Removed as obfuscation of classes wiill change class names

diff --git a/src/jalview/io/FormatFactory.java b/src/jalview/io/FormatFactory.java
deleted file mode 100755 (executable)
index 64abc11..0000000
--- a/src/jalview/io/FormatFactory.java
+++ /dev/null
@@ -1,71 +0,0 @@
-package jalview.io;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.lang.reflect.*;\r
-\r
-public class FormatFactory {\r
-\r
-  public static AlignFile get(int index) {\r
-    try {\r
-      Class c = Class.forName(FormatProperties.getClassName(index));\r
-      Class [] paramTypes = new Class[1];\r
-      paramTypes[0] = SequenceI[].class;\r
-\r
-      Constructor cons = c.getConstructor(null);\r
-\r
-      return (AlignFile)cons.newInstance(null);\r
-    } catch (Exception e) {\r
-      System.err.println("Errore FFactory:"+e);\r
-      return null;\r
-    }\r
-  }\r
-\r
-  public static AlignFile get(int index,String inStr) {\r
-    try {\r
-      Class c = Class.forName(FormatProperties.getClassName(index));\r
-      Class [] paramTypes = new Class[1];\r
-      paramTypes[0] = String.class;\r
-      Constructor cons = c.getConstructor(paramTypes);\r
-\r
-      Object [] params = new Object[1];\r
-      params[0] = inStr;\r
-      return (AlignFile)cons.newInstance(params);\r
-    } catch (Exception e) {\r
-      System.err.println("error2"+e);\r
-      return null;\r
-    }\r
-  }\r
-\r
-  public static AlignFile get(int index,String inFile,String type) {\r
-    try {\r
-\r
-      Class c = Class.forName(FormatProperties.getClassName(index));\r
-      Class [] paramTypes = new Class[2];\r
-      paramTypes[0] = String.class;\r
-      paramTypes[1] = String.class;\r
-      Constructor cons = c.getConstructor(paramTypes);\r
-      Object [] params = new Object[2];\r
-      params[0] = inFile;\r
-      params[1] = type;\r
-\r
-      AlignFile af = (AlignFile)cons.newInstance(params);\r
-\r
-      return af;\r
-    } catch (Exception e) {\r
-      System.err.println("FormatFactory "+e);\r
-      return null;\r
-    }\r
-  }\r
-\r
-  public static AlignFile get(String format) {\r
-    return get(FormatProperties.indexOf(format));\r
-  }\r
-\r
-  public static AlignFile get(String format,String inStr) {\r
-    return get(FormatProperties.indexOf(format),inStr);\r
-  }\r
-  public static AlignFile get(String format,String inFile,String type) {\r
-    return get(FormatProperties.indexOf(format),inFile,type);\r
-  }\r
-}\r

diff --git a/src/jalview/io/FormatProperties.java b/src/jalview/io/FormatProperties.java
deleted file mode 100755 (executable)
index 585f220..0000000
--- a/src/jalview/io/FormatProperties.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998  Michele Clamp\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.\r
- */\r
-\r
-package jalview.io;\r
-\r
-import java.util.*;\r
-\r
-public class FormatProperties {\r
-\r
-  static final int FASTA   = 0;\r
-  static final int MSF     = 1;\r
-  static final int CLUSTAL = 2;\r
-  static final int BLC     = 3;\r
-  static final int PIR     = 4;\r
-  static final int PFAM    = 5;\r
-\r
-  static FormatPropertyVector formats = new FormatPropertyVector();\r
-\r
-  static {\r
-    String prefix = getDefaultClassPrefix();\r
-\r
-    formats.add("FASTA",  prefix + "FastaFile");\r
-    formats.add("MSF",    prefix + "MSFfile");\r
-    formats.add("CLUSTAL",prefix + "ClustalFile");\r
-    formats.add("BLC",    prefix + "BLCFile");\r
-    formats.add("PIR",    prefix + "PIRFile");\r
-    formats.add("PFAM",   prefix + "PfamFile");\r
-  }\r
-\r
-  public static String getDefaultClassPrefix() {\r
-    return "jalview.io.";\r
-  }\r
-\r
-  static int indexOf(String format) {\r
-\r
-    if (format != null) {\r
-       format.toUpperCase();\r
-       if (formats.contains(format)) {\r
-         return formats.indexOf(format);\r
-       }\r
-    }\r
-    return -1;\r
-  }\r
-\r
-  public static String getClassName(int index) {\r
-    return formats.getClassName(index);\r
-  }\r
-\r
-  public static boolean contains(String format) {\r
-\r
-    if (format != null) {\r
-      format.toUpperCase();\r
-\r
-      if (formats.contains(format)) {\r
-        return true;\r
-      }\r
-    }\r
-    return false;\r
-  }\r
-\r
-  public static Vector getFormatNames() {\r
-    return formats.getFormatNames();\r
-  }\r
-\r
-  public static Vector getFormats() {\r
-    return formats.getFormatNames();\r
-  }\r
-}\r

diff --git a/src/jalview/io/FormatProperty.java b/src/jalview/io/FormatProperty.java
deleted file mode 100755 (executable)
index 2e72ee4..0000000
--- a/src/jalview/io/FormatProperty.java
+++ /dev/null
@@ -1,18 +0,0 @@
-package jalview.io;\r
-\r
-public class FormatProperty {\r
-  String description;\r
-  String className;\r
-\r
-  public FormatProperty(String description, String className) {\r
-    this.description = new String(description);\r
-    this.className   = new String(className);\r
-  }\r
-\r
-  public String getClassName() {\r
-    return className;\r
-  }\r
-  public String getDescription() {\r
-    return description;\r
-  }\r
-}\r

diff --git a/src/jalview/io/FormatPropertyVector.java b/src/jalview/io/FormatPropertyVector.java
deleted file mode 100755 (executable)
index 5fc97b3..0000000
--- a/src/jalview/io/FormatPropertyVector.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package jalview.io;\r
-\r
-import java.util.*;\r
-\r
-public class FormatPropertyVector {\r
-  Vector formatProps = new Vector();\r
-  Vector formatDescs = new Vector();\r
-\r
-  public void add(String description,String className) {\r
-    formatProps.addElement(new FormatProperty(description,className));\r
-    formatDescs.addElement(description);\r
-  }\r
-  public Vector getFormatNames() {\r
-    return formatDescs;\r
-  }\r
-\r
-  public String getClassName(int ind) {\r
-    return ((FormatProperty)formatProps.elementAt(ind)).getClassName();\r
-  }\r
-\r
-  public String getSchemeName(int ind) {\r
-    return ((FormatProperty)formatProps.elementAt(ind)).getDescription();\r
-  }\r
-\r
-  public boolean contains(String description) {\r
-    return formatDescs.contains(description);\r
-  }\r
-\r
-  public int indexOf(String description) {\r
-    return formatDescs.indexOf(description);\r
-  }\r
-}\r