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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--MJAbase | +--MJAstate
MAExplorer Open Java API class to access MJAstate methods and data structures. Access get and save state, get additional state info
List of methods available to Plugin-writers
------------------- GET FLAGS ------------------------ get_useDichromasyDisplayFlag() - get "useDichromasyDisplay" flag status get_gangSpotDuplicatesFlag) - get "gangSpotDuplicates" flag status get_presentationViewFlag() - get "presentationView" flag status get_viewFilteredSpotsFlag() - get "viewFilteredSpots" flag status get_useCy5OverCy3Flag() - get "useCy5OverCy3Flag" flag status get_useMouseOverFlag() - get "useMouseOver" flag status get_isZscoreNormFlag() - get "isZscoreNorm" flag status get_useExprProfileOverlayFlag() - get "useExprProfileOverlay" flag status get_updatePseudoArrayImageFlag() - get "updatePseudoArrayImage" flag status get_useRatioDataFlag() - get "useRatioData" flag status get_allowNegQuantDataFlag() - get "allowNegQuantData" flag status get_useHPxySetsDataFlag() - get "useHPxySetsData" flag status get_useHP_E_ListDataFlag() - get "useMeanHP_EdataFlag" flag status get_abortFlag() - get "abortFlag" flag status get_doGCflag() - get "doGCflag" flag status --------------------- SET FLAGS -------------------------------- set_useRatioDataFlag() - set "useRatioData" flag status set_updatePseudoArrayImageFlag() - set "updatePseudoArrayImage" flag status set_isZscoreNormFlag() - set "isZscoreNorm" flag status set_abortFlag() - set "abortFlag" flag status set_doGCflag() - set "doGCflag" flag status --------------------- Change Database --------------------------- openNewFileDB() - open a new .mae database file --------------------- MAEPlugins hash state storage ------------- getPluginHashState() - get state object value from MAEPlugin hash state storage. setPluginHashState() - set state object value from MAEPlugin hash state storage. flushPluginHashState() - flush the MAEPlugin hash state storage to the disk.
This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.
Method Summary | |
boolean |
flushPluginHashState()
flushPluginHashState() - flush the MAEPlugin hash state storage to the disk. |
boolean |
get_abortFlag()
get_abortFlag() - get "abortFlag" flag status |
boolean |
get_allowNegQuantDataFlag()
get_allowNegQuantDataFlag() - get "allowNegQuantData" flag status allow Negative Quantified intensity data |
boolean |
get_doGCFlag()
get_doGCFlag() - get "doGCflag" flag status invoke the Garbage Collector when have time as determined by the main idle loop |
boolean |
get_gangSpotDuplicatesFlag()
get_gangSpotDuplicatesFlag() - get "gangSpotDuplicates" flag status display and report ganged (F1,F2) data else just F1 data |
boolean |
get_isZscoreNormFlag()
get_isZscoreNormFlag() - get "isZscoreNorm" flag status using one of the Zscore normalizations |
boolean |
get_presentationViewFlag()
get_presentationViewFlag() - get "presentationView" flag status use larger fonts and graphics for presentations |
boolean |
get_updatePseudoImgFlag()
get_updatePseudoArrayImageFlag() - get "updatePseudoArrayImage" flag status. |
boolean |
get_useCy5OverCy3Flag()
get_useCy5OverCy3Flag() - get "useCy5OverCy3Flag" flag status Swap Cy3/Cy to Cy5/Cy3 for reporting purposes |
boolean |
get_useDichromasyDisplayFlag()
get_useDichromasyDisplayFlag() - get "useDichromasyDisplay" flag status enable Dichromasy color-blindness display options |
boolean |
get_useExprProfileOverlayFlag()
get_useExprProfileOverlayFlag() - get "useExprProfileOverlay" flag status Plot EP list as overlay 2Dplot else scrollable EP list |
boolean |
get_useHP_E_ListDataFlag()
get_useHP_E_ListDataFlag() - get "useMeanHPeListDataFlag" flag status use mean HP-E 'list' data else single current HP sample data |
boolean |
get_useHPxySetsDataFlag()
get_useHPxySetsDataFlag() - get "useHPxySetsData" flag status use mean HP-X,Y 'sets' data else HP-X,HP-Y single samples data |
boolean |
get_useMouseOverFlag()
get_useMouseOverFlag() - get "useMouseOver" flag status |
boolean |
get_useRatioDataFlag()
get_useRatioDataFlag() - get "useRatioData" flag status data is Cy3/Cy5 ratio else Intensity |
boolean |
get_viewFilteredSpotsFlag()
get_viewFilteredSpotsFlag() - get "viewFilteredSpots" flag status in PseudoArray image show Filtered spots else don't show overlays |
java.lang.String |
getDbEstURL()
getDbEstURL() - get the current url value |
java.lang.String |
getGbid2LocusLinkURL()
getGbid2LocusLinkURL() - get the current url value |
java.lang.String |
getGenBankCloneURL()
getGenBankCloneURL() - get the current url value |
java.lang.String |
getGenBankCloneURLepilogue()
getGenBankCloneURLepilogue() - get the current url value |
java.lang.String |
getGeneBankAccURL()
getGenBankAccURL() - get the current url value |
java.lang.String |
getGeneCardURL()
getGeneCardURL() - get the current url value |
java.lang.String |
getIMAGE2GenBankURL()
getIMAGE2GenBankURL() - get the current url value |
java.lang.String |
getIMAGE2unigeneURL()
getIMAGE2unigeneURL() - get the current url value |
java.lang.String |
getLocusLinkURL()
getLocusLinkURL() - get the current url value |
java.lang.String |
getMAdbURL()
getMAdbURL() - get the current url value |
java.lang.String |
getMedMinerURL()
getMedMinerURL() - get the current url value |
java.lang.String |
getMedMinerURLepilogue()
getMedMinerURLepilogue() - get the current url value |
java.lang.String |
getPirURL()
getPirURL() - get the current url value |
java.lang.Object |
getPluginHashState(java.lang.String pluginName,
java.lang.String varName)
getPluginHashState() - get state object value from MAEPlugin hash state storage. |
boolean |
getPluginHashState(java.lang.String pluginName,
java.lang.String varName,
boolean defValue)
getPluginHashState() - get boolean state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store. |
byte |
getPluginHashState(java.lang.String pluginName,
java.lang.String varName,
byte defValue)
getPluginHashState() - get byte state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store. |
double |
getPluginHashState(java.lang.String pluginName,
java.lang.String varName,
double defValue)
getPluginHashState() - get double state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store. |
float |
getPluginHashState(java.lang.String pluginName,
java.lang.String varName,
float defValue)
getPluginHashState() - get float state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store. |
int |
getPluginHashState(java.lang.String pluginName,
java.lang.String varName,
int defValue)
getPluginHashState() - get int state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store. |
long |
getPluginHashState(java.lang.String pluginName,
java.lang.String varName,
long defValue)
getPluginHashState() - get long state value from MAEPlugin hash state storage This looks for a symbol with the name (pluginName + "." + varName) in the global hash store. |
java.lang.String |
getPluginHashStateFileName()
getPluginHashStateFileName() - get the MAEPlugin hash state disk file name. |
java.lang.String |
getSwissProtURL()
getSwissProtURL() - get the current url value |
java.lang.String |
getUniGeneClusterIdURL()
getUniGeneClusterIdURL() - get the current url value |
java.lang.String |
getUniGeneURL()
getUniGeneURL() - get the current url value |
boolean |
openNewFileDB(java.lang.String dbMAEdir,
java.lang.String maeFilename,
boolean saveOldDBfileFlag)
openNewFileDB() - open a new .mae database file. |
void |
set_abortFlag(boolean flag)
set_abortFlag() - set "abortFlag" flag status |
void |
set_doGCflag(boolean flag)
set_doGCFlag() - set "doGCflag" flag status to invoke the Garbage Collector when have time as determined by main idle loop. |
void |
set_isZscoreNorm(boolean flag)
set_isZscoreNormFlag() - set "isZscoreNorm" flag status using one of the Zscore normalizations. |
void |
set_updatePseudoImgFlag(boolean flag)
set_updatePseudoArrayImageFlag() - set "updatePseudoArrayImage" flag status. |
void |
setDbEstURL(java.lang.String url)
setDbEstURL() - set the url |
void |
setGbid2LocusLinkURL(java.lang.String url)
setGbid2LocusLinkURL() - set the url |
void |
setGenBankAccURL(java.lang.String url)
setGenBankAccURL() - set the url |
void |
setGenBankCloneURL(java.lang.String url)
setGenBankCloneURL() - set the url |
void |
setGenBankCloneURLepilogue(java.lang.String url)
setGenBankCloneURLepilogue() - set the url |
void |
setGeneCardURL(java.lang.String url)
setGeneCardURL() - set the url |
void |
setIMAGE2GenBankURL(java.lang.String url)
setIMAGE2GenBankURL() - set the url |
void |
setIMAGE2unigeneURL(java.lang.String url)
setIMAGE2unigeneURL() - set the url |
void |
setLocusLinkURL(java.lang.String url)
setLocusLinkURL() - set the url |
void |
setMAdbURL(java.lang.String url)
setMAdbURL() - set the url |
void |
setMedMinerURL(java.lang.String url)
setMedMinerURL() - set the url |
void |
setMedMinerURLepilogue(java.lang.String url)
setMedMinerURLepilogue() - set the url |
void |
setPirURL(java.lang.String url)
setPirURL() - set the url |
boolean |
setPluginHashState(java.lang.String pluginName,
java.lang.String varName,
java.lang.Object value)
setPluginHashState() - set state object value from MAEPlugin hash state storage. |
void |
setSwissProtURL(java.lang.String url)
setSwissProtURL() - set the url |
void |
setUniGeneClusterIdURL(java.lang.String url)
setUniGeneClusterIdURL() - set the url |
void |
setUniGeneURL(java.lang.String url)
setUniGeneURL() - set the url |
Methods inherited from class MJAbase |
cvtHashtable2SimpleTable, cvtTable2Hashtable |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
public final boolean get_useDichromasyDisplayFlag()
public final boolean get_gangSpotDuplicatesFlag()
public final boolean get_presentationViewFlag()
public final boolean get_viewFilteredSpotsFlag()
public final boolean get_useCy5OverCy3Flag()
public final boolean get_useMouseOverFlag()
public final boolean get_isZscoreNormFlag()
public final boolean get_useExprProfileOverlayFlag()
public final boolean get_useRatioDataFlag()
public final boolean get_allowNegQuantDataFlag()
public final boolean get_useHPxySetsDataFlag()
public final boolean get_useHP_E_ListDataFlag()
public final boolean get_updatePseudoImgFlag()
public final boolean get_abortFlag()
public final boolean get_doGCFlag()
public final void set_updatePseudoImgFlag(boolean flag)
public final void set_isZscoreNorm(boolean flag)
public final void set_abortFlag(boolean flag)
public final void set_doGCflag(boolean flag)
public final boolean openNewFileDB(java.lang.String dbMAEdir, java.lang.String maeFilename, boolean saveOldDBfileFlag)
dbMAEdir
- - full path of the new database MAE/ 'project' directory.
E.g. "C:/user/test/MAE/" (with appropriate delimiters for the OS you are using).maeFilename
- - name of the .mae startup file to be started
E.g. "Start.mae"saveOldDBfileFlag
- - if set, then save the old DB firstpublic final void setGenBankAccURL(java.lang.String url)
url
- to setpublic final java.lang.String getGeneBankAccURL()
public final void setDbEstURL(java.lang.String url)
url
- to setpublic final java.lang.String getDbEstURL()
public final void setGenBankCloneURL(java.lang.String url)
url
- to setpublic final java.lang.String getGenBankCloneURL()
public final void setGenBankCloneURLepilogue(java.lang.String url)
url
- to setpublic final java.lang.String getGenBankCloneURLepilogue()
public final void setIMAGE2GenBankURL(java.lang.String url)
url
- to setpublic final java.lang.String getIMAGE2GenBankURL()
public final void setIMAGE2unigeneURL(java.lang.String url)
url
- to setpublic final java.lang.String getIMAGE2unigeneURL()
public final void setMAdbURL(java.lang.String url)
url
- to setpublic final java.lang.String getMAdbURL()
public final void setUniGeneURL(java.lang.String url)
url
- to setpublic final java.lang.String getUniGeneURL()
public final void setUniGeneClusterIdURL(java.lang.String url)
url
- to setpublic final java.lang.String getUniGeneClusterIdURL()
public final void setGeneCardURL(java.lang.String url)
url
- to setpublic final java.lang.String getGeneCardURL()
public final void setGbid2LocusLinkURL(java.lang.String url)
url
- to setpublic final java.lang.String getGbid2LocusLinkURL()
public final void setLocusLinkURL(java.lang.String url)
url
- to setpublic final java.lang.String getLocusLinkURL()
public final void setSwissProtURL(java.lang.String url)
url
- to setpublic final java.lang.String getSwissProtURL()
public final void setPirURL(java.lang.String url)
url
- to setpublic final java.lang.String getPirURL()
public final void setMedMinerURL(java.lang.String url)
url
- to setpublic final java.lang.String getMedMinerURL()
public final void setMedMinerURLepilogue(java.lang.String url)
url
- to setpublic final java.lang.String getMedMinerURLepilogue()
public int getPluginHashState(java.lang.String pluginName, java.lang.String varName, int defValue)
pluginName
- of pluginvarName
- of variable in the plugindefValue
- is the default value of variable if not found in hash storepublic byte getPluginHashState(java.lang.String pluginName, java.lang.String varName, byte defValue)
pluginName
- of pluginvarName
- of variable in the plugindefValue
- is the default value of variable if not found in hash storepublic boolean getPluginHashState(java.lang.String pluginName, java.lang.String varName, boolean defValue)
pluginName
- of pluginvarName
- of variable in the plugindefValue
- is the default value of variable if not found in hash storepublic long getPluginHashState(java.lang.String pluginName, java.lang.String varName, long defValue)
pluginName
- of pluginvarName
- of variable in the plugindefValue
- is the default value of variable if not found in hash storepublic float getPluginHashState(java.lang.String pluginName, java.lang.String varName, float defValue)
pluginName
- of pluginvarName
- of variable in the plugindefValue
- is the default value of variable if not found in hash storepublic double getPluginHashState(java.lang.String pluginName, java.lang.String varName, double defValue)
pluginName
- of pluginvarName
- of variable in the plugindefValue
- is the default value of variable if not found in hash storepublic java.lang.Object getPluginHashState(java.lang.String pluginName, java.lang.String varName)
pluginName
- of pluginvarName
- of variable in the pluginpublic boolean setPluginHashState(java.lang.String pluginName, java.lang.String varName, java.lang.Object value)
pluginName
- of pluginvarName
- of variable in the pluginvalue
- of object to savepublic java.lang.String getPluginHashStateFileName()
public boolean flushPluginHashState()
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