Save PaSiMap with Jalview Session

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index ee08d60..3b7ca81 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -769,7 +769,7 @@ public class CalculationChooser extends JPanel
     /*
      * construct the panel and kick off its calculation thread
      */
-    pasimapPanel = new PaSiMapPanel(af.alignPanel, modelName, params);
+    pasimapPanel = new PaSiMapPanel(af.alignPanel, modelName);
     new Thread(pasimapPanel).start();
 
   }

diff --git a/src/jalview/gui/PaSiMapPanel.java b/src/jalview/gui/PaSiMapPanel.java
index 74c7232..4a2d19d 100644 (file)
--- a/src/jalview/gui/PaSiMapPanel.java
+++ b/src/jalview/gui/PaSiMapPanel.java
@@ -98,10 +98,8 @@ public class PaSiMapPanel extends GPaSiMapPanel
    * 
    * @param alignPanel
    * @param modelName
-   * @param params
    */
-  public PaSiMapPanel(AlignmentPanel alignPanel, String modelName,
-          SimilarityParamsI params)
+  public PaSiMapPanel(AlignmentPanel alignPanel, String modelName)
   {
     super(8);  // dim = 8
     this.av = alignPanel.av;

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 3a2089b..5261b23 100755 (executable)
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -516,8 +516,8 @@ public class RotatableCanvas extends JPanel
        {
        rectSelect(rectx1, recty1, rectx2, recty2);
        }
-    */
     }
+    */
 
     repaint();
   }

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 2f4052a..1b458ad 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -77,6 +77,7 @@ import javax.xml.stream.XMLStreamReader;
 
 import jalview.analysis.Conservation;
 import jalview.analysis.PCA;
+import jalview.analysis.PaSiMap;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.FeatureColourI;
@@ -122,6 +123,7 @@ import jalview.gui.JvOptionPane;
 import jalview.gui.OOMWarning;
 import jalview.gui.OverviewPanel;
 import jalview.gui.PCAPanel;
+import jalview.gui.PaSiMapPanel;
 import jalview.gui.PaintRefresher;
 import jalview.gui.SplitFrame;
 import jalview.gui.StructureViewer;
@@ -152,6 +154,7 @@ import jalview.util.jarInputStreamProvider;
 import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.PCAModel;
+import jalview.viewmodel.PaSiMapModel;
 import jalview.viewmodel.ViewportRanges;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
@@ -1432,6 +1435,14 @@ public class Jalview2XML
             savePCA(panel, object);
           }
         }
+       if (frame instanceof PaSiMapPanel)
+       {
+         PaSiMapPanel panel = (PaSiMapPanel) frame;
+         if (panel.getAlignViewport().getAlignment() == jal)
+         {
+           savePaSiMap(panel, object);
+         }
+       }
       }
     }
 
@@ -1980,6 +1991,101 @@ public class Jalview2XML
   }
 
   /**
+   * Writes PaSiMap viewer attributes and computed values to an XML model object and
+   * adds it to the JalviewModel. Any exceptions are reported by logging.
+   * uses the functions from PCA
+   */
+  protected void savePaSiMap(PaSiMapPanel panel, JalviewModel object)
+  {
+    try
+    {
+      PcaViewer viewer = new PcaViewer();
+      viewer.setHeight(panel.getHeight());
+      viewer.setWidth(panel.getWidth());
+      viewer.setXpos(panel.getX());
+      viewer.setYpos(panel.getY());
+      viewer.setTitle(panel.getTitle());
+      PaSiMapModel pasimapModel = panel.getPasimapModel();
+      viewer.setScoreModelName(pasimapModel.getScoreModelName());
+      viewer.setXDim(panel.getSelectedDimensionIndex(X));
+      viewer.setYDim(panel.getSelectedDimensionIndex(Y));
+      viewer.setZDim(panel.getSelectedDimensionIndex(Z));
+      viewer.setBgColour(
+              panel.getRotatableCanvas().getBackgroundColour().getRGB());
+      viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
+      float[] spMin = panel.getRotatableCanvas().getSeqMin();
+      SeqPointMin spmin = new SeqPointMin();
+      spmin.setXPos(spMin[0]);
+      spmin.setYPos(spMin[1]);
+      spmin.setZPos(spMin[2]);
+      viewer.setSeqPointMin(spmin);
+      float[] spMax = panel.getRotatableCanvas().getSeqMax();
+      SeqPointMax spmax = new SeqPointMax();
+      spmax.setXPos(spMax[0]);
+      spmax.setYPos(spMax[1]);
+      spmax.setZPos(spMax[2]);
+      viewer.setSeqPointMax(spmax);
+      viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
+      viewer.setLinkToAllViews(
+              panel.getRotatableCanvas().isApplyToAllViews());
+      /*
+      SimilarityParamsI sp = pasimapModel.getSimilarityParameters();
+      viewer.setIncludeGaps(sp.includeGaps());
+      viewer.setMatchGaps(sp.matchGaps());
+      viewer.setIncludeGappedColumns(sp.includeGappedColumns());
+      viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
+      */
+
+      /*
+       * sequence points on display
+       */
+      for (jalview.datamodel.SequencePoint spt : pasimapModel
+              .getSequencePoints())
+      {
+        SequencePoint point = new SequencePoint();
+        point.setSequenceRef(seqHash(spt.getSequence()));
+        point.setXPos(spt.coord.x);
+        point.setYPos(spt.coord.y);
+        point.setZPos(spt.coord.z);
+        viewer.getSequencePoint().add(point);
+      }
+
+      /*
+       * (end points of) axes on display
+       */
+      for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
+      {
+
+        Axis axis = new Axis();
+        axis.setXPos(p.x);
+        axis.setYPos(p.y);
+        axis.setZPos(p.z);
+        viewer.getAxis().add(axis);
+      }
+
+      /*
+       * raw PaSiMap data (note we are not restoring PaSiMap inputs here -
+       * alignment view, score model, similarity parameters)
+       */
+      PcaDataType data = new PcaDataType();
+      viewer.setPcaData(data);
+      PaSiMap pasimap = pasimapModel.getPasimapData();
+
+      DoubleMatrix pm = new DoubleMatrix();
+      saveDoubleMatrix(pasimap.getPairwiseScores(), pm);
+      data.setPairwiseMatrix(pm);
+
+      DoubleMatrix eigenMatrix = new DoubleMatrix();
+      data.setEigenMatrix(eigenMatrix);
+      saveDoubleMatrix(pasimap.getEigenmatrix(), eigenMatrix);
+
+      object.getPcaViewer().add(viewer);
+    } catch (Throwable t)
+    {
+      Console.error("Error saving PaSiMap: " + t.getMessage());
+    }
+  }
+  /**
    * Stores values from a matrix into an XML element, including (if present) the
    * D or E vectors
    * 
@@ -4398,6 +4504,7 @@ public class Jalview2XML
     {
       loadTrees(jalviewModel, view, af, av, ap);
       loadPCAViewers(jalviewModel, ap);
+      loadPaSiMapViewers(jalviewModel, ap);
       loadPDBStructures(jprovider, jseqs, af, ap);
       loadRnaViewers(jprovider, jseqs, ap);
       loadOverview(view, jalviewModel.getVersion(), af);
@@ -6595,6 +6702,127 @@ public class Jalview2XML
   }
 
   /**
+   * Loads any saved PaSiMAp viewers using the function from PCA
+   * 
+   * @param jms
+   * @param ap
+   */
+  protected void loadPaSiMapViewers(JalviewModel model, AlignmentPanel ap)
+  {
+    try
+    {
+      List<PcaViewer> pcaviewers = model.getPcaViewer();
+      for (PcaViewer viewer : pcaviewers)
+      {
+        String modelName = viewer.getScoreModelName();
+        /*
+        SimilarityParamsI params = new SimilarityParams(
+                viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
+                viewer.isIncludeGaps(),
+                viewer.isDenominateByShortestLength());
+       */
+
+        /*
+         * create the panel (without computing the PaSiMAp)
+         */
+        PaSiMapPanel panel = new PaSiMapPanel(ap, modelName);
+
+        panel.setTitle(viewer.getTitle());
+        panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
+                viewer.getWidth(), viewer.getHeight()));
+
+        boolean showLabels = viewer.isShowLabels();
+        panel.setShowLabels(showLabels);
+        panel.getRotatableCanvas().setShowLabels(showLabels);
+        panel.getRotatableCanvas()
+                .setBgColour(new Color(viewer.getBgColour()));
+        panel.getRotatableCanvas()
+                .setApplyToAllViews(viewer.isLinkToAllViews());
+
+        /*
+         * load PaSiMap output data
+         */
+        ScoreModelI scoreModel = ScoreModels.getInstance()
+                .getScoreModel(modelName, ap);
+        PaSiMap pasimap = new PaSiMap(null, scoreModel, null);
+        PcaDataType pasimapData = viewer.getPcaData();
+
+        MatrixI pairwise = loadDoubleMatrix(pasimapData.getPairwiseMatrix());
+        pasimap.setPairwiseScores(pairwise);
+
+        MatrixI result = loadDoubleMatrix(pasimapData.getEigenMatrix());
+        pasimap.setEigenmatrix(result);
+
+        panel.getPasimapModel().setPaSiMap(pasimap);
+
+        /*
+         * we haven't saved the input data! (JAL-2647 to do)
+         */
+        panel.setInputData(null);
+
+        /*
+         * add the sequence points for the PCA display
+         */
+        List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
+        for (SequencePoint sp : viewer.getSequencePoint())
+        {
+          String seqId = sp.getSequenceRef();
+          SequenceI seq = seqRefIds.get(seqId);
+          if (seq == null)
+          {
+            throw new IllegalStateException(
+                    "Unmatched seqref for PaSiMap: " + seqId);
+          }
+          Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
+          jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
+                  seq, pt);
+          seqPoints.add(seqPoint);
+        }
+        panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
+
+        /*
+         * set min-max ranges and scale after setPoints (which recomputes them)
+         */
+        panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
+        SeqPointMin spMin = viewer.getSeqPointMin();
+        float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
+            spMin.getZPos() };
+        SeqPointMax spMax = viewer.getSeqPointMax();
+        float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
+            spMax.getZPos() };
+        panel.getRotatableCanvas().setSeqMinMax(min, max);
+
+        // todo: hold points list in PCAModel only
+        panel.getPasimapModel().setSequencePoints(seqPoints);
+
+        panel.setSelectedDimensionIndex(viewer.getXDim(), X);
+        panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
+        panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
+
+        // is this duplication needed?
+        panel.setTop(seqPoints.size() - 1);
+        panel.getPasimapModel().setTop(seqPoints.size() - 1);
+
+        /*
+         * add the axes' end points for the display
+         */
+        for (int i = 0; i < 3; i++)
+        {
+          Axis axis = viewer.getAxis().get(i);
+          panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(
+                  axis.getXPos(), axis.getYPos(), axis.getZPos());
+        }
+
+        Desktop.addInternalFrame(panel, MessageManager.formatMessage(
+                "label.calc_title", "PaSiMap", modelName), 475, 450);
+      }
+    } catch (Exception ex)
+    {
+      Console.error("Error loading PaSiMap: " + ex.toString());
+    }
+  }
+
+  /**
    * Creates a new structure viewer window
    * 
    * @param viewerType