package jalview.gui;
import jalview.analysis.AlignSeq;
+import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceGroup;
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;
private static final String DASHES = "---------------------\n";
+ 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 viewport
- * DOCUMENT ME!
+ * contains selected sequences to align
+ * @param endGaps
+ * ~ toggle gaps and the beginning and end of sequences
*/
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 = 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<SequenceI>();
+ public void calculate()
+ {
+ calculate(scoreMatrix);
+ }
- 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());
+ public void calculate(ScoreMatrix sm)
+ {
+ cancelled=false;
+ StringBuilder sb = new StringBuilder(1024);
+
+ sequences = new Vector<SequenceI>();
+ String[] seqStrings;
+ seqs = null;
- SequenceI[] seqs;
- if (isSelection)
+ if (selection != null)
{
- seqs = (SequenceI[]) view
- .getAlignmentAndHiddenColumns(viewport.getGapCharacter())[0];
+ // 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.getAlignment().getSequencesArray();
+ 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 = (viewport.getAlignment().isNucleotide()) ? AlignSeq.DNA
+ String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA
: AlignSeq.PEP;
float[][] scores = new float[seqs.length][seqs.length];
+ float[][] alignmentScores = new float[seqs.length][seqs.length];
double totscore = 0D;
int count = seqs.length;
+ 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();
- if (!first)
+ if (!first && !quiet)
{
- System.out.println(DASHES);
+ jalview.bin.Console.outPrintln(DASHES);
textarea.append(DASHES);
+ sb.append(DASHES);
}
first = false;
- as.printAlignment(System.out);
+ 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);
+
+
+ this.scores = scores;
+ this.alignmentScores = alignmentScores;
- if (count > 2)
+ if (count > 2 && !quiet)
{
printScoreMatrix(seqs, scores, totscore);
}
+
+ 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;
}
/**
double totscore)
{
System.out
- .println("Pairwise alignment scaled similarity score matrix\n");
+ .println("Pairwise alignment scaled similarity score matrix "+getPairwiseSimscoresAsString()+"\n");
for (int i = 0; i < seqs.length; i++)
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
}
{
System.out.print(String.format("%7d", i + 1));
}
- System.out.println();
+ jalview.bin.Console.outPrintln();
for (int i = 0; i < seqs.length; i++)
{
*/
System.out.print(String.format("%7.3f", scores[i][j] / totscore));
}
- System.out.println();
+ jalview.bin.Console.outPrintln();
}
- System.out.println("\n");
+ 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") + ")"
+ : "");
}
/**
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));
+ }
}
git://source.jalview.org / jalview.git / blobdiff