From df0df46c6900f9f425666ccfda9433411b801824 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 14 Sep 2017 10:03:50 +0100
Subject: [PATCH] JAL-2727 method to check if PCAPanel thread is working

---
 src/jalview/gui/CalculationChooser.java |   12 +++++++++++-
 src/jalview/gui/PCAPanel.java           |   15 +++++++++++++++
 2 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index a9f3966..e403dba 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -105,6 +105,11 @@ public class CalculationChooser extends JPanel
 
   List<String> tips = new ArrayList<String>();
 
+  /*
+   * the most recently opened PCA results panel
+   */
+  private PCAPanel pcaPanel;
+
   /**
    * Constructor
    * 
@@ -534,7 +539,7 @@ public class CalculationChooser extends JPanel
               JvOptionPane.WARNING_MESSAGE);
       return;
     }
-    new PCAPanel(af.alignPanel, modelName, params);
+    pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
   }
 
   /**
@@ -592,4 +597,9 @@ public class CalculationChooser extends JPanel
     {
     }
   }
+
+  public PCAPanel getPcaPanel()
+  {
+    return pcaPanel;
+  }
 }
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index f861a7c..9f52d26 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -79,6 +79,8 @@ public class PCAPanel extends GPCAPanel
 
   int top = 0;
 
+  private boolean working;
+
   /**
    * Creates a new PCAPanel object using default score model and parameters
    * 
@@ -234,6 +236,7 @@ public class PCAPanel extends GPCAPanel
       message = MessageManager.getString("label.pca_calculating");
     }
     progress.setProgressBar(message, progId);
+    working = true;
     try
     {
       calcSettings.setEnabled(false);
@@ -252,6 +255,7 @@ public class PCAPanel extends GPCAPanel
     } catch (OutOfMemoryError er)
     {
       new OOMWarning("calculating PCA", er);
+      working = false;
       return;
     } finally
     {
@@ -266,6 +270,7 @@ public class PCAPanel extends GPCAPanel
               .getString("label.principal_component_analysis"), 475, 450);
       this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
     }
+    working = false;
   }
 
   @Override
@@ -788,4 +793,14 @@ public class PCAPanel extends GPCAPanel
     top = t;
     zCombobox.setSelectedIndex(2);
   }
+
+  /**
+   * Answers true if PCA calculation is in progress, else false
+   * 
+   * @return
+   */
+  public boolean isWorking()
+  {
+    return working;
+  }
 }
-- 
1.7.10.2