<p>
Gap open : 12 <br> Gap extend : 2
</p>
- <p>When you select the pairwise alignment option a new window will
- come up which will display the alignments in a text format as they
- are calculated. Also displayed is information about the alignment
- such as alignment score, length and percentage identity between the
- sequences.</p>
- <p> </p>
+ <p>When you select the pairwise alignment option, a new window will
+ come up which displays the alignments in a text format, for example:</p>
+ <p style="font-family:'Lucida Console', monospace">
+ <pre>
+ FER1_SPIOL/5-13 TTMMGMAT<br/>
+ |. .. ||<br/>
+ FER1_MESCR/5-15 TAALSGAT
+ </pre>shows the aligned sequences, where '|' links identical residues, and (for peptide) '.' links residues that have a positive PAM250 score.
+ <p>The window also shows information about the alignment such as alignment score, length and percentage identity between the sequences.</p>
+ <p>A button is also provided to allow you to view the sequences as an alignment.</p>
</body>
</html>
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++)
{
}
}
- output.append(NEWLINE).append(NEWLINE);
+ output.append(NEWLINE);// .append(NEWLINE);
}
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));
import jalview.analysis.AlignSeq;
import jalview.datamodel.Alignment;
-import jalview.datamodel.Sequence;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPairwiseAlignPanel;
import jalview.util.MessageManager;
public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
+ private static final String DASHES = "---------------------\n";
+
AlignmentViewport av;
- Vector sequences;
+ Vector<SequenceI> sequences;
/**
* Creates a new PairwiseAlignPanel object.
*
- * @param av
+ * @param viewport
* DOCUMENT ME!
*/
- public PairwiseAlignPanel(AlignmentViewport av)
+ public PairwiseAlignPanel(AlignmentViewport viewport)
{
super();
- this.av = av;
+ this.av = viewport;
- sequences = new Vector();
+ sequences = new Vector<SequenceI>();
- SequenceI[] seqs;
- String[] seqStrings = av.getViewAsString(true);
+ SequenceGroup selectionGroup = viewport.getSelectionGroup();
+ boolean isSelection = selectionGroup != null
+ && selectionGroup.getSize() > 0;
+ AlignmentView view = viewport.getAlignmentView(isSelection);
+ // String[] seqStrings = viewport.getViewAsString(true);
+ String[] seqStrings = view.getSequenceStrings(viewport
+ .getGapCharacter());
- if (av.getSelectionGroup() == null)
+ SequenceI[] seqs;
+ if (isSelection)
{
- seqs = av.getAlignment().getSequencesArray();
+ seqs = (SequenceI[]) view.getAlignmentAndHiddenColumns(viewport
+ .getGapCharacter())[0];
}
else
{
- seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
+ seqs = av.getAlignment().getSequencesArray();
}
- String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA
+ String type = (viewport.getAlignment().isNucleotide()) ? AlignSeq.DNA
: AlignSeq.PEP;
float[][] scores = new float[seqs.length][seqs.length];
double totscore = 0;
int count = seqs.length;
-
- Sequence seq;
+ boolean first = true;
for (int i = 1; i < count; i++)
{
for (int j = 0; j < i; j++)
{
-
AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
seqStrings[j], type);
as.calcScoreMatrix();
as.traceAlignment();
+ if (!first)
+ {
+ System.out.println(DASHES);
+ textarea.append(DASHES);
+ }
+ first = false;
as.printAlignment(System.out);
- scores[i][j] = (float) as.getMaxScore()
- / (float) as.getASeq1().length;
+ scores[i][j] = as.getMaxScore()
+ / as.getASeq1().length;
totscore = totscore + scores[i][j];
textarea.append(as.getOutput());
for (int i = 0; i < count; i++)
{
- jalview.util.Format.print(System.out, "%s \n",
- ("" + i) + " " + seqs[i].getName());
+ System.out.println(String.format("%d %s", i,
+ seqs[i].getDisplayId(true)));
}
- System.out.println("\n");
-
for (int i = 0; i < count; i++)
{
for (int j = 0; j < i; j++)
{
- jalview.util.Format.print(System.out, "%7.3f",
- scores[i][j] / totscore);
+ System.out.print(String.format("%7.3f", scores[i][j] / totscore));
}
+ System.out.println();
}
System.out.println("\n");
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void viewInEditorButton_actionPerformed(ActionEvent e)
{
- Sequence[] seq = new Sequence[sequences.size()];
+ SequenceI[] seq = new SequenceI[sequences.size()];
for (int i = 0; i < sequences.size(); i++)
{
- seq[i] = (Sequence) sequences.elementAt(i);
+ seq[i] = sequences.elementAt(i);
}
AlignFrame af = new AlignFrame(new Alignment(seq),
--- /dev/null
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+
+import javax.swing.JTextArea;
+
+import junit.extensions.PA;
+
+import org.testng.annotations.Test;
+
+public class PairwiseAlignmentPanelTest
+{
+ @Test(groups = "Functional")
+ public void testConstructor_withSelectionGroup()
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ AlignViewport viewport = af.getViewport();
+ AlignmentI al = viewport.getAlignment();
+
+ /*
+ * select columns 29-36 of sequences 4 and 5 for alignment
+ * Q93XJ9_SOLTU/23-29 L-KAISNV
+ * FER1_PEA/26-32 V-TTTKAF
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(al.getSequenceAt(3), false);
+ sg.addSequence(al.getSequenceAt(4), false);
+ sg.setStartRes(28);
+ sg.setEndRes(35);
+ viewport.setSelectionGroup(sg);
+
+ PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
+
+ String text = ((JTextArea) PA.getValue(testee, "textarea")).getText();
+ String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
+ + "Sequence FER1_PEA/29-32 (Sequence length = 7)\n"
+ + "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n"
+ + " FER1_PEA/29-32 TKAF\n" + " ||.\n"
+ + "Q93XJ9_SOLTU/23-26 LKAI\n" + "Percentage ID = 50.00\n\n";
+ assertEquals(text, expected);
+ }
+
+ /**
+ * This test aligns the same sequences as testConstructor_withSelectionGroup
+ * but as a complete alignment (no selection). Note that in fact the user is
+ * currently required to make a selection in order to calculate pairwise
+ * alignments, so this case does not arise.
+ */
+ @Test(groups = "Functional")
+ public void testConstructor_noSelectionGroup()
+ {
+ String seqs = ">Q93XJ9_SOLTU/23-29\nL-KAISNV\n>FER1_PEA/26-32\nV-TTTKAF\n";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
+ DataSourceType.PASTE);
+ AlignViewport viewport = af.getViewport();
+
+ PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
+
+ String text = ((JTextArea) PA.getValue(testee, "textarea")).getText();
+ String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
+ + "Sequence FER1_PEA/29-32 (Sequence length = 7)\n"
+ + "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n"
+ + " FER1_PEA/29-32 TKAF\n" + " ||.\n"
+ + "Q93XJ9_SOLTU/23-26 LKAI\n" + "Percentage ID = 50.00\n\n";
+ assertEquals(text, expected);
+ }
+}
git://source.jalview.org / jalview.git / commitdiff