From 24ae41ac6530eb119671b2d6cc9db8110d2433e6 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 12 Oct 2007 11:03:00 +0000
Subject: [PATCH] added separator parameter with default of '|' to control the
 list separator to use, and better debug output.

---
 src/jalview/bin/JalviewLite.java |   87 ++++++++++++++++++++++++++++++--------
 1 file changed, 70 insertions(+), 17 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index c61c516..5b103c5 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -210,6 +210,22 @@ public class JalviewLite
     {
       debug = dbg.toLowerCase().equals("true");
     }
+    /**
+     * get the separator parameter if present
+     */
+    String sep = getParameter("separator");
+    if (sep!=null)
+    {
+      if (sep.length()>0)
+      {      separator = sep;
+        if (debug)
+        {
+          System.err.println("Separator set to '"+separator+"'");
+        }
+      } else {
+        throw new Error("Invalid separator parameter - must be non-zero length");
+      }
+    }
     int r = 255;
     int g = 255;
     int b = 255;
@@ -727,17 +743,26 @@ public class JalviewLite
       return file;
     }
   }
-
-  public String[] tabbedListToArray(String list)
+  /**
+   * separator used for separatorList
+   */
+  protected String separator = "|"; // this is a safe(ish) separator - tabs don't work for firefox
+  /**
+   * parse the string into a list
+   * @param list
+   * @return elements separated by separator
+   */
+  public String[] separatorListToArray(String list)
   {
+    int seplen = separator.length();
     if (list==null || list.equals(""))
       return null;
     java.util.Vector jv = new Vector();
     int cp=0,pos;
-    while ((pos=list.indexOf("\t",cp))>cp)
+    while ((pos=list.indexOf(separator,cp))>cp)
     {
       jv.addElement(list.substring(cp,pos));
-      cp = pos+1;
+      cp = pos+seplen;
     }
     if (cp<list.length())
     {
@@ -745,22 +770,33 @@ public class JalviewLite
     }
     if (jv.size()>0)
     { String[] v = new String[jv.size()];
-      jv.copyInto(v);
+      for (int i=0; i<v.length; i++)
+      {
+        v[i] = (String) jv.elementAt(i);
+      }
       jv.removeAllElements();
       if (debug)
       {
-        System.err.println("Array from Tabbed List:\n"+v.length+"\n"+v.toString());
+        System.err.println("Array from '"+separator+"' separated List:\n"+v.length);
+        for (int i=0; i<v.length;i++)
+        {
+          System.err.println("item "+i+" '"+v[i]+"'");
+        }
       }
       return v;
     }
     if (debug)
     {
-      System.err.println("Empty Array from Tabbed List");
+      System.err.println("Empty Array from '"+separator+"' separated List");
     }
     return null;
   }
-
-  public String ArraytotabbedList(String[] list)
+  /**
+   * concatenate the list with separator
+   * @param list
+   * @return concatenated string
+   */
+  public String arrayToSeparatorList(String[] list)
   {
     StringBuffer v = new StringBuffer();
     if (list!=null)
@@ -771,20 +807,21 @@ public class JalviewLite
         {  
           v.append(list[i]); 
         }
-        v.append("\t");
+        v.append(separator);
       }
       if (list[list.length-1]!=null)
       { v.append(list[list.length-1]);
       }
       if (debug)
       {
-        System.err.println("Tabbed List:\n"+v.toString());
+        System.err.println("Returning '"+separator+"' separated List:\n");
+        System.err.println(v);
       }
       return v.toString();
     }
     if (debug)
     {
-      System.err.println("Empty Tabbed List\n");
+      System.err.println("Returning empty '"+separator+"' separated List\n");
     }
     return "";
   }
@@ -794,7 +831,7 @@ public class JalviewLite
    */
   public String getFeatureGroups()
   {
-    String lst = ArraytotabbedList(currentAlignFrame.getFeatureGroups());
+    String lst = arrayToSeparatorList(currentAlignFrame.getFeatureGroups());
     return lst;
   }
   /**
@@ -804,7 +841,7 @@ public class JalviewLite
    */
   public String getFeatureGroupsOn(AlignFrame alf)
   {
-    String lst = ArraytotabbedList(alf.getFeatureGroups());
+    String lst = arrayToSeparatorList(alf.getFeatureGroups());
     return lst;
   }
   /**
@@ -814,7 +851,7 @@ public class JalviewLite
    */
   public String getFeatureGroupsOfState(boolean visible)
   {
-    return ArraytotabbedList(currentAlignFrame.getFeatureGroupsOfState(visible));
+    return arrayToSeparatorList(currentAlignFrame.getFeatureGroupsOfState(visible));
   }
   /**
    * @param alf align frame to get groups of state visible
@@ -824,7 +861,7 @@ public class JalviewLite
    */
   public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
   {
-    return ArraytotabbedList(alf.getFeatureGroupsOfState(visible));
+    return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
   }  /**
    * @param groups tab separated list of group names 
    * @param state true or false
@@ -833,10 +870,26 @@ public class JalviewLite
   public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state)
   {
     boolean st = state;//!(state==null || state.equals("") || state.toLowerCase().equals("false"));
-    alf.setFeatureGroupState(tabbedListToArray(groups), st);
+    alf.setFeatureGroupState(separatorListToArray(groups), st);
   }
   public void setFeatureGroupState(String groups, boolean state)
   {
     setFeatureGroupStateOn(currentAlignFrame, groups, state);
   }
+  /**
+   * List separator string
+   * @return the separator
+   */
+  public String getSeparator()
+  {
+    return separator;
+  }
+  /**
+   * List separator string
+   * @param separator the separator to set
+   */
+  public void setSeparator(String separator)
+  {
+    this.separator = separator;
+  }
 }
-- 
1.7.10.2