public class ModellerDescription
{
/**
- * Translates between a String containing a set of colon-separated values
- * on a single line, and sequence start/end and other properties.
- * See PIRFile IO for its use.
+ * Translates between a String containing a set of colon-separated values on a
+ * single line, and sequence start/end and other properties. See PIRFile IO
+ * for its use.
*/
final String[] seqTypes =
- {
- "sequence", "structure", "structureX", "structureN"};
+ { "sequence", "structure", "structureX", "structureN" };
+
final String[] Fields =
- {
- "objectType", "objectId",
- "startField", "startCode",
- "endField", "endCode",
- "description1", "description2",
- "resolutionField", "tailField"};
+ { "objectType", "objectId", "startField", "startCode", "endField",
+ "endCode", "description1", "description2", "resolutionField",
+ "tailField" };
+
final int TYPE = 0;
+
final int LOCALID = 1;
+
final int START = 2;
+
final int START_CHAIN = 3;
+
final int END = 4;
+
final int END_CHAIN = 5;
+
final int DESCRIPTION1 = 6;
+
final int DESCRIPTION2 = 7;
+
final int RESOLUTION = 8;
+
final int TAIL = 9;
/**
- * 0 is free text or empty
- * 1 is something that parses to an integer, or \@
+ * 0 is free text or empty 1 is something that parses to an integer, or \@
*/
final int Types[] =
- {
- 0, 0, 1, 0, 1, 0, 0, 0, 0, 0
- };
+ { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
+
final char Padding[] =
- {
- ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.'
- };
+ { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.' };
java.util.Hashtable fields = new java.util.Hashtable();
+
ModellerDescription()
{
fields.put(Fields[TAIL], "");
class resCode
{
Integer val;
+
String field;
+
resCode(String f, Integer v)
{
val = v;
{
Integer val = null;
com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
- "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
+ "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
if (!r.search(field))
{
value = r.stringMatched(1);
}
// jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
- // "'");
+ // "'");
try
{
val = Integer.valueOf(value);
return new resCode(field, val); // successful numeric extraction
- }
- catch (Exception e)
+ } catch (Exception e)
{
}
return new resCode(field, null);
{
break;
}
- }
- while (++i < seqTypes.length);
+ } while (++i < seqTypes.length);
if (i < seqTypes.length)
{
i = 1; // continue parsing fields
while (i < TAIL && st.hasMoreTokens())
{
- if ( (field = st.nextToken(":")) != null)
+ if ((field = st.nextToken(":")) != null)
{
// validate residue field value
if (Types[i] == 1)
}
else
{
- // jalview.bin.Cache.log.debug(
- // "Ignoring non-Modeller description: invalid integer-like field '" + field + "'");
+ // jalview.bin.Cache.log.debug(
+ // "Ignoring non-Modeller description: invalid integer-like
+ // field '" + field + "'");
type = -1; /* invalid field! - throw the FieldSet away */
}
;
/**
* make a possibly updated modeller field line for the sequence object
- * @param seq SequenceI
+ *
+ * @param seq
+ * SequenceI
*/
ModellerDescription(SequenceI seq)
{
if (isModellerFieldset())
{
- // Set start and end before we update the type (in the case of a synthesized field set)
+ // Set start and end before we update the type (in the case of a
+ // synthesized field set)
if (getStartNum() != seq.getStart() && getStartCode().val != null)
{
setStartCode(seq.getStart());
// synthesize fields
setStartCode(seq.getStart());
setEndCode(seq.getEnd());
- fields.put(Fields[LOCALID], seq.getName()); // this may be overwritten below...
- // type - decide based on evidence of PDB database references - this also sets the local reference field
+ fields.put(Fields[LOCALID], seq.getName()); // this may be overwritten
+ // below...
+ // type - decide based on evidence of PDB database references - this also
+ // sets the local reference field
int t = 0; // sequence
- if (seq.getDatasetSequence() != null &&
- seq.getDatasetSequence().getDBRef() != null)
+ if (seq.getDatasetSequence() != null
+ && seq.getDatasetSequence().getDBRef() != null)
{
- jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence().getDBRef();
+ jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
+ .getDBRef();
int i, j;
for (i = 0, j = dbr.length; i < j; i++)
{
if (dbr[i] != null)
{
- // JBPNote PDB dbRefEntry needs properties to propagate onto ModellerField
- // JBPNote Need to get info from the user about whether the sequence is the one being modelled, or if it is a template.
- if (dbr[i].getSource().equals(jalview.datamodel.DBRefSource.PDB))
+ // JBPNote PDB dbRefEntry needs properties to propagate onto
+ // ModellerField
+ // JBPNote Need to get info from the user about whether the sequence
+ // is the one being modelled, or if it is a template.
+ if (dbr[i].getSource()
+ .equals(jalview.datamodel.DBRefSource.PDB))
{
fields.put(Fields[LOCALID], dbr[i].getAccessionId());
t = 2;
/**
* Indicate if fields parsed to a modeller-like colon-separated value line
+ *
* @return boolean
*/
boolean isModellerFieldset()
value = (String) fields.get(Fields[i]);
if (value != null && value.length() > 0)
{
- desc += ( (String) fields.get(Fields[i])) + ":";
+ desc += ((String) fields.get(Fields[i])) + ":";
}
else
{
/**
* returns true if sequence object was modifed with a valid modellerField set
- * @param newSeq SequenceI
+ *
+ * @param newSeq
+ * SequenceI
* @return boolean
*/
boolean updateSequenceI(SequenceI newSeq)
git://source.jalview.org / jalview.git / blobdiff