/*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.analysis;
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!! */
/** 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()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getSeq2Start()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getSeq2End()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getSeq1Start()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getSeq1End()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getOutput()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getAStr1()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String getAStr2()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int[] getASeq1()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int[] getASeq2()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public SequenceI getS1()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public SequenceI getS2()
/**
* 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
+ *
+ * @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
*/
- 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;
SeqInit(string1, string2);
}
- public void SeqInit(SequenceI s1,
- String string1,
- SequenceI s2,
- String string2,
- ScoreMatrix scoreMatrix)
+ public void SeqInit(SequenceI s1, String string1, SequenceI s2,
+ String string2, ScoreMatrix scoreMatrix)
{
this.s1 = s1;
this.s2 = s2;
}
/**
- * 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
*/
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)
if (type.equals(AlignSeq.PEP))
{
intToStr = pep;
+ charToInt = ResidueProperties.aaIndex;
defInt = 23;
}
else if (type.equals(AlignSeq.DNA))
{
intToStr = dna;
+ charToInt = ResidueProperties.nucleotideIndex;
defInt = 4;
}
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.");
}
}
}
}
- // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
+ // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
int i = maxi;
int j = maxj;
int trace;
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;
*/
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)));
}
}
// 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(".");
}
// 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)));
}
}
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)
{
/**
* 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)
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;
}
{
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);
}
}
/**
* 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)
/**
* 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)
/**
* 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)
/**
* 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)
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;
}
}
/**
* 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;
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);
}
}
}
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