From e8334005d46d1d4cc064250758068e5a390cff25 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 12 May 2006 08:47:16 +0000
Subject: [PATCH] pass viewport to fileloader, as we need to
 firepropertychange once sequences are added

---
 src/jalview/gui/AlignFrame.java          |    6 +++---
 src/jalview/gui/CutAndPasteTransfer.java |   12 +++++++-----
 src/jalview/gui/Desktop.java             |   20 ++++++++++----------
 src/jalview/io/FileLoader.java           |   16 +++++++++-------
 src/jalview/jbgui/GDesktop.java          |    6 +++---
 5 files changed, 32 insertions(+), 28 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4b1f1f1..359b675 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -203,17 +203,17 @@ public class AlignFrame
 
   public void addFromFile_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport.alignment);
+    Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
   }
 
   public void addFromText_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport.alignment);
+    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
   }
 
   public void addFromURL_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.inputURLMenuItem_actionPerformed(viewport.alignment);
+    Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
   }
 
   /**
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 5d48ea3..ba1e85e 100755
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -40,7 +40,7 @@ import javax.swing.*;
 public class CutAndPasteTransfer extends GCutAndPasteTransfer
 {
 
-  AlignmentI addToThisAlignment;
+  AlignViewport viewport;
 
   public CutAndPasteTransfer()
   {
@@ -57,9 +57,9 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     /**
      * DOCUMENT ME!
      */
-    public void setForInput(AlignmentI alignment)
+    public void setForInput(AlignViewport viewport)
     {
-      addToThisAlignment = alignment;
+      this.viewport = viewport;
       getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);
     }
 
@@ -150,10 +150,12 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
         if (sequences != null)
         {
-          if(addToThisAlignment!=null)
+          if(viewport!=null)
           {
             for(int i=0; i<sequences.length; i++)
-              addToThisAlignment.addSequence(sequences[i]);
+              viewport.getAlignment().addSequence(sequences[i]);
+
+            viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
           }
           else
           {
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 83fc065..09f4b3a 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -341,7 +341,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      *
      * @param e DOCUMENT ME!
      */
-    public void inputLocalFileMenuItem_actionPerformed(jalview.datamodel.AlignmentI alignment)
+    public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
     {
         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
                     "LAST_DIRECTORY"),
@@ -377,8 +377,8 @@ public class Desktop extends jalview.jbgui.GDesktop
                 format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
             }
 
-            if (alignment != null)
-              new FileLoader().LoadFile(alignment, choice, FormatAdapter.FILE, format);
+            if (viewport != null)
+              new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
             else
               new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
         }
@@ -391,7 +391,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      *
      * @param e DOCUMENT ME!
      */
-    public void inputURLMenuItem_actionPerformed(jalview.datamodel.AlignmentI alignment)
+    public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
     {
       // This construct allows us to have a wider textfield
       // for viewing
@@ -433,8 +433,8 @@ public class Desktop extends jalview.jbgui.GDesktop
 
         if (url.toLowerCase().endsWith(".jar"))
         {
-          if (alignment != null)
-            new FileLoader().LoadFile(alignment, url, FormatAdapter.URL, "Jalview");
+          if (viewport != null)
+            new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
           else
             new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
         }
@@ -452,8 +452,8 @@ public class Desktop extends jalview.jbgui.GDesktop
             return;
           }
 
-          if (alignment != null)
-            new FileLoader().LoadFile(alignment, url, FormatAdapter.URL, format);
+          if (viewport != null)
+            new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
           else
             new FileLoader().LoadFile(url, FormatAdapter.URL, format);
         }
@@ -464,10 +464,10 @@ public class Desktop extends jalview.jbgui.GDesktop
      *
      * @param e DOCUMENT ME!
      */
-    public void inputTextboxMenuItem_actionPerformed(jalview.datamodel.AlignmentI alignment)
+    public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
     {
         CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        cap.setForInput(alignment);
+        cap.setForInput(viewport);
         Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
     }
 
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 1785e89..3aaba9e 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -22,9 +22,9 @@ package jalview.io;
 import jalview.gui.AlignFrame;
 import jalview.gui.Jalview2XML;
 import javax.swing.JOptionPane;
+
+import jalview.gui.*;
 import jalview.datamodel.*;
-import jalview.gui.Desktop;
-import jalview.datamodel.SequenceI;
 import java.util.Vector;
 import java.util.StringTokenizer;
 
@@ -33,11 +33,11 @@ public class FileLoader
   String file;
   String protocol;
   String format;
-  AlignmentI alignment;
+  AlignViewport viewport;
 
-  public void LoadFile(AlignmentI alignment, String file, String protocol, String format)
+  public void LoadFile(AlignViewport viewport, String file, String protocol, String format)
   {
-    this.alignment = alignment;
+    this.viewport = viewport;
     LoadFile(file, protocol, format);
   }
 
@@ -148,10 +148,12 @@ public class FileLoader
 
         if ( (sequences != null) && (sequences.length > 0))
         {
-          if(alignment!=null)
+          if(viewport!=null)
           {
             for(int i=0; i<sequences.length; i++)
-              alignment.addSequence(sequences[i]);
+              viewport.getAlignment().addSequence(sequences[i]);
+
+              viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
           }
           else
           {
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index b16c99e..fbf75cc 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -203,7 +203,7 @@ public class GDesktop extends JFrame
      *
      * @param e DOCUMENT ME!
      */
-    protected void inputLocalFileMenuItem_actionPerformed(jalview.datamodel.AlignmentI al)
+    protected void inputLocalFileMenuItem_actionPerformed(jalview.gui.AlignViewport av)
     {
     }
 
@@ -212,7 +212,7 @@ public class GDesktop extends JFrame
      *
      * @param e DOCUMENT ME!
      */
-    protected void inputURLMenuItem_actionPerformed(jalview.datamodel.AlignmentI al)
+    protected void inputURLMenuItem_actionPerformed(jalview.gui.AlignViewport av)
     {
     }
 
@@ -221,7 +221,7 @@ public class GDesktop extends JFrame
      *
      * @param e DOCUMENT ME!
      */
-    protected void inputTextboxMenuItem_actionPerformed(jalview.datamodel.AlignmentI al)
+    protected void inputTextboxMenuItem_actionPerformed(jalview.gui.AlignViewport av)
     {
     }
 
-- 
1.7.10.2