public class AnnotationParser extends java.lang.Object implements JmolAnnotationParser
Modifier and Type | Field and Description |
---|---|
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> |
basePairs |
private java.util.Map<java.lang.String,java.lang.Object> |
dssr |
private java.util.Map<java.lang.String,java.lang.String[]> |
htPar |
private java.util.Map<java.lang.String,java.lang.Object> |
htTemp |
private java.lang.String |
line |
private javajs.util.SB |
message |
private int[] |
next |
private static java.util.Map<java.lang.String,java.lang.String> |
pdbAtomForH |
private javajs.api.GenericLineReader |
reader |
Constructor and Description |
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AnnotationParser() |
Modifier and Type | Method and Description |
---|---|
private void |
addArray(java.util.Map<java.lang.String,java.lang.Object> data,
java.lang.String key,
float[] f) |
private void |
addFloat(java.util.Map<java.lang.String,java.lang.Object> data,
java.lang.String key,
int pt) |
private void |
addMessage(java.lang.String s) |
private void |
addToMessages(java.lang.String s) |
private java.lang.String |
after(java.lang.String s,
java.lang.String key) |
private void |
assignPDBH(java.lang.String group3,
java.lang.String sNames) |
java.lang.String |
calculateDSSRStructure(Viewer vwr,
BS bsAtoms) |
java.lang.String |
catalogStructureUnits(Viewer viewer,
SV map0,
int[] modelAtomIndices,
java.util.Map<java.lang.String,int[]> resMap,
java.lang.Object object,
java.util.Map<java.lang.String,java.lang.Integer> modelMap) |
private boolean |
catalogUnit(Viewer viewer,
float[][] vals,
java.lang.String unitID,
float val,
BS bsAtoms,
int[] modelAtomIndices,
java.util.Map<java.lang.String,int[]> resMap,
java.util.Map<java.lang.String,java.lang.Integer> atomMap,
java.util.Map<java.lang.String,java.lang.Integer> modelMap)
Carried out for each unit
|
javajs.util.Lst<java.lang.Object> |
catalogValidations(Viewer viewer,
SV map0,
int[] modelAtomIndices,
java.util.Map<java.lang.String,int[]> resMap,
java.util.Map<java.lang.String,java.lang.Integer> atomMap,
java.util.Map<java.lang.String,java.lang.Integer> modelMap)
Returns a Lst
|
private void |
extractFloats(java.util.Map<java.lang.String,java.lang.Object> data,
java.lang.String[] names) |
private void |
findAnnotationAtoms(Viewer vwr,
java.lang.String name,
javajs.util.Lst<SV> _list,
java.lang.String key,
BS bs)
find annotations; allows for wild cards InterPro.* where .....
|
private java.lang.String |
fix(java.lang.String nt,
boolean withName)
A.T8 --> [T]8:A N1@A.G2673 --> [G]2673:A.N1
A.US3/4 --> [US3]4:A
|
void |
fixAtoms(int modelIndex,
SV dbObj,
BS bsAddedMask,
int type,
int margin)
Adjusts _atoms bitset to account for added hydrogen atoms.
|
private java.lang.String |
fixKeyDSSR(java.lang.String key) |
java.lang.String |
getAnnotationInfo(Viewer vwr,
SV a,
java.lang.String match,
int type,
int modelIndex)
Get a string report of annotation data
|
private void |
getAnnotationKVPairs(SV a,
java.lang.String match,
java.lang.String dotPath,
javajs.util.SB sb,
java.lang.String pre,
boolean showDetail,
boolean isMappingOnly,
int type)
Construct a nice listing for this annotation, including validation
|
BS |
getAtomBits(Viewer vwr,
java.lang.String key,
java.lang.Object dbObj,
java.util.Map<java.lang.String,java.lang.Object> annotationCache,
int type,
int modelIndex,
BS bsModel) |
javajs.util.Lst<java.lang.Float> |
getAtomValidation(Viewer vwr,
java.lang.String type,
Atom atom)
Get all validation values corresponding to a specific validation type.
|
java.lang.String |
getAttachedAtomForPDBH(java.lang.String group3,
java.lang.String name)
Finds the standard attached heavy atom for a PDB H atom; used in EBI clash
validation.
|
private java.util.Map<java.lang.String,java.lang.Object> |
getBPData(int i0,
java.lang.String type,
boolean readParams) |
private java.lang.String |
getDataKey(int type) |
private void |
getDSSRAtoms(Viewer vwr,
java.lang.String res,
javajs.util.Lst<?> lst,
BS bs,
java.util.Map<java.lang.String,BS> htChains)
parsing a residue designation for tokens in DSSR.
|
private java.lang.String |
getDSSRForModel(Viewer vwr,
int modelIndex) |
java.lang.String |
getHBonds(ModelSet ms,
int modelIndex,
javajs.util.Lst<Bond> vHBonds,
boolean doReport) |
private java.lang.String |
getHeader() |
private void |
getHelixOrStem(int n,
java.lang.String key,
java.lang.String type,
boolean isHelix) |
private javajs.util.Lst<java.lang.Object> |
getLinkNTList(java.lang.String linkStr,
java.lang.String type,
javajs.util.Lst<java.lang.Object> list) |
private SV |
getMainItem(java.util.Map<java.lang.String,SV> data) |
private java.lang.Object |
getNT(java.lang.String s,
boolean isResno) |
private java.util.Map<java.lang.String,java.lang.Object> |
getNTList() |
private void |
getNTs(javajs.util.Lst<java.lang.Object> linkNTList,
javajs.util.Lst<java.lang.Object> lst,
boolean isStem,
boolean isResno) |
private javajs.util.P3 |
getPoint(java.lang.String data) |
javajs.util.Lst<SV> |
initializeAnnotation(SV objAnn,
int type,
int modelIndex)
We create a main list of mappings, where each mapping has _atoms and _path
|
private boolean |
isHeader(java.lang.String line) |
private void |
mapGroups(java.util.Map<java.lang.String,java.lang.String> map) |
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> |
newList(java.lang.String name) |
java.lang.String |
processDSSR(java.util.Map<java.lang.String,java.lang.Object> info,
javajs.api.GenericLineReader reader,
java.lang.String line0,
java.util.Map<java.lang.String,java.lang.String> htGroup1) |
private java.lang.String |
rd() |
private void |
readBulges(int n) |
private void |
readHBonds(int n) |
private javajs.util.Lst<java.lang.String> |
readInfo(java.lang.String key,
int n)
Default for no real processing -- just the lines
|
private void |
readJunctions(int n) |
private void |
readLoops(int n) |
private void |
readMore(java.util.Map<java.lang.String,java.lang.Object> data,
boolean isBP,
boolean isRev) |
private void |
readMotifs(int n) |
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> |
readNTList(java.lang.String ntsKey,
java.lang.String type,
int n) |
private void |
readPairs(int n) |
private void |
readSets(java.lang.String key,
int n,
int nway,
int ptnts) |
private void |
readStacks(int n)
List of 40 coaxial stacks
1 Helix#1 contains 4 stems: [#1,#2,#3,#4]
2 Helix#4 contains 4 stems: [#6,#7,#9,#13]
3 Helix#10 contains 3 stems: [#16,#17,#18]
4 Helix#13 contains 2 stems: [#21,#22]
|
private void |
readStructure() |
private void |
readTurns(int n) |
void |
setAllDSSRParametersForModel(Viewer vwr,
int modelIndex) |
private BS |
setAnnotationAtoms(Viewer vwr,
java.util.Map<java.lang.String,SV> mapping,
int i) |
private NucleicMonomer |
setDSSRPhos(Viewer vwr,
int n,
java.util.Map<java.lang.String,java.lang.Object> bp,
BS bs,
java.util.Map<java.lang.String,BS> htChains) |
private NucleicMonomer |
setDSSRRes(Viewer vwr,
java.lang.String res,
BS bs,
java.util.Map<java.lang.String,BS> htChains) |
private void |
skipHeader()
Numbers are right justified in columns 0-3 followed by a space and a
character;
base-pair data start in column 5, but notes start with "Note: " or " ",
both of which have a space in column 5.
|
private void |
skipTo(java.lang.String key,
boolean startsWith) |
private javajs.api.GenericLineReader reader
private java.lang.String line
private java.util.Map<java.lang.String,java.lang.Object> dssr
private java.util.Map<java.lang.String,java.lang.Object> htTemp
private javajs.util.SB message
private java.util.Map<java.lang.String,java.lang.String[]> htPar
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> basePairs
private int[] next
private static java.util.Map<java.lang.String,java.lang.String> pdbAtomForH
public java.lang.String processDSSR(java.util.Map<java.lang.String,java.lang.Object> info, javajs.api.GenericLineReader reader, java.lang.String line0, java.util.Map<java.lang.String,java.lang.String> htGroup1) throws java.lang.Exception
processDSSR
in interface JmolAnnotationParser
java.lang.Exception
private void mapGroups(java.util.Map<java.lang.String,java.lang.String> map) throws java.lang.Exception
java.lang.Exception
private void readStructure() throws java.lang.Exception
java.lang.Exception
private void readHBonds(int n) throws java.lang.Exception
java.lang.Exception
private void addToMessages(java.lang.String s) throws java.lang.Exception
java.lang.Exception
private void addMessage(java.lang.String s)
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> newList(java.lang.String name)
private void readStacks(int n) throws java.lang.Exception
n
- java.lang.Exception
private javajs.util.Lst<java.lang.String> readInfo(java.lang.String key, int n) throws java.lang.Exception
key
- n
- java.lang.Exception
private void readLoops(int n) throws java.lang.Exception
java.lang.Exception
private void readJunctions(int n) throws java.lang.Exception
java.lang.Exception
private void readBulges(int n) throws java.lang.Exception
java.lang.Exception
private void readSets(java.lang.String key, int n, int nway, int ptnts) throws java.lang.Exception
java.lang.Exception
private void getNTs(javajs.util.Lst<java.lang.Object> linkNTList, javajs.util.Lst<java.lang.Object> lst, boolean isStem, boolean isResno)
private javajs.util.Lst<java.lang.Object> getLinkNTList(java.lang.String linkStr, java.lang.String type, javajs.util.Lst<java.lang.Object> list)
private void readMotifs(int n) throws java.lang.Exception
java.lang.Exception
private void readTurns(int n) throws java.lang.Exception
java.lang.Exception
private void readPairs(int n) throws java.lang.Exception
java.lang.Exception
private java.util.Map<java.lang.String,java.lang.Object> getBPData(int i0, java.lang.String type, boolean readParams) throws java.lang.Exception
i0
- type
- readParams
- helix or base pair, not stemjava.lang.Exception
private void readMore(java.util.Map<java.lang.String,java.lang.Object> data, boolean isBP, boolean isRev) throws java.lang.Exception
java.lang.Exception
private void extractFloats(java.util.Map<java.lang.String,java.lang.Object> data, java.lang.String[] names)
private void addArray(java.util.Map<java.lang.String,java.lang.Object> data, java.lang.String key, float[] f)
private void addFloat(java.util.Map<java.lang.String,java.lang.Object> data, java.lang.String key, int pt)
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> readNTList(java.lang.String ntsKey, java.lang.String type, int n) throws java.lang.Exception
java.lang.Exception
private void getHelixOrStem(int n, java.lang.String key, java.lang.String type, boolean isHelix) throws java.lang.Exception
java.lang.Exception
private javajs.util.P3 getPoint(java.lang.String data)
private java.util.Map<java.lang.String,java.lang.Object> getNTList() throws java.lang.Exception
java.lang.Exception
private java.lang.Object getNT(java.lang.String s, boolean isResno)
private java.lang.String getHeader() throws java.lang.Exception
java.lang.Exception
private void skipHeader() throws java.lang.Exception
java.lang.Exception
private boolean isHeader(java.lang.String line)
private void skipTo(java.lang.String key, boolean startsWith) throws java.lang.Exception
java.lang.Exception
private java.lang.String fix(java.lang.String nt, boolean withName)
nt
- withName
- private java.lang.String after(java.lang.String s, java.lang.String key)
private java.lang.String rd() throws java.lang.Exception
java.lang.Exception
public void setAllDSSRParametersForModel(Viewer vwr, int modelIndex)
setAllDSSRParametersForModel
in interface JmolAnnotationParser
private NucleicMonomer setDSSRPhos(Viewer vwr, int n, java.util.Map<java.lang.String,java.lang.Object> bp, BS bs, java.util.Map<java.lang.String,BS> htChains)
private NucleicMonomer setDSSRRes(Viewer vwr, java.lang.String res, BS bs, java.util.Map<java.lang.String,BS> htChains)
public java.lang.String getHBonds(ModelSet ms, int modelIndex, javajs.util.Lst<Bond> vHBonds, boolean doReport)
getHBonds
in interface JmolAnnotationParser
public java.lang.String calculateDSSRStructure(Viewer vwr, BS bsAtoms)
calculateDSSRStructure
in interface JmolAnnotationParser
private java.lang.String getDSSRForModel(Viewer vwr, int modelIndex)
private void getAnnotationKVPairs(SV a, java.lang.String match, java.lang.String dotPath, javajs.util.SB sb, java.lang.String pre, boolean showDetail, boolean isMappingOnly, int type)
a
- match
- dotPath
- sb
- pre
- showDetail
- isMappingOnly
- type
- private java.lang.String getDataKey(int type)
public java.lang.String catalogStructureUnits(Viewer viewer, SV map0, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> resMap, java.lang.Object object, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
catalogStructureUnits
in interface JmolAnnotationParser
public javajs.util.Lst<java.lang.Object> catalogValidations(Viewer viewer, SV map0, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> resMap, java.util.Map<java.lang.String,java.lang.Integer> atomMap, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
catalogValidations
in interface JmolAnnotationParser
public javajs.util.Lst<SV> initializeAnnotation(SV objAnn, int type, int modelIndex)
initializeAnnotation
in interface JmolAnnotationParser
objAnn
- private void findAnnotationAtoms(Viewer vwr, java.lang.String name, javajs.util.Lst<SV> _list, java.lang.String key, BS bs)
vwr
- name
- _list
- key
- bs
- private BS setAnnotationAtoms(Viewer vwr, java.util.Map<java.lang.String,SV> mapping, int i)
private boolean catalogUnit(Viewer viewer, float[][] vals, java.lang.String unitID, float val, BS bsAtoms, int[] modelAtomIndices, java.util.Map<java.lang.String,int[]> resMap, java.util.Map<java.lang.String,java.lang.Integer> atomMap, java.util.Map<java.lang.String,java.lang.Integer> modelMap)
viewer
- vals
- model-based array of float values for a given validation typeunitID
- val
- bsAtoms
- modelAtomIndices
- resMap
- atomMap
- modelMap
- TODOprivate java.lang.String fixKeyDSSR(java.lang.String key)
private void getDSSRAtoms(Viewer vwr, java.lang.String res, javajs.util.Lst<?> lst, BS bs, java.util.Map<java.lang.String,BS> htChains)
vwr
- res
- lst
- bs
- htChains
- public BS getAtomBits(Viewer vwr, java.lang.String key, java.lang.Object dbObj, java.util.Map<java.lang.String,java.lang.Object> annotationCache, int type, int modelIndex, BS bsModel)
getAtomBits
in interface JmolAnnotationParser
public javajs.util.Lst<java.lang.Float> getAtomValidation(Viewer vwr, java.lang.String type, Atom atom)
getAtomValidation
in interface JmolAnnotationParser
vwr
- type
- e.g. "clashes"atom
- public java.lang.String getAnnotationInfo(Viewer vwr, SV a, java.lang.String match, int type, int modelIndex)
getAnnotationInfo
in interface JmolAnnotationParser
a
- an annotation structure wrapped as a script variablematch
- can contain "mappings" to get those specificallypublic java.lang.String getAttachedAtomForPDBH(java.lang.String group3, java.lang.String name)
group3
- name
- private void assignPDBH(java.lang.String group3, java.lang.String sNames)
public void fixAtoms(int modelIndex, SV dbObj, BS bsAddedMask, int type, int margin)
fixAtoms
in interface JmolAnnotationParser