From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 7 May 2018 09:22:56 +0000 (+0100)
Subject: JAL-1767 JAL-2647 hide 'Input Data..' for PCA loaded from project
X-Git-Tag: Release_2_11_1_0~78^2~9^2~3
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=88e9d982ef43c740e3f29b34156f4f57836a84e3

JAL-1767 JAL-2647 hide 'Input Data..' for PCA loaded from project
---

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 105aa78..7c0dfa9 100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -279,7 +279,7 @@ public class PCAPanel extends EmbmenuFrame
     {
     }
     ;
-    Object[] alAndColsel = pcaModel.getSeqtrings()
+    Object[] alAndColsel = pcaModel.getInputData()
             .getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index c725db8..e4a53ef 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -5961,6 +5961,11 @@ public class Jalview2XML
         panel.pcaModel.setPCA(pca);
 
         /*
+         * we haven't saved the input data! (JAL-2647 to do)
+         */
+        panel.setInputData(null);
+
+        /*
          * add the sequence points for the PCA display
          */
         List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 2ecdb82..f0ba274 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -277,12 +277,15 @@ public class PCAPanel extends GPCAPanel
     printer.start();
   }
 
+  /**
+   * If available, shows the data which formed the inputs for the PCA as a new
+   * alignment
+   */
   @Override
   public void originalSeqData_actionPerformed()
   {
-    // this was cut'n'pasted from the equivalent TreePanel method - we should
-    // make this an abstract function of all jalview analysis windows
-    if (pcaModel.getSeqtrings() == null)
+    // JAL-2647 disabled after load from project (until save to project done)
+    if (pcaModel.getInputData() == null)
     {
       Cache.log.info(
               "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
@@ -290,7 +293,7 @@ public class PCAPanel extends GPCAPanel
     }
     // decide if av alignment is sufficiently different to original data to
     // warrant a new window to be created
-    // create new alignmnt window with hidden regions (unhiding hidden regions
+    // create new alignment window with hidden regions (unhiding hidden regions
     // yields unaligned seqs)
     // or create a selection box around columns in alignment view
     // test Alignment(SeqCigar[])
@@ -304,7 +307,7 @@ public class PCAPanel extends GPCAPanel
     {
     }
 
-    Object[] alAndColsel = pcaModel.getSeqtrings()
+    Object[] alAndColsel = pcaModel.getInputData()
             .getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
@@ -726,4 +729,17 @@ public class PCAPanel extends GPCAPanel
   {
     showLabels.setSelected(show);
   }
+
+  /**
+   * Sets the input data used to calculate the PCA. This is provided for
+   * 'restore from project', which does not currently support this (AL-2647), so
+   * sets the value to null, and hides the menu option for "Input Data...". J
+   * 
+   * @param data
+   */
+  public void setInputData(AlignmentView data)
+  {
+    pcaModel.setInputData(data);
+    originalSeqData.setVisible(data != null);
+  }
 }
diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index bd45bc2..122ad0f 100755
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -62,6 +62,8 @@ public class GPCAPanel extends JInternalFrame
 
   protected JPanel statusPanel = new JPanel();
 
+  protected JMenuItem originalSeqData;
+
   /**
    * Constructor
    */
@@ -238,7 +240,7 @@ public class GPCAPanel extends JInternalFrame
         bgcolour_actionPerformed();
       }
     });
-    JMenuItem originalSeqData = new JMenuItem();
+    originalSeqData = new JMenuItem();
     originalSeqData.setText(MessageManager.getString("label.input_data"));
     originalSeqData.addActionListener(new ActionListener()
     {
diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index a4f57be..1693294 100644
--- 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,