### Get Service Setup Options - Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/databaseservice/SequenceDatabaseSuperService.html

Provides optional configuration settings for setting up or configuring the service. These options are displayed to the user in the interface. If the service requires setup, these options must allow for it. Returns null if no setup options are required.

```java
public Options getSetupOptions()
```

--------------------------------

### SequenceDatabaseSuperService - Apply Setup Options

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/databaseservice/class-use/DatabaseServiceException.html

Applies and saves the specified setup options to the service.

```APIDOC
## POST /sequenceDatabaseSuperService/applySetupOptions

### Description
Applies and saves the provided setup options to the SequenceDatabaseSuperService.

### Method
POST

### Endpoint
/sequenceDatabaseSuperService/applySetupOptions

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
- **setupOptions** (Options) - Required - The setup options to apply.
- **progressListener** (jebl.util.ProgressListener) - Required - A listener for progress updates.

### Request Example
```json
{
  "setupOptions": { ... },
  "progressListener": null
}
```

### Response
#### Success Response (200)
- **void** - This method does not return a value upon successful execution.

#### Response Example
(No response body for void methods)
```

--------------------------------

### Apply Service Setup Options - Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/databaseservice/SequenceDatabaseSuperService.html

Applies and saves the provided setup options. This method is invoked after user interaction with options from getSetupOptions(). It can also handle the initial setup of the service if isSetUp() returns false. It uses a ProgressListener for progress reporting and cancellation.

```java
public void applySetupOptions(Options setupOptions, jebl.util.ProgressListener progressListener) throws DatabaseServiceException
```

--------------------------------

### Sequence Database Service Configuration (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/databaseservice/SequenceDatabaseSuperService.html

Methods related to the configuration and setup of sequence databases. This includes applying setup options, retrieving options for adding databases, and checking if the service is set up. It also allows for overriding default behavior for displaying setup options.

```java
void applySetupOptions​(Options setupOptions, jebl.util.ProgressListener progressListener)

```

```java
Options getAddDatabaseOptions​(DatabaseService.SequenceSearchQueryType databaseType)

```

```java
Options getSetupOptions()

```

```java
boolean isSetUp()

```

--------------------------------

### Java: Get Help for Finding Program

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/GeneiousGridDocumentOperation.html

This method provides an HTML fragment containing instructions for users on how to download the necessary program for local runs. If no specific help is available, it should return null. This is useful for guiding users through setup.

```java
public java.lang.String getHelpForFindingProgram()
```

--------------------------------

### Renaming Example Plugins with Ant Task

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/index.html

Demonstrates how to use the `copyPluginAndRename` Ant task to rename an example plugin. This is a common step when starting a new plugin development based on an existing example.

```xml
<target name="copyPluginAndRename">
    <copy todir="newPluginName" overwrite="true" preservelastmodified="true">
        <fileset dir="examplePluginDir"/>
    </copy>
    <replace dir="newPluginName" token="examplePluginName" value="newPluginName"/>
</target>
```

--------------------------------

### GET /services

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/class-use/GeneiousService.html

Lists all currently installed Geneious services available in the application.

```APIDOC
## GET /services

### Description
Returns a list of all installed GeneiousServices currently registered in the system.

### Method
GET

### Endpoint
/services

### Response
#### Success Response (200)
- **services** (List<GeneiousService>) - A list of all installed services.

#### Response Example
{
  "services": [
    {
      "id": "com.biomatters.geneious.ncbi",
      "name": "NCBI"
    },
    {
      "id": "com.biomatters.geneious.local",
      "name": "Local"
    }
  ]
}
```

--------------------------------

### Method Detail

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/ConstructorWrapper.html

Provides detailed information about the newInstance method.

```APIDOC
## Method Detail

### newInstance

```java
public java.lang.Object newInstance()
```
```

--------------------------------

### Get Start Index of Trailing Gaps

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/SequenceUtilities.html

Determines the start index of the trailing gap characters ('-') in a CharSequence. This index represents the position where the trailing gaps begin.

```java
public static int getTrailingGapsStartIndex(java.lang.CharSequence charSequence)
```

--------------------------------

### Create GTextPane Instances

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/components/GTextPane.html

Demonstrates the constructor usage for initializing a GTextPane component, either empty, with initial text, or with a specific StyledDocument.

```java
GTextPane pane = new GTextPane();
GTextPane paneWithText = new GTextPane("Initial text");
GTextPane paneWithDoc = new GTextPane(new javax.swing.text.DefaultStyledDocument());
```

--------------------------------

### Get Interval Start (Inclusive)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/Interval.html

Retrieves the starting index of the interval, which is inclusive. This method returns a 0-based index representing the beginning of the interval.

```java
public int getFrom()
```

--------------------------------

### POST /options/component/create

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/Options.RadioOption.html

Initializes and returns a graphical component for the option.

```APIDOC
## POST /options/component/create

### Description
Creates a graphical component (JPanel) representing this option, initialized to the current value.

### Method
POST

### Endpoint
/options/component/create

### Response
#### Success Response (200)
- **component** (JPanel) - The graphical representation of the option.

#### Response Example
{
  "component": "[JPanel Instance]"
}
```

--------------------------------

### Get Codon Start Offset

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/SequenceAnnotation.html

Retrieves the offset of the first complete codon relative to the feature's start. This is indicated by the NCBI_CODON_START qualifier.

```java
int | getCodonStart()
```

--------------------------------

### Method Summary

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/ConstructorWrapper.html

Lists the methods available for the ConstructorWrapper class, including inherited methods.

```APIDOC
## Method Summary

All Methods | Instance Methods | Concrete Methods | Modifier and Type | Method | Description
---|---|---|---|---|---
`java.lang.Object` | | | | `newInstance()` | 

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

--------------------------------

### Initialize GEditorPane Constructors

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/components/GEditorPane.html

Demonstrates the different ways to instantiate a GEditorPane object. Options include a default constructor, loading content from a URL object, loading from a string URL, or initializing with a specific content type and text.

```java
public GEditorPane();

public GEditorPane(java.net.URL initialPage) throws java.io.IOException;

public GEditorPane(java.lang.String url) throws java.io.IOException;

public GEditorPane(java.lang.String type, java.lang.String text);
```

--------------------------------

### Get Missing Residues Before Chain Start (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/implementations/structure/PdbDocument.html

Calculates the number of residues preceding the start of a specified chain. The index parameter refers to the ATOM record numbering in the PDB file. Introduced in API 4.700.

```java
public int getChainMissingResiduesBefore(java.lang.String chainIdentifier, int index)
```

--------------------------------

### Get Residue Adjustment Details (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment.html

Provides methods to retrieve the details of a ResidueAdjustment. These methods allow you to get the start and end indices of the residues to be replaced or deleted, and the new residues to be inserted. It also provides a way to get a new sequence if the entire sequence was replaced.

```Java
public int getFirstResidueToReplaceInclusive()
```

```Java
public int getLastResidueToReplaceExclusive()
```

```Java
public java.lang.String getNewResidues()
```

```Java
public ImmutableSequence getNewSequence()
```

--------------------------------

### Constructor: Create WritableDatabaseServiceTree

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/WritableDatabaseServiceTree.html

Initializes a new GUI component to display and select writable database services.

```APIDOC
## Constructor: WritableDatabaseServiceTree

### Description
Creates a new GUI component that allows the user to choose a WritableDatabaseService from the provided root services.

### Parameters
- **roots** (List<WritableDatabaseService>) - Required - The list of root services to display.
- **showNumberOfDocumentsInFolder** (boolean) - Required - Whether to display document counts.
- **documentCountsByService** (Map<WritableDatabaseService, Integer>) - Required - A map containing document counts for each service.

### Request Example
new WritableDatabaseServiceTree(roots, true, countsMap);
```

--------------------------------

### Initialize DummyService

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/databaseservice/WritableDatabaseService.DummyService.html

Constructs a new instance of DummyService with a specified name, unique ID, and icon set. This service acts as a placeholder providing basic identification properties.

```java
public DummyService(java.lang.String name, java.lang.String rootUniqueId, Icons icons)
```

--------------------------------

### GET /sequence-viewer-extensions

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/PluginUtilities.html

Retrieves a list of all SequenceViewerExtension factories provided by currently installed plugins.

```APIDOC
## GET /sequence-viewer-extensions

### Description
Retrieves a list of all SequenceViewerExtension factories provided by all currently installed plugins.

### Method
GET

### Endpoint
/sequence-viewer-extensions

### Response
#### Success Response (200)
- **factories** (List<SequenceViewerExtension.Factory>) - A list of all available sequence viewer extension factories.

#### Response Example
[
  { "factoryName": "ExampleExtensionFactory" }
]
```

--------------------------------

### POST /WritableDatabaseService/DummyService

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/databaseservice/WritableDatabaseService.DummyService.html

Initializes a new dummy service instance which acts as a placeholder with specific naming and icons, providing no functional database operations.

```APIDOC
## POST /WritableDatabaseService/DummyService

### Description
Constructs a new dummy implementation of WritableDatabaseService. This is primarily used for UI elements where a service is required but no actual backend functionality is needed.

### Method
POST

### Endpoint
/WritableDatabaseService/DummyService

### Parameters
#### Request Body
- **name** (String) - Required - The display name of the service.
- **rootUniqueId** (String) - Required - A unique identifier for the root of the service.
- **icons** (Icons) - Required - The icon set to be associated with the service.

### Request Example
{
  "name": "My Dummy Service",
  "rootUniqueId": "com.example.dummy",
  "icons": "default_icon_set"
}

### Response
#### Success Response (200)
- **status** (String) - Confirmation of service initialization.

#### Response Example
{
  "status": "success",
  "serviceId": "com.example.dummy"
}
```

--------------------------------

### GET /operations

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/PluginUtilities.html

Methods for retrieving and managing document operations provided by installed plugins.

```APIDOC
## GET /operations/alignment

### Description
Get a DocumentOperation representation of an AlignmentOperation.

### Method
GET

### Endpoint
/operations/alignment

### Parameters
#### Query Parameters
- **uniqueIdPrefix** (String) - Required - The unique ID prefix for the operation.
- **alphabet** (SequenceDocument.Alphabet) - Required - The alphabet type for the alignment.

### Response
#### Success Response (200)
- **operation** (DocumentOperation) - The requested alignment operation.

## GET /operations/list

### Description
Get a list of all DocumentOperations provided by all currently installed plugins.

### Method
GET

### Endpoint
/operations/list

### Response
#### Success Response (200)
- **operations** (List<DocumentOperation>) - A list of available document operations.
```

--------------------------------

### Get Interval Properties

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/SequenceAnnotationInterval.html

Methods to retrieve the start, end, length, and index boundaries of a sequence annotation interval. These are fundamental for understanding the extent of an annotation on a sequence.

```java
int getFrom();
int getLength();
int getMaximumIndex();
int getMinimumIndex();
int getTo();
```

--------------------------------

### Initialize OligoSequenceDocument

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/implementations/sequence/OligoSequenceDocument.html

Demonstrates how to instantiate an OligoSequenceDocument either from an existing sequence document or by providing raw sequence data.

```java
// Create from existing sequence document
OligoSequenceDocument doc1 = new OligoSequenceDocument(sequenceDocument);

// Create from scratch
OligoSequenceDocument doc2 = new OligoSequenceDocument("Name", "Description", "ATGC", new java.util.Date());
```

--------------------------------

### Retrieve Operation Help

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/DocumentOperation.Wrapper.html

Returns help text in HTML or plain text format to guide users on how to use the operation.

```java
public java.lang.String getHelp() {
	return "Help text or HTML content";
}
```

--------------------------------

### Get Length of Leading Gaps

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/SequenceUtilities.html

Calculates the number of leading gap characters ('-') at the beginning of a CharSequence. This is equivalent to finding the start index of the first non-gap character.

```java
public static int getLeadingGapsLength(java.lang.CharSequence charSequence)
```

--------------------------------

### Initialize ButtonOption

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/Options.ButtonOption.html

Constructors for creating a ButtonOption instance. Options include XML-based initialization, full configuration with icons and alignment, or a simplified version with default centering.

```java
public ButtonOption(org.jdom.Element element) throws XMLSerializationException;

public ButtonOption(java.lang.String name, java.lang.String label, java.lang.String buttonLabel, javax.swing.Icon icon, int alignment);

public ButtonOption(java.lang.String name, java.lang.String label, java.lang.String buttonLabel);
```

--------------------------------

### Get Interval Minimum Index (Inclusive)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/Interval.html

Retrieves the minimum index of the interval, which is inclusive and 0-based. This represents the starting point of the interval.

```java
public int getMin()
```

--------------------------------

### Get Codon Start of Annotation (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/SequenceAnnotation.html

Retrieves the codon start value for a coding feature annotation. It returns the value of the NCBI_CODON_START qualifier if it's between 1 and 3, otherwise returns -1. This method is available since API 4.600 (Geneious 6.0.0).

```java
public int getCodonStart() {
    // Implementation details...
    return -1; // Placeholder
}
```

--------------------------------

### Check Service Setup Status - Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/databaseservice/SequenceDatabaseSuperService.html

Determines if the service is set up and ready for use. If this method returns false, the user cannot select the service as a search target until it is set up using getSetupOptions().

```java
public boolean isSetUp()
```

--------------------------------

### Get Trailing Gaps Start Index

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/SequenceCharSequence.html

Returns the index at which trailing gaps begin in a SequenceCharSequence. If no trailing gaps exist, it returns the sequence's length.

```java
public abstract int getTrailingGapsStartIndex()
```

--------------------------------

### Initialize and Configure EValue

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/implementations/EValue.html

Demonstrates how to instantiate the EValue class and configure the number of decimal places displayed in its string representation.

```java
EValue val = new EValue(0.000012345, 3);
val.setDecimalPlacesDisplayed(4);
System.out.println(val.toString());
```

--------------------------------

### Handle Circular Alignment Properties

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/implementations/DefaultAlignmentDocument.html

Methods to get and set the circular length of an alignment. The circular length defines the gapped length at which the alignment wraps back to the start.

```Java
public int getCircularLength()

public void setCircularLength(int circularLength)
```

--------------------------------

### Constructor Summary

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/ConstructorWrapper.html

Lists the constructors available for the ConstructorWrapper class.

```APIDOC
## Constructor Summary

Constructors | Description
---|---
`ConstructorWrapper​(java.lang.reflect.Constructor constructor)` |
```

--------------------------------

### Use Radio, Combo Box, and Listeners in Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/Options.html

This example illustrates the use of radio options, combo box options, and change listeners. It shows how to group related options, set up dependencies between them, and implement listeners to enforce validation rules, such as ensuring minimum values do not exceed maximum values.

```java
public class OptionsExample3 extends Options {
    private StringOption annotationType;
    private IntegerOption numberOfBasesToTrim;
    private RadioOption<TrimType> trimType;

    public static final TrimType trimByLength = new TrimType("trimByLength","By Length");
    public static final TrimType trimVectors = new TrimType("trimVectors","Vectors");

    public static final Sensitivity sensitivityHigh = new Sensitivity("high","UniVec (High sensitivity)","Recommended when the result will be inspected manually");
    public static final Sensitivity sensitivityLow = new Sensitivity("low","UniVec_Core (Few false positives)","Recommended for automated pipelines");

    private ComboBoxOption<Sensitivity> sensitivity;
    private IntegerOption minimum;
    private IntegerOption maximum;

    public OptionsExample3() {
        annotationType = addStringOption("annotationType","Annotation Type","CDS");
        annotationType.setDescription("The type of annotation to add to the sequence");

        trimType = addRadioOption("trimType","", Arrays.asList(trimByLength,trimVectors),trimByLength, Alignment.VERTICAL_ALIGN);

        numberOfBasesToTrim = addIntegerOption("numberOfBasesToTrim","Number of Bases",5);

        sensitivity = addComboBoxOption("sensitivity","Sensitivity", Arrays.asList(sensitivityHigh, sensitivityLow),sensitivityHigh);

        trimType.addDependent(trimByLength, numberOfBasesToTrim, true);
        trimType.addDependent(trimVectors, sensitivity, true);

        beginAlignHorizontally(null,false);
        minimum = addIntegerOption("min","Between",2,0,10);
        maximum = addIntegerOption("max","and",7,0,10);

        // Add change listeners to ensure that minimum<=maximum :
        minimum.addChangeListener(new SimpleListener() {
            public void objectChanged() {
                if (minimum.getValue()>maximum.getValue()) {
                    maximum.setValue(minimum.getValue());
                }
            }
        });
        maximum.addChangeListener(new SimpleListener() {
            public void objectChanged() {
                if (maximum.getValue()<minimum.getValue()) {
                    minimum.setValue(maximum.getValue());
                }
            }
        });
        endAlignHorizontally();
    }

    public Sensitivity getSensitivity() {
        return sensitivity.getValue();
    }

    public TrimType getTrimType() {
        return trimType.getValue();
    }
}
```

--------------------------------

### Get Writable Database Service Roots

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/PluginUtilities.html

Retrieves the root services for all installed WritableDatabaseServices. This includes local database roots, search result roots, and shared database roots.

```java
public static java.util.List<WritableDatabaseService> getWritableDatabaseServiceRoots()
```

--------------------------------

### Get All Geneious Services

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/PluginUtilities.html

Returns a list of all installed GeneiousServices, including parent and child services. This method retrieves services that may be unavailable or uninitialized, unlike getGeneiousService(String).

```java
public static java.util.List<GeneiousService> getGeneiousServices()
```

--------------------------------

### Implement DocumentOperation Options and Execution

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/DocumentOperation.Wrapper.html

Demonstrates how to define a custom Options class and implement the performOperation method to process documents. This pattern ensures that user-defined options are correctly cast and utilized during the operation execution.

```java
public List<AnnotatedPluginDocument> performOperation(AnnotatedPluginDocument[] documentList, ProgressListener progressListener, Options options) throws DocumentOperationException {
	MyOptions myOptions = (MyOptions) options;
	boolean sampleOptionSelected = myOptions.isSampleOption();
	// Perform logic here
	return null;
}
```

--------------------------------

### Initialize GMenuItem instances

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/components/GMenuItem.html

Demonstrates the various constructor overloads for creating a GMenuItem, allowing for initialization with text, icons, actions, or mnemonics. These constructors mirror the standard javax.swing.JMenuItem functionality.

```java
GMenuItem item1 = new GMenuItem();
GMenuItem item2 = new GMenuItem(icon);
GMenuItem item3 = new GMenuItem("Menu Text");
GMenuItem item4 = new GMenuItem(action);
GMenuItem item5 = new GMenuItem("Menu Text", icon);
GMenuItem item6 = new GMenuItem("Menu Text", KeyEvent.VK_M);
```

--------------------------------

### DocumentViewerFactory: Get Selection Signatures (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/DocumentViewerFactory.html

This method returns an array of DocumentSelectionSignature objects, specifying the types of documents a viewer can accept. In this example, it's configured to accept a single SequenceDocument.

```java
public DocumentSelectionSignature[] getSelectionSignatures(){
    return new DocumentSelectionSignature[]{new DocumentSelectionSignature(SequenceDocument.class,1,1)};
}
```

--------------------------------

### Get Next Selection Range (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/SequenceAnnotationGenerator.SelectionRange.html

Retrieves the next SelectionRange in a chained sequence of selections. This is useful when multiple regions are selected, for example, by ctrl-dragging in the sequence viewer. Returns null if there are no more subsequent ranges.

```java
public SequenceAnnotationGenerator.SelectionRange getNext()
```

--------------------------------

### POST /Label/Constructor

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/components/ProOnlyComponents.Label.html

Initializes a new Label component with specified text and optional license restriction indicators.

```APIDOC
## POST /Label/Constructor

### Description
Creates a new instance of a Label. The constructor allows for optional appending of restricted text based on license status.

### Method
POST

### Endpoint
/Label

### Parameters
#### Request Body
- **text** (String) - Required - The display text for the label.
- **showProOnlyText** (boolean) - Optional - If true, appends "(restricted)" to the label text when disabled due to missing license.

### Request Example
{
  "text": "Advanced Analysis",
  "showProOnlyText": true
}

### Response
#### Success Response (200)
- **status** (String) - Success message indicating component creation.
```

--------------------------------

### Constructor Detail

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/ConstructorWrapper.html

Provides detailed information about the ConstructorWrapper constructor.

```APIDOC
## Constructor Detail

### ConstructorWrapper

```java
public ConstructorWrapper(java.lang.reflect.Constructor constructor)
```
```

--------------------------------

### Interval Accessor Methods

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/Interval.html

Methods to retrieve the start and end points of an interval. Includes methods for getting the maximum and minimum values, with deprecated methods for compatibility and newer methods for clarity.

```java
getFrom()
getTo()
getMax()
getMaxExclusive()
getMaxInclusive()
getMin()
getToExclusive()
getToInclusive()
getLength()
```

--------------------------------

### Get Restricted Name (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/License.html

Retrieves the string used to identify Geneious when no active license is present. The parameter `upperCaseR` controls whether the returned string starts with an uppercase 'R' ('Restricted') or a lowercase 'r' ('restricted').

```java
public static String restrictedName(boolean upperCaseR)

```

--------------------------------

### POST /dialogs/showOptionsDialog

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/components/Dialogs.html

Displays an options dialog and optionally manages persistent storage for the options.

```APIDOC
## POST /dialogs/showOptionsDialog

### Description
Displays an options dialog based on an Options object. Blocks until the user clicks OK or Cancel.

### Method
POST

### Endpoint
/dialogs/showOptionsDialog

### Parameters
#### Request Body
- **options** (Options) - Required - The options to be displayed.
- **dialogTitle** (String) - Required - Title of the dialog and preference key.
- **restoreAndSavePreferences** (boolean) - Required - Whether to restore/save preferences to persistent storage.

### Response
#### Success Response (200)
- **result** (boolean) - false if user canceled, true if clicked OK.

### Response Example
{
  "result": true
}
```

--------------------------------

### Implement Service Metadata Hooks

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/databaseservice/WritableDatabaseService.DummyService.html

Methods for providing service-specific icons and help documentation. Subclasses should override these to integrate with the Geneious UI.

```java
protected Icons _getIcons() {
	// Implementation to return service icons
}

protected String _getHelp() {
	// Implementation to return help text
}
```

--------------------------------

### Get Operation Run Time - Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/OperationRecordDocument.html

Retrieves the start time of the operation as milliseconds since the epoch, obtained from System.currentTimeMillis(). Returns 0 if the time is unknown, which can occur during SnapGene lineage import.

```java
public long getTimeAtWhichOperationWasRun()

Returns: the start time of the operation - obtained from System.currentTimeMillis(). May be 0 if unknown (which happens when importing SnapGene lineage)
```

--------------------------------

### Get Total Sequence Frequency (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/SequenceViewerExtension.StateFrequencies.html

Retrieves the total frequency count of all states within a sequence. This count includes all characters, including gaps. For example, 'GAT--TACA' would return 9.

```Java
public long getTotal()
```

--------------------------------

### POST /FindOptions/constructor

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/class-use/Options.html

Internal constructor for FindOptions configuration.

```APIDOC
## POST /FindOptions/constructor

### Description
Internal constructor for initializing FindOptions. Note: This must only be called by Geneious; do not call it from a plugin.

### Method
POST

### Endpoint
/FindOptions/constructor

### Parameters
#### Request Body
- **text** (String) - Required - Search text.
- **caseSensitive** (boolean) - Required - Whether the search is case-sensitive.
- **isFromStart** (boolean) - Required - Whether to search from the start.
- **isForwards** (boolean) - Required - Search direction.
- **additionalOptions** (Options) - Required - Supplementary configuration options.
```

--------------------------------

### Get Paired Reads as NucleotideSequenceDocument (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/class-use/NucleotideSequenceDocument.html

Provides examples of retrieving paired reads, including normalized and reversed versions, as NucleotideSequenceDocument objects from an AssemblerInput.Read object. This is essential for working with next-generation sequencing data.

```java
NucleotideSequenceDocument mate = read.getMate();
NucleotideSequenceDocument mateNormalized = read.getMateNormalized();
NucleotideSequenceDocument mateNormalizedReversed = read.getMateNormalizedReversed();
NucleotideSequenceDocument firstRead = read.getRead();
NucleotideSequenceDocument firstReadNormalized = read.getReadNormalized();
```

--------------------------------

### GButton Constructors

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/components/GButton.html

Lists the available constructors for the GButton class.

```APIDOC
## GButton Constructors

### Constructor Summary

| Constructor | Description |
|---|---|
| `GButton()` | |
| `GButton(java.lang.String text)` | |
| `GButton(java.lang.String text, boolean small)` | |
| `GButton(java.lang.String text, javax.swing.Icon icon)` | |
| `GButton(javax.swing.Action a)` | |
| `GButton(javax.swing.Icon icon)` | |
```

--------------------------------

### Create Basic Options in Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/Options.html

This example demonstrates how to create simple options for user input, including a text field for annotation type, a checkbox, and an integer field. It shows basic option creation and retrieval of their values.

```java
public class OptionsExample1 extends Options {
    private StringOption annotationType;
    private BooleanOption trimEnds;
    private IntegerOption numberOfBasesToTrim;

    public OptionsExample1() {
        annotationType = addStringOption("annotationType","Annotation Type","CDS");
        annotationType.setDescription("The type of annotation to add to the sequence");
        trimEnds = addBooleanOption("trimEnds","Trim Ends",false);
        numberOfBasesToTrim = addIntegerOption("numberOfBasesToTrim","Number Of Bases To Trim",5);
    }

    public String getAnnotationType() {
        return annotationType.getValue();
    }

    public int getNumberOfBasesToTrim() {
        if (trimEnds.getValue()) {
            return numberOfBasesToTrim.getValue();
        }
        else {
            return 0;
        }
    }
}
```

--------------------------------

### Get Integer Setting with Default - UserEditablePreferences

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/UserEditablePreferences.html

Retrieves an integer value from user editable preferences. If the key does not exist, it adds the key with the provided default value. Keys should ideally start with a fully qualified class name for uniqueness.

```java
public static int getIntSettingIfNotPresent​(java.lang.String key,
                                            int defaultValue)
```

--------------------------------

### Implement Version Support for XML Serialization in Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/SequenceListSummary.html

Demonstrates how to implement the getVersionSupport method to define compatibility levels for different Geneious versions. It uses a switch statement to return the appropriate MajorVersion based on the VersionSupportType.

```java
public Geneious.MajorVersion getVersionSupport(XMLSerializable.VersionSupportType versionType) {
  switch (versionType) {
    case FormatLastExtended:
      return Geneious.MajorVersion.Version10_0;
    case FormatLastChanged:
      return Geneious.MajorVersion.Version9_1;
    case OldestVersionSerializableTo:
      return Geneious.MajorVersion.Version9_0;
    default:
      throw new IllegalArgumentException("Unrecognized VersionSupportType");
  }
}
```

--------------------------------

### Get Version Support for XML Serialization (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/SequenceAnnotation.html

Retrieves the Geneious MajorVersion related to XML serialization compatibility for a class. It supports different version types like FormatLastExtended, FormatLastChanged, and OldestVersionSerializableTo. This is an example implementation.

```java
public Geneious.MajorVersion getVersionSupport(XMLSerializable.VersionSupportType versionType) {
 switch (versionType) {
   case FormatLastExtended:
     //added a new tag to xml in 10.0 that can be safely ignored by older versions
     return Geneious.MajorVersion.Version10_0;
   case FormatLastChanged:
     //renamed a tag in 9.1 meaning that older versions can no longer read the xml from 9.1
     return Geneious.MajorVersion.Version9_1;
   case OldestVersionSerializableTo:
     //this document class can export xml that is compatible with 9.0
     return Geneious.MajorVersion.Version9_0;
   default:
     throw new IllegalArgumentException("Unrecognized VersionSupportType");
 }
 
}
```

--------------------------------

### Initialize SequenceGapInformation

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/implementations/SequenceGapInformation.html

Demonstrates how to instantiate SequenceGapInformation from a gapped sequence or an existing XML element. These constructors are essential for tracking gap positions within biological sequences.

```java
public SequenceGapInformation(java.lang.CharSequence gappedSequence);

public SequenceGapInformation(org.jdom.Element element, SequenceCharSequence gappedCharSequence);
```

--------------------------------

### Get Boolean Setting with Default - UserEditablePreferences

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/UserEditablePreferences.html

Retrieves a boolean value from user editable preferences. If the key is not found, it adds the key with the specified default value. It is recommended that keys start with a fully qualified class name to ensure uniqueness.

```java
public static boolean getBooleanSettingIfNotPresent​(java.lang.String key,
                                                    boolean defaultValue)
```

--------------------------------

### Create GUI Component for Option

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/Options.RadioOption.html

Initializes and returns a JPanel representing the option. This method is called once to create the component, which is then cached for future access.

```java
protected javax.swing.JPanel createComponent()
```

--------------------------------

### Get String Setting with Default - UserEditablePreferences

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/UserEditablePreferences.html

Retrieves a String value from user editable preferences. If the key does not exist, it adds the key with the provided default value. It's recommended that keys start with a fully qualified class name for uniqueness.

```java
public static java.lang.String getStringSettingIfNotPresent​(java.lang.String key,
                                                            java.lang.String defaultValue)
```

--------------------------------

### Initialize GButton Constructors

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/components/GButton.html

Various constructors for creating a GButton instance, mirroring standard JButton functionality with additional support for small-font styling.

```java
public GButton()
public GButton(javax.swing.Icon icon)
public GButton(java.lang.String text, boolean small)
public GButton(java.lang.String text)
public GButton(javax.swing.Action a)
public GButton(java.lang.String text, javax.swing.Icon icon)
```

--------------------------------

### Get Minimum Index of Annotation Interval - Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/SequenceAnnotationInterval.html

Returns the smallest sequence index covered by this interval, calculated as Math.min(getFrom(), getTo()). This value is usually within the range of 1 to the sequence length. If outside this range, it implies the annotation starts before or after the sequence's boundaries.

```java
public int getMinimumIndex()

// Returns: The smallest sequence index covered by this interval, equivalent to Math.min(getFrom(), getTo()).
```

--------------------------------

### Initialize AbstractPluginDocument

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/AbstractPluginDocument.html

Constructs a new document instance. Options include using the current system time or a specific creation date and URN.

```java
public AbstractPluginDocument(java.util.Date created);
public AbstractPluginDocument(java.util.Date created, URN urn);
public AbstractPluginDocument();
```

--------------------------------

### Get Maximum Index of Annotation Interval - Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/SequenceAnnotationInterval.html

Returns the largest sequence index covered by this interval, calculated as Math.max(getFrom(), getTo()). This value is typically within the range of 1 to the sequence length. Values outside this range suggest the annotation extends beyond the sequence's start or end.

```java
public int getMaximumIndex()

// Returns: The largest sequence index covered by this interval, equivalent to Math.max(getFrom(), getTo()).
```

--------------------------------

### Get Component Location Relative to Root Pane

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/GuiUtilities.html

Calculates and returns the location of a given component relative to its root pane. For example, if the component's top-left corner aligns with the root pane's top-left corner, the returned location will be (0,0). It takes a java.awt.Component as input and returns a java.awt.Point.

```java
public static java.awt.Point getLocationRelativeToRootPane​(java.awt.Component component)

```

--------------------------------

### Configure Java Logging Properties (Properties)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/index.html

Shows an example of a Java logging properties file for Geneious. This configuration specifies logging levels for different packages, handler types, and log file patterns, allowing for customized log output.

```Properties
.level=WARNING
com.biomatters.level=INFO
your.package.name.level=FINE
handlers=java.util.logging.FileHandler
java.util.logging.FileHandler.append=true
java.util.logging.FileHandler.formatter=java.util.logging.SimpleFormatter
java.util.logging.FileHandler.pattern=c:\\temp\\geneious.log
```

--------------------------------

### Get Plugin Dependencies - Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/GeneiousPlugin.html

Returns a list of other plugin names or class names that this plugin depends on during initialization. The plugin will not be initialized until all dependencies are initialized and will be shut down before them. May return null if dependencies are unknown. If a dependency is not installed, the plugin will still activate and must handle potential failures gracefully.

```java
public java.util.List<java.lang.String> getDependencies() {
    // Return a list of dependency names or class names
    return null; // Or return a list, e.g., java.util.Arrays.asList("DependencyPluginName");
}
```

--------------------------------

### Get Annotation End Position - Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/SequenceAnnotationInterval.html

Retrieves the end position of an annotation. This position is typically less than the 'from' position for reverse-directed annotations and usually falls within the range of 1 to the sequence length. Values outside this range indicate the annotation starts before or after the sequence ends. Circular sequence handling is described in getFrom().

```java
public int getTo()

// Returns: end position of the annotation
```

--------------------------------

### Initialize FolderView in Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/databaseservice/FolderView.html

Demonstrates how to instantiate a new FolderView object using a list of document fields and a default sorting field, or via XML deserialization.

```java
import com.biomatters.geneious.publicapi.databaseservice.FolderView;
import com.biomatters.geneious.publicapi.documents.DocumentField;
import java.util.List;

// Constructor for a new FolderView
List<DocumentField> fields = ...; // Define your fields
DocumentField defaultSort = ...; // Define default sort field
FolderView folderView = new FolderView(fields, defaultSort);

// Constructor for XML deserialization
// FolderView deserializedView = new FolderView(jdomElement);
```

--------------------------------

### Generate Hardware Fault Recommendations (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/SystemUtilities.html

Constructs an HTML-formatted message detailing potential hardware faults and providing instructions for system hardware checks. It takes an introductory message, the location of the suspected fault, and detailed exception messages as input. The HTML tags are omitted if the intro parameter is null (API 2022.0.0+).

```java
public static String getFaultyHardwareRecommendations(String intro, String machine, String details) {
    // Implementation details...
    return "<html><body><h1>Hardware Issue</h1><p>Details...</p></body></html>"; // Placeholder
}
```

--------------------------------

### Get High DPI Scale (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/SystemUtilities.html

Retrieves the DPI scale factor for the system's highest DPI screen. This method is a fallback and `getHighDPIScale(Graphics2D)` or `getHighDPIScale(GraphicsDevice)` should generally be preferred for accurate behavior across multi-monitor setups. It returns 1 if the graphics object is null. On systems like MacOS Retina, it returns 2.

```java
public static double getHighDPIScale(java.awt.Graphics2D graphics) {
    // Implementation details...
    return 1.0; // Placeholder
}
```

```java
public static double getHighDPIScale(java.awt.GraphicsDevice graphicsDevice) {
    // Implementation details...
    return 1.0; // Placeholder
}
```

--------------------------------

### Manage Option UI Metadata

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/Options.Option.html

Methods to set and retrieve tool-tip descriptions and help text for options. Help text supports HTML and is displayed via a question mark button.

```java
public final String getDescription();
public final void setDescription(String description);
public final void setHelp(String help);
public String getHelp();
```

--------------------------------

### Initialize and Write to OutputStreamToRandomAccessFile

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/OutputStreamToRandomAccessFile.html

Demonstrates how to instantiate the class and use it within a buffered output stream chain to write data to a RandomAccessFile.

```java
import java.io.*;
import com.biomatters.geneious.publicapi.utilities.OutputStreamToRandomAccessFile;

// Usage example
RandomAccessFile raf = new RandomAccessFile("example.bin", "rw");
DataOutputStream dos = new DataOutputStream(new BufferedOutputStream(new OutputStreamToRandomAccessFile(raf)));

dos.writeInt(12345);
dos.flush();
dos.close();
```

--------------------------------

### Install Plugin Silently (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/PluginUtilities.html

Installs and activates a Geneious plugin (.gplugin file) without user interaction. Throws an IOException if installation fails or requires a restart.

```Java
public static void installPluginSilently(java.io.File pluginFile) throws java.io.IOException

```

--------------------------------

### POST /utilities/intlist/create

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/class-use/IntList.html

Utility methods for creating and manipulating IntList objects.

```APIDOC
## POST /utilities/intlist/create

### Description
Creates a new IntList instance from various input formats including arrays or string representations.

### Method
POST

### Endpoint
/com.biomatters.geneious.publicapi.utilities.IntList/forValues

### Parameters
#### Request Body
- **values** (int[]) - Required - Array of integers to populate the list.

### Response
#### Success Response (200)
- **IntList** (object) - The newly created IntList instance.

### Response Example
{
  "values": [10, 20, 30]
}
```

--------------------------------

### Log a Fine Message (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/index.html

A simple Java code example demonstrating how to log a message at the FINE level using Java's standard logging system within a Geneious plugin.

```Java
Logger.getLogger(getClass().getName()).fine("Hello World!");
```

--------------------------------

### Initialize IntegerOption via Constructors

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/Options.IntegerOption.html

Constructors for creating an IntegerOption instance. Options include initialization from an XML element, or defining a name, label, default value, and optional range constraints.

```java
protected IntegerOption(org.jdom.Element element) throws XMLSerializationException;

protected IntegerOption(java.lang.String name, java.lang.String label, java.lang.Integer defaultValue, int minimum, int maximum);

protected IntegerOption(java.lang.String name, java.lang.String label, java.lang.Integer defaultValue);
```

--------------------------------

### Measure and Log Operation Duration (Java)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/Logs.html

Logs a message if an operation's duration exceeds a specified threshold. Best used with the `start()` method to capture the start time. Returns the duration in milliseconds. Requires start time, duration threshold, and a message.

```java
public static long duration(long start, long logIfDurationGreaterThan, java.lang.String message)
```

--------------------------------

### Get Selected Sequences (Deprecated) - Geneious Java

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/SequenceSelection.html

Deprecated method to get the set of selected sequences. Use getSelectedSequenceIndices() instead.

```java
@Deprecated
public java.util.Set<SequenceDocument> getSelectedSequences()
```

--------------------------------

### Creating and Using IntList

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/IntList.html

Demonstrates how to instantiate an IntList using factory methods and access its elements. This class is designed to avoid the overhead of boxing primitive integers into Integer objects.

```java
import com.biomatters.geneious.publicapi.utilities.IntList;

// Create an IntList from varargs
IntList list = IntList.forValues(1, 2, 3, 4, 5);

// Access elements
int first = list.get(0);
int size = list.size();

// Check for existence
boolean containsThree = list.contains(3);

// Convert to array
int[] array = list.toIntArray();
```

--------------------------------

### Initialize and Use FastSaxBuilder

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/xml/FastSaxBuilder.html

Demonstrates how to instantiate the FastSaxBuilder and use its optimized build methods to parse XML from an InputStream with a specified maximum size.

```java
import com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder;
import org.jdom.Document;
import java.io.InputStream;

public class XmlParser {
    public Document parseXml(InputStream inputStream, long sizeInBytes) throws Exception {
        FastSaxBuilder builder = new FastSaxBuilder();
        // Build document with memory optimization
        return builder.build(inputStream, sizeInBytes);
    }
}
```

--------------------------------

### MultiThreadedProcessingSystem Usage Example

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/utilities/MultiThreadedProcessingSystem.html

An example demonstrating how to instantiate and use the MultiThreadedProcessingSystem with NucleotideSequenceDocument objects. It shows setting up the processing system with specific parameters.

```java
final AtomicLong totalLength = new AtomicLong();
MultiThreadedProcessingSystem<NucleotideSequenceDocument> processingSystem = new MultiThreadedProcessingSystem<NucleotideSequenceDocument>("testProcess",10,10,Runtime.getRuntime().availableProcessors()) {

};
```

--------------------------------

### Construct ExtractionOptions with Single Interval

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/implementations/SequenceExtractionUtilities.ExtractionOptions.html

Initializes extraction options with a single start and end position. Supports reverse extraction if end is less than start.

```java
public ExtractionOptions(int extractFrom, int extractTo)
```

--------------------------------

### POST /service/folder-selection

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/plugin/ServiceUtilities.html

Opens a dialog for the user to select a local database folder.

```APIDOC
## POST /service/folder-selection

### Description
Opens a dialog in which the user can choose one of their local database folders.

### Method
POST

### Endpoint
ServiceUtilities.getUserSelectedFolder(Component anyComponentInParentFrame)

### Parameters
#### Request Body
- **anyComponentInParentFrame** (java.awt.Component) - Optional - A component whose parent frame will become the parent frame for the dialog.

### Response
#### Success Response (200)
- **folder** (WritableDatabaseService) - The folder selected by the user, or null if cancelled.
```

--------------------------------

### Construct SequenceAnnotationInterval with Start and End

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/SequenceAnnotationInterval.html

A backwards compatibility constructor that defines an interval by start and end indices. The direction is automatically inferred based on the relative values of the indices.

```java
public SequenceAnnotationInterval(int from, int to)
```

--------------------------------

### Initialize OverlayIcons

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/components/OverlayIcons.html

Demonstrates how to instantiate an OverlayIcons object using a base set of icons and additional overlay icons. The static get method is recommended for better performance through internal caching.

```java
import com.biomatters.geneious.publicapi.components.OverlayIcons;
import com.biomatters.geneious.publicapi.plugin.Icons;

// Basic instantiation
Icons base = getBaseIcons();
Icons overlay = getOverlayIcons();
OverlayIcons myIcons = new OverlayIcons(base, overlay);

// Recommended instantiation using static factory for caching
OverlayIcons cachedIcons = OverlayIcons.get(base, overlay);
```

--------------------------------

### GMenuItem Constructors

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/components/GMenuItem.html

Various constructors for initializing a GMenuItem instance with different configurations such as icons, text, actions, and mnemonics.

```APIDOC
## POST /GMenuItem

### Description
Initializes a new instance of GMenuItem. Supports multiple overloads matching standard JMenuItem initialization patterns.

### Method
POST

### Endpoint
/GMenuItem

### Parameters
#### Request Body
- **text** (String) - Optional - The display text for the menu item.
- **icon** (Icon) - Optional - The icon to display alongside the text.
- **a** (Action) - Optional - The Action to be performed when the item is selected.
- **mnemonic** (int) - Optional - The mnemonic key code.

### Request Example
{
  "text": "New Project",
  "mnemonic": 78
}

### Response
#### Success Response (200)
- **status** (String) - Confirmation of object creation.
```

--------------------------------

### Get Sequence Qualities (Static, All)

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/DefaultNucleotideGraph.html

A static utility method to get all sequence quality scores for a NucleotideGraph. This is equivalent to calling the method with the full sequence length.

```java
public static int[] getSequenceQualities(NucleotideGraph graph)

```

--------------------------------

### AlignmentData Example getVersionSupport Implementation

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/documents/sequence/SequenceListOnDisk.AlignmentData.html

Provides an example implementation for the getVersionSupport method, demonstrating how to handle different VersionSupportType values to return appropriate Geneious major versions.

```java
switch (versionType) {
  case FormatLastExtended:
    //added a new tag to xml in 10.0 that can be safely ignored by older versions
    return Geneious.MajorVersion.Version10_0;
  case FormatLastChanged:
    //renamed a tag in 9.1 meaning that older versions can no longer read the xml from 9.1
    return Geneious.MajorVersion.Version9_1;
  case OldestVersionSerializableTo:
    //this document class can export xml that is compatible with 9.0
    return Geneious.MajorVersion.Version9_0;
  default:
    throw new IllegalArgumentException("Unrecognized VersionSupportType");
}

```

--------------------------------

### POST /alert-panel/show-loading

Source: https://assets.geneious.com/developer/geneious/javadoc/latest/com/biomatters/geneious/publicapi/components/AlertPanel.html

Displays a loading spinner in the alert panel.

```APIDOC
## POST /alert-panel/show-loading

### Description
Displays a loading throbber icon in the panel. This is typically used during background operations.

### Method
POST

### Request Example
{}

### Response
#### Success Response (200)
- **status** (String) - Confirmation that the loading icon is visible.
```