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A
- actionPerformed(ActionEvent) - Method in class apollo.dataadapter.das.DASAdapterGUI.HistoryListener
- apollo.dataadapter.das - package apollo.dataadapter.das
B
- buildGUI() - Method in class apollo.dataadapter.das.DASAdapterGUI
C
- commitChanges(CurationSet) - Method in class apollo.dataadapter.das.DASAdapter
D
- DASAdapter - class apollo.dataadapter.das.DASAdapter.
- DASAdapter(String) - Constructor for class apollo.dataadapter.das.DASAdapter
- DASAdapter() - Constructor for class apollo.dataadapter.das.DASAdapter
- DASAdapterGUI - class apollo.dataadapter.das.DASAdapterGUI.
- DASAdapterGUI(IOOperation) - Constructor for class apollo.dataadapter.das.DASAdapterGUI
- DASAdapterGUI.HistoryListener - class apollo.dataadapter.das.DASAdapterGUI.HistoryListener.
- DASAdapterGUI.HistoryListener() - Constructor for class apollo.dataadapter.das.DASAdapterGUI.HistoryListener
- DASAdapterGUI.LongValidator - class apollo.dataadapter.das.DASAdapterGUI.LongValidator.
- DASAdapterGUI.LongValidator() - Constructor for class apollo.dataadapter.das.DASAdapterGUI.LongValidator
- DASAdapterGUI.SeqListener - class apollo.dataadapter.das.DASAdapterGUI.SeqListener.
- DASAdapterGUI.SeqListener() - Constructor for class apollo.dataadapter.das.DASAdapterGUI.SeqListener
- DASAdapterGUI.ServerListener - class apollo.dataadapter.das.DASAdapterGUI.ServerListener.
- DASAdapterGUI.ServerListener() - Constructor for class apollo.dataadapter.das.DASAdapterGUI.ServerListener
- DASClient - class apollo.dataadapter.das.DASClient.
- This will open a DAS server and provide access
the DSN element data provided by the server
It will: Connect to a datasource Get XML from the data source Parse the XML and provide methods for reading that data - DASClient(String) - Constructor for class apollo.dataadapter.das.DASClient
- DASDsn - interface apollo.dataadapter.das.DASDsn.
- DASFeature - interface apollo.dataadapter.das.DASFeature.
- DASLazySequence - class apollo.dataadapter.das.DASLazySequence.
- I am a Sequence class for implementing lazy load using a DASServer
- DASLazySequence(String, Controller, RangeI, DASServerI, DASDsn, DASSegment) - Constructor for class apollo.dataadapter.das.DASLazySequence
- DASSegment - interface apollo.dataadapter.das.DASSegment.
- I represent the contained in a Segment (as defined by the DAS-spec) needed by Apollo to request features for the segment, and display the features of the segment.
- DASSequence - interface apollo.dataadapter.das.DASSequence.
- I represent the data contained in a dna sequence (as defined by the DAS-spec) needed by Apollo to display a sequence.
- DASServerI - interface apollo.dataadapter.das.DASServerI.
- I represent the capability of a general DASServer, as required by Apollo to make das-data requests.
- dasSeq - Variable in class apollo.dataadapter.das.DASAdapter
- doOperation(Object) - Method in class apollo.dataadapter.das.DASAdapterGUI
- driver - Variable in class apollo.dataadapter.das.DASAdapterGUI
- dsn - Variable in class apollo.dataadapter.das.DASLazySequence
E
- emptyVector - Variable in class apollo.dataadapter.das.DASAdapterGUI
G
- genomeSeq - Variable in class apollo.dataadapter.das.DASAdapter
- getAnalysisRegion(CurationSet) - Method in class apollo.dataadapter.das.DASAdapter
- getAnnotatedRegion() - Method in class apollo.dataadapter.das.DASAdapter
- getCurationSet() - Method in class apollo.dataadapter.das.DASAdapter
- getDASFeatures(FeatureHolder) - Method in class apollo.dataadapter.das.DASClient
- getDASFeatures(FeatureHolder, int, int) - Method in class apollo.dataadapter.das.DASClient
- getDASSequence(DASSequenceDB, String) - Method in class apollo.dataadapter.das.DASClient
- getDASSequenceDB() - Method in class apollo.dataadapter.das.DASClient
- getDNA() - Method in interface apollo.dataadapter.das.DASSequence
- getDNALength() - Method in interface apollo.dataadapter.das.DASSequence
- getDSNs() - Method in interface apollo.dataadapter.das.DASServerI
- getDescription() - Method in interface apollo.dataadapter.das.DASDsn
- getDsn() - Method in class apollo.dataadapter.das.DASLazySequence
- getEnd() - Method in interface apollo.dataadapter.das.DASFeature
- getEntryPoints(DASDsn) - Method in interface apollo.dataadapter.das.DASServerI
- getFeatures(DASDsn, DASSegment[]) - Method in interface apollo.dataadapter.das.DASServerI
- getGroupId() - Method in interface apollo.dataadapter.das.DASFeature
- getGroupTargetStart() - Method in interface apollo.dataadapter.das.DASFeature
- getGroupTargetStop() - Method in interface apollo.dataadapter.das.DASFeature
- getId() - Method in interface apollo.dataadapter.das.DASFeature
- getId() - Method in interface apollo.dataadapter.das.DASSegment
- getId() - Method in interface apollo.dataadapter.das.DASSequence
- getInput() - Method in class apollo.dataadapter.das.DASAdapter
- getInputType() - Method in class apollo.dataadapter.das.DASAdapter
- getLabel() - Method in interface apollo.dataadapter.das.DASFeature
- getLength() - Method in interface apollo.dataadapter.das.DASSegment
- getMapMaster() - Method in interface apollo.dataadapter.das.DASDsn
- getMethodId() - Method in interface apollo.dataadapter.das.DASFeature
- getMethodLabel() - Method in interface apollo.dataadapter.das.DASFeature
- getName() - Method in class apollo.dataadapter.das.DASAdapter
- getNote() - Method in interface apollo.dataadapter.das.DASFeature
- getOrientation() - Method in interface apollo.dataadapter.das.DASFeature
- getOrientation() - Method in interface apollo.dataadapter.das.DASSegment
- getPhase() - Method in interface apollo.dataadapter.das.DASFeature
- getProperties() - Method in class apollo.dataadapter.das.DASAdapterGUI
- getRawAnalysisResults(String) - Method in class apollo.dataadapter.das.DASAdapter
- getResiduesFromSourceImpl(int, int) - Method in class apollo.dataadapter.das.DASLazySequence
- Returns the sequence string
- getScore() - Method in interface apollo.dataadapter.das.DASFeature
- getSegment() - Method in class apollo.dataadapter.das.DASLazySequence
- getSegment() - Method in interface apollo.dataadapter.das.DASSegment
- getSelectedHistory() - Method in class apollo.dataadapter.das.DASAdapterGUI
- getSelectedSeq() - Method in class apollo.dataadapter.das.DASAdapterGUI
- getSelectedServer() - Method in class apollo.dataadapter.das.DASAdapterGUI
- getSequence(String) - Method in class apollo.dataadapter.das.DASAdapter
- getSequence(DbXref) - Method in class apollo.dataadapter.das.DASAdapter
- getSequence(DbXref, int, int) - Method in class apollo.dataadapter.das.DASAdapter
- getSequences(DbXref[]) - Method in class apollo.dataadapter.das.DASAdapter
- getSequences(DbXref[], int[], int[]) - Method in class apollo.dataadapter.das.DASAdapter
- getSequences(DASDsn, DASSegment[]) - Method in interface apollo.dataadapter.das.DASServerI
- getServer() - Method in class apollo.dataadapter.das.DASLazySequence
- getSource() - Method in interface apollo.dataadapter.das.DASDsn
- getSourceId() - Method in interface apollo.dataadapter.das.DASDsn
- getSourceVersion() - Method in interface apollo.dataadapter.das.DASDsn
- getStart() - Method in interface apollo.dataadapter.das.DASFeature
- getStart() - Method in interface apollo.dataadapter.das.DASSegment
- getStart() - Method in interface apollo.dataadapter.das.DASSequence
- getStateInformation() - Method in class apollo.dataadapter.das.DASAdapter
- getStop() - Method in interface apollo.dataadapter.das.DASSegment
- getStop() - Method in interface apollo.dataadapter.das.DASSequence
- getSubSequence(int, int) - Method in class apollo.dataadapter.das.DASLazySequence
- getSubparts() - Method in interface apollo.dataadapter.das.DASSegment
- getSupportedOperations() - Method in class apollo.dataadapter.das.DASAdapter
- getTargetId() - Method in interface apollo.dataadapter.das.DASFeature
- getTargetStart() - Method in interface apollo.dataadapter.das.DASFeature
- getTargetStop() - Method in interface apollo.dataadapter.das.DASFeature
- getType() - Method in class apollo.dataadapter.das.DASAdapter
- getTypeCategory() - Method in interface apollo.dataadapter.das.DASFeature
- getTypeId() - Method in interface apollo.dataadapter.das.DASFeature
- getTypeLabel() - Method in interface apollo.dataadapter.das.DASFeature
- getTypeReference() - Method in interface apollo.dataadapter.das.DASFeature
- getTypeSubparts() - Method in interface apollo.dataadapter.das.DASFeature
- getUI(IOOperation) - Method in class apollo.dataadapter.das.DASAdapter
- getURL() - Method in interface apollo.dataadapter.das.DASServerI
- getVersion() - Method in interface apollo.dataadapter.das.DASSequence
H
- hiLabel - Variable in class apollo.dataadapter.das.DASAdapterGUI
- hiTextBox - Variable in class apollo.dataadapter.das.DASAdapterGUI
- high - Variable in class apollo.dataadapter.das.DASAdapter
- historyLabel - Variable in class apollo.dataadapter.das.DASAdapterGUI
- historyList - Variable in class apollo.dataadapter.das.DASAdapterGUI
- historyVector - Variable in class apollo.dataadapter.das.DASAdapterGUI
- history_listener - Variable in class apollo.dataadapter.das.DASAdapterGUI
I
- init() - Method in class apollo.dataadapter.das.DASAdapter
- initAnalysis(Feature, StrandedFeatureSetI, Hashtable, Hashtable) - Method in class apollo.dataadapter.das.DASAdapter
- initResult(Feature, FeatureSetI, CurationSet, Hashtable) - Method in class apollo.dataadapter.das.DASAdapter
- initSpan(Feature, FeatureSetI) - Method in class apollo.dataadapter.das.DASAdapter
- itemStateChanged(ItemEvent) - Method in class apollo.dataadapter.das.DASAdapterGUI.SeqListener
- itemStateChanged(ItemEvent) - Method in class apollo.dataadapter.das.DASAdapterGUI.ServerListener
K
- keyTyped(KeyEvent) - Method in class apollo.dataadapter.das.DASAdapterGUI.LongValidator
L
- low - Variable in class apollo.dataadapter.das.DASAdapter
- lowLabel - Variable in class apollo.dataadapter.das.DASAdapterGUI
- lowTextBox - Variable in class apollo.dataadapter.das.DASAdapterGUI
M
- MAX_HISTORY_LENGTH - Static variable in class apollo.dataadapter.das.DASAdapterGUI
O
- op - Variable in class apollo.dataadapter.das.DASAdapterGUI
P
- posValidator - Variable in class apollo.dataadapter.das.DASAdapterGUI
- printFeatureInfo(Feature) - Method in class apollo.dataadapter.das.DASAdapter
- props - Variable in class apollo.dataadapter.das.DASAdapterGUI
S
- segment - Variable in class apollo.dataadapter.das.DASLazySequence
- seqLabel - Variable in class apollo.dataadapter.das.DASAdapterGUI
- seqList - Variable in class apollo.dataadapter.das.DASAdapterGUI
- seq_id - Variable in class apollo.dataadapter.das.DASAdapter
- seq_listener - Variable in class apollo.dataadapter.das.DASAdapterGUI
- sequenceHash - Variable in class apollo.dataadapter.das.DASAdapterGUI
- sequenceVector - Variable in class apollo.dataadapter.das.DASAdapterGUI
- server - Variable in class apollo.dataadapter.das.DASAdapter
- server - Variable in class apollo.dataadapter.das.DASLazySequence
- serverLabel - Variable in class apollo.dataadapter.das.DASAdapterGUI
- serverList - Variable in class apollo.dataadapter.das.DASAdapterGUI
- serverVector - Variable in class apollo.dataadapter.das.DASAdapterGUI
- server_listener - Variable in class apollo.dataadapter.das.DASAdapterGUI
- setDNA(String) - Method in interface apollo.dataadapter.das.DASSequence
- setDNALength(String) - Method in interface apollo.dataadapter.das.DASSequence
- setDataAdapter(DataAdapter) - Method in class apollo.dataadapter.das.DASAdapterGUI
- setDescription(String) - Method in interface apollo.dataadapter.das.DASDsn
- setEnd(String) - Method in interface apollo.dataadapter.das.DASFeature
- setFont(Font) - Method in class apollo.dataadapter.das.DASAdapterGUI
- setGroupId(String) - Method in interface apollo.dataadapter.das.DASFeature
- setGroupTargetStart(String) - Method in interface apollo.dataadapter.das.DASFeature
- setGroupTargetStop(String) - Method in interface apollo.dataadapter.das.DASFeature
- setHigh(int) - Method in class apollo.dataadapter.das.DASAdapter
- setId(String) - Method in interface apollo.dataadapter.das.DASFeature
- setId(String) - Method in interface apollo.dataadapter.das.DASSegment
- setId(String) - Method in interface apollo.dataadapter.das.DASSequence
- setLabel(String) - Method in interface apollo.dataadapter.das.DASFeature
- setLength(String) - Method in interface apollo.dataadapter.das.DASSegment
- setLow(int) - Method in class apollo.dataadapter.das.DASAdapter
- setMapMaster(String) - Method in interface apollo.dataadapter.das.DASDsn
- setMethodId(String) - Method in interface apollo.dataadapter.das.DASFeature
- setMethodLabel(String) - Method in interface apollo.dataadapter.das.DASFeature
- setNote(String) - Method in interface apollo.dataadapter.das.DASFeature
- setOrientation(String) - Method in interface apollo.dataadapter.das.DASFeature
- setOrientation(String) - Method in interface apollo.dataadapter.das.DASSegment
- setPhase(String) - Method in interface apollo.dataadapter.das.DASFeature
- setProperties(Properties) - Method in class apollo.dataadapter.das.DASAdapterGUI
- setRange(SeqFeatureI, String, int, int) - Method in class apollo.dataadapter.das.DASAdapter
- setRegion(String) - Method in class apollo.dataadapter.das.DASAdapter
- setScore(String) - Method in interface apollo.dataadapter.das.DASFeature
- setSegment(String) - Method in interface apollo.dataadapter.das.DASSegment
- setSelection(String, Vector, JComboBox) - Method in class apollo.dataadapter.das.DASAdapterGUI
- setSequence(String, DASSequence) - Method in class apollo.dataadapter.das.DASAdapter
- setServer(String) - Method in class apollo.dataadapter.das.DASAdapter
- setSource(String) - Method in interface apollo.dataadapter.das.DASDsn
- setSourceId(String) - Method in interface apollo.dataadapter.das.DASDsn
- setSourceVersion(String) - Method in interface apollo.dataadapter.das.DASDsn
- setStart(String) - Method in interface apollo.dataadapter.das.DASFeature
- setStart(String) - Method in interface apollo.dataadapter.das.DASSegment
- setStart(String) - Method in interface apollo.dataadapter.das.DASSequence
- setStateInformation(Properties) - Method in class apollo.dataadapter.das.DASAdapter
- setStop(String) - Method in interface apollo.dataadapter.das.DASSegment
- setStop(String) - Method in interface apollo.dataadapter.das.DASSequence
- setSubparts(String) - Method in interface apollo.dataadapter.das.DASSegment
- setTargetId(String) - Method in interface apollo.dataadapter.das.DASFeature
- setTargetStart(String) - Method in interface apollo.dataadapter.das.DASFeature
- setTargetStop(String) - Method in interface apollo.dataadapter.das.DASFeature
- setTypeCategory(String) - Method in interface apollo.dataadapter.das.DASFeature
- setTypeId(String) - Method in interface apollo.dataadapter.das.DASFeature
- setTypeLabel(String) - Method in interface apollo.dataadapter.das.DASFeature
- setTypeReference(String) - Method in interface apollo.dataadapter.das.DASFeature
- setTypeSubparts(String) - Method in interface apollo.dataadapter.das.DASFeature
- setURL(String) - Method in class apollo.dataadapter.das.DASClient
- setURL(String) - Method in interface apollo.dataadapter.das.DASServerI
- setVersion(String) - Method in interface apollo.dataadapter.das.DASSequence
- supportedOperations - Variable in class apollo.dataadapter.das.DASAdapter
U
- updateSequences() - Method in class apollo.dataadapter.das.DASAdapterGUI
- url - Variable in class apollo.dataadapter.das.DASClient
V
_
- _beep() - Method in class apollo.dataadapter.das.DASAdapterGUI
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