import java.awt.Color;
import java.awt.Graphics;
+import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
*/
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";
float[][] F;
- int[][] traceback;
+ int[][] traceback; // todo is this actually used?
int[] seq1;
/** DOCUMENT ME!! */
public int seq2start;
- /** DOCUMENT ME!! */
public int seq2end;
int count;
- /** DOCUMENT ME!! */
public float maxscore;
- float pid;
-
int prev = 0;
- int gapOpen = 120;
-
- int gapExtend = 20;
-
StringBuffer output = new StringBuffer();
String type; // AlignSeq.PEP or AlignSeq.DNA
private ScoreMatrix scoreMatrix;
- private static final int GAP_INDEX = -1;
-
/**
* Creates a new AlignSeq object.
*
}
}
- // 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;
/**
* 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
- String s1id = s1.getName(), s2id = s2.getName();
- int maxid = s1.getName().length();
- if (s2.getName().length() > maxid)
- {
- maxid = s2.getName().length();
- }
- if (maxid > 30)
+ String s1id = getAlignedSeq1().getDisplayId(true);
+ String s2id = getAlignedSeq2().getDisplayId(true);
+ int nameLength = Math.max(s1id.length(), s2id.length());
+ if (nameLength > MAX_NAME_LENGTH)
{
- maxid = 30;
+ int truncateBy = nameLength - MAX_NAME_LENGTH;
+ nameLength = MAX_NAME_LENGTH;
// JAL-527 - truncate the sequence ids
- if (s1.getName().length() > maxid)
+ if (s1id.length() > nameLength)
{
- s1id = s1.getName().substring(0, 30);
+ int slashPos = s1id.lastIndexOf('/');
+ s1id = s1id.substring(0, slashPos - truncateBy)
+ + s1id.substring(slashPos);
}
- if (s2.getName().length() > maxid)
+ if (s2id.length() > nameLength)
{
- s2id = s2.getName().substring(0, 30);
+ int slashPos = s2id.lastIndexOf('/');
+ s2id = s2id.substring(0, slashPos - truncateBy)
+ + s2id.substring(slashPos);
}
}
- int len = 72 - maxid - 1;
+ int len = 72 - nameLength - 1;
int nochunks = ((aseq1.length - count) / len)
+ ((aseq1.length - count) % len > 0 ? 1 : 0);
- pid = 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(" : ").append(String.valueOf(s1.getStart()))
- .append(" - ").append(String.valueOf(s1.getEnd()));
+ 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(" : ").append(String.valueOf(s2.getStart()))
- .append(" - ").append(String.valueOf(s2.getEnd()));
+ output.append(nameFormat.form(s2id));
output.append(" (Sequence length = ")
.append(String.valueOf(s2str.length())).append(")")
.append(NEWLINE).append(NEWLINE);
for (int j = 0; j < nochunks; j++)
{
// Print the first aligned sequence
- output.append(new Format("%" + (maxid) + "s").form(s1id)).append(" ");
+ output.append(nameFormat.form(s1id)).append(" ");
for (int i = 0; i < len; i++)
{
}
output.append(NEWLINE);
- output.append(new Format("%" + (maxid) + "s").form(" ")).append(" ");
+ output.append(nameFormat.form(" ")).append(" ");
/*
* Print out the match symbols:
pid++;
output.append("|");
}
- else if (type.equals("pep"))
+ else if (PEP.equals(type))
{
if (pam250.getPairwiseScore(c1, c2) > 0)
{
// Now print the second aligned sequence
output = output.append(NEWLINE);
- output = output.append(new Format("%" + (maxid) + "s").form(s2id))
- .append(" ");
+ output = output.append(nameFormat.form(s2id)).append(" ");
for (int i = 0; i < len; i++)
{
}
pid = pid / (aseq1.length - count) * 100;
- output = output.append(new Format("Percentage ID = %2.2f\n").form(pid));
+ output.append(new Format("Percentage ID = %3.2f\n").form(pid));
+ output.append(NEWLINE);
try
{
os.print(output.toString());
public int findTrace(int i, int j)
{
int t = 0;
- // float pairwiseScore = lookup[seq1[i]][seq2[j]];
float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
s2str.charAt(j));
float max = score[i - 1][j - 1] + (pairwiseScore * 10);
// top left hand element
score[0][0] = scoreMatrix.getPairwiseScore(s1str.charAt(0),
s2str.charAt(0)) * 10;
- E[0][0] = -gapExtend;
+ 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;
float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0),
s2str.charAt(j));
- score[0][j] = max(pairwiseScore * 10, -gapOpen, -gapExtend);
+ score[0][j] = max(pairwiseScore * 10, -GAP_OPEN_COST, -GAP_EXTEND_COST);
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);
+ E[i][0] = -GAP_OPEN_COST;
+ F[i][0] = max(score[i - 1][0] - GAP_OPEN_COST, F[i - 1][0] - GAP_EXTEND_COST);
float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
s2str.charAt(0));
{
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] - 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));
git://source.jalview.org / jalview.git / blobdiff