From d6ad9619070895df810de190dd202b1698632438 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 26 May 2008 09:55:37 +0000
Subject: [PATCH] minor bugfix for case when PDB sequence strings are not
 parsed and added new javascript API methods for getting
 selected sequences
 (https://mantis.lifesci.dundee.ac.uk/view.php?id=32977)

---
 src/jalview/bin/JalviewLite.java |   84 +++++++++++++++++++++++++++++++++++---
 1 file changed, 79 insertions(+), 5 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 4945ec0..c7cc4f3 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -44,16 +44,42 @@ public class JalviewLite
   //The following public methods maybe called
   //externally, eg via javascript in HTML page
   /**
-   * @return list of selected sequences separated by "¬"
+   * @return String list of selected sequence IDs, each terminated by "¬" (&#172;)
    */
   public String getSelectedSequences()
   {
     return getSelectedSequencesFrom(getDefaultTargetFrame());
   }
+  /**
+   * @param sep separator string or null for default
+   * @return String list of selected sequence IDs, each terminated by sep or ("¬" as default)
+   */
+  public String getSelectedSequences(String sep)
+  {
+    return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
+  }
+  /**
+   * @param alf alignframe containing selection
+   * @return String list of selected sequence IDs, each terminated by "¬"
+   *  
+   */
   public String getSelectedSequencesFrom(AlignFrame alf)
   {
+    return getSelectedSequencesFrom(alf, "¬");
+  }
+  /**
+   * get list of selected sequence IDs separated by given separator 
+   * @param alf window containing selection 
+   * @param sep separator string to use - default is "¬"
+   * @return String list of selected sequence IDs, each terminated by the given separator
+   */
+  public String getSelectedSequencesFrom(AlignFrame alf, String sep)
+  {
     StringBuffer result = new StringBuffer("");
-
+    if (sep==null || sep.length()==0)
+    {
+      sep = "¬";
+    }
     if (alf.viewport.getSelectionGroup() != null)
     {
       SequenceI[] seqs = alf.viewport.getSelectionGroup().
@@ -62,13 +88,52 @@ public class JalviewLite
 
       for (int i = 0; i < seqs.length; i++)
       {
-        result.append(seqs[i].getName() + "¬");
+        result.append(seqs[i].getName());
+        result.append(sep); 
       }
     }
 
     return result.toString();
   }
-  
+
+  /**
+   * get sequences selected in current alignFrame and return their alignment in format 'format' either with or without suffix 
+   * @param alf - where selection is
+   * @param format - format of alignment file
+   * @param suffix - "true" to append /start-end string to each sequence ID 
+   * @return selected sequences as flat file or empty string if there was no current selection
+   */
+  public String getSelectedSequencesAsAlignment(String format, String suffix) {
+    return getSelectedSequencesAsAlignmentFrom(currentAlignFrame, format, suffix);
+  }
+
+  /**
+   * get sequences selected in alf and return their alignment in format 'format' either with or without suffix 
+   * @param alf - where selection is
+   * @param format - format of alignment file
+   * @param suffix - "true" to append /start-end string to each sequence ID 
+   * @return selected sequences as flat file or empty string if there was no current selection
+   */
+  public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix)
+  {
+    try
+    {
+      boolean seqlimits = suffix.equalsIgnoreCase("true");
+      if (alf.viewport.getSelectionGroup()!=null)
+      {
+        String reply = new AppletFormatAdapter().formatSequences(format,
+                new Alignment(alf.viewport.getSelectionAsNewSequence()), seqlimits);
+        return reply;
+      }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+      return "Error retrieving alignment in " + format + " format. ";
+    }
+    return "";
+  }
+
   public String getAlignment(String format)
   {
     return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
@@ -703,7 +768,16 @@ public class JalviewLite
             {
               for (int i = 0; i < seqs.length; i++)
               {
-                ( (Sequence) seqs[i]).addPDBId(pdb);
+                if (seqs[i]!=null)
+                {
+                  ( (Sequence) seqs[i]).addPDBId(pdb);
+                } else {
+                  if (JalviewLite.debug)
+                  {
+                    // this may not really be a problem but we give a warning anyway
+                    System.err.println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "+i+")");
+                  }
+                }
               }
 
               if (jmolAvailable)
-- 
1.7.10.2