X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=3eae385a0473f4e266d627a85539abfd55f6fb0e;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=0de81677fa8d7a6a1415095408dbd8155117851b;hpb=85de15725d1b74ba9e0c35a104132206615d8c13;p=jalview.git
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 0de8167..3eae385 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,23 +1,22 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.*;
import java.awt.*;
@@ -27,40 +26,55 @@ import jalview.schemes.*;
import jalview.util.*;
/**
- *
- *
+ *
+ *
* @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", "-"};
+ { "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", "-"
- };
+ { "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!! */
@@ -74,51 +88,67 @@ public class AlignSeq
/** 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!
+ *
+ * @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);
+ 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!
+ *
+ * @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 AlignSeq(SequenceI s1, String string1, SequenceI s2,
+ String string2, String type)
{
- SeqInit(s1, string1, s2, string2, type);
+ SeqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type);
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getMaxScore()
@@ -128,7 +158,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getSeq2Start()
@@ -138,7 +168,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getSeq2End()
@@ -148,7 +178,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getSeq1Start()
@@ -158,7 +188,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getSeq1End()
@@ -168,7 +198,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getOutput()
@@ -178,7 +208,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getAStr1()
@@ -188,7 +218,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getAStr2()
@@ -198,7 +228,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int[] getASeq1()
@@ -208,7 +238,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int[] getASeq2()
@@ -218,7 +248,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public SequenceI getS1()
@@ -228,7 +258,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public SequenceI getS2()
@@ -237,19 +267,16 @@ public class AlignSeq
}
/**
- * 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
+ * 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)
+ public void SeqInit(SequenceI s1, String string1, SequenceI s2,
+ String string2, String type)
{
this.s1 = s1;
this.s2 = s2;
@@ -257,11 +284,16 @@ public class AlignSeq
SeqInit(string1, string2);
}
- public void SeqInit(SequenceI s1,
- String string1,
- SequenceI s2,
- String string2,
- ScoreMatrix scoreMatrix)
+ /**
+ * 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;
@@ -270,8 +302,10 @@ public class AlignSeq
}
/**
- * construct score matrix for string1 and string2 (after removing any existing gaps
- * @param string1
+ * construct score matrix for string1 and string2 (after removing any existing
+ * gaps
+ *
+ * @param string1
* @param string2
*/
private void SeqInit(String string1, String string2)
@@ -281,51 +315,53 @@ public class AlignSeq
if (s1str.length() == 0 || s2str.length() == 0)
{
- output.append("ALL GAPS: " +
- (s1str.length() == 0 ? s1.getName() : " ")
- + (s2str.length() == 0 ? s2.getName() : ""));
+ output.append("ALL GAPS: "
+ + (s1str.length() == 0 ? s1.getName() : " ")
+ + (s2str.length() == 0 ? s2.getName() : ""));
return;
}
- //System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory());
+ // System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory());
seq1 = new int[s1str.length()];
- //System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory());
+ // System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory());
seq2 = new int[s2str.length()];
- //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
+ // System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
score = new int[s1str.length()][s2str.length()];
- //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
+ // System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
E = new int[s1str.length()][s2str.length()];
- //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());
+ // 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());
+ // System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());
seq1 = stringToInt(s1str, type);
- //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());
+ // 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();
+ // 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");
+ // traceAlignment();
+ // tend = System.currentTimeMillis();
+ // System.out.println("Time take to traceback alignment = " + (tend-tstart)
+ // + " ms");
}
private void setDefaultParams(String type)
@@ -348,18 +384,20 @@ public class AlignSeq
if (type.equals(AlignSeq.PEP))
{
intToStr = pep;
- defInt = 23;
+ charToInt = ResidueProperties.aaIndex;
+ defInt = ResidueProperties.maxProteinIndex;
}
else if (type.equals(AlignSeq.DNA))
{
intToStr = dna;
- defInt = 4;
+ charToInt = ResidueProperties.nucleotideIndex;
+ defInt = ResidueProperties.maxNucleotideIndex;
}
else
{
output.append("Wrong type = dna or pep only");
- throw new Error("Unknown Type " + type2 +
- " - dna or pep are the only allowed values.");
+ throw new Error("Unknown Type " + type2
+ + " - dna or pep are the only allowed values.");
}
}
@@ -391,7 +429,7 @@ public class AlignSeq
}
}
- // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
+ // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
int i = maxi;
int j = maxj;
int trace;
@@ -405,15 +443,15 @@ public class AlignSeq
count = (seq1.length + seq2.length) - 1;
- while ( (i > 0) && (j > 0))
+ while ((i > 0) && (j > 0))
{
- if ( (aseq1[count] != defInt) && (i >= 0))
+ if ((aseq1[count] != defInt) && (i >= 0))
{
aseq1[count] = seq1[i];
astr1 = s1str.charAt(i) + astr1;
}
- if ( (aseq2[count] != defInt) && (j > 0))
+ if ((aseq2[count] != defInt) && (j > 0))
{
aseq2[count] = seq2[j];
astr2 = s2str.charAt(j) + astr2;
@@ -463,42 +501,53 @@ public class AlignSeq
*/
public void printAlignment(java.io.PrintStream os)
{
- // TODO: Use original sequence characters rather than re-translated characters in output
+ // 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;
+ 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(" : " + 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");
-
+ 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()) + " ");
+ output.append(new Format("%" + (maxid) + "s").form(s1id) + " ");
for (int i = 0; i < len; i++)
{
- if ( (i + (j * len)) < astr1.length())
+ if ((i + (j * len)) < astr1.length())
{
- output.append(astr1.charAt(i +
- (j * len)));
+ output.append(astr1.charAt(i + (j * len)));
}
}
@@ -508,19 +557,19 @@ public class AlignSeq
// Print out the matching chars
for (int i = 0; i < len; i++)
{
- if ( (i + (j * len)) < astr1.length())
+ 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))))
+ 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)
+ if (ResidueProperties.getPAM250(astr1.charAt(i + (j * len)),
+ astr2.charAt(i + (j * len))) > 0)
{
output.append(".");
}
@@ -538,12 +587,12 @@ public class AlignSeq
// Now print the second aligned sequence
output = output.append("\n");
- output = output.append(new Format("%" + (maxid) + "s").form(s2.getName()) +
- " ");
+ output = output.append(new Format("%" + (maxid) + "s").form(s2id)
+ + " ");
for (int i = 0; i < len; i++)
{
- if ( (i + (j * len)) < astr2.length())
+ if ((i + (j * len)) < astr2.length())
{
output.append(astr2.charAt(i + (j * len)));
}
@@ -553,20 +602,22 @@ public class AlignSeq
}
pid = pid / (float) (aseq1.length - count) * 100;
- output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));
+ output = output.append(new Format("Percentage ID = %2.2f\n\n")
+ .form(pid));
try
{
os.print(output.toString());
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
}
/**
* DOCUMENT ME!
- *
- * @param mat DOCUMENT ME!
+ *
+ * @param mat
+ * DOCUMENT ME!
*/
public void printScoreMatrix(int[][] mat)
{
@@ -604,10 +655,12 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- *
+ *
+ * @param i
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public int findTrace(int i, int j)
@@ -668,8 +721,7 @@ public class AlignSeq
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);
+ score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen, -gapExtend);
traceback[0][j] = 1;
}
@@ -689,13 +741,11 @@ public class AlignSeq
{
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);
+ 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]);
+ 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);
}
}
@@ -703,10 +753,12 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
- * @param gapChar DOCUMENT ME!
- * @param seq DOCUMENT ME!
- *
+ *
+ * @param gapChar
+ * DOCUMENT ME!
+ * @param seq
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public static String extractGaps(String gapChar, String seq)
@@ -724,11 +776,14 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
- * @param i1 DOCUMENT ME!
- * @param i2 DOCUMENT ME!
- * @param i3 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)
@@ -750,10 +805,12 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
- * @param i1 DOCUMENT ME!
- * @param i2 DOCUMENT ME!
- *
+ *
+ * @param i1
+ * DOCUMENT ME!
+ * @param i2
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public int max(int i1, int i2)
@@ -770,10 +827,12 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- * @param type DOCUMENT ME!
- *
+ *
+ * @param s
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public int[] stringToInt(String s, String type)
@@ -792,34 +851,16 @@ public class AlignSeq
try
{
- if (type.equals("pep"))
+ 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] = ResidueProperties.aaIndex[c];
- if (seq1[i] > 23)
- {
- seq1[i] = 23;
- }
- }
- else if (type.equals("dna"))
- {
- seq1[i] = ResidueProperties.nucleotideIndex[c];
- if (seq1[i] > 4)
- {
- seq1[i] = 4;
- }
+ seq1[i] = defInt;
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
- if (type.equals("dna"))
- {
- seq1[i] = 4;
- }
- else
- {
- seq1[i] = 23;
- }
+ seq1[i] = defInt;
}
}
@@ -828,15 +869,20 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param mat DOCUMENT ME!
- * @param n DOCUMENT ME!
- * @param m DOCUMENT ME!
- * @param psize 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 psize)
{
int max = -1000;
int min = 1000;
@@ -866,13 +912,190 @@ public class AlignSeq
int x = psize * i;
int y = psize * j;
- // System.out.println(mat[i][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);
+ // 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)
+ {
+ lastmatch = true;
+ // extend mapping interval.
+ if (lp1 + 1 != alignpos || lp2+1 !=pdbpos)
+ {
+ as1.add(Integer.valueOf(alignpos));
+ as2.add(Integer.valueOf(pdbpos));
+ }
+ lp1 = alignpos;
+ lp2 = pdbpos;
+ }
+ else
+ {
+ 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;
+ }
+
+ /**
+ * 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;
}
}