public class ProteinSequencePane
extends java.lang.Object
Constructor and Description |
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ProteinSequencePane() |
Modifier and Type | Method and Description |
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static double |
formatProteinSequence(javax.swing.JEditorPane editorPane,
java.lang.String cleanSequence,
java.util.ArrayList<java.lang.Integer> selectedPeptideStart,
java.util.ArrayList<java.lang.Integer> selectedPeptideEnd,
int[] coverage)
Formats the protein sequence such that both the covered parts of the sequence
and the peptide selected in the peptide table is highlighted.
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static double |
formatProteinSequence(javax.swing.JEditorPane editorPane,
java.lang.String cleanSequence,
int[] coverage)
Formats the protein sequence such that the covered parts of the sequence
is highlighted.
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static double |
formatProteinSequence(javax.swing.JEditorPane editorPane,
java.lang.String cleanSequence,
int[] coverage,
java.util.TreeMap<java.lang.String,java.lang.String> keyValuePairs,
java.util.HashMap<java.lang.String,java.awt.Color> tagColors,
boolean showModifications,
boolean showVariants,
boolean showCoverage)
Formats the protein sequence such that the covered parts of the sequence
is highlighted.
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static double |
formatProteinSequence(javax.swing.JEditorPane editorPane,
java.lang.String cleanSequence,
int selectedPeptideStart,
int selectedPeptideEnd,
int[] coverage)
Formats the protein sequence such that the covered parts of the sequence
is highlighted.
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static double |
formatProteinSequence(javax.swing.JEditorPane editorPane,
java.lang.String cleanSequence,
int selectedPeptideStart,
int selectedPeptideEnd,
int[] coverage,
java.util.TreeMap<java.lang.String,java.lang.String> aKeyValuePairs,
java.util.HashMap<java.lang.String,java.awt.Color> selectedAnnotationType)
Formats the protein sequence such that both the covered parts of the sequence
and the peptide selected in the peptide table is highlighted.
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public static double formatProteinSequence(javax.swing.JEditorPane editorPane, java.lang.String cleanSequence, int[] coverage, java.util.TreeMap<java.lang.String,java.lang.String> keyValuePairs, java.util.HashMap<java.lang.String,java.awt.Color> tagColors, boolean showModifications, boolean showVariants, boolean showCoverage)
editorPane
- the editor pane to add the formatted sequence tocleanSequence
- the clean protein sequence, i.e., just the amino acid sequencecoverage
- the sequence coverage map with numbers indicating the number
of times a given residue is used, zero means no coverage,
(note: only uses index 1-n)keyValuePairs
- the key value pairs used for PEFF formatingtagColors
- the colors to use for the different tags, key is the tagshowModifications
- if the modifications are to be highlighted or notshowVariants
- if the variants are to be highlighted or notshowCoverage
- if the coverage is to be highlighted or notpublic static double formatProteinSequence(javax.swing.JEditorPane editorPane, java.lang.String cleanSequence, int[] coverage)
editorPane
- the editor pane to add the formatted sequence tocleanSequence
- the clean protein sequence, i.e., just the amino acid sequencecoverage
- the sequence coverage map with numbers indicating the number
of times a given residue is used, zero means no coverage,
(note: only uses index 1-n)public static double formatProteinSequence(javax.swing.JEditorPane editorPane, java.lang.String cleanSequence, int selectedPeptideStart, int selectedPeptideEnd, int[] coverage)
editorPane
- the editor pane to add the formatted sequence tocleanSequence
- the clean protein sequence, i.e., just the amino acid sequenceselectedPeptideStart
- the starting index of the selected peptideselectedPeptideEnd
- the ending index of the selected peptidecoverage
- the sequence coverage map with numbers indicating the number
of times a given residue is used, zero means no coverage,
(note: only uses index 1-n)public static double formatProteinSequence(javax.swing.JEditorPane editorPane, java.lang.String cleanSequence, java.util.ArrayList<java.lang.Integer> selectedPeptideStart, java.util.ArrayList<java.lang.Integer> selectedPeptideEnd, int[] coverage)
editorPane
- the editor pane to add the formatted sequence tocleanSequence
- the clean protein sequence, i.e., just the amino acid sequenceselectedPeptideStart
- the start indexes of the currently selected peptideselectedPeptideEnd
- the end indexes if the currently selected peptidecoverage
- the sequence coverage map with numbers indicating the number
of times a given residue is used, zero means no coverage,
(note: only uses index 1-n)public static double formatProteinSequence(javax.swing.JEditorPane editorPane, java.lang.String cleanSequence, int selectedPeptideStart, int selectedPeptideEnd, int[] coverage, java.util.TreeMap<java.lang.String,java.lang.String> aKeyValuePairs, java.util.HashMap<java.lang.String,java.awt.Color> selectedAnnotationType)
editorPane
- the editor pane to add the formatted sequence tocleanSequence
- the clean protein sequence, i.e., just the amino acid sequenceselectedPeptideStart
- the start index of the currently selected peptideselectedPeptideEnd
- the end index if the currently selected peptidecoverage
- the sequence coverage map with numbers indicating the number
of times a given residue is used, zero means no coverage,
(note: only uses index 1-n)aKeyValuePairs
- the key value pairs used for PEFF formatingselectedAnnotationType
- the colors to use for the different tags, key is the tagCopyright © 2013. All Rights Reserved.