+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
-import java.util.Vector;
+
+import java.util.List;
+
import com.stevesoft.pat.Regex;
+
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.
- */
- final String[] seqTypes =
- {
- "sequence", "structure", "structureX", "structureN"};
- final String[] Fields =
- {
- "objectType", "objectId",
- "startField", "startCode",
- "endField", "endCode",
- "description1", "description2",
- "resolutionField", "tailField"};
+ /**
+ * 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" };
+
+ final String[] Fields = { "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
- };
- final char Padding[] =
- {
- ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.'
- };
+ final int Types[] = { 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;
resCode(int v)
{
- val = new Integer(v);
+ val = Integer.valueOf(v);
field = val.toString();
}
};
private resCode validResidueCode(String field)
{
Integer val = null;
- com.stevesoft.pat.Regex r = new Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
+ Regex r = new Regex(
+ "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
if (!r.search(field))
{
{
value = r.stringMatched(1);
}
- jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
- "'");
+ // Cache.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);
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)
field = st.nextToken(":");
do
{
- if (seqTypes[i].compareToIgnoreCase(field) == 0)
+ if (seqTypes[i].equalsIgnoreCase(field))
{
break;
}
- }
- while (++i < seqTypes.length);
+ } while (++i < seqTypes.length);
if (i < seqTypes.length)
{
+ st.nextToken(); // skip ':'
// valid seqType for modeller
type = i;
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)
+ 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
+ {
+ // Cache.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);
}
/**
* 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)
- if (getStartNum() != seq.getStart() && getStartCode().val != null)
+ // Set start and end before we update the type (in the case of a
+ // synthesized field set)
+ 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());
}
// 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().getDBRefs() != null)
{
- Vector dbr = seq.getDatasetSequence().getDBRef();
- int i, j;
- for (i = 0, j = dbr.size(); i < j; i++)
+ List<DBRefEntry> dbr = seq.getDatasetSequence().getDBRefs();
+ for (int i = 0, ni = dbr.size(); i < ni; i++)
{
- jalview.datamodel.DBRefEntry dref = (jalview.datamodel.DBRefEntry)
- dbr.get(i);
- if (dref != null)
+ DBRefEntry dbri = dbr.get(i);
+ if (dbri != 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 (dref.getSource().equals("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 (dbri.getSource()
+ .equals(jalview.datamodel.DBRefSource.PDB))
{
- fields.put(Fields[LOCALID], dref.getAccessionId());
+ fields.put(Fields[LOCALID], dbri.getAccessionId());
t = 2;
break;
}
/**
* 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
{
{
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();
}
/**
* returns true if sequence object was modifed with a valid modellerField set
- * @param newSeq SequenceI
+ *
+ * @param newSeq
+ * SequenceI
* @return boolean
*/
boolean updateSequenceI(SequenceI newSeq)
{
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());
}
return false;
}
}
-
git://source.jalview.org / jalview.git / blobdiff