X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=d912b2942dcdc86e7fbb909dc71940e4c8fd843f;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=bd87bb2d7d7718a3928fb26b0c9d09d1607aa853;hpb=f3bc67915e61855d87866b4a614fe7a953813408;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index bd87bb2..d912b29 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -27,10 +27,10 @@ import jalview.schemes.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
-
 import java.io.*;
-
 import javax.swing.*;
+import java.beans.*;
+
 
 
 /**
@@ -96,11 +96,39 @@ public class AlignmentPanel extends GAlignmentPanel
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
+    final AlignmentPanel ap = this;
+    av.addPropertyChangeListener(new PropertyChangeListener()
+    {
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        if (evt.getPropertyName().equals("alignment"))
+        {
+          PaintRefresher.Refresh(ap,
+                                 av.getSequenceSetId(),
+                                 true,
+                                 true);
+          alignmentChanged();
+        }
+      }
+      });
 
     adjustAnnotationHeight();
 
   }
 
+  public void alignmentChanged()
+  {
+    av.alignmentChanged(this);
+
+    if (overviewPanel != null)
+      overviewPanel.updateOverviewImage();
+
+    alignFrame.updateEditMenuBar();
+
+    repaint();
+  }
+
+
 
   /**
    * DOCUMENT ME!
@@ -285,7 +313,6 @@ public class AlignmentPanel extends GAlignmentPanel
         annotationSpaceFillerHolder.getWidth(),
         height));
 
-    annotationPanel.repaint();
     repaint();
   }
 
@@ -684,21 +711,21 @@ public class AlignmentPanel extends GAlignmentPanel
     Color currentColor = null;
     Color currentTextColor = null;
 
-    pg.setFont(new Font(av.getFont().getName(),
-                        Font.ITALIC,
-                        av.getFont().getSize()));
+    pg.setFont(idPanel.idCanvas.idfont);
+
+    SequenceI seq;
     for (int i = startSeq; i < endSeq; i++)
     {
+      seq = av.getAlignment().getSequenceAt(i);
       if ( (av.getSelectionGroup() != null) &&
-          av.getSelectionGroup().getSequences(false).contains(
-              av.getAlignment().getSequenceAt(i)))
+          av.getSelectionGroup().getSequences(null).contains(seq))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
       }
       else
       {
-        currentColor = av.getAlignment().getSequenceAt(i).getColor();
+        currentColor = av.getSequenceColour(seq);
         currentTextColor = Color.black;
       }
 
@@ -708,10 +735,17 @@ public class AlignmentPanel extends GAlignmentPanel
 
       pg.setColor(currentTextColor);
 
-      String string = av.getAlignment().getSequenceAt(i).getDisplayId
-          ( av.getShowJVSuffix());
+      int xPos = 0;
+      if (av.rightAlignIds)
+      {
+        fm = pg.getFontMetrics();
+        xPos = idWidth - fm.stringWidth(
+            seq.getDisplayId(av.getShowJVSuffix())
+            ) - 4;
+      }
 
-      pg.drawString(string, 0,
+      pg.drawString(seq.getDisplayId( av.getShowJVSuffix()),
+                    xPos,
                     ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
                     (av.getCharHeight() / 5));
     }
@@ -792,18 +826,23 @@ public class AlignmentPanel extends GAlignmentPanel
     pg.setClip(0, pi * pheight, pwidth, pheight);
 
     int ypos = hgap;
-    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
-                           av.getFont().getSize());
-    pg.setFont(italic);
+
+
 
     do
     {
       for (int i = 0; i < av.alignment.getHeight(); i++)
       {
+        pg.setFont(idPanel.idCanvas.idfont);
         SequenceI s = av.alignment.getSequenceAt(i);
         String string = s.getDisplayId( av.getShowJVSuffix());
-
-        pg.drawString(string, 0,
+        int xPos = 0;
+        if (av.rightAlignIds)
+        {
+          FontMetrics fm = pg.getFontMetrics();
+          xPos = idWidth - fm.stringWidth( string ) - 4;
+        }
+        pg.drawString(string, xPos,
                       ( (i * av.charHeight) + ypos + av.charHeight) -
                       (av.charHeight / 5));
       }
@@ -815,7 +854,6 @@ public class AlignmentPanel extends GAlignmentPanel
 
         pg.setFont(av.getFont());
         labels.drawComponent(pg, idWidth);
-        pg.setFont(italic);
         pg.translate(+3,
                      -ypos -
                      (av.getAlignment().getHeight() * av.charHeight));
@@ -862,7 +900,10 @@ public class AlignmentPanel extends GAlignmentPanel
       if (System.getProperty("java.awt.headless") != null
           && System.getProperty("java.awt.headless").equals("true"))
       {
-        width = alignFrame.getWidth() - 22;
+        width = alignFrame.getWidth()
+            - vscroll.getPreferredSize().width
+            - alignFrame.getInsets().left
+            - alignFrame.getInsets().right;
       }
       else
         width = seqPanel.getWidth() + getVisibleIdWidth();
@@ -873,6 +914,9 @@ public class AlignmentPanel extends GAlignmentPanel
       height += annotationPanel.adjustPanelHeight() + 3;
     }
 
+    try
+    {
+
     jalview.util.ImageMaker im;
     if(type==jalview.util.ImageMaker.PNG)
       im  = new jalview.util.ImageMaker(this,
@@ -885,8 +929,6 @@ public class AlignmentPanel extends GAlignmentPanel
                                        "Create EPS file from alignment",
                                         width, height, file, alignFrame.getTitle() );
 
-    try
-    {
       if (av.getWrapAlignment())
       {
         if(im.getGraphics()!=null)
@@ -1071,11 +1113,14 @@ public class AlignmentPanel extends GAlignmentPanel
   {
     int seqPanelWidth = seqPanel.seqCanvas.getWidth();
 
-    //If headless, seqPanel will have 0 width
     if (System.getProperty("java.awt.headless") != null
-              && System.getProperty("java.awt.headless").equals("true"))
+        && System.getProperty("java.awt.headless").equals("true"))
     {
-      seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth();
+      seqPanelWidth = alignFrame.getWidth()
+          - getVisibleIdWidth()
+          - vscroll.getPreferredSize().width
+          - alignFrame.getInsets().left
+          - alignFrame.getInsets().right;
     }
 
     int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(