pass viewport to fileloader, as we need to firepropertychange once sequences are...

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4b1f1f1..359b675 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -203,17 +203,17 @@ public class AlignFrame
 \r
   public void addFromFile_actionPerformed(ActionEvent e)\r
   {\r
-    Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport.alignment);\r
+    Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);\r
   }\r
 \r
   public void addFromText_actionPerformed(ActionEvent e)\r
   {\r
-    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport.alignment);\r
+    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);\r
   }\r
 \r
   public void addFromURL_actionPerformed(ActionEvent e)\r
   {\r
-    Desktop.instance.inputURLMenuItem_actionPerformed(viewport.alignment);\r
+    Desktop.instance.inputURLMenuItem_actionPerformed(viewport);\r
   }\r
 \r
   /**\r

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 5d48ea3..ba1e85e 100755 (executable)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -40,7 +40,7 @@ import javax.swing.*;
 public class CutAndPasteTransfer extends GCutAndPasteTransfer\r
 {\r
 \r
-  AlignmentI addToThisAlignment;\r
+  AlignViewport viewport;\r
 \r
   public CutAndPasteTransfer()\r
   {\r
@@ -57,9 +57,9 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     /**\r
      * DOCUMENT ME!\r
      */\r
-    public void setForInput(AlignmentI alignment)\r
+    public void setForInput(AlignViewport viewport)\r
     {\r
-      addToThisAlignment = alignment;\r
+      this.viewport = viewport;\r
       getContentPane().add(inputButtonPanel, java.awt.BorderLayout.SOUTH);\r
     }\r
 \r
@@ -150,10 +150,12 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 \r
         if (sequences != null)\r
         {\r
-          if(addToThisAlignment!=null)\r
+          if(viewport!=null)\r
           {\r
             for(int i=0; i<sequences.length; i++)\r
-              addToThisAlignment.addSequence(sequences[i]);\r
+              viewport.getAlignment().addSequence(sequences[i]);\r
+\r
+            viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
           }\r
           else\r
           {\r

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 83fc065..09f4b3a 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -341,7 +341,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      *\r
      * @param e DOCUMENT ME!\r
      */\r
-    public void inputLocalFileMenuItem_actionPerformed(jalview.datamodel.AlignmentI alignment)\r
+    public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)\r
     {\r
         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
                     "LAST_DIRECTORY"),\r
@@ -377,8 +377,8 @@ public class Desktop extends jalview.jbgui.GDesktop
                 format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);\r
             }\r
 \r
-            if (alignment != null)\r
-              new FileLoader().LoadFile(alignment, choice, FormatAdapter.FILE, format);\r
+            if (viewport != null)\r
+              new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);\r
             else\r
               new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);\r
         }\r
@@ -391,7 +391,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      *\r
      * @param e DOCUMENT ME!\r
      */\r
-    public void inputURLMenuItem_actionPerformed(jalview.datamodel.AlignmentI alignment)\r
+    public void inputURLMenuItem_actionPerformed(AlignViewport viewport)\r
     {\r
       // This construct allows us to have a wider textfield\r
       // for viewing\r
@@ -433,8 +433,8 @@ public class Desktop extends jalview.jbgui.GDesktop
 \r
         if (url.toLowerCase().endsWith(".jar"))\r
         {\r
-          if (alignment != null)\r
-            new FileLoader().LoadFile(alignment, url, FormatAdapter.URL, "Jalview");\r
+          if (viewport != null)\r
+            new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");\r
           else\r
             new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");\r
         }\r
@@ -452,8 +452,8 @@ public class Desktop extends jalview.jbgui.GDesktop
             return;\r
           }\r
 \r
-          if (alignment != null)\r
-            new FileLoader().LoadFile(alignment, url, FormatAdapter.URL, format);\r
+          if (viewport != null)\r
+            new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);\r
           else\r
             new FileLoader().LoadFile(url, FormatAdapter.URL, format);\r
         }\r
@@ -464,10 +464,10 @@ public class Desktop extends jalview.jbgui.GDesktop
      *\r
      * @param e DOCUMENT ME!\r
      */\r
-    public void inputTextboxMenuItem_actionPerformed(jalview.datamodel.AlignmentI alignment)\r
+    public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)\r
     {\r
         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
-        cap.setForInput(alignment);\r
+        cap.setForInput(viewport);\r
         Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
     }\r
 \r

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 1785e89..3aaba9e 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -22,9 +22,9 @@ package jalview.io;
 import jalview.gui.AlignFrame;\r
 import jalview.gui.Jalview2XML;\r
 import javax.swing.JOptionPane;\r
+\r
+import jalview.gui.*;\r
 import jalview.datamodel.*;\r
-import jalview.gui.Desktop;\r
-import jalview.datamodel.SequenceI;\r
 import java.util.Vector;\r
 import java.util.StringTokenizer;\r
 \r
@@ -33,11 +33,11 @@ public class FileLoader
   String file;\r
   String protocol;\r
   String format;\r
-  AlignmentI alignment;\r
+  AlignViewport viewport;\r
 \r
-  public void LoadFile(AlignmentI alignment, String file, String protocol, String format)\r
+  public void LoadFile(AlignViewport viewport, String file, String protocol, String format)\r
   {\r
-    this.alignment = alignment;\r
+    this.viewport = viewport;\r
     LoadFile(file, protocol, format);\r
   }\r
 \r
@@ -148,10 +148,12 @@ public class FileLoader
 \r
         if ( (sequences != null) && (sequences.length > 0))\r
         {\r
-          if(alignment!=null)\r
+          if(viewport!=null)\r
           {\r
             for(int i=0; i<sequences.length; i++)\r
-              alignment.addSequence(sequences[i]);\r
+              viewport.getAlignment().addSequence(sequences[i]);\r
+\r
+              viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
           }\r
           else\r
           {\r

diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index b16c99e..fbf75cc 100755 (executable)
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -203,7 +203,7 @@ public class GDesktop extends JFrame
      *\r
      * @param e DOCUMENT ME!\r
      */\r
-    protected void inputLocalFileMenuItem_actionPerformed(jalview.datamodel.AlignmentI al)\r
+    protected void inputLocalFileMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
     {\r
     }\r
 \r
@@ -212,7 +212,7 @@ public class GDesktop extends JFrame
      *\r
      * @param e DOCUMENT ME!\r
      */\r
-    protected void inputURLMenuItem_actionPerformed(jalview.datamodel.AlignmentI al)\r
+    protected void inputURLMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
     {\r
     }\r
 \r
@@ -221,7 +221,7 @@ public class GDesktop extends JFrame
      *\r
      * @param e DOCUMENT ME!\r
      */\r
-    protected void inputTextboxMenuItem_actionPerformed(jalview.datamodel.AlignmentI al)\r
+    protected void inputTextboxMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
     {\r
     }\r
 \r