From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 25 Jul 2024 14:04:14 +0000 (+0100)
Subject: Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f2439f8196e6cd04fd42683c2cb73d7486f886f4;p=jalview.git

Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation

 Conflicts:
	src/jalview/gui/AlignFrame.java
	src/jalview/gui/CalculationChooser.java
	src/jalview/viewmodel/AlignmentViewport.java
---

f2439f8196e6cd04fd42683c2cb73d7486f886f4
diff --cc src/jalview/gui/AlignFrame.java
index de8d1a0,8336626..febcd0c
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -73,6 -72,8 +73,7 @@@ import javax.swing.JLayeredPane
  import javax.swing.JMenu;
  import javax.swing.JMenuItem;
  import javax.swing.JPanel;
+ import javax.swing.JProgressBar;
 -import javax.swing.JRadioButtonMenuItem;
  import javax.swing.JScrollPane;
  import javax.swing.SwingUtilities;
  
diff --cc src/jalview/gui/CalculationChooser.java
index 8c8bf21,f8986b6..b831f43
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@@ -593,18 -669,19 +674,15 @@@ public class CalculationChooser extend
      return filtered;
    }
  
-   
    protected List<String> getApplicableSecondaryStructureSources()
    {
 -    AlignmentAnnotation[] annotations = af.getViewport().getAlignment()
 -            .getAlignmentAnnotation();
 -
 -    List<String> ssSources = AlignmentUtils
 -            .getSecondaryStructureSources(annotations);
 -    // List<String> ssSources =
 -    // AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
 -
 +    AlignmentAnnotation[] annotations = af.getViewport().getAlignment().getAlignmentAnnotation();
 +    
-     //List<String> ssSources = AlignmentUtils.getSecondaryStructureSources(annotations);
 +    List<String> ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
-     
 +                 
      return ssSources;
    }
-   
+ 
    /**
     * Open and calculate the selected tree or PCA on 'OK'
     */
diff --cc src/jalview/gui/PCAPanel.java
index 0bcb0da,091f79e..1bf1e76
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@@ -32,10 -32,9 +32,11 @@@ import java.awt.print.PrinterException
  import java.awt.print.PrinterJob;
  
  import javax.swing.ButtonGroup;
 +import javax.swing.JLabel;
  import javax.swing.JMenuItem;
+ import javax.swing.JProgressBar;
  import javax.swing.JRadioButtonMenuItem;
 +import javax.swing.SwingConstants;
  import javax.swing.event.InternalFrameAdapter;
  import javax.swing.event.InternalFrameEvent;