(java.io.PrintStream os)
- {
- // 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;
-
- 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)]]));
- }
- }
-
- output = output .append("\n\n");
- }
-
- 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++)
- {
- // 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();
- }
- }
-
- /**
- * 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)
- {
- 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] = 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);
- }
- }
- }
-
-
-
- /**
- * 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())
- {
- newString.append( str.nextToken() );
- }
-
- 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;
- }
-
- if (i3 > max)
- {
- max = i3;
- }
-
- 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;
- }
-
- 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');
- }
-
-
- 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;
- }
- }
- }
-
- 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++)
- {
- 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 jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.ScoreMatrix;
+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.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.StringTokenizer;
+
+/**
+ *
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignSeq
+{
+ public static final String PEP = "pep";
+
+ public static final String DNA = "dna";
+
+ static String[] dna =
+ { "A", "C", "G", "T", "-" };
+
+ // "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;
+
+ private int[] charToInt;
+
+ /**
+ * 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.toUpperCase(), s2, string2.toUpperCase(), 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;
+ }
+
+ /**
+ *
+ * @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 sequences with custom substitution matrix
+ *
+ * @param s1
+ * - sequence 1
+ * @param string1
+ * - string to use for s1
+ * @param s2
+ * - sequence 2
+ * @param string2
+ * - string to use for s2
+ * @param scoreMatrix
+ * - substitution matrix to use for alignment
+ */
+ 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)
+ {
+ output.append("ALL GAPS: "
+ + (s1str.length() == 0 ? s1.getName() : " ")
+ + (s2str.length() == 0 ? s2.getName() : ""));
+ return;
+ }
+
+ // 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))
+ {
+ lookup = ResidueProperties.getDefaultPeptideMatrix();
+ }
+ else if (type.equals(AlignSeq.DNA))
+ {
+ lookup = ResidueProperties.getDefaultDnaMatrix();
+ }
+ }
+
+ private void setType(String type2)
+ {
+ this.type = type2;
+ if (type.equals(AlignSeq.PEP))
+ {
+ intToStr = pep;
+ charToInt = ResidueProperties.aaIndex;
+ defInt = ResidueProperties.maxProteinIndex;
+ }
+ else if (type.equals(AlignSeq.DNA))
+ {
+ intToStr = dna;
+ charToInt = ResidueProperties.nucleotideIndex;
+ defInt = ResidueProperties.maxNucleotideIndex;
+ }
+ else
+ {
+ output.append("Wrong type = dna or pep only");
+ throw new Error(MessageManager.formatMessage("error.unknown_type_dna_or_pep", new String[]{type2}));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ 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 = s1str.charAt(i) + astr1;
+ }
+
+ if ((aseq2[count] != defInt) && (j > 0))
+ {
+ aseq2[count] = seq2[j];
+ astr2 = s2str.charAt(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 = s1str.charAt(i) + astr1;
+ }
+
+ if (aseq2[count] != defInt)
+ {
+ aseq2[count] = seq2[j];
+ astr2 = s2str.charAt(j) + astr2;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void printAlignment(java.io.PrintStream os)
+ {
+ // TODO: Use original sequence characters rather than re-translated
+ // characters in output
+ // Find the biggest id length for formatting purposes
+ String s1id = s1.getName(), s2id = s2.getName();
+ int maxid = s1.getName().length();
+ if (s2.getName().length() > maxid)
+ {
+ maxid = s2.getName().length();
+ }
+ if (maxid > 30)
+ {
+ maxid = 30;
+ // JAL-527 - truncate the sequence ids
+ if (s1.getName().length() > maxid)
+ {
+ s1id = s1.getName().substring(0, 30);
+ }
+ if (s2.getName().length() > maxid)
+ {
+ s2id = s2.getName().substring(0, 30);
+ }
+ }
+ 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(s1id) + " ");
+
+ for (int i = 0; i < len; i++)
+ {
+ if ((i + (j * len)) < astr1.length())
+ {
+ output.append(astr1.charAt(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 ((i + (j * len)) < astr1.length())
+ {
+ if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
+ && !jalview.util.Comparison.isGap(astr1.charAt(i
+ + (j * len))))
+ {
+ pid++;
+ output.append("|");
+ }
+ else if (type.equals("pep"))
+ {
+ if (ResidueProperties.getPAM250(astr1.charAt(i + (j * len)),
+ astr2.charAt(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(s2id)
+ + " ");
+
+ for (int i = 0; i < len; i++)
+ {
+ if ((i + (j * len)) < astr2.length())
+ {
+ output.append(astr2.charAt(i + (j * len)));
+ }
+ }
+
+ output = output.append("\n\n");
+ }
+
+ pid = pid / (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++)
+ {
+ // 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();
+ }
+ }
+
+ /**
+ * 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)
+ {
+ 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] = 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);
+ }
+ }
+ }
+
+ /**
+ * 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())
+ {
+ newString.append(str.nextToken());
+ }
+
+ 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;
+ }
+
+ if (i3 > max)
+ {
+ max = i3;
+ }
+
+ 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;
+ }
+
+ 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');
+ }
+
+ try
+ {
+ seq1[i] = charToInt[c]; // set accordingly from setType
+ if (seq1[i] < 0 || seq1[i] > defInt) // set from setType: 23 for
+ // peptides, or 4 for NA.
+ {
+ seq1[i] = defInt;
+ }
+
+ } catch (Exception e)
+ {
+ seq1[i] = defInt;
+ }
+ }
+
+ 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++)
+ {
+ 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;
+ int 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();
+
+ 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 = Comparison.PID(seqi, seqj);
+
+ // 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;
+ }
+}