From 2b9c6a8948800edf58dd055631920654729fd675 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 21 Mar 2005 09:55:17 +0000
Subject: [PATCH] correct eps png bug missing last 2 lines

---
 src/jalview/gui/AlignFrame.java     |   33 +++++++--------------------------
 src/jalview/gui/AlignmentPanel.java |   28 ++++++++++++++++++++++++----
 2 files changed, 31 insertions(+), 30 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 867de61..ca9903c 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -116,31 +116,12 @@ public class AlignFrame extends GAlignFrame
 
   protected void createPNG_actionPerformed(ActionEvent e)
   {
-    int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;
-    int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();
-
-    if(!viewport.getWrapAlignment())
-    {
-      height = viewport.alignment.getHeight() * viewport.charHeight;
-      width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
-    }
-
-    alignPanel.makePNG( width, height);
+    alignPanel.makePNG();
   }
 
   protected void epsFile_actionPerformed(ActionEvent e)
   {
-    int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;
-    int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();
-
-    if(!viewport.getWrapAlignment())
-    {
-      height = viewport.alignment.getHeight() * viewport.charHeight;
-      width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
-    }
-
-    alignPanel.makeEPS( width, height);
-
+    alignPanel.makeEPS();
   }
 
 
@@ -1051,7 +1032,7 @@ if ( viewport.getConservationSelected() )
     // Need visual-delay indication here.
     public void run()
        {
-         jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
+      /*   jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
          Vector sv = viewport.getAlignment().getSequences();
          SequenceI[] seqs = new SequenceI[sv.size()];
 
@@ -1097,12 +1078,12 @@ if ( viewport.getConservationSelected() )
   }
   public void jpredMenuItem_actionPerformed(ActionEvent e)
     {
-      JInternalFrame frame = new JInternalFrame();
-      JPredClient ct = new JPredClient((SequenceI)
-                                       viewport.getAlignment().getSequences().elementAt(0));
+    //  JInternalFrame frame = new JInternalFrame();
+//      JPredClient ct = new JPredClient((SequenceI)
+    ///                                   viewport.getAlignment().getSequences().elementAt(0));
     }
 
-
+*/}}
   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
     // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 4a2e3f1..76fc8d5 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -434,7 +434,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     }
 
     // draw main sequence panel
-    pg.translate(idWidth,0);
+    pg.translate(idWidth+4,0);
     pg.setClip(0,0,pwidth-idWidth, pheight);
     seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
 
@@ -492,7 +492,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     }
 
     // draw main sequence panel
-    pg.translate(idWidth,0);
+    pg.translate(idWidth+4,0);
     seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
 
 
@@ -501,8 +501,17 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   }
 
 
-  public void makeEPS(int width, int height)
+  public void makeEPS()
   {
+    int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
+    int width = seqPanel.getWidth() + idPanel.getWidth();
+
+    if (!av.getWrapAlignment())
+    {
+      height = (av.alignment.getHeight()+1) * av.charHeight + 30;
+      width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
+    }
+
     try
     {
       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
@@ -534,8 +543,19 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     }
   }
 
-  public void makePNG(int width, int height)
+  public void makePNG()
   {
+      int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
+      int width = seqPanel.getWidth() + idPanel.getWidth();
+
+      if (!av.getWrapAlignment())
+      {
+        height = (av.alignment.getHeight()+1) * av.charHeight + 30;
+        width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
+      }
+
+
+
     try
     {
       jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-- 
1.7.10.2