public class MultipleAlignmentDisplay
extends java.lang.Object
MultipleAlignment
s.
Currently supported: Alignment Panel Display, select aligned residues by PDB code, JmolPanel display.
Constructor and Description |
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MultipleAlignmentDisplay() |
Modifier and Type | Method and Description |
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static MultipleAlignmentJmol |
display(MultipleAlignment multAln)
Display a MultipleAlignment with a JmolPanel.
|
static java.util.List<java.lang.String> |
getPDBresnum(int structNum,
MultipleAlignment multAln,
Atom[] ca)
Utility method used in the
MultipleAlignmentJmol panel, when the aligned residues of a
structure in the alignment have to be selected for formatting (coloring and style). |
static void |
showAlignmentImage(MultipleAlignment multAln,
java.lang.String result)
Creates a new Frame with the String output representation of the
MultipleAlignment . |
static void |
showMultipleAligmentPanel(MultipleAlignment multAln,
AbstractAlignmentJmol jmol,
ColorBrewer colorPattelete)
Creates a new Frame with the MultipleAlignment Sequence Panel.
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public static final java.util.List<java.lang.String> getPDBresnum(int structNum, MultipleAlignment multAln, Atom[] ca)
MultipleAlignmentJmol
panel, when the aligned residues of a
structure in the alignment have to be selected for formatting (coloring and style).structNum
- the structure index (row) of the alignmentmultAln
- the MultipleAlignment that contains the equivalent positionsca
- the atom array of the structure specified (corresponding to the structure index)public static void showMultipleAligmentPanel(MultipleAlignment multAln, AbstractAlignmentJmol jmol, ColorBrewer colorPattelete) throws StructureException
multAln
- jmol
- colors
- StructureException
public static void showAlignmentImage(MultipleAlignment multAln, java.lang.String result)
MultipleAlignment
.multAln
- result
- String outputpublic static MultipleAlignmentJmol display(MultipleAlignment multAln) throws StructureException
multAln
- StructureException