Serialized Form
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Package edu.mssm.crover.tools |
refseq
java.lang.String refseq
range
java.lang.String range
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Package edu.mssm.crover.tools.blast |
|
Package edu.mssm.crover.tools.blast.parsers |
|
Package edu.mssm.crover.tools.blast.parsers.xml.v2 |
_blastOutput_Program
java.lang.String _blastOutput_Program
_blastOutput_Version
java.lang.String _blastOutput_Version
_blastOutput_Reference
java.lang.String _blastOutput_Reference
_blastOutput_Db
java.lang.String _blastOutput_Db
_blastOutput_QueryID
java.lang.String _blastOutput_QueryID
_blastOutput_QueryDef
java.lang.String _blastOutput_QueryDef
_blastOutput_QueryLen
int _blastOutput_QueryLen
_has_blastOutput_QueryLen
boolean _has_blastOutput_QueryLen
- keeps track of state for field: _blastOutput_QueryLen
_blastOutput_Param
BlastOutput_Param _blastOutput_Param
_blastOutput_Iterations
BlastOutput_Iterations _blastOutput_Iterations
_iteration
Iteration _iteration
_parameters
Parameters _parameters
_hspList
java.util.ArrayList _hspList
_hit_Num
int _hit_Num
_has_hit_Num
boolean _has_hit_Num
- keeps track of state for field: _hit_Num
_hit_Id
java.lang.String _hit_Id
_hit_Def
java.lang.String _hit_Def
_hit_Accession
java.lang.String _hit_Accession
_hit_Len
int _hit_Len
_has_hit_Len
boolean _has_hit_Len
- keeps track of state for field: _hit_Len
_hit_Hsps
Hit_Hsps _hit_Hsps
_hsp_Num
int _hsp_Num
_has_hsp_Num
boolean _has_hsp_Num
- keeps track of state for field: _hsp_Num
_hsp_BitScore
java.math.BigDecimal _hsp_BitScore
_hsp_Score
int _hsp_Score
_has_hsp_Score
boolean _has_hsp_Score
- keeps track of state for field: _hsp_Score
_hsp_Evalue
double _hsp_Evalue
_has_hsp_Evalue
boolean _has_hsp_Evalue
- keeps track of state for field: _hsp_Evalue
_hsp_QueryFrom
int _hsp_QueryFrom
_has_hsp_QueryFrom
boolean _has_hsp_QueryFrom
- keeps track of state for field: _hsp_QueryFrom
_hsp_QueryTo
int _hsp_QueryTo
_has_hsp_QueryTo
boolean _has_hsp_QueryTo
- keeps track of state for field: _hsp_QueryTo
_hsp_HitFrom
int _hsp_HitFrom
_has_hsp_HitFrom
boolean _has_hsp_HitFrom
- keeps track of state for field: _hsp_HitFrom
_hsp_HitTo
int _hsp_HitTo
_has_hsp_HitTo
boolean _has_hsp_HitTo
- keeps track of state for field: _hsp_HitTo
_hsp_QueryFrame
int _hsp_QueryFrame
_has_hsp_QueryFrame
boolean _has_hsp_QueryFrame
- keeps track of state for field: _hsp_QueryFrame
_hsp_HitFrame
int _hsp_HitFrame
_has_hsp_HitFrame
boolean _has_hsp_HitFrame
- keeps track of state for field: _hsp_HitFrame
_hsp_Identity
int _hsp_Identity
_has_hsp_Identity
boolean _has_hsp_Identity
- keeps track of state for field: _hsp_Identity
_hsp_Positive
int _hsp_Positive
_has_hsp_Positive
boolean _has_hsp_Positive
- keeps track of state for field: _hsp_Positive
_hsp_Gaps
int _hsp_Gaps
_has_hsp_Gaps
boolean _has_hsp_Gaps
- keeps track of state for field: _hsp_Gaps
_hsp_AlignLen
int _hsp_AlignLen
_has_hsp_AlignLen
boolean _has_hsp_AlignLen
- keeps track of state for field: _hsp_AlignLen
_hsp_Qseq
java.lang.String _hsp_Qseq
_hsp_Hseq
java.lang.String _hsp_Hseq
_hsp_Midline
java.lang.String _hsp_Midline
_hitList
java.util.ArrayList _hitList
_statistics
Statistics _statistics
_iteration_IterNum
int _iteration_IterNum
_has_iteration_IterNum
boolean _has_iteration_IterNum
- keeps track of state for field: _iteration_IterNum
_iteration_Hits
Iteration_Hits _iteration_Hits
_iteration_Stat
Iteration_Stat _iteration_Stat
_iteration_Message
java.lang.String _iteration_Message
_parameters_Matrix
java.lang.String _parameters_Matrix
_parameters_Expect
double _parameters_Expect
_has_parameters_Expect
boolean _has_parameters_Expect
- keeps track of state for field: _parameters_Expect
_parameters_GapOpen
int _parameters_GapOpen
_has_parameters_GapOpen
boolean _has_parameters_GapOpen
- keeps track of state for field: _parameters_GapOpen
_parameters_GapExtend
int _parameters_GapExtend
_has_parameters_GapExtend
boolean _has_parameters_GapExtend
- keeps track of state for field: _parameters_GapExtend
_parameters_Filter
java.lang.String _parameters_Filter
_statistics_DbNum
int _statistics_DbNum
_has_statistics_DbNum
boolean _has_statistics_DbNum
- keeps track of state for field: _statistics_DbNum
_statistics_DbLen
int _statistics_DbLen
_has_statistics_DbLen
boolean _has_statistics_DbLen
- keeps track of state for field: _statistics_DbLen
_statistics_HspLen
int _statistics_HspLen
_has_statistics_HspLen
boolean _has_statistics_HspLen
- keeps track of state for field: _statistics_HspLen
_statistics_EffSpace
java.lang.String _statistics_EffSpace
_statistics_Kappa
java.math.BigDecimal _statistics_Kappa
_statistics_Lambda
java.math.BigDecimal _statistics_Lambda
_statistics_Entropy
java.math.BigDecimal _statistics_Entropy
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Package edu.mssm.crover.tools.blast.parsers.xml.v1 |
_blastOutput_Program
java.lang.String _blastOutput_Program
_blastOutput_Version
java.lang.String _blastOutput_Version
_blastOutput_Reference
java.lang.String _blastOutput_Reference
_blastOutput_Db
java.lang.String _blastOutput_Db
_blastOutput_QueryID
java.lang.String _blastOutput_QueryID
_blastOutput_QueryDef
java.lang.String _blastOutput_QueryDef
_blastOutput_QueryLen
java.lang.String _blastOutput_QueryLen
_blastOutput_QuerySeq
java.lang.String _blastOutput_QuerySeq
_blastOutput_IterNum
java.lang.String _blastOutput_IterNum
_blastOutput_Hits
BlastOutput_Hits _blastOutput_Hits
_blastOutput_Param
BlastOutput_Param _blastOutput_Param
_blastOutput_Stat
BlastOutput_Stat _blastOutput_Stat
_blastOutput_Message
java.lang.String _blastOutput_Message
_hitList
java.util.ArrayList _hitList
_parameters
Parameters _parameters
_statistics
Statistics _statistics
_hit_Num
java.lang.String _hit_Num
_hit_Id
java.lang.String _hit_Id
_hit_Def
java.lang.String _hit_Def
_hit_Accession
java.lang.String _hit_Accession
_hit_Len
java.lang.String _hit_Len
_hit_Hsps
Hit_Hsps _hit_Hsps
_hspList
java.util.ArrayList _hspList
_hsp_Num
java.lang.String _hsp_Num
_hsp_Score
java.lang.String _hsp_Score
_hsp_Evalue
java.lang.String _hsp_Evalue
_hsp_QueryFrom
java.lang.String _hsp_QueryFrom
_hsp_QueryTo
java.lang.String _hsp_QueryTo
_hsp_HitFrom
java.lang.String _hsp_HitFrom
_hsp_HitTo
java.lang.String _hsp_HitTo
_hsp_PatternFrom
java.lang.String _hsp_PatternFrom
_hsp_PatternTo
java.lang.String _hsp_PatternTo
_hsp_QueryFrame
java.lang.String _hsp_QueryFrame
_hsp_HitFrame
java.lang.String _hsp_HitFrame
_hsp_Identity
java.lang.String _hsp_Identity
_hsp_Positive
java.lang.String _hsp_Positive
_hsp_Gaps
java.lang.String _hsp_Gaps
_hsp_Density
java.lang.String _hsp_Density
_hsp_Qseq
java.lang.String _hsp_Qseq
_hsp_Hseq
java.lang.String _hsp_Hseq
_hsp_Midline
java.lang.String _hsp_Midline
_parameters_Matrix
java.lang.String _parameters_Matrix
_parameters_Expect
java.lang.String _parameters_Expect
_parameters_Include
java.lang.String _parameters_Include
_parameters_ScMatch
java.lang.String _parameters_ScMatch
_parameters_ScMismatch
java.lang.String _parameters_ScMismatch
_parameters_GapOpen
java.lang.String _parameters_GapOpen
_parameters_GapExtend
java.lang.String _parameters_GapExtend
_parameters_Filter
java.lang.String _parameters_Filter
_parameters_Pattern
java.lang.String _parameters_Pattern
_parameters_EntrezQuery
java.lang.String _parameters_EntrezQuery
_statistics_DbNum
java.lang.String _statistics_DbNum
_statistics_DbLen
java.lang.String _statistics_DbLen
_statistics_HspLen
java.lang.String _statistics_HspLen
_statistics_EffSpace
java.lang.String _statistics_EffSpace
_statistics_Kappa
java.lang.String _statistics_Kappa
_statistics_Lambda
java.lang.String _statistics_Lambda
_statistics_Entropy
java.lang.String _statistics_Entropy
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Package edu.mssm.crover.tools.blast.parsers.xml.v3 |
_blastOutput_Program
java.lang.String _blastOutput_Program
_blastOutput_Version
java.lang.String _blastOutput_Version
_blastOutput_Reference
java.lang.String _blastOutput_Reference
_blastOutput_Db
java.lang.String _blastOutput_Db
_blastOutput_QueryID
java.lang.String _blastOutput_QueryID
_blastOutput_QueryDef
java.lang.String _blastOutput_QueryDef
_blastOutput_QueryLen
int _blastOutput_QueryLen
_has_blastOutput_QueryLen
boolean _has_blastOutput_QueryLen
- keeps track of state for field: _blastOutput_QueryLen
_blastOutput_Param
BlastOutput_Param _blastOutput_Param
_blastOutput_Iterations
BlastOutput_Iterations _blastOutput_Iterations
_iteration
Iteration _iteration
_parameters
Parameters _parameters
_hspList
java.util.ArrayList _hspList
_hit_Num
int _hit_Num
_has_hit_Num
boolean _has_hit_Num
- keeps track of state for field: _hit_Num
_hit_Id
java.lang.String _hit_Id
_hit_Def
java.lang.String _hit_Def
_hit_Accession
java.lang.String _hit_Accession
_hit_Len
int _hit_Len
_has_hit_Len
boolean _has_hit_Len
- keeps track of state for field: _hit_Len
_hit_Hsps
Hit_Hsps _hit_Hsps
_hsp_Num
int _hsp_Num
_has_hsp_Num
boolean _has_hsp_Num
- keeps track of state for field: _hsp_Num
_hsp_BitScore
java.math.BigDecimal _hsp_BitScore
_hsp_Score
int _hsp_Score
_has_hsp_Score
boolean _has_hsp_Score
- keeps track of state for field: _hsp_Score
_hsp_Evalue
double _hsp_Evalue
_has_hsp_Evalue
boolean _has_hsp_Evalue
- keeps track of state for field: _hsp_Evalue
_hsp_QueryFrom
int _hsp_QueryFrom
_has_hsp_QueryFrom
boolean _has_hsp_QueryFrom
- keeps track of state for field: _hsp_QueryFrom
_hsp_QueryTo
int _hsp_QueryTo
_has_hsp_QueryTo
boolean _has_hsp_QueryTo
- keeps track of state for field: _hsp_QueryTo
_hsp_HitFrom
int _hsp_HitFrom
_has_hsp_HitFrom
boolean _has_hsp_HitFrom
- keeps track of state for field: _hsp_HitFrom
_hsp_HitTo
int _hsp_HitTo
_has_hsp_HitTo
boolean _has_hsp_HitTo
- keeps track of state for field: _hsp_HitTo
_hsp_QueryFrame
int _hsp_QueryFrame
_has_hsp_QueryFrame
boolean _has_hsp_QueryFrame
- keeps track of state for field: _hsp_QueryFrame
_hsp_HitFrame
int _hsp_HitFrame
_has_hsp_HitFrame
boolean _has_hsp_HitFrame
- keeps track of state for field: _hsp_HitFrame
_hsp_Identity
int _hsp_Identity
_has_hsp_Identity
boolean _has_hsp_Identity
- keeps track of state for field: _hsp_Identity
_hsp_Positive
int _hsp_Positive
_has_hsp_Positive
boolean _has_hsp_Positive
- keeps track of state for field: _hsp_Positive
_hsp_Gaps
int _hsp_Gaps
_has_hsp_Gaps
boolean _has_hsp_Gaps
- keeps track of state for field: _hsp_Gaps
_hsp_AlignLen
int _hsp_AlignLen
_has_hsp_AlignLen
boolean _has_hsp_AlignLen
- keeps track of state for field: _hsp_AlignLen
_hsp_Qseq
java.lang.String _hsp_Qseq
_hsp_Hseq
java.lang.String _hsp_Hseq
_hsp_Midline
java.lang.String _hsp_Midline
_hitList
java.util.ArrayList _hitList
_statistics
Statistics _statistics
_iteration_IterNum
int _iteration_IterNum
_has_iteration_IterNum
boolean _has_iteration_IterNum
- keeps track of state for field: _iteration_IterNum
_iteration_Hits
Iteration_Hits _iteration_Hits
_iteration_Stat
Iteration_Stat _iteration_Stat
_iteration_Message
java.lang.String _iteration_Message
_parameters_Matrix
java.lang.String _parameters_Matrix
_parameters_Expect
double _parameters_Expect
_has_parameters_Expect
boolean _has_parameters_Expect
- keeps track of state for field: _parameters_Expect
_parameters_ScMatch
int _parameters_ScMatch
_has_parameters_ScMatch
boolean _has_parameters_ScMatch
- keeps track of state for field: _parameters_ScMatch
_parameters_ScMismatch
int _parameters_ScMismatch
_has_parameters_ScMismatch
boolean _has_parameters_ScMismatch
- keeps track of state for field: _parameters_ScMismatch
_parameters_GapOpen
int _parameters_GapOpen
_has_parameters_GapOpen
boolean _has_parameters_GapOpen
- keeps track of state for field: _parameters_GapOpen
_parameters_GapExtend
int _parameters_GapExtend
_has_parameters_GapExtend
boolean _has_parameters_GapExtend
- keeps track of state for field: _parameters_GapExtend
_parameters_Filter
java.lang.String _parameters_Filter
_statistics_DbNum
int _statistics_DbNum
_has_statistics_DbNum
boolean _has_statistics_DbNum
- keeps track of state for field: _statistics_DbNum
_statistics_DbLen
int _statistics_DbLen
_has_statistics_DbLen
boolean _has_statistics_DbLen
- keeps track of state for field: _statistics_DbLen
_statistics_HspLen
int _statistics_HspLen
_has_statistics_HspLen
boolean _has_statistics_HspLen
- keeps track of state for field: _statistics_HspLen
_statistics_EffSpace
java.lang.String _statistics_EffSpace
_statistics_Kappa
java.math.BigDecimal _statistics_Kappa
_statistics_Lambda
java.math.BigDecimal _statistics_Lambda
_statistics_Entropy
java.math.BigDecimal _statistics_Entropy
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Package edu.mssm.crover.tools.tissue |
hash
java.util.WeakHashMap hash
|
Package edu.mssm.crover.tools.tissue.xml |
_expectationValue
double _expectationValue
_has_expectationValue
boolean _has_expectationValue
- keeps track of state for field: _expectationValue
_maxErrorRate
double _maxErrorRate
_has_maxErrorRate
boolean _has_maxErrorRate
- keeps track of state for field: _maxErrorRate
_database
java.lang.String _database
_searchDate
java.lang.String _searchDate
_minimumLength
int _minimumLength
_has_minimumLength
boolean _has_minimumLength
- keeps track of state for field: _minimumLength
_bValue
int _bValue
_has_bValue
boolean _has_bValue
- keeps track of state for field: _bValue
_vValue
int _vValue
_has_vValue
boolean _has_vValue
- keeps track of state for field: _vValue
_querySequenceList
java.util.ArrayList _querySequenceList
_ac
java.lang.String _ac
_tokey
int _tokey
_has_tokey
boolean _has_tokey
- keeps track of state for field: _tokey
_residueCodes
java.lang.String _residueCodes
_type
java.lang.String _type
_ac
java.lang.String _ac
_hitList
java.util.ArrayList _hitList
_tokeyList
java.util.ArrayList _tokeyList
_id
int _id
_has_id
boolean _has_id
- keeps track of state for field: _id
_rawTissue
java.lang.String _rawTissue
_organism
java.lang.String _organism
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Package edu.mssm.crover.tools.mapstrength |
|
Package edu.mssm.crover.webapps.dimlib.parsers.xml |
_references
References _references
_description
java.lang.String _description
_phenotypeList
java.util.ArrayList _phenotypeList
_wildType_Protein
WildType_Protein _wildType_Protein
_other_Protein
Other_Protein _other_Protein
_wildType_Residues
java.lang.String _wildType_Residues
_mutated_Residues
java.lang.String _mutated_Residues
_linkList
java.util.ArrayList _linkList
_genericPosition
java.lang.String _genericPosition
_absolutePosition
int _absolutePosition
_has_absolutePosition
boolean _has_absolutePosition
- keeps track of state for field: _absolutePosition
_wildTypeAa
java.lang.String _wildTypeAa
_submitter
Submitter _submitter
_protein
Protein _protein
_genericPosition
java.lang.String _genericPosition
_absolutePosition
int _absolutePosition
_has_absolutePosition
boolean _has_absolutePosition
- keeps track of state for field: _absolutePosition
_insertedAa
java.lang.String _insertedAa
_db
java.lang.String _db
_ac
java.lang.String _ac
_submitter
Submitter _submitter
_mutations
Mutations _mutations
_annotations
Annotations _annotations
_mutantList
java.util.ArrayList _mutantList
_items
java.util.ArrayList _items
_insertionList
java.util.ArrayList _insertionList
_deletionList
java.util.ArrayList _deletionList
_pointMutationList
java.util.ArrayList _pointMutationList
_chimeraList
java.util.ArrayList _chimeraList
_db
java.lang.String _db
_ac
java.lang.String _ac
_organism
java.lang.String _organism
_start
int _start
_has_start
boolean _has_start
- keeps track of state for field: _start
_end
int _end
_has_end
boolean _has_end
- keeps track of state for field: _end
_pmid
int _pmid
_has_pmid
boolean _has_pmid
- keeps track of state for field: _pmid
_genericPosition
java.lang.String _genericPosition
_absolutePosition
int _absolutePosition
_has_absolutePosition
boolean _has_absolutePosition
- keeps track of state for field: _absolutePosition
_wildTypeAa
java.lang.String _wildTypeAa
_mutantAa
java.lang.String _mutantAa
_name
java.lang.String _name
_family
java.lang.String _family
_organism
java.lang.String _organism
_dblinks
Dblinks _dblinks
_tm_Domain
Tm_Domain _tm_Domain
_sequence
java.lang.String _sequence
_mutants
Mutants _mutants
_snps
Snps _snps
_paperList
java.util.ArrayList _paperList
_urlList
java.util.ArrayList _urlList
_submitter
Submitter _submitter
_seq_Before
java.lang.String _seq_Before
_seq_After
java.lang.String _seq_After
_allowed_Bases
java.lang.String _allowed_Bases
_forward_Pcr_Primer
java.lang.String _forward_Pcr_Primer
_reverse_Pcr_Primer
java.lang.String _reverse_Pcr_Primer
_pcr_Product_Length
java.lang.String _pcr_Product_Length
_snpList
java.util.ArrayList _snpList
_name
java.lang.String _name
_email
java.lang.String _email
_tm_SegmentList
java.util.ArrayList _tm_SegmentList
_start
int _start
_has_start
boolean _has_start
- keeps track of state for field: _start
_end
int _end
_has_end
boolean _has_end
- keeps track of state for field: _end
_href
java.lang.String _href
_start
int _start
_has_start
boolean _has_start
- keeps track of state for field: _start
_end
int _end
_has_end
boolean _has_end
- keeps track of state for field: _end
|
Package edu.mssm.crover.webapps.dimlib.lw |
protein
WildTypeProtein protein
mutant
MutantProtein mutant
add_mutation
cuttingedge.lw.form.Action add_mutation
add_inhibitor_binding
cuttingedge.lw.form.Action add_inhibitor_binding
remove_inhibitor_binding
cuttingedge.lw.form.Action remove_inhibitor_binding
validate
cuttingedge.lw.form.Action validate
activity
cuttingedge.lw.form.LOV activity
expression_level
cuttingedge.lw.form.LOV expression_level
vmax
cuttingedge.lw.form.Switch vmax
michaelis_constant
cuttingedge.lw.form.Switch michaelis_constant
substrate_binding
cuttingedge.lw.form.Switch substrate_binding
inhibitor_binding
cuttingedge.lw.form.Switch inhibitor_binding
affinity_labeling_site
cuttingedge.lw.form.Switch affinity_labeling_site
chemical_modification_site
cuttingedge.lw.form.Switch chemical_modification_site
ion_effect
cuttingedge.lw.form.Switch ion_effect
temperature_effect
cuttingedge.lw.form.Switch temperature_effect
electrophysiology
cuttingedge.lw.form.Switch electrophysiology
transporter_modification
cuttingedge.lw.form.LOV transporter_modification
transporter_localization
cuttingedge.lw.form.LOV transporter_localization
expression_system
cuttingedge.lw.form.LOV expression_system
assay_system
cuttingedge.lw.form.LOV assay_system
cell_type_used
cuttingedge.lw.form.Input cell_type_used
vector_type_used
cuttingedge.lw.form.Input vector_type_used
mai
MutantAdditionalInfo mai
messages
cuttingedge.lw.form.Data messages
modify_alignment
cuttingedge.lw.form.Action modify_alignment
protein
WildTypeProtein protein
save_alignment
cuttingedge.lw.form.Action save_alignment
back_to_create
cuttingedge.lw.form.Action back_to_create
from_creation
boolean from_creation
search_type
cuttingedge.lw.form.LOV search_type
aln_keyword
cuttingedge.lw.form.Input aln_keyword
select
cuttingedge.lw.form.Action select
alns_found
cuttingedge.lw.form.LOV alns_found
view_aln
cuttingedge.lw.form.Action view_aln
view_aln_subset
cuttingedge.lw.form.Action view_aln_subset
pm
javax.jdo.PersistenceManager pm
chosen_sequences
cuttingedge.lw.form.LOV chosen_sequences
view_aln
cuttingedge.lw.form.Action view_aln
view_aln_subset
cuttingedge.lw.form.Action view_aln_subset
alnChosen
ArcadiaAlignment alnChosen
pm
javax.jdo.PersistenceManager pm
seqs
ArcadiaAlignedSequence[] seqs
hdatInSeq
boolean hdatInSeq
modify_alignment
cuttingedge.lw.form.Action modify_alignment
protein
WildTypeProtein protein
absolute_number
cuttingedge.lw.form.Input absolute_number
get_generic_number
cuttingedge.lw.form.Action get_generic_number
confirmed
boolean confirmed
size
java.lang.String size
pm
javax.jdo.PersistenceManager pm
size_lov
cuttingedge.lw.form.LOV size_lov
num_res_lov
cuttingedge.lw.form.LOV num_res_lov
format_lov
cuttingedge.lw.form.LOV format_lov
links_lov
cuttingedge.lw.form.LOV links_lov
bold
boolean bold
svg
boolean svg
links
boolean links
links_value
java.lang.String links_value
seqsToDisplay
java.lang.String[] seqsToDisplay
seqsHash
java.util.HashSet seqsHash
useDSI
boolean useDSI
chosSeqs
cuttingedge.lw.form.LOV chosSeqs
hdatInSeq
boolean hdatInSeq
firstItem
java.lang.String firstItem
confirmed
boolean confirmed
protein
WildTypeProtein protein
confirm
cuttingedge.lw.form.Action confirm
family_output
cuttingedge.lw.form.Output family_output
protein_output
cuttingedge.lw.form.Output protein_output
organism_output
cuttingedge.lw.form.Output organism_output
sequence_output
cuttingedge.lw.form.MultiLineOutput sequence_output
pm
javax.jdo.PersistenceManager pm
foreach_mutant
cuttingedge.lw.form.ForEach foreach_mutant
foreach_mutation
cuttingedge.lw.form.ForEach foreach_mutation
foreach_pmid
cuttingedge.lw.form.ForEach foreach_pmid
foreach_url
cuttingedge.lw.form.ForEach foreach_url
foreach_phenotype
cuttingedge.lw.form.ForEach foreach_phenotype
mutant_form
cuttingedge.lw.form.Form mutant_form
mutation_form
cuttingedge.lw.form.Form mutation_form
pmid_form
cuttingedge.lw.form.Form pmid_form
url_form
cuttingedge.lw.form.Form url_form
phenotype_form
cuttingedge.lw.form.Form phenotype_form
DEFAULT_SEQ_LINE_LENGTH
int DEFAULT_SEQ_LINE_LENGTH
confirmed
boolean confirmed
pm
javax.jdo.PersistenceManager pm
DEFAULT_SEQ_LINE_LENGTH
int DEFAULT_SEQ_LINE_LENGTH
errors
java.util.Collection errors
instructions
cuttingedge.lw.form.Output instructions
position
cuttingedge.lw.form.Input position
mutation
cuttingedge.lw.form.Input mutation
validate
cuttingedge.lw.form.Action validate
description
cuttingedge.lw.form.Input description
see_alignment
cuttingedge.lw.form.Action see_alignment
protein
WildTypeProtein protein
mutant
MutantProtein mutant
add_mutation
cuttingedge.lw.form.Action add_mutation
add_additional_info
cuttingedge.lw.form.Action add_additional_info
add_additional_info_new
cuttingedge.lw.form.Action add_additional_info_new
phenotype
cuttingedge.lw.form.Input phenotype
pmid
cuttingedge.lw.form.Input pmid
url
cuttingedge.lw.form.Input url
pmid_vector
java.util.Vector pmid_vector
url_vector
java.util.Vector url_vector
phenotype_vector
java.util.Vector phenotype_vector
desc
java.lang.String desc
sub_name
java.lang.String sub_name
sub_email
java.lang.String sub_email
submitter_name
cuttingedge.lw.form.Input submitter_name
submitter_email
cuttingedge.lw.form.Input submitter_email
errors
java.util.Collection errors
get_data_form
cuttingedge.lw.form.Action get_data_form
vip
java.util.Vector vip
mai
MutantAdditionalInfo mai
ma
MutantAdditionalInfo ma
MutationForm
cuttingedge.lw.form.Form MutationForm
PMIDForm
cuttingedge.lw.form.Form PMIDForm
URLForm
cuttingedge.lw.form.Form URLForm
PhenotypeForm
cuttingedge.lw.form.Form PhenotypeForm
seqBefore
cuttingedge.lw.form.Input seqBefore
seqAfter
cuttingedge.lw.form.Input seqAfter
allowedBases
cuttingedge.lw.form.Input allowedBases
forwardPCRPrimer
cuttingedge.lw.form.Input forwardPCRPrimer
reversePCRPrimer
cuttingedge.lw.form.Input reversePCRPrimer
productLength
cuttingedge.lw.form.Input productLength
submit
cuttingedge.lw.form.Action submit
snp
SNP snp
submitter_name
cuttingedge.lw.form.Input submitter_name
submitter_email
cuttingedge.lw.form.Input submitter_email
errors
java.util.Collection errors
confirmation
boolean confirmation
session
cuttingedge.lw.ServletSession session
pm
javax.jdo.PersistenceManager pm
servletContext
javax.servlet.ServletContext servletContext
protein
WildTypeProtein protein
m_protein
MutantProtein m_protein
mpmai
MutantAdditionalInfo mpmai
mutant_collection
java.util.Collection mutant_collection
new_mutant_collection
java.util.Collection new_mutant_collection
existing_mutant_ids
java.util.Collection existing_mutant_ids
snp
SNP snp
snp_collection
java.util.Collection snp_collection
new_snp_collection
java.util.Collection new_snp_collection
existing_snp_ids
java.util.Collection existing_snp_ids
new_acs
java.util.Vector new_acs
aln_name
java.lang.String aln_name
aln_desc
java.lang.String aln_desc
aln_seqs
ArcadiaAlignedSequence[] aln_seqs
aln
ArcadiaAlignment aln
submitter
SubmitterInfo submitter
query_keyword
java.lang.String query_keyword
storedRequest
javax.servlet.http.HttpServletRequest storedRequest
pm
javax.jdo.PersistenceManager pm
pm
javax.jdo.PersistenceManager pm
p_found
cuttingedge.lw.form.LOV p_found
instructions
cuttingedge.lw.form.Output instructions
create_new_protein
cuttingedge.lw.form.Action create_new_protein
mutation
cuttingedge.lw.form.Input mutation
validate
cuttingedge.lw.form.Action validate
protein_keyword
cuttingedge.lw.form.Input protein_keyword
protein_search
cuttingedge.lw.form.LOV protein_search
organism
cuttingedge.lw.form.LOV organism
search
cuttingedge.lw.form.Action search
not_found
cuttingedge.lw.form.Output not_found
or_new
cuttingedge.lw.form.Output or_new
create
cuttingedge.lw.form.Action create
pm
javax.jdo.PersistenceManager pm
pfv
java.util.Vector pfv
submissionType
java.lang.String submissionType
family
cuttingedge.lw.form.LOV family
family_other
cuttingedge.lw.form.Input family_other
seq_name
cuttingedge.lw.form.Input seq_name
organism_name
cuttingedge.lw.form.LOV organism_name
sequence
cuttingedge.lw.form.Input sequence
database
cuttingedge.lw.form.LOV database
accession
cuttingedge.lw.form.Input accession
position
cuttingedge.lw.form.Input position
mutation
cuttingedge.lw.form.Input mutation
validate
cuttingedge.lw.form.Action validate
heading
cuttingedge.lw.form.Output heading
intro
cuttingedge.lw.form.Output intro
not_found
cuttingedge.lw.form.Output not_found
protein_keyword
cuttingedge.lw.form.Input protein_keyword
protein_search
cuttingedge.lw.form.LOV protein_search
organism
cuttingedge.lw.form.LOV organism
search
cuttingedge.lw.form.Action search
confirm
cuttingedge.lw.form.Action confirm
pm
javax.jdo.PersistenceManager pm
tm_input
cuttingedge.lw.form.Input tm_input
tm_lov
cuttingedge.lw.form.LOV tm_lov
tm_num_lov
cuttingedge.lw.form.LOV tm_num_lov
add_tm
cuttingedge.lw.form.Action add_tm
tm_ann
TmDomain_Annotation tm_ann
main_keyword
java.lang.String main_keyword
input_sequence
java.lang.String input_sequence
submitter_name
cuttingedge.lw.form.Input submitter_name
submitter_email
cuttingedge.lw.form.Input submitter_email
errors
java.util.Collection errors
submissionType
java.lang.String submissionType
messages
cuttingedge.lw.form.Data messages
affinity_labeling_site
java.lang.String affinity_labeling_site
chemical_modification_site
java.lang.String chemical_modification_site
phosphorylation
java.lang.String phosphorylation
input_family
java.lang.String input_family
input_other_family
java.lang.String input_other_family
input_name
java.lang.String input_name
print_sequence
java.lang.String print_sequence
input_organism
java.lang.String input_organism
input_ac
java.lang.String input_ac
input_db
java.lang.String input_db
TMForm
cuttingedge.lw.form.Form TMForm
s_name
java.lang.String s_name
s_email
java.lang.String s_email
protein_keyword
cuttingedge.lw.form.Input protein_keyword
select
cuttingedge.lw.form.Action select
advanced
cuttingedge.lw.form.Action advanced
extended
cuttingedge.lw.form.Action extended
keyword
java.lang.String keyword
mutant
cuttingedge.lw.form.LOV mutant
organism
cuttingedge.lw.form.LOV organism
heading
cuttingedge.lw.form.Output heading
protein_search
cuttingedge.lw.form.LOV protein_search
sort_criteria
cuttingedge.lw.form.LOV sort_criteria
protein_keyword
cuttingedge.lw.form.Input protein_keyword
select
cuttingedge.lw.form.Action select
advanced
cuttingedge.lw.form.Action advanced
add_criteria
cuttingedge.lw.form.Action add_criteria
keyword
java.lang.String keyword
mutant
cuttingedge.lw.form.LOV mutant
organism
cuttingedge.lw.form.LOV organism
heading
cuttingedge.lw.form.Output heading
protein_search
cuttingedge.lw.form.LOV protein_search
sort_criteria
cuttingedge.lw.form.LOV sort_criteria
fieldName1
cuttingedge.lw.form.LOV fieldName1
fieldEffect1
cuttingedge.lw.form.LOV fieldEffect1
fieldValue1
cuttingedge.lw.form.Input fieldValue1
relation1
cuttingedge.lw.form.LOV relation1
fieldName2
cuttingedge.lw.form.LOV fieldName2
fieldEffect2
cuttingedge.lw.form.LOV fieldEffect2
fieldValue2
cuttingedge.lw.form.Input fieldValue2
relation2
cuttingedge.lw.form.LOV relation2
fieldName3
cuttingedge.lw.form.LOV fieldName3
fieldEffect3
cuttingedge.lw.form.LOV fieldEffect3
fieldValue3
cuttingedge.lw.form.Input fieldValue3
text
cuttingedge.lw.form.Data text
currentKeyword
java.lang.String currentKeyword
currentKeywordValue
java.lang.String currentKeywordValue
currentField
java.lang.String currentField
currentEffect
java.lang.String currentEffect
currentOrganism
java.lang.String currentOrganism
searchFields
boolean searchFields
tmp
java.lang.String tmp
mutantOrProtein
java.lang.String mutantOrProtein
organismSelected
java.lang.String organismSelected
allKeywords
java.util.ArrayList allKeywords
allKeywordValues
java.util.ArrayList allKeywordValues
allFields
java.util.ArrayList allFields
allEffects
java.util.ArrayList allEffects
aln_name
cuttingedge.lw.form.Input aln_name
aln_desc
cuttingedge.lw.form.Input aln_desc
aln_submitter_name
cuttingedge.lw.form.Input aln_submitter_name
aln_submitter_email
cuttingedge.lw.form.Input aln_submitter_email
browse
cuttingedge.lw.form.Action browse
pm
javax.jdo.PersistenceManager pm
DEFAULT_SEQ_LINE_LENGTH
int DEFAULT_SEQ_LINE_LENGTH
submissionType
java.lang.String submissionType
submission_method
cuttingedge.lw.form.LOV submission_method
start_submission
cuttingedge.lw.form.Action start_submission
heading
cuttingedge.lw.form.Output heading
submissionType
java.lang.String submissionType
protein
java.lang.String protein
view_type
java.lang.String view_type
selections
cuttingedge.lw.form.Output selections
view
cuttingedge.lw.form.Output view
heading
cuttingedge.lw.form.Output heading
name
cuttingedge.lw.form.Input name
residues
cuttingedge.lw.form.Input residues
foreach
cuttingedge.lw.form.ForEach foreach
pm
javax.jdo.PersistenceManager pm
proteins_found
cuttingedge.lw.form.LOV proteins_found
mutants_found
cuttingedge.lw.form.LOV mutants_found
views
cuttingedge.lw.form.LOV views
choose_prot_view
cuttingedge.lw.form.Action choose_prot_view
choose_mut_view
cuttingedge.lw.form.Action choose_mut_view
attributes
cuttingedge.lw.form.LOV attributes
heading
cuttingedge.lw.form.Output heading
pm
javax.jdo.PersistenceManager pm
foreach_protein
cuttingedge.lw.form.ForEach foreach_protein
p_form
cuttingedge.lw.form.Form p_form
old_wtpv
java.util.Vector old_wtpv
old_mpv
java.util.Vector old_mpv
mut_num_ids
int mut_num_ids
prot_num_acs
int prot_num_acs
molecule_type
java.lang.String molecule_type
mm
MutationManager mm
sort_criteria
cuttingedge.lw.form.LOV sort_criteria
main_keyword
java.lang.String main_keyword
main_group
java.lang.String main_group
organism_in
java.lang.String organism_in
sort_type_in
java.lang.String sort_type_in
protein_keyword
cuttingedge.lw.form.Input protein_keyword
organism_lov
cuttingedge.lw.form.LOV organism_lov
search
cuttingedge.lw.form.Action search
refine
cuttingedge.lw.form.Action refine
protein_search
cuttingedge.lw.form.LOV protein_search
mutant
cuttingedge.lw.form.LOV mutant
proteins_found
cuttingedge.lw.form.LOV proteins_found
mutants_found
cuttingedge.lw.form.LOV mutants_found
views
cuttingedge.lw.form.LOV views
choose_prot_view
cuttingedge.lw.form.Action choose_prot_view
choose_mut_view
cuttingedge.lw.form.Action choose_mut_view
attributes
cuttingedge.lw.form.LOV attributes
heading
cuttingedge.lw.form.Output heading
pm
javax.jdo.PersistenceManager pm
foreach_protein
cuttingedge.lw.form.ForEach foreach_protein
p_form
cuttingedge.lw.form.Form p_form
old_wtpv
java.util.Vector old_wtpv
old_mpv
java.util.Vector old_mpv
mut_num_ids
int mut_num_ids
prot_num_acs
int prot_num_acs
molecule_type
java.lang.String molecule_type
mm
MutationManager mm
sort_criteria
cuttingedge.lw.form.LOV sort_criteria
main_keyword
java.lang.String main_keyword
main_group
java.lang.String main_group
organism_in
java.lang.String organism_in
sort_type_in
java.lang.String sort_type_in
protein_keyword
cuttingedge.lw.form.Input protein_keyword
organism_lov
cuttingedge.lw.form.LOV organism_lov
search
cuttingedge.lw.form.Action search
protein_search
cuttingedge.lw.form.LOV protein_search
mutant
cuttingedge.lw.form.LOV mutant
mutantOrProtein
java.lang.String mutantOrProtein
allKeywords
java.util.ArrayList allKeywords
allKeywordValues
java.util.ArrayList allKeywordValues
allFields
java.util.ArrayList allFields
allEffects
java.util.ArrayList allEffects
organismSelected
java.lang.String organismSelected
itemsToDisplay
java.util.ArrayList itemsToDisplay
sortField
java.lang.String sortField
search_type
cuttingedge.lw.form.LOV search_type
organism
cuttingedge.lw.form.LOV organism
select
cuttingedge.lw.form.Action select
pm
javax.jdo.PersistenceManager pm
mm
MutationManager mm
snps_found
cuttingedge.lw.form.LOV snps_found
no_snps_found
cuttingedge.lw.form.Output no_snps_found
choose_snp
cuttingedge.lw.form.Action choose_snp
snps_tbl
java.util.Hashtable snps_tbl
snp_query
cuttingedge.lw.form.Action snp_query
pm
javax.jdo.PersistenceManager pm
mutant_query
cuttingedge.lw.form.Action mutant_query
number_query
cuttingedge.lw.form.Action number_query
alignment_query
cuttingedge.lw.form.Action alignment_query
snp_query
cuttingedge.lw.form.Action snp_query
paper_query
cuttingedge.lw.form.Action paper_query
submit
cuttingedge.lw.form.Action submit
submit_aln
cuttingedge.lw.form.Action submit_aln
goToPersistentTest
cuttingedge.lw.form.Action goToPersistentTest
submit_snp
cuttingedge.lw.form.Action submit_snp
heading
cuttingedge.lw.form.Output heading
pm
javax.jdo.PersistenceManager pm
fiData
cuttingedge.lw.form.FileInput fiData
submit_aln
cuttingedge.lw.form.Action submit_aln
imported_seqs
BiologicalSequence[] imported_seqs
errors
java.util.Collection errors
fiData
cuttingedge.lw.form.FileInput fiData
submit
cuttingedge.lw.form.Action submit
mutant
MutantProtein mutant
submission
DimlibSubmission submission
c
java.util.Collection c
pm
javax.jdo.PersistenceManager pm
validator
XMLValidator validator
isXMLerror
boolean isXMLerror
wtp
WildTypeProtein wtp
errors
java.util.Collection errors
submitter
SubmitterInfo submitter
submission_type
java.lang.String submission_type
snp
SNP snp
diagram_type
cuttingedge.lw.form.LOV diagram_type
mutation_query
cuttingedge.lw.form.Action mutation_query
protein
WildTypeProtein protein
view_type
java.lang.String view_type
attributes
java.lang.String attributes
molecule_type
java.lang.String molecule_type
selections
cuttingedge.lw.form.Output selections
view
cuttingedge.lw.form.Data view
textview
cuttingedge.lw.form.MultiLineOutput textview
heading
cuttingedge.lw.form.Output heading
attribute
cuttingedge.lw.form.LOV attribute
change_attributes
cuttingedge.lw.form.Action change_attributes
caveat
cuttingedge.lw.form.Output caveat
see_alignment
cuttingedge.lw.form.Action see_alignment
mutation_form
cuttingedge.lw.form.Form mutation_form
phenotype_form
cuttingedge.lw.form.Form phenotype_form
url_form
cuttingedge.lw.form.Form url_form
pmid_form
cuttingedge.lw.form.Form pmid_form
ac_form
cuttingedge.lw.form.Form ac_form
DEFAULT_SEQ_LINE_LENGTH
int DEFAULT_SEQ_LINE_LENGTH
all_acs
boolean all_acs
changeAcOption
cuttingedge.lw.form.Action changeAcOption
submitter
cuttingedge.lw.form.Output submitter
d_type
java.lang.String d_type
pm
javax.jdo.PersistenceManager pm
mm
MutationManager mm
protein_keyword
cuttingedge.lw.form.Input protein_keyword
protein_search
cuttingedge.lw.form.LOV protein_search
organism_keyword
cuttingedge.lw.form.LOV organism_keyword
search
cuttingedge.lw.form.Action search
heading
cuttingedge.lw.form.Output heading
pm
javax.jdo.PersistenceManager pm
submissionType
java.lang.String submissionType
template
cuttingedge.lw.form.Action template
browse
cuttingedge.lw.form.Action browse
submission_type
java.lang.String submission_type
|
Package edu.mssm.crover.webapps.dimlib.util |
|
Package edu.mssm.crover.webapps.ims.lw |
imsuser
IMSUser imsuser
sessionParam1
java.lang.Object sessionParam1
sessionParam2
java.lang.Object sessionParam2
alSubstrates
java.util.ArrayList alSubstrates
alKinases
java.util.ArrayList alKinases
alProducts
java.util.ArrayList alProducts
pp
PhosphoParams pp
servletContext
javax.servlet.ServletContext servletContext
dbType
java.lang.String dbType
imsDBName
java.lang.String imsDBName
userdir
java.lang.String userdir
submcat
java.lang.String submcat
|
Package edu.mssm.crover.webapps.ims.input |
nextForm
IMSUserHome nextForm
submit
cuttingedge.lw.form.Action submit
addFile
cuttingedge.lw.form.Action addFile
inTitle
cuttingedge.lw.form.Input inTitle
inFName
cuttingedge.lw.form.Input inFName
fiData
cuttingedge.lw.form.FileInput fiData
currentSubm
Submission currentSubm
alValidation
java.util.ArrayList alValidation
alValidationSummary
java.util.ArrayList alValidationSummary
feValidation
cuttingedge.lw.form.ForEach feValidation
feValidationSummary
cuttingedge.lw.form.ForEach feValidationSummary
outValidation
cuttingedge.lw.form.Output outValidation
outValidationSummary
cuttingedge.lw.form.Output outValidationSummary
isPrototype
boolean isPrototype
session
cuttingedge.lw.ServletSession session
nextForm
UpdateProfileForm nextForm
createSubmissionForm
CreateSubmissionForm createSubmissionForm
update
cuttingedge.lw.form.Action update
createSubmission
cuttingedge.lw.form.Action createSubmission
createSubm2
cuttingedge.lw.form.Action createSubm2
searchSubmission
cuttingedge.lw.form.Action searchSubmission
outWelcome
cuttingedge.lw.form.Output outWelcome
lnkBrowse
cuttingedge.lw.form.Link lnkBrowse
userHome
IMSUserHome userHome
insert
cuttingedge.lw.form.Action insert
cancel
cuttingedge.lw.form.Action cancel
inSTitle
cuttingedge.lw.form.Input inSTitle
sTitle
java.lang.String sTitle
session
cuttingedge.lw.ServletSession session
registrationForm
RegistrationForm registrationForm
userHome
IMSUserHome userHome
iUsername
cuttingedge.lw.form.Input iUsername
iPassword
cuttingedge.lw.form.Input iPassword
login
cuttingedge.lw.form.Action login
register
cuttingedge.lw.form.Action register
update
cuttingedge.lw.form.Action update
username
java.lang.String username
password
java.lang.String password
fswitch
cuttingedge.lw.form.FormSwitch fswitch
le
LoginExpression le
fe
cuttingedge.lw.form.ForEach fe
nextForm
LoginForm nextForm
frmReg
RegistrationForm frmReg
alAffIn
java.util.ArrayList alAffIn
alAddressIn
java.util.ArrayList alAddressIn
submit
cuttingedge.lw.form.Action submit
newAff
Affiliation newAff
nextForm
RegisterAffForm nextForm
alIMSUserIn
java.util.ArrayList alIMSUserIn
frmReg
RegistrationForm frmReg
submit
cuttingedge.lw.form.Action submit
aUploadFile
cuttingedge.lw.form.Action aUploadFile
aSaveSubmission
cuttingedge.lw.form.Action aSaveSubmission
lnkWizard
cuttingedge.lw.form.Link lnkWizard
aCancel
cuttingedge.lw.form.Action aCancel
outGreeting
cuttingedge.lw.form.Output outGreeting
aPhosphoProto
cuttingedge.lw.form.Action aPhosphoProto
nextForm
IMSUserHome nextForm
aSearch
cuttingedge.lw.form.Action aSearch
aUserHome
cuttingedge.lw.form.Action aUserHome
inTitle
cuttingedge.lw.form.Input inTitle
inFName
cuttingedge.lw.form.Input inFName
ofeList
cuttingedge.lw.form.OutputForEach ofeList
nextForm
LoginForm nextForm
alIMSUserIn
java.util.ArrayList alIMSUserIn
alAddressIn
java.util.ArrayList alAddressIn
currentUser
IMSUser currentUser
s
com.odi.Session s
update
cuttingedge.lw.form.Action update
is
InsertSubmission is
userHome
IMSUserHome userHome
submit
cuttingedge.lw.form.Action submit
addFile
cuttingedge.lw.form.Action addFile
cancel
cuttingedge.lw.form.Action cancel
aReturn
cuttingedge.lw.form.Action aReturn
inFName
cuttingedge.lw.form.Input inFName
fiData
cuttingedge.lw.form.FileInput fiData
currentSubm
Submission currentSubm
|
Package edu.mssm.crover.webapps.ims.input.prototype |
alInputs
java.util.ArrayList alInputs
alDescs
java.util.ArrayList alDescs
outGreeting
cuttingedge.lw.form.Output outGreeting
aSelect
cuttingedge.lw.form.Action aSelect
pp
PhosphoParams pp
aProcess
cuttingedge.lw.form.Action aProcess
ss
SearchSelect ss
ssp
SearchSelectParams ssp
ims_ss
IMSServletSession ims_ss
lovSelected
cuttingedge.lw.form.LOV lovSelected
aDelete
cuttingedge.lw.form.Action aDelete
inKeyword
cuttingedge.lw.form.Input inKeyword
lovSearchType
cuttingedge.lw.form.LOV lovSearchType
aSearch
cuttingedge.lw.form.Action aSearch
alSearch
cuttingedge.lw.form.event.ActionListener alSearch
lovSelections
cuttingedge.lw.form.LOV lovSelections
aSelect
cuttingedge.lw.form.Action aSelect
ssp
SearchSelectParams ssp
ims_ss
IMSServletSession ims_ss
aProcess
cuttingedge.lw.form.Action aProcess
ss
SearchSelect ss
ssp
SearchSelectParams ssp
ims_ss
IMSServletSession ims_ss
lovIType
cuttingedge.lw.form.LOV lovIType
aSelect
cuttingedge.lw.form.Action aSelect
outGreeting
cuttingedge.lw.form.Output outGreeting
ims_ss
IMSServletSession ims_ss
outGreeting
cuttingedge.lw.form.Output outGreeting
outReaction
cuttingedge.lw.form.Output outReaction
aSubmit
cuttingedge.lw.form.Action aSubmit
|
Package edu.mssm.crover.webapps.ims.lwtest |
session
cuttingedge.lw.ServletSession session
fe
cuttingedge.lw.form.ForEach fe
m_alOut
java.util.ArrayList m_alOut
aReset
cuttingedge.lw.form.Action aReset
input
cuttingedge.lw.form.Input input
session
cuttingedge.lw.ServletSession session
iClassName
cuttingedge.lw.form.Input iClassName
submit
cuttingedge.lw.form.Action submit
className
java.lang.String className
fswitch
cuttingedge.lw.form.FormSwitch fswitch
se
SwitchExpression se
m_alOut
java.util.ArrayList m_alOut
m_iData
cuttingedge.lw.form.Input m_iData
m_aSubmit
cuttingedge.lw.form.Action m_aSubmit
|
Package edu.mssm.crover.webapps.ims.util |
|
Package edu.mssm.crover.webapps.ims.control |
liForm
LoginForm liForm
frmRU
RegisterUserForm frmRU
frmRA
RegisterAffForm frmRA
session
cuttingedge.lw.ServletSession session
newUser
IMSUser newUser
userAffiliation
Affiliation userAffiliation
|
Package edu.mssm.crover.webapps.tmprop.lw |
back
cuttingedge.lw.form.Action back
ftp3d_method
cuttingedge.lw.form.LOV ftp3d_method
back
cuttingedge.lw.form.Action back
ftp_method
cuttingedge.lw.form.LOV ftp_method
window
cuttingedge.lw.form.Input window
back
cuttingedge.lw.form.Action back
hdp_method
cuttingedge.lw.form.LOV hdp_method
window_min
cuttingedge.lw.form.Input window_min
window_max
cuttingedge.lw.form.Input window_max
back
cuttingedge.lw.form.Action back
vol_method
cuttingedge.lw.form.LOV vol_method
servletContext
javax.servlet.ServletContext servletContext
hydro_option
boolean hydro_option
volume_option
boolean volume_option
ci_option
boolean ci_option
lfp_option
boolean lfp_option
ft_option
boolean ft_option
ft3d_option
boolean ft3d_option
hdp_method_equal
boolean hdp_method_equal
hdp_method_weighted
boolean hdp_method_weighted
window_min
java.lang.String window_min
window_max
java.lang.String window_max
vol_method_equal
boolean vol_method_equal
vol_method_weighted
boolean vol_method_weighted
ftp_method_var
boolean ftp_method_var
ftp_method_ci
boolean ftp_method_ci
ftp_method_hdp
boolean ftp_method_hdp
ftp_method_sdvol
boolean ftp_method_sdvol
window
java.lang.String window
ftp3d_method_var
boolean ftp3d_method_var
ftp3d_method_ci
boolean ftp3d_method_ci
ftp3d_method_hdp
boolean ftp3d_method_hdp
ftp3d_method_sdvol
boolean ftp3d_method_sdvol
base_name
java.lang.String base_name
email_adress
java.lang.String email_adress
alignment
java.lang.String alignment
ref_sequence
java.lang.String ref_sequence
options_h
cuttingedge.lw.form.Switch options_h
options_v
cuttingedge.lw.form.Switch options_v
options_ci
cuttingedge.lw.form.Switch options_ci
options_lfp
cuttingedge.lw.form.Switch options_lfp
options_ft
cuttingedge.lw.form.Switch options_ft
options_ft3d
cuttingedge.lw.form.Switch options_ft3d
alignment
cuttingedge.lw.form.Input alignment
reference_sequence
cuttingedge.lw.form.Input reference_sequence
base_name
cuttingedge.lw.form.Input base_name
email
cuttingedge.lw.form.Input email
browse_alignment
cuttingedge.lw.form.Action browse_alignment
browse_reference_sequence
cuttingedge.lw.form.Action browse_reference_sequence
run
cuttingedge.lw.form.Action run
clear
cuttingedge.lw.form.Action clear
hydro_options
cuttingedge.lw.form.Action hydro_options
volume_options
cuttingedge.lw.form.Action volume_options
ft_options
cuttingedge.lw.form.Action ft_options
ft3d_options
cuttingedge.lw.form.Action ft3d_options
select_hydro
cuttingedge.lw.form.Action select_hydro
deselect_hydro
cuttingedge.lw.form.Action deselect_hydro
select_volume
cuttingedge.lw.form.Action select_volume
deselect_volume
cuttingedge.lw.form.Action deselect_volume
select_ci
cuttingedge.lw.form.Action select_ci
deselect_ci
cuttingedge.lw.form.Action deselect_ci
select_lfp
cuttingedge.lw.form.Action select_lfp
deselect_lfp
cuttingedge.lw.form.Action deselect_lfp
select_ft
cuttingedge.lw.form.Action select_ft
deselect_ft
cuttingedge.lw.form.Action deselect_ft
select_ft3d
cuttingedge.lw.form.Action select_ft3d
deselect_ft3d
cuttingedge.lw.form.Action deselect_ft3d
fiData
cuttingedge.lw.form.FileInput fiData
|
Package edu.mssm.crover.webapps.tissueinfo |
selectedTissuesForm
cuttingedge.lw.form.Form selectedTissuesForm
selectedTissues
java.util.Vector selectedTissues
formName
java.lang.String formName
formLabel
java.lang.String formLabel
sqlProfileQuery
java.lang.String sqlProfileQuery
genbankAccession
java.lang.String genbankAccession
rForm
ReportForm rForm
organismChoice
java.lang.String organismChoice
organismTable
java.lang.String organismTable
stylesheet
java.lang.String stylesheet
pfForm
ProfileForm pfForm
organismChoice
java.lang.String organismChoice
organismTable
java.lang.String organismTable
acc
cuttingedge.lw.form.Input acc
stylesheet
java.lang.String stylesheet
ESTForm
cuttingedge.lw.form.Form ESTForm
genbankAccession
java.lang.String genbankAccession
ESTVector
java.util.Vector ESTVector
organismChoice
java.lang.String organismChoice
organismTable
java.lang.String organismTable
stylesheet
java.lang.String stylesheet
ncbiurl
java.lang.String ncbiurl
sqlQuery
java.lang.String sqlQuery
selectedExpressedTissuesForm
cuttingedge.lw.form.Form selectedExpressedTissuesForm
selectedSpecificTissuesForm
cuttingedge.lw.form.Form selectedSpecificTissuesForm
expressedTissues
java.util.Vector expressedTissues
specificTissues
java.util.Vector specificTissues
expressedForm
GetForm expressedForm
specificForm
GetForm specificForm
organismChoice
java.lang.String organismChoice
stylesheet
java.lang.String stylesheet
ncbiurl
java.lang.String ncbiurl
searchForm
SearchForm searchForm
selectedExpressedTissuesForm
cuttingedge.lw.form.Form selectedExpressedTissuesForm
selectedSpecificTissuesForm
cuttingedge.lw.form.Form selectedSpecificTissuesForm
selectedExpressedTissues
java.util.Vector selectedExpressedTissues
selectedSpecificTissues
java.util.Vector selectedSpecificTissues
lovExp
cuttingedge.lw.form.LOV lovExp
lovSpec
cuttingedge.lw.form.LOV lovSpec
expressedForm
GetForm expressedForm
specificForm
GetForm specificForm
organismChoice
java.lang.String organismChoice
organismTable
java.lang.String organismTable
tiForm
TissueInfoForm tiForm
pForm
ProfileSearchForm pForm
organismChoice
java.lang.String organismChoice
lovOrg
cuttingedge.lw.form.LOV lovOrg
stylesheet
java.lang.String stylesheet
organismKey
java.lang.String organismKey
organismTable
java.lang.String organismTable
|
Package edu.mssm.crover.webapps.util |
logFile
java.lang.String logFile
referPage
java.lang.String referPage
nextPage
java.lang.String nextPage
legalPage
java.lang.String legalPage
application
java.lang.String application
agree
java.lang.String agree
disagree
java.lang.String disagree
remoteAddr
java.lang.String remoteAddr
complete
java.lang.String complete
|
Package edu.mssm.crover.domain2d |
hideFirst
boolean hideFirst
hideLast
boolean hideLast
spacer
java.awt.geom.Point2D spacer
xOffset
double xOffset
yOffset
double yOffset
preferred_size
java.awt.Dimension preferred_size
model
BetaStrandModel model
defaultCS
ResidueColorScheme defaultCS
positions
int[] positions
colors
java.awt.Color[] colors
sunum
int sunum
ri
Domain2D_Annotation.RenderingInfo[] ri
li
Domain2D_Annotation.LayoutInfo[] li
start
int start
- start position on the sequence.
end
int end
- end position on the sequence.
spacer
java.awt.Point spacer
direction
java.awt.Point direction
readObject
private void readObject(java.io.ObjectInputStream s)
throws java.lang.ClassNotFoundException,
java.io.IOException
renderingClassName
java.lang.String renderingClassName
id
java.lang.String id
kind
java.lang.String kind
template
LoopTemplate template
contained
java.util.Vector contained
solver
Solver solver
size
ConstrainedPoint size
last_domain
Domain2D last_domain
bgColor
java.awt.Color bgColor
lastMinuteDrawings
java.util.Vector lastMinuteDrawings
resolution
int resolution
page_width
float page_width
page_height
float page_height
xoffset
int xoffset
yoffset
int yoffset
minWidth
int minWidth
minHeight
int minHeight
preferredWidth
int preferredWidth
preferredHeight
int preferredHeight
rgf
ResidueGlyphFactory rgf
model
ResidueModel model
start
int start
end
int end
entryDirection
java.awt.geom.Point2D entryDirection
exitDirection
java.awt.geom.Point2D exitDirection
EllipseSpool
EllipsisGlyph[] EllipseSpool
numres_fit
int numres_fit
spacer
java.awt.geom.Point2D spacer
numres
int numres
needreset
boolean needreset
template
LoopTemplate template
templateSelector
LoopTemplateSelector templateSelector
renderingstate
int renderingstate
xmin
double xmin
ymin
double ymin
xmax
double xmax
ymax
double ymax
xoffset
double xoffset
yoffset
double yoffset
model
FreeLoopModel model
helix_layout
HelixLayout helix_layout
model
HelixModel model
backgroundImage
java.awt.Image backgroundImage
hideFirst
boolean hideFirst
hideLast
boolean hideLast
model
HelixModel model
rgf
ResidueGlyphFactory rgf
xoffset
int xoffset
yoffset
int yoffset
minWidth
int minWidth
minHeight
int minHeight
preferredWidth
int preferredWidth
preferredHeight
int preferredHeight
start
int start
end
int end
id
java.lang.String id
opacity
boolean opacity
hideFirst
boolean hideFirst
hideLast
boolean hideLast
spacer
java.awt.geom.Point2D spacer
x0_text
float x0_text
y0_text
float y0_text
start_index
int start_index
end_index
int end_index
radius
float radius
model
ProteinSegmentModel model
printable_area
java.awt.geom.Dimension2D printable_area
start_range
java.lang.String start_range
end_range
java.lang.String end_range
URL
java.lang.String URL
classname
java.lang.String classname
border
int border
singleLineStroke
java.awt.Stroke singleLineStroke
model
ResidueModel model
shape
int shape
outline
boolean outline
- Sets the shape of this cresidue glyph.
- See Also:
ResidueGlyph.CIRCLE_SHAPE,
public void setShape(int shape) { this.shape=shape; } obsolete
boldStroke
java.awt.Stroke boldStroke
ml
BrushingMouseListener ml
position
ConstrainedPoint position
numbering
boolean numbering
diagram
Diagram diagram
exclusions
java.awt.geom.Rectangle2D[] exclusions
quickDraw
boolean quickDraw
rgf
ResidueGlyphFactory rgf
start
ConstrainedPoint start
end
ConstrainedPoint end
delta_start
ConstrainedPoint delta_start
delta_end
ConstrainedPoint delta_end
first
ResidueGlyph first
last
ResidueGlyph last
rmf
ResidueModelFactory rmf
rgra
ResidueGlyphRenderingAttributes rgra
solver
Solver solver
position
ConstrainedPoint position
id
java.lang.String id
mouseListener
BrushingMouseListener mouseListener
start
ConstrainedPoint start
end
ConstrainedPoint end
rgf
ResidueGlyphFactory rgf
stroke
java.awt.Stroke stroke
color
java.awt.Color color
position
ReflexPoint position
|
Package edu.mssm.crover.domain2d.rbdg.xml |
_defineList
java.util.ArrayList _defineList
- Define a new color. Defined colors can be referenced by name
throughout the input file.
_colorScheme
ColorScheme _colorScheme
- Selects the color-scheme. Can be either GPCRDB or monotonous.
_residueColorList
java.util.ArrayList _residueColorList
- Color one residue on the sequence. Residue position
numbering starts at 1.
_name
java.lang.String _name
_residueBackground
ResidueBackground _residueBackground
- Fill color for the background of a residue
_cpointList
java.util.ArrayList _cpointList
- A control point. x and y coordinates are doubles.
_x
double _x
_has_x
boolean _has_x
- keeps track of state for field: _x
_y
double _y
_has_y
boolean _has_y
- keeps track of state for field: _y
_color
java.lang.String _color
_red
int _red
_has_red
boolean _has_red
- keeps track of state for field: _red
_green
int _green
_has_green
boolean _has_green
- keeps track of state for field: _green
_blue
int _blue
_has_blue
boolean _has_blue
- keeps track of state for field: _blue
_colors
Colors _colors
- Groups color-related options
_elipses
Elipses _elipses
- Groups elipses related options
_links
Links _links
- Describes hyperlinks attached to various components of the
diagram.
_options
Options _options
- Groups options that can affect how the diagram is rendered.
_output
Output _output
- Groups options related to the diagram output.
_tmBundle
TmBundle _tmBundle
- Use the bundle to layout integral membrane proteins. Specify
the number of transmembrane (TM) segment to display, and the
bundle will automatically calculate the layout of the
diagram. Attributes of the bundle include the direction the
N-term will take (up or down). Ids must also be generated
for each subunit the tm-bundle contains, so that subunits
can be referenced by the secondary -structure section of the
diagram. The N and C-term X and Y attributes relate to the
spacer values that can be used when drawing the diagram.
_subunitList
java.util.ArrayList _subunitList
- Each subunit is located on the page according to the
location and spacer of the subunit that preceeds it. The
location of the first subunit is determined so that the
complete diagram is visible. At the time of writing, the
following types of subunits are available (all types should
be entered starting with edu.mssm.crover.domain2d):
FreeLoop, ExtremityDomain (for N-terms), CtermDomain,
HelicalDomain, BetaStrandDomain, ProteinSegmentDomain
_x
int _x
_has_x
boolean _has_x
- keeps track of state for field: _x
_y
int _y
_has_y
boolean _has_y
- keeps track of state for field: _y
_to
int _to
_has_to
boolean _has_to
- keeps track of state for field: _to
_from
int _from
_has_from
boolean _has_from
- keeps track of state for field: _from
_excludeList
java.util.ArrayList _excludeList
- Excludes elipses from a range of residues.
_includeList
java.util.ArrayList _includeList
- Allows elipses to be included in a range of residues.
_residueRange
java.lang.String _residueRange
_format
FormatType _format
_filename
java.lang.String _filename
_filename
java.lang.String _filename
_residueRange
java.lang.String _residueRange
_residueList
java.util.ArrayList _residueList
- Links a residue to a URL. This feature is supported for all
types of export (GIF,JPG, SVG, etc). Residue position
numbering starts at 1.
_subunitRefList
java.util.ArrayList _subunitRefList
- Links a subunit to a URL. The subunit is referenced by id.
The url attribute provides the URL. For non-SVG outputs,
only subunits of type
edu.mssm.crover.domain2d.ProteinSegmentDomain can be linked
to a URL. the SVG export supports this feature for any type
of subunit.
_residueShapeList
java.util.ArrayList _residueShapeList
- Determines how individual residues will be rendered.
Attributes determine when and what type of shape is used to
render a residue. When can be either linked or nothing.
"linked" selects residues that are hyperlinked. "other"
select all the other residues. Three shapes are supported:
rectangular, circular, and octogonal.
_imageList
java.util.ArrayList _imageList
- Select options for an image output of the diagram.
_page
Page _page
- Generates an XML document that describes one diagram. This
document will contain information suitable to generate HTML
pages that embed the diagram images. When provided, the
template attribute names an XSL stylesheet that will be set
in the document.
_imageMap
ImageMap _imageMap
- Output an image map document. Currently not supported. (maps
are embedded in the XML produced.)
_template
java.lang.String _template
_filename
java.lang.String _filename
_diagramName
java.lang.String _diagramName
_name
java.lang.String _name
- Name of the protein
_residueCodes
java.lang.String _residueCodes
- Residues of the protein
_secondaryStructure
SecondaryStructure _secondaryStructure
- Defines the secondary structure for this protein.
_diagramLayout
DiagramLayout _diagramLayout
- Describes the graphical arrangement of secondary structure
units on the 2D page.
_protein
Protein _protein
- Describes the protein to be rendered.
_diagram
Diagram _diagram
- Groups the main sections that determine how the diagram will
appear.
_position
int _position
_has_position
boolean _has_position
- keeps track of state for field: _position
_url
java.lang.String _url
_color
java.lang.String _color
_position
int _position
_has_position
boolean _has_position
- keeps track of state for field: _position
_color
java.lang.String _color
_when
java.lang.String _when
- When to use the shape. Values can be linked (when residue is
linked), or nothing (when residue is not linked).
_shape
java.lang.String _shape
_segmentList
java.util.ArrayList _segmentList
- Defines the limits of of segment of secondary structure.
Segments should span non overlapping parts of the sequence.
_disulfideBridgeList
java.util.ArrayList _disulfideBridgeList
- Describes a disulfide bridge. A yellow line is drawn on the
diagram between the to and from residues.
_start
int _start
_has_start
boolean _has_start
- keeps track of state for field: _start
_end
int _end
_has_end
boolean _has_end
- keeps track of state for field: _end
_mapto
java.lang.String _mapto
_x
int _x
_has_x
boolean _has_x
- keeps track of state for field: _x
_y
int _y
_has_y
boolean _has_y
- keeps track of state for field: _y
_id
java.lang.String _id
_type
java.lang.String _type
_direction
Direction _direction
- Direction is a vector(x,y) which indicates the orientation
of a subunit (helix or loop) within the plane.
_spacer
Spacer _spacer
- The separation between the first residue of the subunit and
the last, on the page.
_controlPoints
ControlPoints _controlPoints
- Use only when subunit type is FreeLoop, Nterm or Cterm.
Provides control points for the shape of the loop (Bezier
control points). Control points are defined in a 2D space
centered on the position of the first residue of the
subunit. Thus, the first control point must have position
(0,0). The last control point should be placed such that it
matches the spacer of the subunit. The other control points
can be placed to control the shape of the path along which
residues of the subunit will be laid out.
_id
java.lang.String _id
_url
java.lang.String _url
_tmNumber
int _tmNumber
_has_tmNumber
boolean _has_tmNumber
- keeps track of state for field: _tmNumber
_tmIdPrefix
java.lang.String _tmIdPrefix
_ntermId
java.lang.String _ntermId
_ctermId
java.lang.String _ctermId
_direction
java.lang.String _direction
_nTermX
int _nTermX
_has_nTermX
boolean _has_nTermX
- keeps track of state for field: _nTermX
_nTermY
int _nTermY
_has_nTermY
boolean _has_nTermY
- keeps track of state for field: _nTermY
_cTermX
int _cTermX
_has_cTermX
boolean _has_cTermX
- keeps track of state for field: _cTermX
_cTermY
int _cTermY
_has_cTermY
boolean _has_cTermY
- keeps track of state for field: _cTermY
|
Package edu.mssm.crover.domain2d.rbdg.xml.types |
type
int type
stringValue
java.lang.String stringValue
|
Package edu.mssm.crover.domain2d.rbdg.layout.xml |
_cpointList
java.util.ArrayList _cpointList
- A control point. x and y coordinates are doubles.
_x
double _x
_has_x
boolean _has_x
- keeps track of state for field: _x
_y
double _y
_has_y
boolean _has_y
- keeps track of state for field: _y
_tmBundle
TmBundle _tmBundle
- Use the bundle to layout integral membrane proteins. Specify
the number of transmembrane (TM) segment to display, and the
bundle will automatically calculate the layout of the
diagram. Attributes of the bundle include the direction the
N-term will take (up or down). Ids must also be generated
for each subunit the tm-bundle contains, so that subunits
can be referenced by the secondary -structure section of the
diagram.
_subunitList
java.util.ArrayList _subunitList
- Each subunit is located on the page according to the
location and spacer of the subunit that preceeds it. The
location of the first subunit is determined so that the
complete diagram is visible. At the time of writing, the
following types of subunits are available (all types should
be entered starting with edu.mssm.crover.domain2d):
FreeLoop, NtermDomain, CtermDomain, HelicalDomain,
BetaStrandDomain, ProteinSegmentDomain
_x
int _x
_has_x
boolean _has_x
- keeps track of state for field: _x
_y
int _y
_has_y
boolean _has_y
- keeps track of state for field: _y
_x
int _x
_has_x
boolean _has_x
- keeps track of state for field: _x
_y
int _y
_has_y
boolean _has_y
- keeps track of state for field: _y
_id
java.lang.String _id
_type
java.lang.String _type
_direction
Direction _direction
- Direction is a vector(x,y) which indicates the orientation
of a subunit (helix or loop) within the plane.
_spacer
Spacer _spacer
- The separation between the first residue of the subunit and
the last, on the page.
_controlPoints
ControlPoints _controlPoints
- Use only when subunit type is FreeLoop, Nterm or Cterm.
Provides control points for the shape of the loop (Bezier
control points). Control points are defined in a 2D space
centered on the position of the first residue of the
subunit. Thus, the first control point must have position
(0,0). The last control point should be placed such that it
matches the spacer of the subunit. The other control points
can be placed to control the shape of the path along which
residues of the subunit will be laid out.
_tmNumber
int _tmNumber
_has_tmNumber
boolean _has_tmNumber
- keeps track of state for field: _tmNumber
_tmIdPrefix
java.lang.String _tmIdPrefix
_ntermId
java.lang.String _ntermId
_ctermId
java.lang.String _ctermId
_direction
java.lang.String _direction
_nTermX
int _nTermX
_has_nTermX
boolean _has_nTermX
- keeps track of state for field: _nTermX
_nTermY
int _nTermY
_has_nTermY
boolean _has_nTermY
- keeps track of state for field: _nTermY
_cTermX
int _cTermX
_has_cTermX
boolean _has_cTermX
- keeps track of state for field: _cTermX
_cTermY
int _cTermY
_has_cTermY
boolean _has_cTermY
- keeps track of state for field: _cTermY
|
Package edu.mssm.crover.scentral |
reason
int reason
reason
int reason
lastModificationDate
java.sql.Date lastModificationDate
principalID
java.lang.String principalID
name
java.lang.String name
description
java.lang.String description
object_id
int object_id
creation_date
java.sql.Date creation_date
cause
java.lang.Exception cause
service
WebService service
creationTime
java.util.Date creationTime
- When was this user record created ?
diagnostic
java.lang.String diagnostic
userID
java.lang.String userID
firstName
java.lang.String firstName
middleName
java.lang.String middleName
lastName
java.lang.String lastName
title
java.lang.String title
email
java.lang.String email
password
java.lang.String password
affiliation
java.lang.String affiliation
company
java.lang.String company
department
java.lang.String department
address1
java.lang.String address1
address2
java.lang.String address2
city
java.lang.String city
zip
java.lang.String zip
country
java.lang.String country
state
java.lang.String state
phoneNumber
java.lang.String phoneNumber
faxNumber
java.lang.String faxNumber
recordID
java.lang.String recordID
accessed
boolean accessed
lastLogin
java.util.Date lastLogin
readObject
private void readObject(java.io.ObjectInputStream s)
throws java.lang.ClassNotFoundException,
java.io.IOException
- Takes care of initializing transient variables,
they are null just after the default deserialization.
They must be initialized so that the session can be
used immediately after being deserialized.
If you subclass UserSession, and add transient variable,
you have to implement a new private, readObject method to
take care of deserializing them.
This method of yours must install the menu_bar (specific
to your service). If it does not, it will get a null value
via getMenuBar().
currentPage
java.lang.String currentPage
recordID
java.lang.String recordID
|
Package edu.mssm.crover.ims |
|
Package edu.mssm.crover.ims.tasks |
|
Package edu.mssm.crover.ims.tasks.results |
file
java.io.File file
value
long value
value
SequenceTaskData value
file_content
byte[] file_content
value
java.lang.String value
|
Package edu.mssm.crover.ims.tasks.engines |
data
byte[] data
f
java.io.File f
tiquery_taskid
java.lang.String[] tiquery_taskid
organism
java.lang.String organism
organism
java.lang.String organism
masking_taskid
java.lang.String masking_taskid
file
FileTaskData file
file
FileTaskData file
database
java.lang.String database
eValue
double eValue
mbr
java.io.File mbr
taskid_mask
java.lang.String taskid_mask
from_taskid
boolean from_taskid
data
AnnotatedBioSequence[] data
file
java.io.File file
data
int[] data
megablast_taskid
java.lang.String megablast_taskid
database
java.lang.String database
e_value
double e_value
max_error
double max_error
required_length
int required_length
assemble_hsps
boolean assemble_hsps
tiout
java.io.File tiout
timegablast_taskid
java.lang.String timegablast_taskid
tissuelist_taskid
java.lang.String tissuelist_taskid
tiqoutprefix
java.lang.String tiqoutprefix
tiq_args
java.lang.String[] tiq_args
|
Package edu.mssm.crover.ims.tasks.groups |
|
Package edu.mssm.crover.ims.tasks.rmi |
failedTermination
boolean failedTermination
data
TaskData data
tm
TaskManagerRMIServer tm
taskID
java.lang.String taskID
taskType
java.lang.String taskType
tm
TaskManager tm
|
Class edu.mssm.crover.ims.tasks.rmi.TaskManagerRMIServerImpl_Stub implements Serializable |
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Package edu.mssm.crover.ims.submissions |
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Package edu.mssm.crover.tables |
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Package edu.mssm.crover.tables.readers |
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Package edu.mssm.crover.tables.treatments |
expected
java.lang.Class expected
inadequate
java.lang.Class inadequate
treatment
java.lang.Class treatment
origin
java.lang.Exception origin
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Package edu.mssm.crover.tables.writers |
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Package edu.mssm.crover.webservices.rbde |
sequence
AnnotatedBioSequence sequence
cacs
ColorAnnotationsColorScheme cacs
defaultColorScheme
ResidueColorScheme defaultColorScheme
elipsOK
boolean[] elipsOK
need_rebuild_image
boolean need_rebuild_image
need_repaint_image
boolean need_repaint_image
last_image_time
long last_image_time
image_time_adjusted_in_advance
boolean image_time_adjusted_in_advance
image_scale_factor
double image_scale_factor
Nterm_dir
java.awt.Point Nterm_dir
test_int
int test_int
sequence
AnnotatedBioSequence sequence
cacs
ColorAnnotationsColorScheme cacs
defaultColorScheme
ResidueColorScheme defaultColorScheme
elipsOK
boolean[] elipsOK
need_rebuild_image
boolean need_rebuild_image
need_repaint_image
boolean need_repaint_image
last_image_time
long last_image_time
image_time_adjusted_in_advance
boolean image_time_adjusted_in_advance
image_scale_factor
double image_scale_factor
Nterm_dir
java.awt.Point Nterm_dir
sequence
AnnotatedBioSequence sequence
cacs
ColorAnnotationsColorScheme cacs
defaultColorScheme
ResidueColorScheme defaultColorScheme
elipsOK
boolean[] elipsOK
need_rebuild_image
boolean need_rebuild_image
need_repaint_image
boolean need_repaint_image
last_image_time
long last_image_time
image_time_adjusted_in_advance
boolean image_time_adjusted_in_advance
image_scale_factor
double image_scale_factor
Nterm_dir
java.awt.Point Nterm_dir
layout
java.lang.String layout
readObject
private void readObject(java.io.ObjectInputStream s)
throws java.lang.ClassNotFoundException,
java.io.IOException
diagram
CustomizedDiagram diagram
diagram_info
LibraryObjectInfo diagram_info
color_annotation
Color_Annotation color_annotation
error
boolean error
diagram_id
int diagram_id
name
java.lang.String name
description
java.lang.String description
list_form_diagram_id
int list_form_diagram_id
title
java.lang.String title
title
java.lang.String title
diagram_id
int diagram_id
name
java.lang.String name
description
java.lang.String description
list_form_diagram_id
int list_form_diagram_id
SERVE_FRAMESET_DOCUMENT
int SERVE_FRAMESET_DOCUMENT
- See Also:
- Constant Field Values
filename
java.lang.String filename
diagram_id
int diagram_id
name
java.lang.String name
description
java.lang.String description
list_form_diagram_id
int list_form_diagram_id
log
Log log
log
Log log
SERVE_FRAMESET_DOCUMENT
int SERVE_FRAMESET_DOCUMENT
- See Also:
- Constant Field Values
title
java.lang.String title
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Package edu.mssm.crover.cli |
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Package edu.mssm.crover.imports |
reason
java.lang.String reason
line
int line
reason
java.lang.String reason
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Package edu.mssm.crover.db |
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Package edu.mssm.crover.bturns |
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Package edu.mssm.crover.odmg.objectstore.util |
vect
com.odi.util.OSVector vect
theHashCode
int theHashCode
allowDuplicates
boolean allowDuplicates
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Package edu.mssm.crover.mutations.drivers |
origin
java.lang.Exception origin
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Package edu.mssm.crover.corba.servers.sequences |
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Package edu.mssm.crover.util |
changes
java.beans.PropertyChangeSupport changes
pushListeners
java.util.Vector pushListeners
URLString
java.lang.String URLString
URLContent
java.lang.StringBuffer URLContent
dummyparser
RemoveHTMLTags dummyparser
sequence
Sequence sequence
changes
java.beans.PropertyChangeSupport changes
pushListeners
java.util.Vector pushListeners
descr
java.lang.String descr
invisible
boolean invisible
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Package edu.mssm.crover.representation |
align_data
java.lang.String[] align_data
seqs
BiologicalSequence[] seqs
short_name
java.lang.String short_name
origin
BiologicalOrigin origin
origin
BiologicalOrigin origin
Annotations
java.util.Vector Annotations
shortname
java.lang.String shortname
color
java.awt.Color color
- Uses a String representation of java.awt.Color, so
that it can be serialized in the database.
residuePositions
int[] residuePositions
first_res
int first_res
second_res
int second_res
domain_type
java.lang.String domain_type
start
java.lang.Integer start
end
java.lang.Integer end
domain_type
java.lang.String domain_type
color_str
java.lang.String color_str
extd_domain_type
java.lang.String extd_domain_type
extd_sunum
int extd_sunum
extd_starts
int[] extd_starts
extd_ends
int[] extd_ends
extd_types
int[] extd_types
resnum
java.lang.Integer resnum
url
java.net.URL url
inexistant_residue
char inexistant_residue
dbname
java.lang.String dbname
ac
java.lang.String ac
shortname
java.lang.String shortname
sequences
BiologicalSequence[] sequences
alignment
char[][] alignment
positions
int positions
seq_short_name
java.lang.String seq_short_name
flagged_residues
int[] flagged_residues
info
java.lang.String[] info
domain_type
java.lang.String domain_type
sunum
int sunum
starts
int[] starts
ends
int[] ends
types
int[] types
sequence
java.lang.String sequence
short_name
java.lang.String short_name
annots
Annotations annots
- Annotations are serialized
origin
BiologicalOrigin origin
Ntermx
int Ntermx
Ntermy
int Ntermy
Ctermx
int Ctermx
Ctermy
int Ctermy
sunum
int sunum
starts
int[] starts
ends
int[] ends
nterm_location
int nterm_location
resnum
java.lang.Integer resnum
url
java.net.URL url
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Package edu.mssm.crover.joe |
fComponentsAdjusted
boolean fComponentsAdjusted
aboutLabel
javax.swing.JLabel aboutLabel
copyrightLabel
javax.swing.JLabel copyrightLabel
empty1
javax.swing.JLabel empty1
empty2
javax.swing.JLabel empty2
JPanel1
javax.swing.JPanel JPanel1
okButton
javax.swing.JButton okButton
properties
java.util.Properties properties
frameSizeAdjusted
boolean frameSizeAdjusted
newIcon
com.symantec.itools.javax.swing.icons.ImageIcon newIcon
openIcon
com.symantec.itools.javax.swing.icons.ImageIcon openIcon
saveIcon
com.symantec.itools.javax.swing.icons.ImageIcon saveIcon
cutIcon
com.symantec.itools.javax.swing.icons.ImageIcon cutIcon
copyIcon
com.symantec.itools.javax.swing.icons.ImageIcon copyIcon
pasteIcon
com.symantec.itools.javax.swing.icons.ImageIcon pasteIcon
aboutIcon
com.symantec.itools.javax.swing.icons.ImageIcon aboutIcon
saveFileDialog
java.awt.FileDialog saveFileDialog
openFileDialog
java.awt.FileDialog openFileDialog
JPanel2
javax.swing.JPanel JPanel2
JToolBar1
javax.swing.JToolBar JToolBar1
JToolBarSeparator1
com.symantec.itools.javax.swing.JToolBarSeparator JToolBarSeparator1
aboutButton
javax.swing.JButton aboutButton
JToolBarSeparator3
com.symantec.itools.javax.swing.JToolBarSeparator JToolBarSeparator3
previousButton
javax.swing.JButton previousButton
nextButton
javax.swing.JButton nextButton
attachButton
javax.swing.JButton attachButton
detachButton
javax.swing.JButton detachButton
moveButton
javax.swing.JButton moveButton
JoeMenuBar
javax.swing.JMenuBar JoeMenuBar
fileMenu
javax.swing.JMenu fileMenu
openItem
javax.swing.JMenuItem openItem
saveItem
javax.swing.JMenuItem saveItem
saveAsItem
javax.swing.JMenuItem saveAsItem
JSeparator1
javax.swing.JSeparator JSeparator1
exitItem
javax.swing.JMenuItem exitItem
JMenu2
javax.swing.JMenu JMenu2
JMenuItem3
javax.swing.JMenuItem JMenuItem3
JMenuItem5
javax.swing.JMenuItem JMenuItem5
JMenuItem4
javax.swing.JMenuItem JMenuItem4
ToolsMenu
javax.swing.JMenu ToolsMenu
helpMenu
javax.swing.JMenu helpMenu
aboutItem
javax.swing.JMenuItem aboutItem
JMenuItem2
javax.swing.JMenuItem JMenuItem2
log
Log log
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Package edu.mssm.crover.beans |
tabbedPane
javax.swing.JTabbedPane tabbedPane
contained
java.util.Hashtable contained
last_selected_tab_title
java.lang.String last_selected_tab_title
NOT_SET
java.lang.String NOT_SET
focus_listeners
java.util.Vector focus_listeners
buttonsInTabs
boolean buttonsInTabs
- Toggle the display of interaction buttons immediately following the tab
content. The buttons allow the user to attach and detach the
content of the time without external control. They could be
useful at development time but are better replaced latter by
external controls (these one can be located at a fixed position).
frame
javax.swing.JFrame frame
internal
javax.swing.JInternalFrame internal
desk
LooseTabbedPane.DesktopElement desk
tabname
java.lang.String tabname
tabbedpane
javax.swing.JTabbedPane tabbedpane
ltp
LooseTabbedPane ltp
title
java.lang.String title
contained
java.util.Vector contained
associated_frame
LooseTabbedPane.AttachedFrame associated_frame
ltp
LooseTabbedPane ltp
title
java.lang.String title
state
int state
in_desk_title
java.lang.String in_desk_title
detachedState
javax.swing.JPanel detachedState
attachedState
java.awt.Component attachedState
detachButton
javax.swing.JButton detachButton
type
int type
tab_title
java.lang.String tab_title
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Package edu.mssm.crover.ssedit |
sequence
BiologicalSequence sequence
range
SequenceRange range
rmf
ResidueModelFactory rmf
lineWidth
int lineWidth
rmf
ResidueModelFactory rmf
model
SecondaryStructure_Annotation model
sequence
BiologicalSequence sequence
changes
java.beans.PropertyChangeSupport changes
Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.