X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fviewmodel%2FPaSiMapModel.java;fp=src%2Fjalview%2Fviewmodel%2FPaSiMapModel.java;h=a0e5174748d46d8d8a97cb84619832271109f99b;hb=ce59cf0845b1420b9382d91e4df1de78c00885d1;hp=0000000000000000000000000000000000000000;hpb=8b4b6dc36c3f57292ce9d8484ce5005eaec77262;p=jalview.git

diff --git a/src/jalview/viewmodel/PaSiMapModel.java b/src/jalview/viewmodel/PaSiMapModel.java
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+/*
+ * 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;
+  }
+}