X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignmentPanel.java;h=efbc6af31bd1fa6103c805f68c450c221e412c00;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=51fd62cd9afca13b5cf9a723a4a5bfc8ac443219;hpb=e5ea4030e3d64c871eae90f4acf22cb5f0ded979;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignmentPanel.java b/src/jalview/jbgui/GAlignmentPanel.java
index 51fd62c..efbc6af 100755
--- a/src/jalview/jbgui/GAlignmentPanel.java
+++ b/src/jalview/jbgui/GAlignmentPanel.java
@@ -1,86 +1,135 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.jbgui;
 
-import java.awt.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JPanel;
+import javax.swing.JScrollBar;
+import javax.swing.JScrollPane;
+import javax.swing.border.Border;
 
 public class GAlignmentPanel extends JPanel
 {
   protected JPanel sequenceHolderPanel = new JPanel();
+
   protected JScrollBar vscroll = new JScrollBar();
-  protected  JScrollBar hscroll = new JScrollBar();
+
+  protected JScrollBar hscroll = new JScrollBar();
+
   protected JPanel seqPanelHolder = new JPanel();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   BorderLayout borderLayout3 = new BorderLayout();
-  JPanel jPanel2 = new JPanel();
-  BorderLayout borderLayout2 = new BorderLayout();
-  protected JPanel scorePanelHolder = new JPanel();
+
   protected JPanel scalePanelHolder = new JPanel();
+
   protected JPanel idPanelHolder = new JPanel();
+
   BorderLayout borderLayout5 = new BorderLayout();
+
   protected JPanel idSpaceFillerPanel1 = new JPanel();
-  protected JPanel idSpaceFillerPanel = new JPanel();
-  BorderLayout borderLayout4 = new BorderLayout();
+
+  public JPanel annotationSpaceFillerHolder = new JPanel();
+
   BorderLayout borderLayout6 = new BorderLayout();
+
   ButtonGroup buttonGroup1 = new ButtonGroup();
+
   BorderLayout borderLayout7 = new BorderLayout();
 
+  JPanel hscrollHolder = new JPanel();
+
+  BorderLayout borderLayout10 = new BorderLayout();
+
+  protected JPanel hscrollFillerPanel = new JPanel();
+
+  BorderLayout borderLayout11 = new BorderLayout();
+
+  public JScrollPane annotationScroller = new JScrollPane();
+
+  Border border1;
+
+  BorderLayout borderLayout4 = new BorderLayout();
+
   public GAlignmentPanel()
   {
     try
     {
       jbInit();
-    }
-    catch(Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
   }
+
   private void jbInit() throws Exception
   {
+    border1 = BorderFactory.createLineBorder(Color.gray, 1);
     idPanelHolder.setBorder(null);
     idPanelHolder.setPreferredSize(new Dimension(70, 10));
     this.setLayout(borderLayout7);
-    sequenceHolderPanel.setMaximumSize(new Dimension(2147483647, 2147483647));
+    sequenceHolderPanel
+            .setMaximumSize(new Dimension(2147483647, 2147483647));
     sequenceHolderPanel.setMinimumSize(new Dimension(150, 150));
     sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
     sequenceHolderPanel.setLayout(borderLayout3);
     seqPanelHolder.setLayout(borderLayout1);
-    jPanel2.setBackground(new Color(212, 208, 230));
-    jPanel2.setBorder(null);
-    jPanel2.setLayout(borderLayout2);
     scalePanelHolder.setBackground(Color.white);
     scalePanelHolder.setMinimumSize(new Dimension(10, 80));
     scalePanelHolder.setPreferredSize(new Dimension(10, 30));
     scalePanelHolder.setLayout(borderLayout6);
-    scorePanelHolder.setBackground(Color.white);
-    scorePanelHolder.setPreferredSize(new Dimension(10, 80));
-    scorePanelHolder.setLayout(borderLayout4);
     idPanelHolder.setLayout(borderLayout5);
     idSpaceFillerPanel1.setBackground(Color.white);
     idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
-    idSpaceFillerPanel.setBackground(Color.white);
-    idSpaceFillerPanel.setPreferredSize(new Dimension(10, 80));
+    idSpaceFillerPanel1.setLayout(borderLayout11);
+    annotationSpaceFillerHolder.setBackground(Color.white);
+    annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
+    annotationSpaceFillerHolder.setLayout(borderLayout4);
     hscroll.setOrientation(JScrollBar.HORIZONTAL);
-    vscroll.setEnabled(true);
-    sequenceHolderPanel.add(scorePanelHolder, BorderLayout.SOUTH);
-    sequenceHolderPanel.add(scalePanelHolder,  BorderLayout.NORTH);
-    sequenceHolderPanel.add(seqPanelHolder,  BorderLayout.CENTER);
-    this.add(jPanel2, BorderLayout.CENTER);
-    jPanel2.add(sequenceHolderPanel, BorderLayout.CENTER);
+    hscrollHolder.setLayout(borderLayout10);
+    hscrollFillerPanel.setBackground(Color.white);
+    hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+    hscrollHolder.setBackground(Color.white);
+    annotationScroller.setBorder(null);
+    annotationScroller.setPreferredSize(new Dimension(10, 80));
+    this.setPreferredSize(new Dimension(220, 166));
+
+    sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
+    sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
     seqPanelHolder.add(vscroll, BorderLayout.EAST);
-    seqPanelHolder.add(hscroll, BorderLayout.SOUTH);
+    sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
+
+    // jPanel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
     this.add(idPanelHolder, BorderLayout.WEST);
-    idPanelHolder.add(idSpaceFillerPanel1,  BorderLayout.NORTH);
-    idPanelHolder.add(idSpaceFillerPanel,  BorderLayout.SOUTH);
+    idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
+    idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
+    this.add(hscrollHolder, BorderLayout.SOUTH);
+    hscrollHolder.add(hscroll, BorderLayout.CENTER);
+    hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
+    this.add(sequenceHolderPanel, BorderLayout.CENTER);
   }
-
-
 }