--- /dev/null
+/*
+ * 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.viewmodel;
+
+import jalview.analysis.PaSiMap;
+import jalview.api.RotatableCanvasI;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.Point;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.gui.PairwiseAlignPanel;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.util.List;
+import java.util.Vector;
+
+public class PaSiMapModel
+{
+ /*
+ * inputs
+ */
+ private AlignmentViewport inputData;
+
+ private final SequenceI[] seqs;
+
+ /*
+ * options - score model, nucleotide / protein
+ */
+ private ScoreModelI scoreModel;
+
+ private boolean nucleotide = false;
+
+ /*
+ * outputs
+ */
+ private PaSiMap pasimap;
+
+ int top;
+
+ private List<SequencePoint> points;
+
+ /**
+ * Constructor given sequence data, score model and score calculation
+ * parameter options.
+ *
+ * @param seqData
+ * @param sqs
+ * @param nuc
+ * @param modelName
+ * @param params
+ */
+ public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs, boolean nuc,
+ ScoreModelI modelName)
+ {
+ inputData = seqData;
+ seqs = sqs;
+ nucleotide = nuc;
+ scoreModel = modelName;
+ }
+
+ /**
+ * Performs the PaSiMap calculation (in the same thread) and extracts result data
+ * needed for visualisation by PaSiMapPanel
+ */
+ public void calculate(PairwiseAlignPanel pap)
+ {
+ pasimap = new PaSiMap(inputData, scoreModel, pap);
+ pasimap.run(); // executes in same thread, wait for completion
+
+ // Now find the component coordinates
+ int ii = 0;
+
+ while ((ii < seqs.length) && (seqs[ii] != null))
+ {
+ ii++;
+ }
+
+ int width = pasimap.getWidth();
+ int height = pasimap.getHeight();
+ top = width;
+
+ points = new Vector<>();
+ Point[] scores = pasimap.getComponents(width - 1, width - 2, width - 3, 1);
+
+ for (int i = 0; i < height; i++)
+ {
+ SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
+ points.add(sp);
+ }
+ }
+
+ public void updateRc(RotatableCanvasI rc)
+ {
+ rc.setPoints(points, pasimap.getHeight());
+ }
+
+ public boolean isNucleotide()
+ {
+ return nucleotide;
+ }
+
+ public void setNucleotide(boolean nucleotide)
+ {
+ this.nucleotide = nucleotide;
+ }
+
+ /**
+ * Answers the index of the principal dimension of the PaSiMap
+ *
+ * @return
+ */
+ public int getTop()
+ {
+ return top;
+ }
+
+ public void setTop(int t)
+ {
+ top = t;
+ }
+
+ /**
+ * Updates the 3D coordinates for the list of points to the given dimensions.
+ * Principal dimension is getTop(). Next greatest eigenvector is getTop()-1.
+ * Note - pasimap.getComponents starts counting the spectrum from rank-2 to zero,
+ * rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1 ..)
+ *
+ * @param dim1
+ * @param dim2
+ * @param dim3
+ */
+ public void updateRcView(int dim1, int dim2, int dim3)
+ {
+ // note: actual indices for components are dim1-1, etc (patch for JAL-1123)
+ Point[] scores = pasimap.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 1);
+
+ for (int i = 0; i < pasimap.getHeight(); i++)
+ {
+ points.get(i).coord = scores[i];
+ }
+ }
+
+ public String getDetails()
+ {
+ return pasimap.getDetails();
+ }
+
+ public String getAlignmentOutput()
+ {
+ return pasimap.getAlignmentOutput();
+ }
+
+ public AlignmentViewport getInputData()
+ {
+ return inputData;
+ }
+
+ public void setInputData(AlignmentViewport data)
+ {
+ inputData = data;
+ }
+
+ public String getPointsasCsv(boolean transformed, int xdim, int ydim,
+ int zdim)
+ {
+ StringBuffer csv = new StringBuffer();
+ csv.append("\"Sequence\"");
+ if (transformed)
+ {
+ csv.append(",");
+ csv.append(xdim);
+ csv.append(",");
+ csv.append(ydim);
+ csv.append(",");
+ csv.append(zdim);
+ }
+ else
+ {
+ for (int d = 1, dmax = (int) pasimap.getDim(); d <= dmax; d++)
+ {
+ csv.append("," + d);
+ }
+ }
+ csv.append("\n");
+ for (int s = 0; s < seqs.length; s++)
+ {
+ csv.append("\"" + seqs[s].getName() + "\"");
+ if (!transformed)
+ {
+ double[] fl = pasimap.component(s);
+ for (int d = fl.length - 1; d >= 0; d--)
+ {
+ csv.append(",");
+ csv.append(fl[d]);
+ }
+ } else {
+ Point p = points.get(s).coord;
+ csv.append(",").append(p.x);
+ csv.append(",").append(p.y);
+ csv.append(",").append(p.z);
+ }
+ csv.append("\n");
+ }
+ return csv.toString();
+ }
+
+ public String getScoreModelName()
+ {
+ return scoreModel == null ? "" : scoreModel.getName();
+ }
+
+ public void setScoreModel(ScoreModelI sm)
+ {
+ this.scoreModel = sm;
+ }
+
+ public List<SequencePoint> getSequencePoints()
+ {
+ return points;
+ }
+
+ public void setSequencePoints(List<SequencePoint> sp)
+ {
+ points = sp;
+ }
+
+ /**
+ * Answers the object holding the values of the computed PaSiMap
+ *
+ * @return
+ */
+ public PaSiMap getPasimapData()
+ {
+ return pasimap;
+ }
+
+ public void setPaSiMap(PaSiMap data)
+ {
+ pasimap = data;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff