From f13833b55dc6e05e5630b8dc465059a5cd2848a8 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 1 May 2007 16:34:53 +0000
Subject: [PATCH] setVisible flag sent to EditNameDialog

---
 src/jalview/appletgui/APopupMenu.java       |    6 +++---
 src/jalview/appletgui/AnnotationLabels.java |   16 ++++++++++++++--
 src/jalview/appletgui/AnnotationPanel.java  |    8 +++++---
 src/jalview/appletgui/EditNameDialog.java   |   11 +++++++----
 4 files changed, 29 insertions(+), 12 deletions(-)

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 41b5076..300eb94 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -307,7 +307,7 @@ public class APopupMenu
           "Group Description",
           ap.alignFrame,
           "Edit Group Name / Description",
-          500,100);
+          500,100, true);
 
       if (dialog.accept)
       {
@@ -342,7 +342,7 @@ public class APopupMenu
 
                                                    ap.alignFrame,
                                                    "Edit Sequence",
-                                                   500, 100);
+                                                   500, 100, true);
 
         if (dialog.accept)
         {
@@ -499,7 +499,7 @@ public class APopupMenu
         "Sequence Description",
         ap.alignFrame,
         "Edit Sequence Name / Description",
-        500,100);
+        500,100, true);
 
     if (dialog.accept)
     {
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 1884a08..5ddaa5e 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -157,19 +157,31 @@ public class AnnotationLabels
 
   boolean editLabelDescription(AlignmentAnnotation annotation)
   {
+    Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
+                                    +ap.av.getGapCharacter()+"\"",
+                                    annotation.padGaps);
+
     EditNameDialog dialog = new EditNameDialog(
         annotation.label,
         annotation.description,
-        "       Annotation Label",
+        "      Annotation Label",
         "Annotation Description",
         ap.alignFrame,
         "Edit Annotation Name / Description",
-        500, 100);
+        500, 180, false);
+
+    Panel empty = new Panel(new FlowLayout());
+    empty.add(padGaps);
+    dialog.add(empty);
+    dialog.pack();
+
+    dialog.setVisible(true);
 
     if (dialog.accept)
     {
       annotation.label = dialog.getName();
       annotation.description = dialog.getDescription();
+      annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
       repaint();
       return true;
     }
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 101bddf..ee9e159 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -225,7 +225,7 @@ public class AnnotationPanel
   String enterLabel(String text, String label)
   {
     EditNameDialog dialog = new EditNameDialog(text,null,label,null,
-        ap.alignFrame,"Enter Label", 400,200);
+        ap.alignFrame,"Enter Label", 400,200, true);
 
     if(dialog.accept)
       return dialog.getName();
@@ -370,8 +370,8 @@ public class AnnotationPanel
   {
     // setHeight of panels
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
     int height = 0;
+
     if (aa != null)
     {
       for (int i = 0; i < aa.length; i++)
@@ -387,6 +387,7 @@ public class AnnotationPanel
         {
           aa[i].height += av.charHeight;
         }
+
         if (aa[i].hasIcons)
         {
           aa[i].height += 16;
@@ -394,13 +395,14 @@ public class AnnotationPanel
 
         if (aa[i].graph > 0)
         {
-          aa[i].height += GRAPH_HEIGHT;
+          aa[i].height += aa[i].graphHeight;
         }
 
         if (aa[i].height == 0)
         {
           aa[i].height = 20;
         }
+
         height += aa[i].height;
       }
     }
diff --git a/src/jalview/appletgui/EditNameDialog.java b/src/jalview/appletgui/EditNameDialog.java
index ca029c8..46325d9 100644
--- a/src/jalview/appletgui/EditNameDialog.java
+++ b/src/jalview/appletgui/EditNameDialog.java
@@ -49,16 +49,18 @@ public class EditNameDialog extends JVDialog
                         String label2,
                         Frame owner,
                         String title,
-                        int width, int height)
+                        int width, int height, boolean display)
   {
     super(owner, title, true, width, height);
 
+    Font mono = new Font("Monospaced", Font.PLAIN, 12);
     Panel panel = new Panel(new BorderLayout());
     Panel panel2 = new Panel(new BorderLayout());
 
     id = new TextField(name, 40);
+    id.setFont(mono);
     Label label = new Label(label1);
-    label.setFont(new Font("Monospaced", Font.PLAIN, 12));
+    label.setFont(mono);
 
     panel2.add(label, BorderLayout.WEST);
     panel2.add(id, BorderLayout.CENTER);
@@ -69,13 +71,14 @@ public class EditNameDialog extends JVDialog
     {
       panel2 = new Panel(new BorderLayout());
       description = new TextField(desc, 40);
+      description.setFont(mono);
       label = new Label(label2);
-      label.setFont(new Font("Monospaced", Font.PLAIN, 12));
+      label.setFont(mono);
       panel2.add(label, BorderLayout.WEST);
       panel2.add(description, BorderLayout.CENTER);
       panel.add(panel2, BorderLayout.CENTER);
     }
     setMainPanel(panel);
-    setVisible(true);
+    setVisible(display);
   }
 }
-- 
1.7.10.2