rearranged project structure

diff --git a/JalviewX.jpx b/JalviewX.jpx
index 04da67d..b8d68cb 100755 (executable)
--- a/JalviewX.jpx
+++ b/JalviewX.jpx
@@ -1,29 +1,43 @@
-<?xml version="1.0" encoding="UTF-8"?>\r
-<!--JBuilder XML Project-->\r
-<project>\r
-  <property category="debug.0" name="SmartStepRedefineClasses" value="0"/>\r
-  <property category="debug.0" name="SmartStepSkipStaticInitializers" value="0"/>\r
-  <property category="debug.0" name="SmartStepSkipSynthetics" value="0"/>\r
-  <property category="javaFormatting" name="EventStyle" value="0"/>\r
-  <property category="javaFormatting" name="classBraceNextLine" value="1"/>\r
-  <property category="javaFormatting" name="methodBraceNextLine" value="1"/>\r
-  <property category="javaFormatting" name="otherBraceNextLine" value="1"/>\r
-  <property category="javaFormatting" name="packageThreshold" value="0"/>\r
-  <property category="javaFormatting" name="throwsOnNewLine" value="1"/>\r
-  <property category="serverservices" name="single.server.name" value="Tomcat 4.0"/>\r
-  <property category="sys" name="BackupPath" value="bak"/>\r
-  <property category="sys" name="Company" value="Dundee University"/>\r
-  <property category="sys" name="CompanyLabel" value="Company:"/>\r
-  <property category="sys" name="Copyright" value="Copyright (c) 2004"/>\r
-  <property category="sys" name="CopyrightLabel" value="Copyright:"/>\r
-  <property category="sys" name="DefaultPath" value="src"/>\r
-  <property category="sys" name="DocPath" value="doc"/>\r
-  <property category="sys" name="IncludeTestPath" value="1"/>\r
-  <property category="sys" name="JDK" value="java version 1.4.2_01-b06"/>\r
-  <property category="sys" name="JvmVersion" value="1.2"/>\r
-  <property category="sys" name="Libraries" value="Axis;Regex"/>\r
-  <property category="sys" name="OutPath" value="classes"/>\r
-  <property category="sys" name="SourcePath" value="src;test"/>\r
-  <property category="sys" name="TestPath" value="test"/>\r
-  <property category="sys" name="WorkingDirectory" value="."/>\r
-</project>\r
+<?xml version="1.0" encoding="UTF-8"?>
+<!--JBuilder XML Project-->
+<project>
+  <property category="debug.0" name="SmartStepRedefineClasses" value="0"/>
+  <property category="debug.0" name="SmartStepSkipStaticInitializers" value="0"/>
+  <property category="debug.0" name="SmartStepSkipSynthetics" value="0"/>
+  <property category="javaFormatting" name="EventStyle" value="0"/>
+  <property category="javaFormatting" name="classBraceNextLine" value="1"/>
+  <property category="javaFormatting" name="methodBraceNextLine" value="1"/>
+  <property category="javaFormatting" name="otherBraceNextLine" value="1"/>
+  <property category="javaFormatting" name="packageThreshold" value="0"/>
+  <property category="javaFormatting" name="throwsOnNewLine" value="1"/>
+  <property category="optimize.0" name="OptimizableType" value="com.borland.jbuilder.optimize.IntroOptimizeitProfiler"/>
+  <property category="runtime.0" name="BuildTargetOnRun" value="com.borland.jbuilder.build.ProjectBuilder$ProjectBuildAction;make"/>
+  <property category="runtime.0" name="ConfigurationName" value="JalviewX"/>
+  <property category="runtime.0" name="RunnableType" value="com.borland.jbuilder.runtime.ApplicationRunner"/>
+  <property category="runtime.0" name="application.class" value="jalview.bin.Jalview"/>
+  <property category="serverservices" name="single.server.name" value="Tomcat 4.0"/>
+  <property category="sys" name="AuthorLabel" value="@author"/>
+  <property category="sys" name="BackupPath" value="bak"/>
+  <property category="sys" name="Company" value="Dundee University"/>
+  <property category="sys" name="CompanyLabel" value="Company:"/>
+  <property category="sys" name="Copyright" value="Copyright (c) 2004"/>
+  <property category="sys" name="CopyrightLabel" value="Copyright:"/>
+  <property category="sys" name="DefaultPath" value="src"/>
+  <property category="sys" name="Description" value=""/>
+  <property category="sys" name="DescriptionLabel" value="Description:"/>
+  <property category="sys" name="DocPath" value="doc"/>
+  <property category="sys" name="ExcludeClassEnabled" value="0"/>
+  <property category="sys" name="IncludeTestPath" value="1"/>
+  <property category="sys" name="JDK" value="java version 1.4.2_01-b06"/>
+  <property category="sys" name="JvmVersion" value="1.2"/>
+  <property category="sys" name="Libraries" value="axis;regex;javah"/>
+  <property category="sys" name="OutPath" value="classes"/>
+  <property category="sys" name="SourcePath" value="src;test"/>
+  <property category="sys" name="TestPath" value="test"/>
+  <property category="sys" name="Title" value=""/>
+  <property category="sys" name="TitleLabel" value="Title:"/>
+  <property category="sys" name="Version" value="1.0"/>
+  <property category="sys" name="VersionLabel" value="@version"/>
+  <property category="sys" name="WorkingDirectory" value="."/>
+  <file path="build.xml"/>
+</project>

diff --git a/lib/axis-ant.jar b/lib/axis-ant.jar
deleted file mode 100755 (executable)
index 9cb30a9..0000000
Binary files a/lib/axis-ant.jar and /dev/null differ

diff --git a/lib/jhindexer b/lib/jhindexer
deleted file mode 100755 (executable)
index e84a1b2..0000000
--- a/lib/jhindexer
+++ /dev/null
@@ -1,49 +0,0 @@
-#! /bin/sh
-# This builds a search database 
-
-# Cygwin support.  $cygwin _must_ be set to either true or false.
-case "`uname`" in
-  CYGWIN*) cygwin=true ;;
-  *) cygwin=false ;;
-esac
-
-# For Cygwin, ensure paths are in UNIX format before anything is touched
-if $cygwin; then
-  [ -n "$JAVAHELP_HOME" ] &&
-    JAVAHELP_HOME=`cygpath --unix "$JAVAHELP_HOME"`
-fi
-
-if [ "$JAVAHELP_HOME" = "" ] ; then
-  # try to find jhindexer
-  if [ -d /opt/javahelp ] ; then 
-    JAVAHELP_HOME=/opt/javahelp
-  fi
-
-  if [ -d ${HOME}/opt/jhindexer ] ; then 
-    JAVAHELP_HOME=${HOME}/opt/javahelp
-  fi
-
-  ## resolve links - $0 may be a link to javahelp's home
-  PRG=$0
-  progname=`basename $0`
-  
-  while [ -h "$PRG" ] ; do
-    ls=`ls -ld "$PRG"`
-    link=`expr "$ls" : '.*-> \(.*\)$'`
-    if expr "$link" : '.*/.*' > /dev/null; then
-       PRG="$link"
-    else
-       PRG="`dirname $PRG`/$link"
-    fi
-  done
-  
-  JAVAHELP_HOME=`dirname "$PRG"`/../..
-
-fi
-
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin; then
-  JAVAHELP_HOME=`cygpath --path --windows "$JAVAHELP_HOME"`
-fi
-
-java -jar $JAVAHELP_HOME/javahelp/bin/jhindexer.jar "$@"

diff --git a/lib/jhindexer.jar b/lib/jhindexer.jar
deleted file mode 100755 (executable)
index 5e54263..0000000
Binary files a/lib/jhindexer.jar and /dev/null differ