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'STRAP:multiple sequence alignments '
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Package charite.christo

Interface Summary
CanBeStopped  
ChRunnable  
Colored Implemented by colored objects.
CommandInterpreter Command interpreters can interpret commands given as a command line.
Disposable Implemented by objects such as dialogs or plugins that can be disposed.
FileEditor  
FloatValue Implemented by objects that can return float values.
HasControlPanel Implemented by objects that can contain a GUI where the user can manipulate the inner state.
HasID  
HasImage  
HasModiCount  
HasName  
HasNativeExec  
HasPanel Implemented by objects that have a GUI.
HasPrgParas  
HasPropertyMap  
HasRenderer For the Tree and List renderers
HasRendererModiCount For the Tree and List renderers
HasScore This interface denotes objects that have a numeric value which is a score.
HasSharedControlPanel Provides a GUI where the user can change the settings for a group of objects.
HasWeakRef  
IsEnabled  
NeedsInternet  
NeedsSharedInstance  
PaintHook  
PreferredSize  
ProcessEv  
TooltipProvider  
WhenCreatedWhenModified  
 

Class Summary
AbstractInteractiveFileProcessor  
AbstractProxy  
AnonymousFTP  
AnonymousFTPPROXY HELP The standard Java way to fetch files from the Internet fails for some FTP-addresses.
AnsiEscape  
Archive  
BA  
BasicExecutable HELP
ButColor Opens a JColorChooser.
CacheResult HELP Some procedures are computationally expensive such as BLAST searches or 3D superpositions and results are stored on HD
Implementation: Several results are stored within one file.
ChAppleScript  
ChAquaScrollBarUI  
ChButton  
ChCatdoc  
ChClassLoader1  
ChCodeViewer  
ChCombo extended choice box
ChComparator  
ChCompilerJavac  
ChCompilerJavacPROXY  
ChConstants  
ChDelay This utility class manages threads.
ChEnv In Java1.4 the shell variables are read by calling the command "set".
ChExec execute external programs Several alternative command lines can be set.
ChExecSecurity  
ChFile  
ChFileChooser  
ChFileFilter  
ChFrame  
ChHttpClient  
ChHttpClientPROXY HELP
ChIcon HELP Image icons are a visual aid to recognize proteins and residue annotations.
ChInStream  
ChJarSignersHardLinker A utility class for working around the java webstart jar signing/security bug see http://bugs.sun.com/view_bug.do?bug_id=6967414 and http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6805618
ChJavadoc Utility classes for Javadoc.
ChJCheckBox the extended button class
ChJHighlighter  
ChJList HELP This list supports WIKI:Drag_and_drop (Watch movie STRING:ChConstants#MOVIE_Export_Proteins STRING:ChConstants#MOVIE_Drag_to_another_STRAP STRING:ChConstants#MOVIE_Drag_protein_to_3D STRING:ChConstants#MOVIE_Sequence_Features_in_3D) Reordering WIKI:Context_menu (Watch movie STRING:ChConstants#MOVIE_Context_Menu) Keep window always visible: You may want to set the window "Floating on top".
ChJMenu  
ChJMenuBar  
ChJnlp  
ChJOrtho  
ChJOrthoPROXY HELP Home:http://www.inetsoftware.de/other-products/jortho
License of JOrtho: GPL
ChJScrollPane  
ChJTable  
ChJTextPane HELP
ChJTree  
ChListSelectionModel  
ChLogger  
ChMap<K,V>  
ChMetalScrollBarUI  
ChMsg Some modale message dialogs
ChMsgDia Some modale message dialogs
ChPanel  
ChPdfUtils  
ChPdfUtilsPROXY HELP Home: http://pdfbox.apache.org/
License of JPdf: Apache License v2.0
ChPubmed HELP
ChRegex putln(ChRegex.replace(ChRegex.pattern("(34)"), " $1$1 ", "12345678"));
ChRenderer This list cell renderer is used for list components that contain java classes
ChScriptPanel  
ChScrollBar  
ChSet<E>  
ChSlider convenient extension of JSlider
ChSprite  
ChStdout HELP
ChTableLayout Container that arranges components horizontally.
ChTableModel  
ChTabPane A reimplementation of tabbed pane since JTabbedPane does not work very well
ChTar  
ChTarPROXY HELP Home: http://www.gjt.org/servlets/JCVSlet/list/ice/com/ice/tar/
License of tar.zip: tar/doc/LICENSE says: "...You are free to use this work in any way you wish..."
ChTextArea  
ChTextComponents Utilities for TextComponents
ChTextField  
ChTextReplacement  
ChTextView  
ChThread Periodically calls Runnable objects.
ChTokenizer A fast Tokenizer
ChTransferable HELP

Objects are dragged with the mouse and dropped on a target (see WIKI:Drag_and_drop).
Actions which are performed when objects are dropped on certain targets.
D r o p p e d   O b j e c t s Drop target Proteins Residue selections Hetero groups Images
Proteins
  		Copy selection to protein Add heteros to protein Set icon image
Residue selections
  		Set background image
3D-View
  		Add 3D-structure to view Highlight atoms/amino acids in 3D Add hetero structure to view
Alignment panel
  		Load or un-hide protein Copy selection to protein Add heteros to protein
Tree-node "Hidden"
  		Hide proteins Desktop or file browser
  		Copy protein file Write PDB-file
ChTreeModel  
ChUtils Static utility methods.
ChUtils.EvLi  
ChWindowsScrollBarUI  
ChZip to extract jar packages
CollapseComponent HELP Tool-bars and menu-bars waste space on the screen.
Customize HELP The customize-dialogs are used to set program options.
DesktopUtils  
DialogExecuteOnFile HELP With this dialog obtainable from the "plugin"-menu shell programs can be run on files or character sequences.
DialogFindInText views html and plain text
DialogStringMatch HELP Items in graphical list components can be selected using string pattern.
DNA_Util  
EvAdapter  
ExecByRegex HELP This Dialog allows to apply shell commands to selected text regions and object IDs.
FileEditorEclipse Opens a file in Eclipse.
FilePopup HELP This list shows currently downloaded files.
Stalled downloads are recognized by a file size that does not change for a long time.
They can block the program flow.
FreeMemoryBar Displays the free memory
FullClassName  
GraphEdge An Edge for a graph
GraphNode A node for a graph
GraphSun A graphical representation of a graph adjusting the node distances dynamically.
HelpCommands  
Hex2bin  
HtmlDoc  
HtmlDocEditorKit HELP
Preparing document for printing:
When printing, backgrounds are automatically turned to white.
PACKAGE:charite.christo.strap. PACKAGE:charite.christo.protein. INCLUDE_DOC2:StrapAlign INCLUDE_DOC2:StrapUtils
HtmlDocElement For the generation of the documentation of STRAP
HtmlUtil  
Hyperrefs Selections of Residues (sors) can refere to URLs or database entries.
Insecure All potentially dangerous file operations such as file modification or running native code are chaneled through this class.
InteractiveDownload HELP
J_JavaEditor J is a fast text editor written in Java and distributed under the GNU General Public License.
JListModel  
LAFChooser  
ListOrTreeNeedsRepaint  
Microsoft HELP
Windows differs to standard OS with respect to File separator character "\" instead of "/".
NativeTools  
NCBI_separateEntries HELP This utility allows to split a multiple sequences file where the sections are separated by a line containing only two slashes.
OccurInText Find places of patterns in text
PDB_separateChains HELP Proteins read from a PDB-file are selected.
PrgParas  
PrgParasGUI  
Range  
Ratio  
RenameFile  
RendererNumberAsOval  
ScrollLabel  
Sil  
SourcefilesInJarfile Lists all java source files in a give jar file
Strings2Tree  
TabItemTipIcon Obtains texts for tabs of JTabbedPane, menu item texts, tool=tips and tabs.
TextMatches  
UniqueList<T>  
Web HELP

Internet and Web-proxy

In some institutions all Internet connections are going through a Web proxy (see WIKI:Proxy_server).
 

Overview   Package  Class  Tree  Deprecated  Index  Help 
'STRAP:multiple sequence alignments '
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'The most important classes are StrapAlign, Protein and StrapEvent.'