JAL-2962 rename run method (as not a Runnable)

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index fc1d359..a32f785 100644 (file)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -134,7 +134,7 @@ public class PCAPanel extends EmbmenuFrame
     {
       nuclSetting.setState(pcaModel.isNucleotide());
       protSetting.setState(!pcaModel.isNucleotide());
-      pcaModel.run();
+      pcaModel.calculate();
       // ////////////////
       xCombobox.select(0);
       yCombobox.select(1);

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index ec7994f..641105b 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -173,7 +173,7 @@ public class PCAPanel extends GPCAPanel
     working = true;
     try
     {
-      pcaModel.run();
+      pcaModel.calculate();
       // ////////////////
       xCombobox.setSelectedIndex(0);
       yCombobox.setSelectedIndex(1);

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index db0f4dd..aa7c938 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -81,7 +81,7 @@ public class PCAModel
    * Performs the PCA calculation (in the same thread) and extracts result data
    * needed for visualisation by PCAPanel
    */
-  public void run()
+  public void calculate()
   {
     pca = new PCA(seqstrings, scoreModel, similarityParams);
     pca.run(); // executes in same thread, wait for completion