From 74333501ca7e85ea8f5d6f6d7c6787cf9d5e7c0e Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Fri, 3 Feb 2006 17:46:25 +0000 Subject: [PATCH] Java 1.1 compatible --- src/jalview/io/ModellerDescription.java | 752 +++++++++++++++---------------- 1 file changed, 376 insertions(+), 376 deletions(-) diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java index 457a6ae..13e48b4 100755 --- a/src/jalview/io/ModellerDescription.java +++ b/src/jalview/io/ModellerDescription.java @@ -1,376 +1,376 @@ -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; - } -} - +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].equalsIgnoreCase(field) ) + { + 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.elementAt(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; + } +} + -- 1.7.10.2