| Modifier and Type | Method and Description |
|---|---|
void |
AlignmentEditor.removeCanceledTMPFls(Utilities util,
java.lang.String newTreeFile,
boolean selected)
Remove temporary files created for PhyML execution resulting from cancelation.
|
java.lang.String[] |
AlignmentEditor.renamePhymlFiles(Utilities util,
java.lang.String newTreeFile,
boolean selected)
Rename PhyML files created on directory chosen to
the name specified by user.
|
java.lang.String |
ResultsView.saveCurrentTable(java.lang.String tofilename,
Utilities util)
Write current visible table to file.
|
| Constructor and Description |
|---|
AlignmentOperations(Utilities utilities)
Alignment operations constructor.
|
CodemlTP(Utilities utilities) |
DatamonkeyTP(Utilities utilities)
Initialize Datamonkey tab.
|
GUIAlignmentEditor(java.io.File seqfile,
java.lang.String flFormat,
java.lang.String treeFile,
Utilities utilities)
Creates new form GUIAlignmentEditor
|
GUIAlignmentFiltering(java.lang.String sourceloc,
java.util.HashMap<java.lang.String,java.lang.String> codonstable,
Utilities utilities)
Creates new form GUIAlignmentFiltering
|
GUIAlignmentFiltering(java.lang.String sourceloc,
java.lang.String codonsfile,
Utilities utilities)
Creates new form GUIAlignmentFiltering
|
GUICodemlOptions(CodemlOptions codemlopts,
Utilities utilities,
boolean visible)
Creates new form GUICodemlOptions.
|
GUIFileFormatConverter(Utilities utilities)
Creates new form GUIFileFormatConverter
|
GUIGnuplotOptions(java.lang.String datafile,
boolean radical,
Utilities utilities)
Creates new form GnuplotOptions
|
GUIPDBTool(ResultsN3DTP combtp,
Utilities utilities)
Creates new form GUIPDBTool
|
GUIPhyMLOptions(Utilities utilities)
Creates new form GUIPhyMLOptions
|
GUIPreferences(Utilities utilities)
Creates new form GUIPreferences
|
GUIProtToSwissModel(FileFormatConverter filefc,
ResultsN3DTP smparse,
Utilities utilities)
Creates new form GUIProtToSwissModel
|
GUIProtToSwissModel(ResultsN3DTP smparse,
Utilities utilities)
Creates new form GUIProtToSwissModel
Initialization is performed from the window itself. |
GUIResultsView(java.lang.String file0,
java.lang.String file1,
java.lang.String distLbl,
Utilities utilities)
Creates new form GUIResultsView
|
ProtToSwissModel(java.lang.String targetSeq,
java.lang.String targetSeqName,
java.lang.String templateSeq,
java.lang.String templateSeqName,
java.lang.String templatePDBidChain,
java.lang.String emailadd,
java.lang.String projTitle,
Utilities utilities)
Use for Alignment Mode.
Uses a refresh timer of 30 seconds (default) when waiting for results to be ready. |
ProtToSwissModel(java.lang.String aasequence,
java.lang.String emailadd,
java.lang.String projtitle,
java.lang.String templatepdbid,
java.lang.String templatechain,
java.lang.String templatefile,
Utilities utilities)
Use for Automated Mode.
Uses a refresh timer of 30 seconds (default) when waiting for results to be ready. |
ProtToSwissModel(Utilities utilities)
Generic constructor for access to class values.
This is an empty constructor, use another constructor for doing submission of sequences in any of the project modes. |
ResultsN3DTP(Utilities utilities)
Initialize ResultsN3D with empty fields.
|
TreeSAAPTP(Utilities utilities)
Initialize TreeSAAP Panel resources
|