GenericLoadParseQueryXML (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- spim.fiji.plugin.queryXML.GenericLoadParseQueryXML<AS,S,V,D,L,X>

Type Parameters:: AS -; S -; V -; D -; L -

Direct Known Subclasses:: LoadParseQueryXML

public class GenericLoadParseQueryXML<AS extends AbstractSpimData<S>,S extends AbstractSequenceDescription<V,D,L>,V extends BasicViewSetup,D extends BasicViewDescription<V>,L extends BasicImgLoader,X extends XmlIoAbstractSpimData<S,AS>>
extends Object

Interface for interactive parsing of spimdata XMLs

Author:: Stephan Preibisch (stephan.preibisch@gmx.de)

Field Summary

Fields
Modifier and Type	Field and Description
`protected HashMap<String,List<Entity>>`	`allAttributeInstances`
`protected HashMap<String,Integer>`	`attributeChoice`
`protected static String[]`	`attributeChoiceList`
`protected HashMap<String,List<Entity>>`	`attributeInstancesToProcess`
`protected ArrayList<String>`	`attributes`
`protected String`	`buttonText`
`protected String`	`clusterExt`
`static String[]`	`clusterOptions1`
`protected Color`	`color`
`protected Comparator<String>`	`comparator`
`protected AS`	`data`
`static boolean`	`debugRandomClusterHash`
`static HashMap<String,Integer>`	`defaultAttributeChoice`
`static HashMap<String,Integer>`	`defaultAttributeEntityIndex`
`static HashMap<String,String>`	`defaultAttributePatternString`
`static HashMap<String,boolean[]>`	`defaultAttributeSelectedEntities`
`static int`	`defaultClusterOption1`
`static String`	`defaultXMLfilename`
`protected static String`	`errorMsg1`
`protected GenericDialog`	`gd`
`protected static String`	`goodMsg1`
`protected X`	`io`
`protected ActionListener`	`listener`
`protected String`	`message1`
`protected String`	`message2`
`protected static String`	`neutralMsg1`
`protected static String`	`noMsg2`
`protected boolean`	`returnfalse`
`protected ArrayList<TimePoint>`	`timepointsToProcess`
`protected static String`	`warningMsg1`
`protected String`	`xmlfilename`

Constructor Summary

Constructors
Constructor and Description

GenericLoadParseQueryXML(X io)
Constructor for the class needs an appropriate IO module

Constructors
Constructor and Description
`GenericLoadParseQueryXML(X io)` Constructor for the class needs an appropriate IO module

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addButton(String buttonText, ActionListener listener)`
`protected void`	`addListeners(GenericDialog gd, TextField tf, Label label1, Label label2)`
`protected static String[]`	`buildEntityList(String attributeName, List<? extends Entity> entityList, boolean addTitle)`
`protected static String[]`	`buildTimepointList(List<TimePoint> tpList, boolean addTitle)`
`protected String`	`createUniqueName()`
`String`	`getClusterExtension()`
`Comparator<String>`	`getComparator()`
`AS`	`getData()`
`GenericDialog`	`getGenericDialog()`
`X`	`getIO()`
`List<TimePoint>`	`getTimePointsToProcess()`
`ArrayList<V>`	`getViewSetupsToProcess()`
`String`	`getXMLFileName()`
`protected static String[]`	`makeChoiceList(String attribute)`
`protected AS`	`parseXML(String xmlFilename)`
`protected <E extends Entity> boolean`	`query(int choice, String attribute, List<E> allEntities, List<E> entitiesToProcess)`
`protected boolean`	`queryDetails()`
`static int`	`queryIndividualEntry(String name, String[] list, int defaultSelection)` Querys a single element from the list
`static boolean[]`	`queryMultipleEntries(String name, String[] list, boolean[] defaultSelection)` Querys a multiple element from the list
`static boolean[]`	`queryPattern(String name, String[] list, String[] defaultSelectionArray)` Querys a pattern of element from the list
`boolean`	`queryXML()`
`boolean`	`queryXML(List<String> specifyAttributes)`
`boolean`	`queryXML(String query)`
`boolean`	`queryXML(String query, List<String> specifyAttributes)`
`boolean`	`queryXML(String additionalTitle, String query, List<String> specifyAttributes)` Asks the user for a valid XML (real time parsing)
`void`	`setComparator(Comparator<String> comparator)` Sets the comparator used to sort the Attributes in a specific order for display, can be null Note that Timepoint (XmlKeys.TIMEPOINTS_TIMEPOINT_TAG) is always the last entry no matter what as it is special
`void`	`setReturnFalse(boolean value)`
`protected boolean`	`tryParsing(String xmlfile, boolean parseAllTypes)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

defaultXMLfilename

public static String defaultXMLfilename

debugRandomClusterHash

public static boolean debugRandomClusterHash

goodMsg1
```
protected static String goodMsg1
```

warningMsg1
```
protected static String warningMsg1
```

errorMsg1
```
protected static String errorMsg1
```

neutralMsg1
```
protected static String neutralMsg1
```

noMsg2
```
protected static String noMsg2
```

attributeChoiceList

protected static String[] attributeChoiceList

clusterOptions1

public static final String[] clusterOptions1

defaultClusterOption1

public static int defaultClusterOption1

defaultAttributeChoice

public static HashMap<String,Integer> defaultAttributeChoice

defaultAttributeEntityIndex

public static HashMap<String,Integer> defaultAttributeEntityIndex

defaultAttributePatternString

public static HashMap<String,String> defaultAttributePatternString

defaultAttributeSelectedEntities

public static HashMap<String,boolean[]> defaultAttributeSelectedEntities

attributeChoice

protected HashMap<String,Integer> attributeChoice

io

protected final X extends XmlIoAbstractSpimData<S,AS> io

comparator

protected Comparator<String> comparator

message1
```
protected String message1
```

message2
```
protected String message2
```

color
```
protected Color color
```

data

protected AS extends AbstractSpimData<S> data

xmlfilename
```
protected String xmlfilename
```

timepointsToProcess

protected ArrayList<TimePoint> timepointsToProcess

attributes
```
protected ArrayList<String> attributes
```

allAttributeInstances

protected HashMap<String,List<Entity>> allAttributeInstances

attributeInstancesToProcess

protected HashMap<String,List<Entity>> attributeInstancesToProcess

clusterExt
```
protected String clusterExt
```

buttonText
```
protected String buttonText
```

listener
```
protected ActionListener listener
```

gd
```
protected GenericDialog gd
```

returnfalse
```
protected boolean returnfalse
```

Constructor Detail
- GenericLoadParseQueryXML
```
public GenericLoadParseQueryXML(X io)
```
  Constructor for the class needs an appropriate IO module
  
  Parameters:
  
  io -

Method Detail

getIO
```
public X getIO()
```
Returns:

the i/o object used to parse the XML

getData
```
public AS getData()
```
Returns:

the SpimData object parsed from the xml

getXMLFileName
```
public String getXMLFileName()
```
Returns:

The location of the xml file

getTimePointsToProcess
```
public List<TimePoint> getTimePointsToProcess()
```
Returns:

All timepoints that should be processed

getViewSetupsToProcess
```
public ArrayList<V> getViewSetupsToProcess()
```
Returns:

All ViewSetups that should be processed per timepoint (based on the selected attributes)

setComparator
```
public void setComparator(Comparator<String> comparator)
```
Sets the comparator used to sort the Attributes in a specific order for display, can be null Note that Timepoint (XmlKeys.TIMEPOINTS_TIMEPOINT_TAG) is always the last entry no matter what as it is special

Parameters:

comparator -

getComparator

public Comparator<String> getComparator()

queryXML
```
public boolean queryXML()
```

queryXML

public boolean queryXML(List<String> specifyAttributes)

queryXML

public boolean queryXML(String query)

queryXML

public boolean queryXML(String query,
                        List<String> specifyAttributes)

addButton

public void addButton(String buttonText,
                      ActionListener listener)

getGenericDialog

public GenericDialog getGenericDialog()

setReturnFalse

public void setReturnFalse(boolean value)

queryXML
```
public boolean queryXML(String additionalTitle,
                        String query,
                        List<String> specifyAttributes)
```
Asks the user for a valid XML (real time parsing)

Parameters:

specifyAttributes - - set of attributes the user should be asked if he/she wants to select a subset of them

Returns:

null if cancelled or timepointlistsize = 0

getClusterExtension
```
public String getClusterExtension()
```

createUniqueName
```
protected String createUniqueName()
```

queryIndividualEntry
```
public static int queryIndividualEntry(String name,
                                       String[] list,
                                       int defaultSelection)
```
Querys a single element from the list

Parameters:

name - - type of elements (e.g. "Timepoint")

list - - list of available elements

defaultSelection - - default selection

Returns:

the selection or -1 if cancelled

queryMultipleEntries

public static boolean[] queryMultipleEntries(String name,
                                             String[] list,
                                             boolean[] defaultSelection)

Querys a multiple element from the list

Parameters:: name - - type of elements (e.g. "Timepoints"); list - - list of available elements; defaultSelection - - default selection
Returns:: the selection or null if cancelled

queryPattern
```
public static boolean[] queryPattern(String name,
                                     String[] list,
                                     String[] defaultSelectionArray)
```
Querys a pattern of element from the list

Parameters:

name - - type of elements (e.g. "Timepoints")

list - - list of available elements

defaultSelectionArray - - default selection (array of size 1 to be able to return it)

Returns:

the selection or null if cancelled

query

protected <E extends Entity> boolean query(int choice,
                                           String attribute,
                                           List<E> allEntities,
                                           List<E> entitiesToProcess)

queryDetails
```
protected boolean queryDetails()
```

buildTimepointList

protected static String[] buildTimepointList(List<TimePoint> tpList,
                                             boolean addTitle)

buildEntityList

protected static String[] buildEntityList(String attributeName,
                                          List<? extends Entity> entityList,
                                          boolean addTitle)

makeChoiceList

protected static String[] makeChoiceList(String attribute)

tryParsing

protected boolean tryParsing(String xmlfile,
                             boolean parseAllTypes)

parseXML

protected AS parseXML(String xmlFilename)
               throws SpimDataException

Throws:: SpimDataException

addListeners

protected void addListeners(GenericDialog gd,
                            TextField tf,
                            Label label1,
                            Label label2)

Class GenericLoadParseQueryXML<AS extends AbstractSpimData<S>,S extends AbstractSequenceDescription<V,D,L>,V extends BasicViewSetup,D extends BasicViewDescription<V>,L extends BasicImgLoader,X extends XmlIoAbstractSpimData<S,AS>>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

defaultXMLfilename

debugRandomClusterHash

goodMsg1

warningMsg1

errorMsg1

neutralMsg1

noMsg2

attributeChoiceList

clusterOptions1

defaultClusterOption1

defaultAttributeChoice

defaultAttributeEntityIndex

defaultAttributePatternString

defaultAttributeSelectedEntities

attributeChoice

io

comparator

message1

message2

color

data

xmlfilename

timepointsToProcess

attributes

allAttributeInstances

attributeInstancesToProcess

clusterExt

buttonText

listener

gd

returnfalse

Constructor Detail

GenericLoadParseQueryXML

Method Detail

getIO

getData

getXMLFileName

getTimePointsToProcess

getViewSetupsToProcess

setComparator

getComparator

queryXML

queryXML

queryXML

queryXML

addButton

getGenericDialog

setReturnFalse

queryXML

getClusterExtension

createUniqueName

queryIndividualEntry

queryMultipleEntries

queryPattern

query

queryDetails

buildTimepointList

buildEntityList

makeChoiceList

tryParsing

parseXML

addListeners