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jalview::bin::JalviewLite Class Reference

Inheritance diagram for jalview::bin::JalviewLite:
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Collaboration diagram for jalview::bin::JalviewLite:
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List of all members.

Classes

class  LoadingThread
class  LoadJmolThread

Public Member Functions

boolean addPdbFile (AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile)
String arrayToSeparatorList (String[] list)
String arrayToSeparatorList (String[] list, String separator)
void destroy ()
String getAlignment (String format)
String getAlignment (String format, String suffix)
String getAlignmentFrom (AlignFrame alf, String format)
String getAlignmentFrom (AlignFrame alf, String format, String suffix)
String getAlignmentOrder ()
String getAlignmentOrderFrom (AlignFrame alf, String sep)
String getAlignmentOrderFrom (AlignFrame alf)
String getAnnotation ()
String getAnnotationFrom (AlignFrame alf)
Vector getAppletWindow (Class class1)
Color getDefaultColourParameter (String colparam, Color defcolour)
boolean getDefaultParameter (String name, boolean def)
AlignFrame getDefaultTargetFrame ()
String getFeatureGroups ()
String getFeatureGroupsOfState (boolean visible)
String getFeatureGroupsOfStateOn (AlignFrame alf, boolean visible)
String getFeatureGroupsOn (AlignFrame alf)
String getFeatures (String format)
String getFeaturesFrom (AlignFrame alf, String format)
Vector getJsExecQueue ()
String getJsMessage (String messageclass, String viewId)
String getSelectedSequences ()
String getSelectedSequences (String sep)
String getSelectedSequencesAsAlignment (String format, String suffix)
String getSelectedSequencesAsAlignmentFrom (AlignFrame alf, String format, String suffix)
String getSelectedSequencesFrom (AlignFrame alf)
String getSelectedSequencesFrom (AlignFrame alf, String sep)
String getSeparator ()
StructureSelectionManager getStructureSelectionManager ()
void highlight (String sequenceId, String position, String alignedPosition)
abstract void highlightIn (AlignFrame alf, String sequenceId, String position, String alignedPosition)
void highlightIn (final AlignFrame alf, final String sequenceId, final String position, final String alignedPosition)
void init ()
boolean isAlignPdbStructures ()
boolean isJsMessageSetChanged (String string, String string2, String[] colcommands)
AlignFrame loadAlignment (String text, String title)
void loadAnnotation (String annotation)
void loadAnnotationFrom (AlignFrame alf, String annotation)
abstract void mouseOverStructure (String pdbResNum, String chain, String pdbfile)
void mouseOverStructure (final String pdbResNum, final String chain, final String pdbfile)
AlignFrame newView ()
AlignFrame newView (String name)
AlignFrame newViewFrom (AlignFrame alf, String name)
AlignFrame newViewFrom (AlignFrame alf)
void openJalviewHelpUrl ()
String orderAlignmentBy (AlignFrame alf, String order, String undoName, String sep)
String orderBy (String order, String undoName)
String orderBy (String order, String undoName, String sep)
void paint (Graphics g)
void removeJavascriptListener (AlignFrame af, String listener)
abstract void scrollViewToColumnIn (AlignFrame alf, String leftHandColumn)
void scrollViewToColumnIn (final AlignFrame alf, final String leftHandColumn)
abstract void scrollViewToIn (AlignFrame alf, String topRow, String leftHandColumn)
void scrollViewToIn (final AlignFrame alf, final String topRow, final String leftHandColumn)
void scrollViewToRowIn (final AlignFrame alf, final String topRow)
abstract void scrollViewToRowIn (AlignFrame alf, String topRow)
void select (String sequenceIds, String columns)
void select (String sequenceIds, String columns, String sep)
void selectIn (AlignFrame alf, String sequenceIds, String columns)
abstract void selectIn (AlignFrame alf, String sequenceIds, String columns, String sep)
void selectIn (final AlignFrame alf, String sequenceIds, String columns, String sep)
String[] separatorListToArray (String list)
String[] separatorListToArray (String list, String separator)
void setExecutor (JSFunctionExec jsFunctionExec2)
void setFeatureGroupState (String groups, boolean state)
void setFeatureGroupStateOn (final AlignFrame alf, final String groups, boolean state)
abstract void setFeatureGroupStateOn (AlignFrame alf, String groups, boolean state)
void setJsMessageSet (String messageclass, String viewId, String[] colcommands)
void setMouseoverListener (String listener)
void setMouseoverListener (AlignFrame af, String listener)
void setSelectionListener (AlignFrame af, String listener)
void setSelectionListener (String listener)
void setSeparator (String separator)
void setStructureListener (String listener, String modelSet)
void showURL (String url, String target)
void start ()
void stop ()

Static Public Member Functions

static void addFrame (final Frame frame, String title, int width, int height)
static String getBuildDate ()
static String getVersion ()

Public Attributes

AlignFrame currentAlignFrame = null
boolean jmolAvailable = false
boolean jsfallbackEnabled = false
boolean useXtrnalSviewer = false

Static Public Attributes

static boolean debug = false
static int lastFrameX = 200
static int lastFrameY = 200

Protected Member Functions

void setAlignPdbStructures (boolean alignPdbStructures)

Protected Attributes

String separator = "" + ((char) 0x00AC)

Package Attributes

boolean embedded = false
String file = "No file"
boolean fileFound = true
AlignFrame initialAlignFrame = null
Button launcher = new Button("Start Jalview")
static String version = null

Static Package Attributes

static String builddate = null

Private Member Functions

void callInitCallback ()
String resolveUrlForLocalOrAbsolute (String url, URL localref)
void tidyUp ()

Static Private Member Functions

static void initBuildDetails ()

Private Attributes

boolean alignPdbStructures = false
boolean checkedForJmol = false
boolean checkForJmol = true
Vector
< jalview.javascript.JSFunctionExec
javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>()
Vector jsExecQueue = new Vector()
jalview.javascript.JSFunctionExec jsFunctionExec
Hashtable< String, long[]> jshashes = new Hashtable<String, long[]>()
Hashtable< String, Hashtable
< String, String[]> > 
jsmessages = new Hashtable<String, Hashtable<String, String[]>>()

Detailed Description

Jalview Applet. Runs in Java 1.18 runtime

Author:
$author$
Version:
Revision:
1.92

Definition at line 70 of file JalviewLite.java.


The documentation for this class was generated from the following file:

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