X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=832f5198781b804b055ee48f596c5bd6fc570b1c;hb=3889d8cc311503f8d40d9618acec1b0f4baf2aec;hp=c9ae0446605b4fa6ed1ac598379c789d6c76aed2;hpb=f55e45cc5d9db13675e9de77c45bd7b657da08ac;p=jalview.git
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index c9ae044..832f519 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,23 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 file is part of Jalview.
*
- * 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 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.analysis;
-
import java.util.*;
import java.awt.*;
@@ -113,17 +111,17 @@ public class AlignSeq
String type;
- private int[] charToInt;
+ private int[] charToInt;
/**
* Creates a new AlignSeq object.
*
* @param s1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param s2
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public AlignSeq(SequenceI s1, SequenceI s2, String type)
{
@@ -135,16 +133,16 @@ public class AlignSeq
* Creates a new AlignSeq object.
*
* @param s1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param s2
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
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);
}
/**
@@ -268,18 +266,13 @@ 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
+ * 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
+ * DNA or PEPTIDE
*/
public void SeqInit(SequenceI s1, String string1, SequenceI s2,
String string2, String type)
@@ -290,6 +283,14 @@ public class AlignSeq
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)
{
@@ -303,7 +304,7 @@ public class AlignSeq
* construct score matrix for string1 and string2 (after removing any existing
* gaps
*
- * @param string1
+ * @param string1
* @param string2
*/
private void SeqInit(String string1, String string2)
@@ -383,13 +384,13 @@ public class AlignSeq
{
intToStr = pep;
charToInt = ResidueProperties.aaIndex;
- defInt = 23;
+ defInt = ResidueProperties.maxProteinIndex;
}
else if (type.equals(AlignSeq.DNA))
{
intToStr = dna;
charToInt = ResidueProperties.nucleotideIndex;
- defInt = 4;
+ defInt = ResidueProperties.maxNucleotideIndex;
}
else
{
@@ -502,12 +503,25 @@ public class AlignSeq
// 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;
@@ -526,8 +540,7 @@ public class AlignSeq
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++)
{
@@ -573,8 +586,7 @@ 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++)
@@ -604,7 +616,7 @@ public class AlignSeq
* DOCUMENT ME!
*
* @param mat
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void printScoreMatrix(int[][] mat)
{
@@ -644,9 +656,9 @@ public class AlignSeq
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param j
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -718,7 +730,7 @@ public class AlignSeq
{
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;
}
@@ -742,9 +754,9 @@ public class AlignSeq
* DOCUMENT ME!
*
* @param gapChar
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -765,11 +777,11 @@ public class AlignSeq
* DOCUMENT ME!
*
* @param i1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param i2
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param i3
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -794,9 +806,9 @@ public class AlignSeq
* DOCUMENT ME!
*
* @param i1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param i2
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -816,9 +828,9 @@ public class AlignSeq
* DOCUMENT ME!
*
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -839,11 +851,12 @@ public class AlignSeq
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.
+ 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;
@@ -857,15 +870,15 @@ public class AlignSeq
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param mat
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param n
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param m
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param psize
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public static void displayMatrix(Graphics g, int[][] mat, int n, int m,
int psize)
@@ -907,4 +920,185 @@ public class AlignSeq
}
}
}
+
+ /**
+ * 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)
+ {
+ as1.add(Integer.valueOf(alignpos));
+ lp1 = alignpos;
+ }
+
+ if (lp2 + 1 != pdbpos)
+ {
+ as2.add(Integer.valueOf(pdbpos));
+ 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;
+ }
}