From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 22 Sep 2005 15:49:51 +0000 (+0000)
Subject: Create instance of FormatAdapter
X-Git-Tag: Release_2_06~20
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=008ad05ffd2964c864cdab0f18dff2fb36c82242;p=jalview.git

Create instance of FormatAdapter
---

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 3da1401..988aadd 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -121,7 +121,7 @@ public class AlignFrame
     jalview.bin.JalviewLite.addFrame(frame,
                                      "Alignment output - " + e.getActionCommand(),
                                      600, 500);
-    cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
+    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
                                               viewport.getAlignment().
                                               getSequences()));
   }
diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index f8c3756..90bd343 100755
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -74,7 +74,7 @@ public class CutAndPasteTransfer
     SequenceI[] sequences = null;
 
     String format = IdentifyFile.Identify(text, "Paste");
-    sequences = FormatAdapter.readFile(text, "Paste", format);
+    sequences = new FormatAdapter().readFile(text, "Paste", format);
 
     if (sequences != null)
     {
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index c9ec391..75f5991 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -107,7 +107,7 @@ public class JalviewLite extends Applet
       }
 
       String format = jalview.io.IdentifyFile.Identify(args[0],"File");
-      SequenceI[] sequences = FormatAdapter.readFile(args[0], "File", format);
+      SequenceI[] sequences = new FormatAdapter().readFile(args[0], "File", format);
 
       if ( (sequences != null) && (sequences.length > 0))
       {
@@ -228,7 +228,7 @@ public class JalviewLite extends Applet
         public void run()
         {
             SequenceI[] sequences = null;
-            sequences = FormatAdapter.readFile(file, protocol, format);
+            sequences = new FormatAdapter().readFile(file, protocol, format);
 
             if ((sequences != null) && (sequences.length > 0))
             {
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a020116..9243e99 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -279,7 +279,7 @@ public class AlignFrame
     }
     else
     {
-      String output = FormatAdapter.formatSequences(format,
+      String output = new FormatAdapter().formatSequences(format,
           viewport.getAlignment().
           getSequences());
       if (output == null)
@@ -315,7 +315,7 @@ public class AlignFrame
     Desktop.addInternalFrame(cap,
                              "Alignment output - " + e.getActionCommand(), 600,
                              500);
-    cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
+    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
                                               viewport.getAlignment().
                                               getSequences()));
   }
@@ -685,7 +685,7 @@ public class AlignFrame
       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
 
       String format = IdentifyFile.Identify(str, "Paste");
-      SequenceI[] sequences = FormatAdapter.readFile(str, "Paste", format);
+      SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", format);
 
 
       if (newAlignment)
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 10f9777..219ad4b 100755
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -123,7 +123,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
         if (FormatAdapter.formats.contains(format))
         {
-            sequences = FormatAdapter.readFile(getText(), "Paste", format);
+            sequences = new FormatAdapter().readFile(getText(), "Paste", format);
         }
 
         if (sequences != null)
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index e9735ed..26aff08 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -80,7 +80,7 @@ public class FileLoader
     {
       if (FormatAdapter.formats.contains(format))
       {
-        sequences = FormatAdapter.readFile(file, protocol, format);
+        sequences = new FormatAdapter().readFile(file, protocol, format);
       }
 
       if ( (sequences != null) && (sequences.length > 0))
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 18bf76a..61c2331 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -45,6 +45,8 @@ public class FormatAdapter
         formats.addElement("PFAM");
     }
 
+    AlignFile afile = null;
+
     /**
      * DOCUMENT ME!
      *
@@ -54,12 +56,10 @@ public class FormatAdapter
      *
      * @return DOCUMENT ME!
      */
-    public static SequenceI[] readFile(String inFile, String type, String format)
+    public SequenceI[] readFile(String inFile, String type, String format)
     {
         try
         {
-            AlignFile afile = null;
-
             if (format.equals("FASTA"))
             {
                 afile = new FastaFile(inFile, type);
@@ -101,6 +101,7 @@ public class FormatAdapter
         return null;
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -109,7 +110,7 @@ public class FormatAdapter
      *
      * @return DOCUMENT ME!
      */
-    public static String formatSequences(String format, Vector seqs)
+    public String formatSequences(String format, Vector seqs)
     {
         SequenceI[] s = new SequenceI[seqs.size()];
 
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 8ece84d..872d490 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -166,7 +166,7 @@ public class GFinder
         public void run()
         {
           String str = textfield.getText();
-          SequenceI[] sequences = FormatAdapter.readFile(str, "Paste", "FASTA");
+          SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", "FASTA");
           if(sequences!=null && sequences.length>0)
           {
             str = jalview.analysis.AlignSeq.extractGaps(