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 Details

  • Method Details

    • 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)