/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.gui;
import jalview.analysis.AlignSeq;
+import jalview.analysis.scoremodels.ScoreMatrix;
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;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.math.MiscMath;
import java.awt.event.ActionEvent;
import java.util.Vector;
public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
- AlignViewport av;
+ private static final String DASHES = "---------------------\n";
- Vector sequences;
+ private float[][] scores;
+
+ private float[][] alignmentScores; // scores used by PaSiMap
+
+ private int GAP_OPEN_COST;
+
+ private int GAP_EXTEND_COST;
+
+ AlignmentViewport av;
+
+ Vector<SequenceI> sequences;
+
+ private String alignmentOutput;
+
+ private boolean quiet;
+
+ private boolean discardAlignments;
+
+ private boolean endGaps;
+
+ // for listening
+ public static final String TOTAL = "total";
+
+ public static final String PROGRESS = "progress";
+
+ protected static final String ETA = "eta_in_minutes";
+
+ public static final String PROGRESSCOMPLETE = "finished_stop_progress";
+ public static final String PROGRESSMESSAGE = "message_in_progress";
+
+ private volatile boolean cancelled;
+
+ private long total;
+
+ private long progress;
+
+ private SequenceGroup selection;
+
+ /**
+ * input sequences
+ */
+ private SequenceI[] seqs = null;
+
+ private ScoreMatrix scoreMatrix;
+
+ /**
+ * remaining time
+ */
+ private double etime=Double.NaN;
/**
* Creates a new PairwiseAlignPanel object.
*
- * @param av
- * DOCUMENT ME!
+ * @param viewport
+ * contains selected sequences to align
+ * @param endGaps
+ * ~ toggle gaps and the beginning and end of sequences
*/
- public PairwiseAlignPanel(AlignViewport av)
+ public PairwiseAlignPanel(AlignmentViewport viewport)
+ {
+ this(viewport, null, false, 120, 20, true, null); // default penalties used
+ // in AlignSeq
+ }
+
+ public PairwiseAlignPanel(AlignmentViewport viewport, ScoreMatrix params)
+ {
+ this(viewport, null, false, 120, 20, true, params); // default penalties
+ // used in AlignSeq
+ }
+
+ public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps,
+ int gapOpenCost, int gapExtendCost)
+ {
+ this(viewport, null, endGaps, gapOpenCost, gapExtendCost, true, null);
+ }
+
+ /**
+ * Create a new pairwise alignpanel with specified parameters and score model,
+ * and optionally start the calculation
+ *
+ * @param viewport
+ * @param selection
+ * @param endGaps
+ * @param gapOpenCost
+ * @param gapExtendCost
+ * @param run
+ * @param scoreMatrix
+ */
+ public PairwiseAlignPanel(AlignmentViewport viewport,
+ SequenceGroup selection, boolean endGaps, int gapOpenCost,
+ int gapExtendCost, boolean run, ScoreMatrix scoreMatrix)
{
super();
- this.av = av;
+ this.av = viewport;
+ this.GAP_OPEN_COST = gapOpenCost;
+ this.GAP_EXTEND_COST = gapExtendCost;
+ this.endGaps = endGaps;
+ this.selection = selection;
+ this.total = av.getAlignment().getHeight();
+ total = (total*total-total)/2;
+ this.scoreMatrix = scoreMatrix;
+ if (run)
+ {
+ calculate();
+ }
+ }
- sequences = new Vector();
+ public void calculate()
+ {
+ calculate(scoreMatrix);
+ }
+
+ public void calculate(ScoreMatrix sm)
+ {
+ cancelled=false;
+ StringBuilder sb = new StringBuilder(1024);
- SequenceI[] seqs;
- String[] seqStrings = av.getViewAsString(true);
+ sequences = new Vector<SequenceI>();
+ String[] seqStrings;
+ seqs = null;
- if (av.getSelectionGroup() == null)
+ if (selection != null)
{
- seqs = av.getAlignment().getSequencesArray();
+ // given a set of sequences to compare
+ seqs = selection.getSelectionAsNewSequences(av.getAlignment());
+ seqStrings = new String[seqs.length];
+ int s = 0;
+ for (SequenceI seq : seqs)
+ {
+ seqStrings[s++] = seq.getSequenceAsString();
+ }
}
else
{
- seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
+ SequenceGroup selectionGroup = av.getSelectionGroup();
+ boolean isSelection = selectionGroup != null
+ && selectionGroup.getSize() > 0;
+ AlignmentView view = av.getAlignmentView(isSelection);
+ seqStrings = view.getSequenceStrings(av.getGapCharacter());
+ if (isSelection)
+ {
+ seqs = (SequenceI[]) view
+ .getAlignmentAndHiddenColumns(av.getGapCharacter())[0];
+ }
+ else
+ {
+ seqs = av.getAlignment().getSequencesArray();
+ }
}
String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA
: AlignSeq.PEP;
float[][] scores = new float[seqs.length][seqs.length];
- double totscore = 0;
+ float[][] alignmentScores = new float[seqs.length][seqs.length];
+ double totscore = 0D;
int count = seqs.length;
-
- Sequence seq;
+ int fracprogress=0;
+ boolean first = true;
+ long time=System.currentTimeMillis();
+ long fprogress = 0;
+ firePropertyChange(TOTAL, 0, 500);
for (int i = 1; i < count; i++)
{
+ // fill diagonal alignmentScores with Float.NaN
+ alignmentScores[i - 1][i - 1] = Float.NaN;
for (int j = 0; j < i; j++)
{
-
+ if (cancelled)
+ {
+ alignmentOutput = "Alignment was cancelled.";
+ return;
+ }
AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
- seqStrings[j], type);
+ seqStrings[j], type, GAP_OPEN_COST, GAP_EXTEND_COST);
+
+ if (sm != null)
+ {
+ as.setScoreMatrix(sm);
+ }
if (as.s1str.length() == 0 || as.s2str.length() == 0)
{
}
as.calcScoreMatrix();
- as.traceAlignment();
+ if (endGaps)
+ {
+ as.traceAlignmentWithEndGaps();
+ }
+ else
+ {
+ as.traceAlignment();
+ }
+ as.scoreAlignment();
- as.printAlignment(System.out);
- scores[i][j] = (float) as.getMaxScore()
- / (float) as.getASeq1().length;
+ if (!first && !quiet)
+ {
+ jalview.bin.Console.outPrintln(DASHES);
+ textarea.append(DASHES);
+ sb.append(DASHES);
+ }
+ first = false;
+ if (!discardAlignments)
+ {
+ as.printAlignment(System.out);
+ }
+ scores[i][j] = as.getMaxScore() / as.getASeq1().length;
+ alignmentScores[i][j] = as.getAlignmentScore();
totscore = totscore + scores[i][j];
-
- textarea.append(as.getOutput());
- sequences.add(as.getAlignedSeq1());
- sequences.add(as.getAlignedSeq2());
+ if (!quiet)
+ {
+ textarea.append(as.getOutput());
+ sb.append(as.getOutput());
+ }
+ if (!discardAlignments)
+ {
+ sequences.add(as.getAlignedSeq1());
+ sequences.add(as.getAlignedSeq2());
+ }
+ ++fprogress;
+ }
+ if (i<count)
+ {
+ int newfracprogress=(int) Math.floor((500.0*(double)fprogress)/((double)total));
+ // need to fake a different starting value until we have an ETA calculated
+ firePropertyChange(PROGRESS, fracprogress, newfracprogress);
+ fracprogress = newfracprogress;
+ progress=fprogress;
+ // remaining time in minutes ~ is remaining*(elapsed time)/progress;
+ double lasteta=etime;
+ double rate = ((double)(System.currentTimeMillis()-time))/(double)progress;
+ etime = rate*(total-progress)/60000;
+ firePropertyChange(ETA, lasteta,etime);
}
}
+ alignmentScores[count - 1][count - 1] = Float.NaN;
+ // done - mark progress as indeterminate again
+ firePropertyChange(TOTAL, -1, -2);
+
- if (count > 2)
+ this.scores = scores;
+ this.alignmentScores = alignmentScores;
+
+ if (count > 2 && !quiet)
{
- System.out
- .println("Pairwise alignment scaled similarity score matrix\n");
+ printScoreMatrix(seqs, scores, totscore);
+ }
- for (int i = 0; i < count; i++)
- {
- jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
- + seqs[i].getName());
- }
+ alignmentOutput = sb.toString();
+ }
+
+ public boolean hasEta()
+ {
+ return etime>0;
+ }
+ public double getEta()
+ {
+ return etime;
+ }
+ /**
+ * stops the run() loop ASAP
+ */
+ public void cancel()
+ {
+ cancelled=true;
+ }
+
+ public float[][] getScores()
+ {
+ return this.scores;
+ }
+
+ public float[][] getAlignmentScores()
+ {
+ return this.alignmentScores;
+ }
+
+ public String getAlignmentOutput()
+ {
+ return this.alignmentOutput;
+ }
+
+ /**
+ * Prints a matrix of seqi-seqj pairwise alignment scores to sysout
+ *
+ * @param seqs
+ * @param scores
+ * @param totscore
+ */
+ protected void printScoreMatrix(SequenceI[] seqs, float[][] scores,
+ double totscore)
+ {
+ System.out
+ .println("Pairwise alignment scaled similarity score matrix "+getPairwiseSimscoresAsString()+"\n");
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ jalview.bin.Console.outPrintln(
+ String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
+ }
- System.out.println("\n");
+ /*
+ * table heading columns for sequences 1, 2, 3...
+ */
+ System.out.print("\n ");
+ for (int i = 0; i < seqs.length; i++)
+ {
+ System.out.print(String.format("%7d", i + 1));
+ }
+ jalview.bin.Console.outPrintln();
- for (int i = 0; i < count; i++)
+ for (int i = 0; i < seqs.length; i++)
+ {
+ System.out.print(String.format("%3d", i + 1));
+ for (int j = 0; j < i; j++)
{
- for (int j = 0; j < i; j++)
- {
- jalview.util.Format.print(System.out, "%7.3f", scores[i][j]
- / totscore);
- }
+ /*
+ * as a fraction of tot score, outputs are 0 <= score <= 1
+ */
+ System.out.print(String.format("%7.3f", scores[i][j] / totscore));
}
-
- System.out.println("\n");
+ jalview.bin.Console.outPrintln();
}
+
+ jalview.bin.Console.outPrintln("\n");
+ }
+
+ public String getPairwiseSimscoresAsString()
+ {
+ return (scoreMatrix != null
+ ? " (" + scoreMatrix.getName() + ", open=" + GAP_OPEN_COST
+ + ", extend=" + GAP_EXTEND_COST
+ + (endGaps ? ", with endGaps" : ", no endGaps") + ")"
+ : "");
}
/**
* @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),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
Desktop.addInternalFrame(af,
- MessageManager.getString("label.pairwise_aligned_sequences"),
+ MessageManager.getString("label.pairwise_aligned_sequences")+" "+getPairwiseSimscoresAsString(),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
+
+ public long getTotal()
+ {
+ return total;
+ }
+
+ public long getProgress()
+ {
+ return progress;
+ }
+
+ public SequenceI[] getInputSequences()
+ {
+ return seqs;
+ }
+
+ /**
+ * Set to true to suppress output of progress to Console.stdout or GUI
+ *
+ * @param quiet
+ */
+ public void setQuiet(boolean quiet)
+ {
+ this.quiet = quiet;
+ }
+
+ /**
+ * @return true if no textual alignment report was generated
+ */
+ public boolean isQuiet()
+ {
+ return quiet;
+ }
+
+ /**
+ * set this if you are only interested in final alignment scores
+ *
+ * @param discard
+ */
+ public void setDiscardAlignments(boolean discard)
+ {
+ discardAlignments = discard;
+ }
+
+ /**
+ * @return true if no alignments were saved
+ * @return
+ */
+ public boolean isDiscardAlignments()
+ {
+ return discardAlignments;
+ }
+
+ /**
+ *
+ * @return true if the calculation was cancelled before completion
+ */
+ public boolean isCancelled()
+ {
+ return cancelled;
+ }
+
+ /**
+ * sends status updates to the progress bar for this panel
+ * @param type - PROGRESSMESSAGE or PROGRESSCOMPLETE
+ * @param message - the message (may be internationalised key)
+ */
+ public void updateProgress(String type, String message)
+ {
+ firePropertyChange(type, "", MessageManager.getStringOrReturn("progress", message));
+ }
}