-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import java.awt.event.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class PairwiseAlignPanel extends GPairwiseAlignPanel\r
-{\r
-\r
- AlignViewport av;\r
- Vector sequences;\r
-\r
- /**\r
- * Creates a new PairwiseAlignPanel object.\r
- *\r
- * @param av DOCUMENT ME!\r
- */\r
- public PairwiseAlignPanel(AlignViewport av)\r
- {\r
- super();\r
- this.av = av;\r
-\r
- sequences = new Vector();\r
-\r
- SequenceI [] seqs;\r
- String [] seqStrings = av.getViewAsString(true);\r
-\r
- if(av.getSelectionGroup()==null)\r
- {\r
- seqs = av.alignment.getSequencesArray();\r
- }\r
- else\r
- {\r
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
- }\r
-\r
-\r
- float[][] scores = new float[seqs.length][seqs.length];\r
- double totscore = 0;\r
- int count = seqs.length;\r
-\r
- Sequence seq;\r
-\r
- for (int i = 1; i < count; i++)\r
- {\r
- for (int j = 0; j < i; j++)\r
- {\r
-\r
- AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],\r
- seqs[j], seqStrings[j], "pep");\r
-\r
- if(as.s1str.length()==0 || as.s2str.length()==0)\r
- {\r
- continue;\r
- }\r
-\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
-\r
-\r
- as.printAlignment(System.out);\r
- scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
- totscore = totscore + scores[i][j];\r
-\r
- textarea.append(as.getOutput());\r
- seq = new Sequence(as.getS1().getName(),\r
- as.getAStr1(),\r
- as.getS1().getStart(),\r
- as.getS1().getEnd()\r
- );\r
- sequences.add(seq);\r
-\r
- seq = new Sequence(as.getS2().getName(),\r
- as.getAStr2(),\r
- as.getS2().getStart(),\r
- as.getS2().getEnd() );\r
- sequences.add(seq);\r
- }\r
- }\r
-\r
- if (count > 2)\r
- {\r
- System.out.println(\r
- "Pairwise alignment scaled similarity score matrix\n");\r
-\r
- for (int i = 0; i < count; i++)\r
- {\r
- jalview.util.Format.print(System.out, "%s \n",\r
- ("" + i) + " " +\r
- seqs[i].getName());\r
- }\r
-\r
- System.out.println("\n");\r
-\r
- for (int i = 0; i < count; i++)\r
- {\r
- for (int j = 0; j < i; j++)\r
- {\r
- jalview.util.Format.print(System.out, "%7.3f",\r
- scores[i][j] / totscore);\r
- }\r
- }\r
-\r
- System.out.println("\n");\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void viewInEditorButton_actionPerformed(ActionEvent e)\r
- {\r
- Sequence[] seq = new Sequence[sequences.size()];\r
-\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- seq[i] = (Sequence) sequences.elementAt(i);\r
- }\r
-\r
- AlignFrame af = new AlignFrame(new Alignment(seq));\r
- Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",\r
- AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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.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;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PairwiseAlignPanel extends GPairwiseAlignPanel
+{
+
+ 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
+ * 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();
+ }
+ }
+
+ public void calculate()
+ {
+ calculate(scoreMatrix);
+ }
+
+ public void calculate(ScoreMatrix sm)
+ {
+ cancelled=false;
+ StringBuilder sb = new StringBuilder(1024);
+
+ sequences = new Vector<SequenceI>();
+ String[] seqStrings;
+ seqs = null;
+
+ if (selection != null)
+ {
+ // 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
+ {
+ 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];
+ 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, GAP_OPEN_COST, GAP_EXTEND_COST);
+
+ if (sm != null)
+ {
+ as.setScoreMatrix(sm);
+ }
+
+ if (as.s1str.length() == 0 || as.s2str.length() == 0)
+ {
+ continue;
+ }
+
+ as.calcScoreMatrix();
+ if (endGaps)
+ {
+ as.traceAlignmentWithEndGaps();
+ }
+ else
+ {
+ as.traceAlignment();
+ }
+ as.scoreAlignment();
+
+ 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];
+ 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 && !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;
+ }
+
+ /**
+ * 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)));
+ }
+
+ /*
+ * 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 < seqs.length; i++)
+ {
+ System.out.print(String.format("%3d", i + 1));
+ for (int j = 0; j < i; j++)
+ {
+ /*
+ * as a fraction of tot score, outputs are 0 <= score <= 1
+ */
+ System.out.print(String.format("%7.3f", scores[i][j] / totscore));
+ }
+ 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") + ")"
+ : "");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void viewInEditorButton_actionPerformed(ActionEvent e)
+ {
+ SequenceI[] seq = new SequenceI[sequences.size()];
+
+ for (int i = 0; i < sequences.size(); 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")+" "+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