/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
private java.util.Hashtable parseDescription(String desc)
{
java.util.Hashtable fields = new java.util.Hashtable();
- java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":");
+ java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":",
+ true);
+
String field;
int type = -1;
if (st.countTokens() > 0)
if (i < seqTypes.length)
{
+ st.nextToken(); // skip ':'
// valid seqType for modeller
type = i;
i = 1; // continue parsing fields
{
if ((field = st.nextToken(":")) != null)
{
- // validate residue field value
- if (Types[i] == 1)
+ if (!field.equals(":"))
{
- resCode val = validResidueCode(field);
- if (val != null)
+ // validate residue field value
+ if (Types[i] == 1)
{
- fields.put(new String(Fields[i] + "num"), val);
+ resCode val = validResidueCode(field);
+ if (val != null)
+ {
+ fields.put(new String(Fields[i] + "num"), val);
+ }
+ else
+ {
+ // jalview.bin.Cache.log.debug(
+ // "Ignoring non-Modeller description: invalid integer-like
+ // field '" + field + "'");
+ type = -1; /* invalid field! - throw the FieldSet away */
+ }
+ ;
}
- else
+ fields.put(Fields[i++], field);
+ if (st.hasMoreTokens())
{
- // jalview.bin.Cache.log.debug(
- // "Ignoring non-Modeller description: invalid integer-like
- // field '" + field + "'");
- type = -1; /* invalid field! - throw the FieldSet away */
+ st.nextToken(); // skip token sep.
}
- ;
}
- fields.put(Fields[i++], field);
+ else
+ {
+ i++;
+ }
}
}
if (i == TAIL)
// slurp remaining fields
while (st.hasMoreTokens())
{
- field += ":" + st.nextToken(":");
+ String tl = st.nextToken(":");
+ field += tl.equals(":") ? tl : (":" + tl);
}
fields.put(Fields[TAIL], field);
}
{
// Set start and end before we update the type (in the case of a
// synthesized field set)
- if (getStartNum() != seq.getStart() && getStartCode().val != null)
+ if (getStartCode() == null
+ || (getStartNum() != seq.getStart() && getStartCode().val != null))
{
+ // unset or user updated sequence start position
setStartCode(seq.getStart());
}
- if (getEndNum() != seq.getEnd() && getStartCode().val != null)
+ if (getEndCode() == null
+ || (getEndNum() != seq.getEnd() && getStartCode() != null && getStartCode().val != null))
{
setEndCode(seq.getEnd());
}
{
int start = 0;
resCode val = getStartCode();
- if (val.val != null)
+ if (val != null && val.val != null)
{
return val.val.intValue();
}
{
int end = 0;
resCode val = getEndCode();
- if (val.val != null)
+ if (val != null && val.val != null)
{
return val.val.intValue();
}
{
if (isModellerFieldset())
{
- if (getStartCode().val != null)
+ resCode rc = getStartCode();
+ if (rc != null && rc.val != null)
{
newSeq.setStart(getStartNum());
}
{
newSeq.setStart(1);
}
- if (getEndCode().val != null)
+ rc = getEndCode();
+ if (rc != null && rc.val != null)
{
newSeq.setEnd(getEndNum());
}