X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=3771a577cda01475f0362d5ecb0692c42ed898d1;hb=0705a85fe0a3d391e5aba360340a0c342c898366;hp=ef84548ea138d51ab92252b39181c7394930fc63;hpb=5e34f249e1565c22cad33fb37037047236ba8eca;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index ef84548..3771a57 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -22,13 +22,9 @@ package jalview.appletgui;
 import java.awt.*;
 import java.awt.event.*;
 
-import jalview.analysis.*;
 import jalview.datamodel.*;
-import jalview.jbappletgui.*;
-import jalview.schemes.*;
 
-public class AlignmentPanel
-    extends GAlignmentPanel implements AdjustmentListener
+public class AlignmentPanel extends Panel implements AdjustmentListener
 {
 
   AlignViewport av;
@@ -48,6 +44,15 @@ public class AlignmentPanel
 
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
     if(System.getProperty("os.name").startsWith("Mac"))
       MAC = true;
 
@@ -172,6 +177,9 @@ public class AlignmentPanel
     hscrollFillerPanel.setSize(d);
 
     alignFrame.pack();
+
+    if(overviewPanel!=null)
+          overviewPanel.updateOverviewImage();
   }
 
   public void setIdWidth(int w, int h)
@@ -203,14 +211,7 @@ public class AlignmentPanel
     while (i < al.getHeight() && al.getSequenceAt(i) != null)
     {
       SequenceI s = al.getSequenceAt(i);
-      if (av.getShowFullId())
-      {
-        id = s.getDisplayId();
-      }
-      else
-      {
-        id = s.getName();
-      }
+      id = s.getDisplayId(av.getShowJVSuffix());
 
       if (fm.stringWidth(id) > idWidth)
       {
@@ -271,21 +272,33 @@ public class AlignmentPanel
 
   public void setAnnotationVisible(boolean b)
   {
-    annotationSpaceFillerHolder.setVisible(b);
-    annotationScroller.setVisible(b);
+    if (!av.wrapAlignment)
+    {
+      annotationSpaceFillerHolder.setVisible(b);
+      annotationScroller.setVisible(b);
+    }
     validate();
     repaint();
   }
 
   public void setWrapAlignment(boolean wrap)
   {
+    av.startSeq = 0;
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
 
-    av.setShowAnnotation(!wrap);
-    annotationScroller.setVisible(!wrap);
-    annotationSpaceFillerHolder.setVisible(!wrap);
+    if (wrap)
+    {
+      annotationScroller.setVisible(false);
+      annotationSpaceFillerHolder.setVisible(false);
+    }
+    else if (av.showAnnotation)
+    {
+      annotationScroller.setVisible(true);
+      annotationSpaceFillerHolder.setVisible(true);
+    }
+
     idSpaceFillerPanel1.setVisible(!wrap);
 
     validate();
@@ -464,19 +477,14 @@ public class AlignmentPanel
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
     annotationSpaceFillerHolder.setSize(d.width,
                                         annotationPanel.getSize().height);
-    alabels.setSize(d.width, annotationPanel.getSize().height);
 
-    alabels.repaint();
-    idPanel.idCanvas.repaint();
-    seqPanel.seqCanvas.repaint();
-    scalePanel.repaint();
-    annotationPanel.repaint();
+    alabels.setSize(d.width, annotationPanel.getSize().height);
 
     if (av.getWrapAlignment())
     {
       int max = av.alignment.getWidth() /
           seqPanel.seqCanvas.
-          getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
+          getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +1;
       vscroll.setMaximum(max);
       vscroll.setUnitIncrement(1);
       vscroll.setVisibleAmount(1);
@@ -486,5 +494,86 @@ public class AlignmentPanel
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
+    alabels.repaint();
+    idPanel.idCanvas.repaint();
+    seqPanel.seqCanvas.repaint();
+    scalePanel.repaint();
+    annotationPanel.repaint();
+
+    if (getBounds() == g.getClipBounds())
+    {
+      if (overviewPanel != null)
+        overviewPanel.updateOverviewImage();
+    }
+
+  }
+
+  protected Panel sequenceHolderPanel = new Panel();
+  protected Scrollbar vscroll = new Scrollbar();
+  protected Scrollbar hscroll = new Scrollbar();
+  protected Panel seqPanelHolder = new Panel();
+  BorderLayout borderLayout1 = new BorderLayout();
+  BorderLayout borderLayout3 = new BorderLayout();
+  protected Panel scalePanelHolder = new Panel();
+  protected Panel idPanelHolder = new Panel();
+  BorderLayout borderLayout5 = new BorderLayout();
+  protected Panel idSpaceFillerPanel1 = new Panel();
+  public Panel annotationSpaceFillerHolder = new Panel();
+  BorderLayout borderLayout6 = new BorderLayout();
+  BorderLayout borderLayout7 = new BorderLayout();
+  Panel hscrollHolder = new Panel();
+  BorderLayout borderLayout10 = new BorderLayout();
+  protected Panel hscrollFillerPanel = new Panel();
+  BorderLayout borderLayout11 = new BorderLayout();
+  public Panel annotationScroller = new Panel();
+  BorderLayout borderLayout4 = new BorderLayout();
+  BorderLayout borderLayout2 = new BorderLayout();
+
+  private void jbInit() throws Exception {
+      //  idPanelHolder.setPreferredSize(new Dimension(70, 10));
+      this.setLayout(borderLayout7);
+
+      //   sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+      sequenceHolderPanel.setLayout(borderLayout3);
+      seqPanelHolder.setLayout(borderLayout1);
+      scalePanelHolder.setBackground(Color.white);
+
+      // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
+      scalePanelHolder.setLayout(borderLayout6);
+      idPanelHolder.setLayout(borderLayout5);
+      idSpaceFillerPanel1.setBackground(Color.white);
+
+      //  idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
+      idSpaceFillerPanel1.setLayout(borderLayout11);
+      annotationSpaceFillerHolder.setBackground(Color.white);
+
+      //  annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
+      annotationSpaceFillerHolder.setLayout(borderLayout4);
+      hscroll.setOrientation(Scrollbar.HORIZONTAL);
+      hscrollHolder.setLayout(borderLayout10);
+      hscrollFillerPanel.setBackground(Color.white);
+
+      //  hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+      hscrollHolder.setBackground(Color.white);
+
+      //    annotationScroller.setPreferredSize(new Dimension(10, 80));
+      //  this.setPreferredSize(new Dimension(220, 166));
+      seqPanelHolder.setBackground(Color.white);
+      idPanelHolder.setBackground(Color.white);
+      annotationScroller.setLayout(borderLayout2);
+      sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
+      sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
+      seqPanelHolder.add(vscroll, BorderLayout.EAST);
+      sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
+
+      //  Panel3.add(secondaryPanelHolder,  BorderLayout.SOUTH);
+      this.add(idPanelHolder, BorderLayout.WEST);
+      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);
   }
+
 }