after merge

[jalview.git] / src / jalview / appletgui / AlignmentPanel.java

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 7332a1a..3771a57 100755 (executable)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -23,10 +23,8 @@ import java.awt.*;
 import java.awt.event.*;\r
 \r
 import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
 \r
-public class AlignmentPanel\r
-    extends GAlignmentPanel implements AdjustmentListener\r
+public class AlignmentPanel extends Panel implements AdjustmentListener\r
 {\r
 \r
   AlignViewport av;\r
@@ -46,6 +44,15 @@ public class AlignmentPanel
 \r
   public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
   {\r
+    try\r
+    {\r
+      jbInit();\r
+    }\r
+    catch (Exception e)\r
+    {\r
+      e.printStackTrace();\r
+    }\r
+\r
     if(System.getProperty("os.name").startsWith("Mac"))\r
       MAC = true;\r
 \r
@@ -204,14 +211,7 @@ public class AlignmentPanel
     while (i < al.getHeight() && al.getSequenceAt(i) != null)\r
     {\r
       SequenceI s = al.getSequenceAt(i);\r
-      if (av.getShowFullId())\r
-      {\r
-        id = s.getDisplayId();\r
-      }\r
-      else\r
-      {\r
-        id = s.getName();\r
-      }\r
+      id = s.getDisplayId(av.getShowJVSuffix());\r
 \r
       if (fm.stringWidth(id) > idWidth)\r
       {\r
@@ -484,7 +484,7 @@ public class AlignmentPanel
     {\r
       int max = av.alignment.getWidth() /\r
           seqPanel.seqCanvas.\r
-          getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);\r
+          getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +1;\r
       vscroll.setMaximum(max);\r
       vscroll.setUnitIncrement(1);\r
       vscroll.setVisibleAmount(1);\r
@@ -500,5 +500,80 @@ public class AlignmentPanel
     scalePanel.repaint();\r
     annotationPanel.repaint();\r
 \r
+    if (getBounds() == g.getClipBounds())\r
+    {\r
+      if (overviewPanel != null)\r
+        overviewPanel.updateOverviewImage();\r
+    }\r
+\r
+  }\r
+\r
+  protected Panel sequenceHolderPanel = new Panel();\r
+  protected Scrollbar vscroll = new Scrollbar();\r
+  protected Scrollbar hscroll = new Scrollbar();\r
+  protected Panel seqPanelHolder = new Panel();\r
+  BorderLayout borderLayout1 = new BorderLayout();\r
+  BorderLayout borderLayout3 = new BorderLayout();\r
+  protected Panel scalePanelHolder = new Panel();\r
+  protected Panel idPanelHolder = new Panel();\r
+  BorderLayout borderLayout5 = new BorderLayout();\r
+  protected Panel idSpaceFillerPanel1 = new Panel();\r
+  public Panel annotationSpaceFillerHolder = new Panel();\r
+  BorderLayout borderLayout6 = new BorderLayout();\r
+  BorderLayout borderLayout7 = new BorderLayout();\r
+  Panel hscrollHolder = new Panel();\r
+  BorderLayout borderLayout10 = new BorderLayout();\r
+  protected Panel hscrollFillerPanel = new Panel();\r
+  BorderLayout borderLayout11 = new BorderLayout();\r
+  public Panel annotationScroller = new Panel();\r
+  BorderLayout borderLayout4 = new BorderLayout();\r
+  BorderLayout borderLayout2 = new BorderLayout();\r
+\r
+  private void jbInit() throws Exception {\r
+      //  idPanelHolder.setPreferredSize(new Dimension(70, 10));\r
+      this.setLayout(borderLayout7);\r
+\r
+      //   sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));\r
+      sequenceHolderPanel.setLayout(borderLayout3);\r
+      seqPanelHolder.setLayout(borderLayout1);\r
+      scalePanelHolder.setBackground(Color.white);\r
+\r
+      // scalePanelHolder.setPreferredSize(new Dimension(10, 30));\r
+      scalePanelHolder.setLayout(borderLayout6);\r
+      idPanelHolder.setLayout(borderLayout5);\r
+      idSpaceFillerPanel1.setBackground(Color.white);\r
+\r
+      //  idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));\r
+      idSpaceFillerPanel1.setLayout(borderLayout11);\r
+      annotationSpaceFillerHolder.setBackground(Color.white);\r
+\r
+      //  annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));\r
+      annotationSpaceFillerHolder.setLayout(borderLayout4);\r
+      hscroll.setOrientation(Scrollbar.HORIZONTAL);\r
+      hscrollHolder.setLayout(borderLayout10);\r
+      hscrollFillerPanel.setBackground(Color.white);\r
+\r
+      //  hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));\r
+      hscrollHolder.setBackground(Color.white);\r
+\r
+      //    annotationScroller.setPreferredSize(new Dimension(10, 80));\r
+      //  this.setPreferredSize(new Dimension(220, 166));\r
+      seqPanelHolder.setBackground(Color.white);\r
+      idPanelHolder.setBackground(Color.white);\r
+      annotationScroller.setLayout(borderLayout2);\r
+      sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);\r
+      sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);\r
+      seqPanelHolder.add(vscroll, BorderLayout.EAST);\r
+      sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);\r
+\r
+      //  Panel3.add(secondaryPanelHolder,  BorderLayout.SOUTH);\r
+      this.add(idPanelHolder, BorderLayout.WEST);\r
+      idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);\r
+      idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);\r
+      this.add(hscrollHolder, BorderLayout.SOUTH);\r
+      hscrollHolder.add(hscroll, BorderLayout.CENTER);\r
+      hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);\r
+      this.add(sequenceHolderPanel, BorderLayout.CENTER);\r
   }\r
+\r
 }\r