From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 15 Aug 2006 10:02:12 +0000 (+0000)
Subject: WRITEABLE_FORMATS and READABLE_FORMATS string []
X-Git-Tag: Release_2_1~63
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=32a259190463ee06a81886db9d7843b565dea6df;p=jalview.git

WRITEABLE_FORMATS and READABLE_FORMATS string []
---

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index b26bd74..449b83a 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -89,11 +89,10 @@ public class APopupMenu
       e.printStackTrace();
     }
 
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-2; i++)
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
-      MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
-                                     elementAt(
-                                         i));
+      MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );
+
       item.addActionListener(this);
       outputmenu.add(item);
     }
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1ff729d..eb6fe49 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1937,12 +1937,11 @@ public void itemStateChanged(ItemEvent evt)
       MenuItem item;
 
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-2; i++)
+      for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
       {
 
-        item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
-                            elementAt(
-                                i));
+        item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+
         item.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 53d55f3..10efeeb 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -337,6 +337,7 @@ public class JalviewLite extends Applet
               param = getParameter("showFeatureSettings");
               if(param !=null && param.equalsIgnoreCase("true"))
               {
+                currentAlignFrame.viewport.showSequenceFeatures(true);
                 currentAlignFrame.featureSettings_actionPerformed();
               }
 
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 2bb456b..5c9c941 100755
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -169,7 +169,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
         String format = new IdentifyFile().Identify(getText(), "Paste");
         SequenceI[] sequences = null;
 
-        if (FormatAdapter.formats.contains(format))
+        if (FormatAdapter.isValidFormat(format))
         {
           try{
             sequences = new FormatAdapter().readFile(getText(), "Paste", format);
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 9764f4a..e89eb28 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -115,11 +115,10 @@ public class PopupMenu extends JPopupMenu
         colours.add(PIDColour);
         colours.add(BLOSUM62Colour);
 
-        for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-2; i++)
+        for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
         {
-          JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
-                                         elementAt(
-                                             i));
+          JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
+
           item.addActionListener(new java.awt.event.ActionListener()
           {
             public void actionPerformed(ActionEvent e)
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 99c1d5e..f3d8e29 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -364,7 +364,7 @@ public class SequenceFetcher
     String format = new IdentifyFile().Identify(result, "Paste");
     SequenceI[] sequences = null;
 
-    if (FormatAdapter.formats.contains(format))
+    if (FormatAdapter.isValidFormat(format))
     {
       sequences = null;
       try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index ba5b8a0..1de01e6 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -32,26 +32,22 @@
     public class AppletFormatAdapter
     {
         /** DOCUMENT ME!! */
-        public static final Vector formats = new Vector();
+        public static final String [] READABLE_FORMATS = new String[]
+        {
+            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB"
+        };
+
+        public static final String [] WRITEABLE_FORMATS = new String[]
+            {
+            "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"
+        };
+
 
         public static String INVALID_CHARACTERS = "Contains invalid characters";
 
         public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
                                                  "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";
 
-        static
-        {
-            formats.addElement("BLC");
-            formats.addElement("CLUSTAL");
-            formats.addElement("FASTA");
-            formats.addElement("MSF");
-            formats.addElement("PileUp");
-            formats.addElement("PIR");
-            formats.addElement("PFAM");
-            formats.addElement("STH");
-            formats.addElement("PDB");
-        }
-
 
         public static String FILE = "File";
         public static String URL = "URL";
@@ -62,6 +58,16 @@
         AlignFile afile = null;
         String inFile;
 
+        public static final boolean isValidFormat(String format)
+        {
+          boolean valid = false;
+          for(int i=0; i<READABLE_FORMATS.length; i++)
+            if(READABLE_FORMATS[i].equalsIgnoreCase(format))
+              return true;
+
+          return valid;
+        }
+
         /**
          * DOCUMENT ME!
          *
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 0fc4aa8..10e0bf8 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -138,7 +138,7 @@ public class FileLoader
       {
         String errorMessage = AppletFormatAdapter.SUPPORTED_FORMATS;
 
-        if (FormatAdapter.formats.contains(format))
+        if (FormatAdapter.isValidFormat(format))
         {
           try
           {
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 496585b..1b03e19 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -148,11 +148,10 @@ public class GAlignFrame
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-2; i++)
+      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
       {
-        JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
-                             elementAt(
-                                 i));
+        JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
+
         item.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 08d7271..ec3f737 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -406,7 +406,7 @@ public class JPredClient
           String format = new jalview.io.IdentifyFile().Identify(result.getAligfile(),
               "Paste");
 
-          if (jalview.io.FormatAdapter.formats.contains(format))
+          if (jalview.io.FormatAdapter.isValidFormat(format))
           {
             al = new Alignment(new FormatAdapter().readFile(
                 result.getAligfile(), "Paste", format));