X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=65fd1100b8e8a7f2cdc33f1d1a90f80aaa3076bf;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=2fcc593ccd718e1d13caf7e92080ba66451527b7;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 2fcc593..65fd110 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,76 +1,101 @@
/*
- * 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
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
+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";
- /** 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));
- }
+ private static final String NEWLINE = System.lineSeparator();
+
+ float[][] score;
+
+ float[][] E;
+
+ float[][] F;
+
+ int[][] traceback; // todo is this actually used?
- 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!! */
@@ -82,63 +107,66 @@ public class AlignSeq
/** DOCUMENT ME!! */
public int seq2start;
- /** DOCUMENT ME!! */
public int seq2end;
+
int count;
- /** DOCUMENT ME!! */
- public int maxscore;
- float pid;
+ public float maxscore;
+
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;
+
+ String type; // AlignSeq.PEP or AlignSeq.DNA
+
+ private ScoreMatrix scoreMatrix;
/**
* Creates a new AlignSeq object.
- *
- * @param s1 DOCUMENT ME!
- * @param s2 DOCUMENT ME!
- * @param type DOCUMENT ME!
+ *
+ * @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);
+ 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(Locale.ROOT), s2,
+ string2.toUpperCase(Locale.ROOT), type);
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
- public int getMaxScore()
+ public float getMaxScore()
{
return maxscore;
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getSeq2Start()
@@ -148,7 +176,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getSeq2End()
@@ -158,7 +186,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getSeq1Start()
@@ -168,7 +196,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getSeq1End()
@@ -178,7 +206,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getOutput()
@@ -188,7 +216,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getAStr1()
@@ -198,7 +226,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getAStr2()
@@ -208,7 +236,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int[] getASeq1()
@@ -218,7 +246,7 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int[] getASeq2()
@@ -227,150 +255,101 @@ public class AlignSeq
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ *
+ * @return aligned instance of Seq 1
*/
- public SequenceI getS1()
+ public SequenceI getAlignedSeq1()
{
- return s1;
+ 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;
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ *
+ * @return aligned instance of Seq 2
*/
- public SequenceI getS2()
+ public SequenceI getAlignedSeq2()
{
- return s2;
+ 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;
}
/**
- * 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;
setDefaultParams(type);
- SeqInit(string1, string2);
- }
-
- public void SeqInit(SequenceI s1,
- String string1,
- SequenceI s2,
- String string2,
- ScoreMatrix scoreMatrix)
- {
- this.s1 = s1;
- this.s2 = s2;
- setType(scoreMatrix.isDNA() ? AlignSeq.DNA : AlignSeq.PEP);
- lookup = scoreMatrix.getMatrix();
+ seqInit(string1, string2);
}
/**
- * construct score matrix for string1 and string2 (after removing any existing gaps
+ * construct score matrix for string1 and string2 (after removing any existing
+ * gaps
+ *
* @param string1
* @param string2
*/
- private void SeqInit(String string1, String 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() : ""));
+ 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()];
+ score = new float[s1str.length()][s2str.length()];
- //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
- score = new int[s1str.length()][s2str.length()];
+ E = new float[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()];
+ F = new float[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);
+ seq1 = indexEncode(s1str);
- if (type.equals(AlignSeq.PEP))
- {
- lookup = ResidueProperties.getDefaultPeptideMatrix();
- }
- else if (type.equals(AlignSeq.DNA))
- {
- lookup = ResidueProperties.getDefaultDnaMatrix();
- }
+ seq2 = indexEncode(s2str);
}
- private void setType(String type2)
+ private void setDefaultParams(String moleculeType)
{
- this.type = type2;
- if (type.equals(AlignSeq.PEP))
- {
- intToStr = pep;
- defInt = 23;
- }
- else if (type.equals(AlignSeq.DNA))
- {
- intToStr = dna;
- defInt = 4;
- }
- else
+ if (!PEP.equals(moleculeType) && !DNA.equals(moleculeType))
{
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(MessageManager
+ .formatMessage("error.unknown_type_dna_or_pep", new String[]
+ { moleculeType }));
}
+
+ type = moleculeType;
+ scoreMatrix = ScoreModels.getInstance()
+ .getDefaultModel(PEP.equals(type));
}
/**
@@ -379,7 +358,7 @@ public class AlignSeq
public void traceAlignment()
{
// Find the maximum score along the rhs or bottom row
- int max = -9999;
+ float max = -Float.MAX_VALUE;
for (int i = 0; i < seq1.length; i++)
{
@@ -401,11 +380,10 @@ public class AlignSeq
}
}
- // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
int i = maxi;
int j = maxj;
int trace;
- maxscore = score[i][j] / 10;
+ maxscore = score[i][j] / 10f;
seq1end = maxi + 1;
seq2end = maxj + 1;
@@ -413,21 +391,17 @@ public class AlignSeq
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))
+ 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;
- }
+ aseq1[count] = seq1[i];
+ sb1.append(s1str.charAt(i));
+ aseq2[count] = seq2[j];
+ sb2.append(s2str.charAt(j));
trace = findTrace(i, j);
@@ -439,14 +413,14 @@ public class AlignSeq
else if (trace == 1)
{
j--;
- aseq1[count] = defInt;
- astr1 = "-" + astr1.substring(1);
+ aseq1[count] = GAP_INDEX;
+ sb1.replace(sb1.length() - 1, sb1.length(), "-");
}
else if (trace == -1)
{
i--;
- aseq2[count] = defInt;
- astr2 = "-" + astr2.substring(1);
+ aseq2[count] = GAP_INDEX;
+ sb2.replace(sb2.length() - 1, sb2.length(), "-");
}
count--;
@@ -455,83 +429,114 @@ public class AlignSeq
seq1start = i + 1;
seq2start = j + 1;
- if (aseq1[count] != defInt)
+ if (aseq1[count] != GAP_INDEX)
{
aseq1[count] = seq1[i];
- astr1 = intToStr[seq1[i]] + astr1;
+ sb1.append(s1str.charAt(i));
}
- if (aseq2[count] != defInt)
+ if (aseq2[count] != GAP_INDEX)
{
aseq2[count] = seq2[j];
- astr2 = intToStr[seq2[j]] + astr2;
+ 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(java.io.PrintStream os)
+ 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
- int maxid = s1.getName().length();
-
- if (s2.getName().length() > maxid)
+ String s1id = getAlignedSeq1().getDisplayId(true);
+ String s2id = getAlignedSeq2().getDisplayId(true);
+ int nameLength = Math.max(s1id.length(), s2id.length());
+ if (nameLength > MAX_NAME_LENGTH)
{
- maxid = s2.getName().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 - 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");
+ 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 ");
- output.append(new Format("%" + maxid + "s").form(s1.getName()));
- output.append(" : " + s1.getStart() + " - " + s1.getEnd() +
- " (Sequence length = " +
- s1str.length() + ")\n");
+ 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(new Format("%" + maxid + "s").form(s2.getName()));
- output.append(" : " + s2.getStart() + " - " + s2.getEnd() +
- " (Sequence length = " +
- s2str.length() + ")\n\n");
+ 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(new Format("%" + (maxid) + "s").form(s1.getName()) + " ");
+ output.append(nameFormat.form(s1id)).append(" ");
for (int i = 0; i < len; i++)
{
- if ( (count + i + (j * len)) < aseq1.length)
+ if ((i + (j * len)) < astr1.length())
{
- output.append(new Format("%s").form(intToStr[aseq1[count + i +
- (j * len)]]));
+ output.append(astr1.charAt(i + (j * len)));
}
}
- output.append("\n");
- output.append(new Format("%" + (maxid) + "s").form(" ") + " ");
+ output.append(NEWLINE);
+ output.append(nameFormat.form(" ")).append(" ");
- // Print out the matching chars
+ /*
+ * 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 ( (count + i + (j * len)) < aseq1.length)
+ if ((i + (j * len)) < astr1.length())
{
- if (intToStr[aseq1[count + i + (j * len)]].equals(
- intToStr[aseq2[count + i + (j * len)]]) &&
- !intToStr[aseq1[count + i + (j * len)]].equals("-"))
+ 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 (type.equals("pep"))
+ else if (PEP.equals(type))
{
- if (ResidueProperties.getPAM250(
- intToStr[aseq1[count + i + (j * len)]],
- intToStr[aseq2[count + i + (j * len)]]) > 0)
+ if (pam250.getPairwiseScore(c1, c2) > 0)
{
output.append(".");
}
@@ -548,84 +553,47 @@ 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(NEWLINE);
+ output = output.append(nameFormat.form(s2id)).append(" ");
for (int i = 0; i < len; i++)
{
- if ( (count + i + (j * len)) < aseq1.length)
+ if ((i + (j * len)) < astr2.length())
{
- output.append(new Format("%s").form(intToStr[aseq2[count + i +
- (j * len)]]));
+ output.append(astr2.charAt(i + (j * len)));
}
}
- output = output.append("\n\n");
+ output.append(NEWLINE).append(NEWLINE);
}
- pid = pid / (float) (aseq1.length - count) * 100;
- output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));
-
+ 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 mat DOCUMENT ME!
- */
- public void printScoreMatrix(int[][] mat)
- {
- int n = seq1.length;
- int m = seq2.length;
-
- for (int i = 0; i < n; i++)
+ } catch (Exception ex)
{
- // 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!
- *
+ *
+ * @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);
+ float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
+ s2str.charAt(j));
+ float max = score[i - 1][j - 1] + (pairwiseScore * 10);
if (F[i][j] > max)
{
@@ -669,19 +637,23 @@ public class AlignSeq
int m = seq2.length;
// top left hand element
- score[0][0] = lookup[seq1[0]][seq2[0]] * 10;
- E[0][0] = -gapExtend;
+ 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] - gapOpen, E[0][j - 1] - gapExtend);
- F[0][j] = -gapExtend;
+ E[0][j] = max(score[0][j - 1] - GAP_OPEN_COST,
+ E[0][j - 1] - GAP_EXTEND_COST);
+ F[0][j] = -GAP_EXTEND_COST;
- score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen,
- -gapExtend);
+ 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;
}
@@ -689,10 +661,13 @@ public class AlignSeq
// 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);
+ E[i][0] = -GAP_OPEN_COST;
+ F[i][0] = max(score[i - 1][0] - GAP_OPEN_COST,
+ F[i - 1][0] - GAP_EXTEND_COST);
- score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]);
+ 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;
}
@@ -701,30 +676,38 @@ 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);
-
- score[i][j] = max(score[i - 1][j - 1] +
- (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][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);
}
}
}
/**
- * DOCUMENT ME!
- *
- * @param gapChar DOCUMENT ME!
- * @param seq DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * 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 gapChar, String seq)
+ public static String extractGaps(String gapChars, String seq)
{
- StringTokenizer str = new StringTokenizer(seq, gapChar);
- StringBuffer newString = new StringBuffer();
+ if (gapChars == null || seq == null)
+ {
+ return null;
+ }
+ StringTokenizer str = new StringTokenizer(seq, gapChars);
+ StringBuilder newString = new StringBuilder(seq.length());
while (str.hasMoreTokens())
{
@@ -736,25 +719,28 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
- * @param i1 DOCUMENT ME!
- * @param i2 DOCUMENT ME!
- * @param i3 DOCUMENT ME!
- *
+ *
+ * @param f1
+ * DOCUMENT ME!
+ * @param f2
+ * DOCUMENT ME!
+ * @param f3
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
- public int max(int i1, int i2, int i3)
+ private static float max(float f1, float f2, float f3)
{
- int max = i1;
+ float max = f1;
- if (i2 > i1)
+ if (f2 > f1)
{
- max = i2;
+ max = f2;
}
- if (i3 > max)
+ if (f3 > max)
{
- max = i3;
+ max = f3;
}
return max;
@@ -762,90 +748,65 @@ public class AlignSeq
/**
* DOCUMENT ME!
- *
- * @param i1 DOCUMENT ME!
- * @param i2 DOCUMENT ME!
- *
+ *
+ * @param f1
+ * DOCUMENT ME!
+ * @param f2
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
- public int max(int i1, int i2)
+ private static float max(float f1, float f2)
{
- int max = i1;
+ float max = f1;
- if (i2 > i1)
+ if (f2 > f1)
{
- max = i2;
+ max = f2;
}
return max;
}
/**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- * @param type DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Converts the character string to an array of integers which are the
+ * corresponding indices to the characters in the score matrix
+ *
+ * @param s
+ *
+ * @return
*/
- public int[] stringToInt(String s, String type)
+ int[] indexEncode(String s)
{
- int[] seq1 = new int[s.length()];
+ int[] encoded = 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;
- }
- }
+ encoded[i] = scoreMatrix.getMatrixIndex(c);
}
- return seq1;
+ return encoded;
}
/**
* 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)
{
+ // TODO method doesn't seem to be referenced anywhere delete??
int max = -1000;
int min = 1000;
@@ -874,13 +835,299 @@ 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)
+ {
+ // 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;
}
}