JAL-3725 restrict mapped virtual feature location to mapped region

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

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index a4f57be..1693294 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -37,7 +37,7 @@ public class PCAModel
   /*
    * inputs
    */
-  private final AlignmentView seqstrings;
+  private AlignmentView inputData;
 
   private final SequenceI[] seqs;
 
@@ -72,7 +72,7 @@ public class PCAModel
   public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
           ScoreModelI modelName, SimilarityParamsI params)
   {
-    seqstrings = seqData;
+    inputData = seqData;
     seqs = sqs;
     nucleotide = nuc;
     scoreModel = modelName;
@@ -85,7 +85,7 @@ public class PCAModel
    */
   public void calculate()
   {
-    pca = new PCA(seqstrings, scoreModel, similarityParams);
+    pca = new PCA(inputData, scoreModel, similarityParams);
     pca.run(); // executes in same thread, wait for completion
 
     // Now find the component coordinates
@@ -166,9 +166,14 @@ public class PCAModel
     return pca.getDetails();
   }
 
-  public AlignmentView getSeqtrings()
+  public AlignmentView getInputData()
   {
-    return seqstrings;
+    return inputData;
+  }
+
+  public void setInputData(AlignmentView data)
+  {
+    inputData = data;
   }
 
   public String getPointsasCsv(boolean transformed, int xdim, int ydim,