com.compomics.util.gui.protein

Class ProteinSequencePane

java.lang.Object

com.compomics.util.gui.protein.ProteinSequencePane

public class ProteinSequencePane
extends Object

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.

Author:

Harald Barsnes

Constructor Summary

Constructors

Constructor and Description
ProteinSequencePane()

Method Summary

Modifier and Type	Method and Description
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

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ProteinSequencePane

public ProteinSequencePane()

Method Detail

formatProteinSequence

public 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. The result is inserted into the provided JEditorPane.

Parameters:

editorPane - the editor pane to add the formatted sequence to

cleanSequence - the clean protein sequence, i.e., just the amino acid sequence

coverage - 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 formating

tagColors - the colors to use for the different tags, key is the tag

showModifications - if the modifications are to be highlighted or not

showVariants - if the variants are to be highlighted or not

showCoverage - if the coverage is to be highlighted or not

Returns:

the calculated sequence coverage in percent (0-100)

formatProteinSequence

public static double formatProteinSequence(JEditorPane editorPane,
                                           String cleanSequence,
                                           int[] coverage)

Formats the protein sequence such that the covered parts of the sequence is highlighted. The result is inserted into the provided JEditorPane.

Parameters:

editorPane - the editor pane to add the formatted sequence to

cleanSequence - the clean protein sequence, i.e., just the amino acid sequence

coverage - 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)

Returns:

the calculated sequence coverage in percent (0-100)

formatProteinSequence

public 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. The result is inserted into the provided JEditorPane.

Parameters:

editorPane - the editor pane to add the formatted sequence to

cleanSequence - the clean protein sequence, i.e., just the amino acid sequence

selectedPeptideStart - the starting index of the selected peptide

selectedPeptideEnd - the ending index of the selected peptide

coverage - 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)

Returns:

the calculated sequence coverage in percent (0-100)

formatProteinSequence

public 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. The result is inserted into the provided JEditorPane. This method accounts for redundancies of the selected peptide in the protein sequence

Parameters:

editorPane - the editor pane to add the formatted sequence to

cleanSequence - the clean protein sequence, i.e., just the amino acid sequence

selectedPeptideStart - the start indexes of the currently selected peptide

selectedPeptideEnd - the end indexes if the currently selected peptide

coverage - 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)

Returns:

the calculated sequence coverage in percent (0-100)

formatProteinSequence

public 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. The result is inserted into the provided JEditorPane.

Parameters:

editorPane - the editor pane to add the formatted sequence to

cleanSequence - the clean protein sequence, i.e., just the amino acid sequence

selectedPeptideStart - the start index of the currently selected peptide

selectedPeptideEnd - the end index if the currently selected peptide

coverage - 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 formating

selectedAnnotationType - the colors to use for the different tags, key is the tag

Returns:

the calculated sequence coverage in percent (0-100)