public class AnnotationParser extends Object implements JmolAnnotationParser
Modifier and Type | Field and Description |
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private static Map<String,String> |
pdbAtomForH |
Constructor and Description |
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AnnotationParser() |
Modifier and Type | Method and Description |
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private void |
assignPDBH(String group3,
String sNames) |
String |
calculateDSSRStructure(Viewer vwr,
BS bsAtoms) |
String |
catalogStructureUnits(Viewer viewer,
SV map0,
int[] modelAtomIndices,
Map<String,int[]> resMap,
Object object,
Map<String,Integer> modelMap) |
private boolean |
catalogUnit(Viewer viewer,
float[][] vals,
String unitID,
float val,
BS bsAtoms,
int[] modelAtomIndices,
Map<String,int[]> resMap,
Map<String,Integer> atomMap,
Map<String,Integer> modelMap)
Carried out for each unit
|
javajs.util.Lst<Object> |
catalogValidations(Viewer viewer,
SV map0,
int[] modelAtomIndices,
Map<String,int[]> resMap,
Map<String,Integer> atomMap,
Map<String,Integer> modelMap)
Returns a Lst
|
private void |
findAnnotationAtoms(Viewer vwr,
String name,
javajs.util.Lst<SV> _list,
String key,
BS bs)
find annotations; allows for wild cards InterPro.* where .....
|
void |
fixAtoms(int modelIndex,
SV dbObj,
BS bsAddedMask,
int type,
int margin)
Adjusts _atoms bitset to account for added hydrogen atoms.
|
String |
fixDSSRJSONMap(Map<String,Object> map) |
String |
getAnnotationInfo(Viewer vwr,
SV a,
String match,
int type,
int modelIndex)
Get a string report of annotation data
|
private void |
getAnnotationKVPairs(SV a,
String match,
String dotPath,
javajs.util.SB sb,
String pre,
boolean showDetail,
boolean isMappingOnly,
int type)
Construct a nice listing for this annotation, including validation
|
BS |
getAtomBits(Viewer vwr,
String key,
Object dbObj,
Map<String,Object> annotationCache,
int type,
int modelIndex,
BS bsModel) |
javajs.util.Lst<Float> |
getAtomValidation(Viewer vwr,
String type,
Atom atom)
Get all validation values corresponding to a specific validation type.
|
String |
getAttachedAtomForPDBH(String group3,
String name)
Finds the standard attached heavy atom for a PDB H atom; used in EBI clash
validation.
|
void |
getBasePairs(Viewer vwr,
int modelIndex) |
private String |
getDataKey(int type) |
String |
getHBonds(ModelSet ms,
int modelIndex,
javajs.util.Lst<Bond> vHBonds,
boolean doReport) |
private SV |
getMainItem(Map<String,SV> 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 BS |
setAnnotationAtoms(Viewer vwr,
Map<String,SV> mapping,
int i) |
void |
setGroup1(ModelSet ms,
int modelIndex) |
private void getAnnotationKVPairs(SV a, String match, String dotPath, javajs.util.SB sb, String pre, boolean showDetail, boolean isMappingOnly, int type)
a
- match
- dotPath
- sb
- pre
- showDetail
- isMappingOnly
- type
- private String getDataKey(int type)
public String catalogStructureUnits(Viewer viewer, SV map0, int[] modelAtomIndices, Map<String,int[]> resMap, Object object, Map<String,Integer> modelMap)
catalogStructureUnits
in interface JmolAnnotationParser
public javajs.util.Lst<Object> catalogValidations(Viewer viewer, SV map0, int[] modelAtomIndices, Map<String,int[]> resMap, Map<String,Integer> atomMap, Map<String,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, String name, javajs.util.Lst<SV> _list, String key, BS bs)
vwr
- name
- _list
- key
- bs
- private boolean catalogUnit(Viewer viewer, float[][] vals, String unitID, float val, BS bsAtoms, int[] modelAtomIndices, Map<String,int[]> resMap, Map<String,Integer> atomMap, Map<String,Integer> modelMap)
viewer
- vals
- model-based array of float values for a given validation typeunitID
- val
- bsAtoms
- modelAtomIndices
- resMap
- atomMap
- modelMap
- TODOpublic BS getAtomBits(Viewer vwr, String key, Object dbObj, Map<String,Object> annotationCache, int type, int modelIndex, BS bsModel)
getAtomBits
in interface JmolAnnotationParser
public javajs.util.Lst<Float> getAtomValidation(Viewer vwr, String type, Atom atom)
getAtomValidation
in interface JmolAnnotationParser
vwr
- type
- e.g. "clashes"atom
- public String getAnnotationInfo(Viewer vwr, SV a, 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 String getAttachedAtomForPDBH(String group3, String name)
group3
- name
- public void fixAtoms(int modelIndex, SV dbObj, BS bsAddedMask, int type, int margin)
fixAtoms
in interface JmolAnnotationParser
public void getBasePairs(Viewer vwr, int modelIndex)
getBasePairs
in interface JmolAnnotationParser
public String calculateDSSRStructure(Viewer vwr, BS bsAtoms)
calculateDSSRStructure
in interface JmolAnnotationParser
public String fixDSSRJSONMap(Map<String,Object> map)
fixDSSRJSONMap
in interface JmolAnnotationParser
public String getHBonds(ModelSet ms, int modelIndex, javajs.util.Lst<Bond> vHBonds, boolean doReport)
getHBonds
in interface JmolAnnotationParser
public void setGroup1(ModelSet ms, int modelIndex)
setGroup1
in interface JmolAnnotationParser