Stockholm parser added

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index be4a599..b26bd74 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -89,7 +89,7 @@ public class APopupMenu
       e.printStackTrace();\r
     }\r
 \r
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-1; i++)\r
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-2; i++)\r
     {\r
       MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
                                      elementAt(\r

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 9ba6cca..1ff729d 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1937,7 +1937,7 @@ public void itemStateChanged(ItemEvent evt)
       MenuItem item;\r
 \r
       // dynamically fill save as menu with available formats\r
-      for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)\r
+      for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-2; i++)\r
       {\r
 \r
         item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 35ca39b..9764f4a 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -115,7 +115,7 @@ public class PopupMenu extends JPopupMenu
         colours.add(PIDColour);\r
         colours.add(BLOSUM62Colour);\r
 \r
-        for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)\r
+        for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-2; i++)\r
         {\r
           JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
                                          elementAt(\r

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 8d2d796..ba5b8a0 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -48,6 +48,7 @@
             formats.addElement("PileUp");\r
             formats.addElement("PIR");\r
             formats.addElement("PFAM");\r
+            formats.addElement("STH");\r
             formats.addElement("PDB");\r
         }\r
 \r
@@ -57,6 +58,7 @@
         public static String PASTE = "Paste";\r
         public static String CLASSLOADER = "ClassLoader";\r
 \r
+\r
         AlignFile afile = null;\r
         String inFile;\r
 \r
@@ -112,6 +114,11 @@
               {\r
                 afile = new MCview.PDBfile(inFile, type);\r
               }\r
+              else if (format.equals("STH"))\r
+              {\r
+                afile = new StockholmFile(inFile, type);\r
+              }\r
+\r
 \r
               return afile.getSeqsAsArray();\r
             }\r
@@ -196,6 +203,11 @@
                 {\r
                     afile = new PfamFile();\r
                 }\r
+                else if (format.equalsIgnoreCase("STH"))\r
+                {\r
+                  afile = new StockholmFile();\r
+                }\r
+\r
 \r
                 afile.addJVSuffix(jvsuffix);\r
 \r

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 348b085..5d39383 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -76,6 +76,13 @@ public class IdentifyFile
             {\r
                 data = data.toUpperCase();\r
 \r
+                if ( (data.indexOf("# STOCKHOLM") > -1))\r
+                {\r
+                  reply = "STH";\r
+\r
+                  break;\r
+                }\r
+\r
                 if ((data.indexOf("#") == 0) || (data.length() < 1))\r
                 {\r
                     continue;\r

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index b7c903e..496585b 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -148,7 +148,7 @@ public class GAlignFrame
       setJMenuBar(alignFrameMenuBar);\r
 \r
       // dynamically fill save as menu with available formats\r
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)\r
+      for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-2; i++)\r
       {\r
         JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
                              elementAt(\r