From 98e5ebe726c30cca66c22541ddb98228d914805a Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 8 Feb 2006 15:25:50 +0000
Subject: [PATCH] FormatAdapter throws exception

---
 src/jalview/bin/JalviewLite.java         |   25 +++++++++++++++++--------
 src/jalview/gui/CutAndPasteTransfer.java |   16 ++++++++--------
 src/jalview/jbgui/GFinder.java           |    4 +++-
 3 files changed, 28 insertions(+), 17 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index a26b9d0..c4e17fb 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -127,8 +127,13 @@ public class JalviewLite extends Applet
       }
 
       String format = jalview.io.IdentifyFile.Identify(args[0],"File");
-      SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);
-
+      SequenceI[] sequences = null;
+     try{
+       sequences = new AppletFormatAdapter().readFile(args[0], "File", format);
+     }catch(java.io.IOException ex)
+     {
+       ex.printStackTrace();
+     }
       if ( (sequences != null) && (sequences.length > 0))
       {
         AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);
@@ -247,8 +252,13 @@ public class JalviewLite extends Applet
         public void run()
         {
             SequenceI[] sequences = null;
-            sequences = new AppletFormatAdapter().readFile(file, protocol, format);
-
+            try{
+              sequences = new AppletFormatAdapter().readFile(file, protocol,
+                  format);
+            }catch(java.io.IOException ex)
+            {
+              ex.printStackTrace();
+            }
             if ((sequences != null) && (sequences.length > 0))
             {
               currentAlignFrame = new AlignFrame(new Alignment(sequences),
@@ -263,12 +273,11 @@ public class JalviewLite extends Applet
                 if (treeFile != null)
                 {
                   if (treeFile.indexOf("://") == -1)
-                  treeFile = getCodeBase() + treeFile;
+                    treeFile = getCodeBase() + treeFile;
 
                   try
                   {
-                    jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
-                        getCodeBase() + treeFile, "URL");
+                    jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, "URL");
                     fin.parse();
 
                     if (fin.getTree() != null)
@@ -276,7 +285,7 @@ public class JalviewLite extends Applet
                       TreePanel tp = null;
                       tp = new TreePanel(currentAlignFrame.viewport,
                                          currentAlignFrame.viewport.getAlignment().getSequences(),
-                                         fin, "FromFile", applet.getCodeBase() + treeFile);
+                                         fin, "FromFile", treeFile);
                       addFrame(tp, treeFile, 600, 500);
                       currentAlignFrame.addTreeMenuItem(tp, treeFile);
                     }
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index be2cf97..31a756b 100755
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -134,7 +134,15 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
         if (FormatAdapter.formats.contains(format))
         {
+          try{
             sequences = new FormatAdapter().readFile(getText(), "Paste", format);
+          }catch(java.io.IOException ex)
+          {
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                  "Couldn't read the pasted text.\n" +ex.toString(),
+                                                  "Error parsing text",
+                                                  JOptionPane.WARNING_MESSAGE);
+          }
         }
 
         if (sequences != null)
@@ -161,14 +169,6 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
             {
             }
         }
-        else
-        {
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                "Couldn't read the pasted text.\n" +
-                "Formats currently supported are\n" +
-                "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",
-                "Error parsing text", JOptionPane.WARNING_MESSAGE);
-        }
     }
 
     /**
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index ed03a80..2fe4e14 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -164,7 +164,9 @@ public class GFinder
         public void run()
         {
           String str = textfield.getText();
-          SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", "FASTA");
+          SequenceI[] sequences = null;
+          try{new FormatAdapter().readFile(str, "Paste", "FASTA");}
+          catch(Exception ex){}
           if(sequences!=null && sequences.length>0)
           {
             str = jalview.analysis.AlignSeq.extractGaps(
-- 
1.7.10.2