--- /dev/null
+package jalview.io;
+
+import jalview.datamodel.SequenceI;
+import java.util.Vector;
+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"};
+ 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 \@
+ */
+ 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;
+ field = f;
+ }
+
+ resCode(int v)
+ {
+ val = new Integer(v);
+ field = val.toString();
+ }
+ };
+
+ private resCode validResidueCode(String field)
+ {
+ Integer val = null;
+ com.stevesoft.pat.Regex r = new Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
+
+ if (!r.search(field))
+ {
+ return null; // invalid
+ }
+ String value = r.stringMatched(3);
+ if (value == null)
+ {
+ 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)
+ {
+ }
+ 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, ":");
+ String field;
+ int type = -1;
+ if (st.countTokens() > 0)
+ {
+ // parse colon-fields
+ int i = 0;
+ field = st.nextToken(":");
+ do
+ {
+ if (seqTypes[i].compareToIgnoreCase(field) == 0)
+ {
+ break;
+ }
+ }
+ while (++i < seqTypes.length);
+
+ if (i < seqTypes.length)
+ {
+ // valid seqType for modeller
+ type = i;
+ i = 1; // continue parsing fields
+ while (i < TAIL && st.hasMoreTokens())
+ {
+ if ( (field = st.nextToken(":")) != null)
+ {
+ // validate residue field value
+ if (Types[i] == 1)
+ {
+ 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 */
+ }
+ ;
+ }
+ fields.put(Fields[i++], field);
+ }
+ }
+ if (i == TAIL)
+ {
+ // slurp remaining fields
+ while (st.hasMoreTokens())
+ {
+ field += ":" + st.nextToken(":");
+ }
+ fields.put(Fields[TAIL], field);
+ }
+ }
+ }
+ if (type == -1)
+ {
+ // object is not a proper ModellerPIR object
+ fields = new java.util.Hashtable();
+ fields.put(Fields[TAIL], new String(desc));
+ }
+ else
+ {
+ fields.put(Fields[TYPE], seqTypes[type]);
+ }
+ return fields;
+ }
+
+ ModellerDescription(String desc)
+ {
+ if (desc == null)
+ {
+ desc = "";
+ }
+ fields = parseDescription(desc);
+ }
+
+ void setStartCode(int v)
+ {
+ resCode r;
+ fields.put(Fields[START] + "num", r = new resCode(v));
+ fields.put(Fields[START], r.field);
+ }
+
+ void setEndCode(int v)
+ {
+ resCode r;
+ fields.put(Fields[END] + "num", r = new resCode(v));
+ fields.put(Fields[END], r.field);
+ }
+
+ /**
+ * make a possibly updated modeller field line for the sequence object
+ * @param seq SequenceI
+ */
+ ModellerDescription(SequenceI seq)
+ {
+
+ if (seq.getDescription() != null)
+ {
+ fields = parseDescription(seq.getDescription());
+ }
+
+ 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)
+ {
+ setStartCode(seq.getStart());
+ }
+
+ if (getEndNum() != seq.getEnd() && getStartCode().val != null)
+ {
+ setEndCode(seq.getEnd());
+ }
+ }
+ else
+ {
+ // 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
+ int t = 0; // sequence
+ if (seq.getDatasetSequence() != null &&
+ seq.getDatasetSequence().getDBRef() != null)
+ {
+ Vector dbr = seq.getDatasetSequence().getDBRef();
+ int i, j;
+ for (i = 0, j = dbr.size(); i < j; i++)
+ {
+ jalview.datamodel.DBRefEntry dref = (jalview.datamodel.DBRefEntry)
+ dbr.get(i);
+ if (dref != 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"))
+ {
+ fields.put(Fields[LOCALID], dref.getAccessionId());
+ t = 2;
+ break;
+ }
+ }
+ }
+ }
+ fields.put(Fields[TYPE], seqTypes[t]);
+ }
+
+ }
+
+ /**
+ * Indicate if fields parsed to a modeller-like colon-separated value line
+ * @return boolean
+ */
+ boolean isModellerFieldset()
+ {
+ return (fields.containsKey(Fields[TYPE]));
+ }
+
+ String getDescriptionLine()
+ {
+ String desc = "";
+ int lastfield = Fields.length - 1;
+
+ if (isModellerFieldset())
+ {
+ String value;
+ // try to write a minimal modeller field set, so..
+
+ // find the last valid field in the entry
+
+ for (; lastfield > 6; lastfield--)
+ {
+ if (fields.containsKey(Fields[lastfield]))
+ {
+ break;
+ }
+ }
+
+ for (int i = 0; i < lastfield; i++)
+ {
+ value = (String) fields.get(Fields[i]);
+ if (value != null && value.length() > 0)
+ {
+ desc += ( (String) fields.get(Fields[i])) + ":";
+ }
+ else
+ {
+ desc += Padding[i] + ":";
+ }
+ }
+ }
+ // just return the last field if no others were defined.
+ if (fields.containsKey(Fields[lastfield]))
+ {
+ desc += (String) fields.get(Fields[lastfield]);
+ }
+ else
+ {
+ desc += ".";
+ }
+ return desc;
+ }
+
+ int getStartNum()
+ {
+ int start = 0;
+ resCode val = getStartCode();
+ if (val.val != null)
+ {
+ return val.val.intValue();
+ }
+ return start;
+ }
+
+ resCode getStartCode()
+ {
+ if (isModellerFieldset() && fields.containsKey(Fields[START] + "num"))
+ {
+ return (resCode) fields.get(Fields[START] + "num");
+ }
+ return null;
+ }
+
+ resCode getEndCode()
+ {
+ if (isModellerFieldset() && fields.containsKey(Fields[END] + "num"))
+ {
+ return (resCode) fields.get(Fields[END] + "num");
+ }
+ return null;
+ }
+
+ int getEndNum()
+ {
+ int end = 0;
+ resCode val = getEndCode();
+ if (val.val != null)
+ {
+ return val.val.intValue();
+ }
+ return end;
+ }
+
+ /**
+ * returns true if sequence object was modifed with a valid modellerField set
+ * @param newSeq SequenceI
+ * @return boolean
+ */
+ boolean updateSequenceI(SequenceI newSeq)
+ {
+ if (isModellerFieldset())
+ {
+ if (getStartCode().val != null)
+ {
+ newSeq.setStart(getStartNum());
+ }
+ else
+ {
+ newSeq.setStart(1);
+ }
+ if (getEndCode().val != null)
+ {
+ newSeq.setEnd(getEndNum());
+ }
+ else
+ {
+ newSeq.setEnd(newSeq.getStart() + newSeq.getLength());
+ }
+ return true;
+ }
+ return false;
+ }
+}
+
\r
while ( (line = nextLine()) != null)\r
{\r
- if(line.length()==0)\r
+ if (line.length() == 0)\r
{\r
//System.out.println("blank line");\r
continue;\r
}\r
-\r
+ if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)\r
+ {\r
+ continue;\r
+ }\r
Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));\r
\r
sequence = new StringBuffer();\r
}\r
}\r
\r
- if(sequence.length()>0)\r
+ if (sequence.length() > 0)\r
{\r
sequence.setLength(sequence.length() - 1);\r
-\r
newSeq.setSequence(sequence.toString());\r
seqs.addElement(newSeq);\r
+ ModellerDescription md = new ModellerDescription(newSeq.\r
+ getDescription());\r
+ md.updateSequenceI(newSeq);\r
}\r
}\r
}\r
String seq = s[i].getSequence();\r
seq = seq + "*";\r
\r
- out.append(">P1;" + printId(s[i]) + "\n");\r
-\r
- if(s[i].getDescription()!=null)\r
- out.append(s[i].getDescription()+"\n");\r
+ if (is_NA)\r
+ {\r
+ // modeller doesn't really do nucleotides, so we don't do anything fancy\r
+ // Nucleotide sequence tags should have a >DL; prefix\r
+ out.append(">P1;" + s[i].getName() + "\n"); // JBPNote Should change >P to >N\r
+ if (s[i].getDescription() == null)\r
+ {\r
+ out.append(s[i].getName() + " " +\r
+ (s[i].getEnd() - s[i].getStart() + 1));\r
+ out.append(is_NA ? " bases\n" : " residues\n");\r
+ }\r
+ else\r
+ {\r
+ out.append(s[i].getDescription()+"\n");\r
+ }\r
+ }\r
else\r
{\r
- out.append(s[i].getName()+" "+ (s[i].getEnd() - s[i].getStart() + 1));\r
- out.append( is_NA ? " bases\n" : " residues\n");\r
+ out.append(">P1;" + s[i].getName() + "\n");\r
+ ModellerDescription md = new ModellerDescription(s[i]);\r
+ out.append(md.getDescriptionLine() + "\n");\r
}\r
int nochunks = (seq.length() / len) + 1;\r
\r
git://source.jalview.org / jalview.git / commitdiff