From e5e719a4db6db7d165261151d4638547923fa5d2 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 14 Aug 2006 16:10:00 +0000
Subject: [PATCH] Stockholm parser added

---
 src/jalview/appletgui/APopupMenu.java   |    2 +-
 src/jalview/appletgui/AlignFrame.java   |    2 +-
 src/jalview/gui/PopupMenu.java          |    2 +-
 src/jalview/io/AppletFormatAdapter.java |   12 ++++++++++++
 src/jalview/io/IdentifyFile.java        |    7 +++++++
 src/jalview/jbgui/GAlignFrame.java      |    2 +-
 6 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index be4a599..b26bd74 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -89,7 +89,7 @@ public class APopupMenu
       e.printStackTrace();
     }
 
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-1; i++)
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-2; i++)
     {
       MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
                                      elementAt(
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 9ba6cca..1ff729d 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1937,7 +1937,7 @@ 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(); i++)
+      for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-2; i++)
       {
 
         item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 35ca39b..9764f4a 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -115,7 +115,7 @@ public class PopupMenu extends JPopupMenu
         colours.add(PIDColour);
         colours.add(BLOSUM62Colour);
 
-        for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)
+        for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-2; i++)
         {
           JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
                                          elementAt(
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 8d2d796..ba5b8a0 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -48,6 +48,7 @@
             formats.addElement("PileUp");
             formats.addElement("PIR");
             formats.addElement("PFAM");
+            formats.addElement("STH");
             formats.addElement("PDB");
         }
 
@@ -57,6 +58,7 @@
         public static String PASTE = "Paste";
         public static String CLASSLOADER = "ClassLoader";
 
+
         AlignFile afile = null;
         String inFile;
 
@@ -112,6 +114,11 @@
               {
                 afile = new MCview.PDBfile(inFile, type);
               }
+              else if (format.equals("STH"))
+              {
+                afile = new StockholmFile(inFile, type);
+              }
+
 
               return afile.getSeqsAsArray();
             }
@@ -196,6 +203,11 @@
                 {
                     afile = new PfamFile();
                 }
+                else if (format.equalsIgnoreCase("STH"))
+                {
+                  afile = new StockholmFile();
+                }
+
 
                 afile.addJVSuffix(jvsuffix);
 
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 348b085..5d39383 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -76,6 +76,13 @@ public class IdentifyFile
             {
                 data = data.toUpperCase();
 
+                if ( (data.indexOf("# STOCKHOLM") > -1))
+                {
+                  reply = "STH";
+
+                  break;
+                }
+
                 if ((data.indexOf("#") == 0) || (data.length() < 1))
                 {
                     continue;
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index b7c903e..496585b 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -148,7 +148,7 @@ public class GAlignFrame
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)
+      for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-2; i++)
       {
         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
                              elementAt(
-- 
1.7.10.2