JAL-1767 refactoring and tidying of RotatableCanvas and related

[jalview.git] / src / jalview / viewmodel / PCAModel.java

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index aa7c938..3403887 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -25,6 +25,7 @@ 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;
 
@@ -99,7 +100,7 @@ public class PCAModel
     top = height - 1;
 
     points = new Vector<>();
-    float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+    Point[] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
 
     for (int i = 0; i < height; i++)
     {
@@ -146,7 +147,7 @@ public class PCAModel
   public void updateRcView(int dim1, int dim2, int dim3)
   {
     // note: actual indices for components are dim1-1, etc (patch for JAL-1123)
-    float[][] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
+    Point[] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
 
     for (int i = 0; i < pca.getHeight(); i++)
     {
@@ -202,13 +203,10 @@ public class PCAModel
       }
       else
       {
-        // output current x,y,z coords for points
-        fl = getPointPosition(s);
-        for (int d = 0; d < fl.length; d++)
-        {
-          csv.append(",");
-          csv.append(fl[d]);
-        }
+        Point p = points.elementAt(s).coord;
+        csv.append(",").append(p.x);
+        csv.append(",").append(p.y);
+        csv.append(",").append(p.z);
       }
       csv.append("\n");
     }
@@ -223,10 +221,10 @@ public class PCAModel
   public double[] getPointPosition(int s)
   {
     double pts[] = new double[3];
-    float[] p = points.elementAt(s).coord;
-    pts[0] = p[0];
-    pts[1] = p[1];
-    pts[2] = p[2];
+    Point p = points.elementAt(s).coord;
+    pts[0] = p.x;
+    pts[1] = p.y;
+    pts[2] = p.z;
     return pts;
   }