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java.lang.Objectcom.compomics.util.gui.protein.ProteinSequencePane
public class ProteinSequencePane
This class contains a method that formats a given protein sequence such that both the covered parts of the sequence and the peptide selected in the peptide table is highlighted. The result is inserted into a JEditorPane.
Constructor Summary | |
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ProteinSequencePane()
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Method Summary | |
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static double |
formatProteinSequence(JEditorPane editorPane,
String cleanSequence,
ArrayList<Integer> selectedPeptideStart,
ArrayList<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. |
static double |
formatProteinSequence(JEditorPane editorPane,
String cleanSequence,
int[] coverage)
Formats the protein sequence such that the covered parts of the sequence is highlighted. |
static double |
formatProteinSequence(JEditorPane editorPane,
String cleanSequence,
int[] coverage,
TreeMap<String,String> keyValuePairs,
HashMap<String,Color> tagColors,
boolean showModifications,
boolean showVariants,
boolean showCoverage)
Formats the protein sequence such that the covered parts of the sequence is highlighted. |
static double |
formatProteinSequence(JEditorPane editorPane,
String cleanSequence,
int selectedPeptideStart,
int selectedPeptideEnd,
int[] coverage)
Formats the protein sequence such that the covered parts of the sequence is highlighted. |
static double |
formatProteinSequence(JEditorPane editorPane,
String cleanSequence,
int selectedPeptideStart,
int selectedPeptideEnd,
int[] coverage,
TreeMap<String,String> aKeyValuePairs,
HashMap<String,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. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ProteinSequencePane()
Method Detail |
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public static double formatProteinSequence(JEditorPane editorPane, String cleanSequence, int[] coverage, TreeMap<String,String> keyValuePairs, HashMap<String,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 not
public static double formatProteinSequence(JEditorPane editorPane, 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(JEditorPane editorPane, 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(JEditorPane editorPane, String cleanSequence, ArrayList<Integer> selectedPeptideStart, ArrayList<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(JEditorPane editorPane, String cleanSequence, int selectedPeptideStart, int selectedPeptideEnd, int[] coverage, TreeMap<String,String> aKeyValuePairs, HashMap<String,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 tag
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