How to Change Highlighting Color in Java Swing Textarea? and Also, Change the Beginning of Text Corresponding to the Highlighting Location

Hightlight and change Color of Text in JTextArea

You can use JComponent#setForeground(Color) - But not on JTextArea. It's not designed for that purpose. Instead, use a JEditorPane or JTextPane.

On these components you can also use HTML tags, like:

"<html>My text: <font color=\"blue\">" + myString + "</font></html>"

You can change the background of the JTextArea using JTextArea#setBackground (If that what you mean).

How to change text color in the JTextArea?

JTextArea is meant to entertain Plain Text. The settings applied to a single character applies to whole of the document in JTextArea. But with JTextPane or JEditorPane you have the choice, to colour your String Literals as per your liking. Here with the help of JTextPane, you can do it like this :

import java.awt.*;

import java.awt.event.*;

import javax.swing.*;

import javax.swing.border.*;

import javax.swing.text.AttributeSet;
import javax.swing.text.SimpleAttributeSet;
import javax.swing.text.StyleConstants;
import javax.swing.text.StyleContext;

public class TextPaneTest extends JFrame
{
    private JPanel topPanel;
    private JTextPane tPane;

    public TextPaneTest()
    {
        topPanel = new JPanel();        

        setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        setLocationRelativeTo(null);            

        EmptyBorder eb = new EmptyBorder(new Insets(10, 10, 10, 10));

        tPane = new JTextPane();                
        tPane.setBorder(eb);
        //tPane.setBorder(BorderFactory.createLineBorder(Color.DARK_GRAY));
        tPane.setMargin(new Insets(5, 5, 5, 5));

        topPanel.add(tPane);

        appendToPane(tPane, "My Name is Too Good.\n", Color.RED);
        appendToPane(tPane, "I wish I could be ONE of THE BEST on ", Color.BLUE);
        appendToPane(tPane, "Stack", Color.DARK_GRAY);
        appendToPane(tPane, "Over", Color.MAGENTA);
        appendToPane(tPane, "flow", Color.ORANGE);

        getContentPane().add(topPanel);

        pack();
        setVisible(true);   
    }

    private void appendToPane(JTextPane tp, String msg, Color c)
    {
        StyleContext sc = StyleContext.getDefaultStyleContext();
        AttributeSet aset = sc.addAttribute(SimpleAttributeSet.EMPTY, StyleConstants.Foreground, c);

        aset = sc.addAttribute(aset, StyleConstants.FontFamily, "Lucida Console");
        aset = sc.addAttribute(aset, StyleConstants.Alignment, StyleConstants.ALIGN_JUSTIFIED);

        int len = tp.getDocument().getLength();
        tp.setCaretPosition(len);
        tp.setCharacterAttributes(aset, false);
        tp.replaceSelection(msg);
    }

    public static void main(String... args)
    {
        SwingUtilities.invokeLater(new Runnable()
            {
                public void run()
                {
                    new TextPaneTest();
                }
            });
    }
}

here is the Output :

JTextPane

Highlight Text In JTextArea In Presence of Duplicate Lines

You had it almost all by yourself there were few issues though.

You should use getSelectionStart() rather than getCaretPosition().
Highlight should start from index not from index-1.

Please see the example below. Select what you want to highlight right click on the textArea or press the button to highlight your selection:

public class HighlightingTextArea {    
    public static void main(String[] args) {    
        SwingUtilities.invokeLater(new Runnable() {    
            @Override
            public void run() {
                final JTextArea textArea = new JTextArea(10, 44);
                textArea.append("AAAA\nBBBB\nAAAA\nCCCC\nDDDD\nAAAA");
                JButton b = new JButton(new AbstractAction("highlight") {    
                    @Override
                    public void actionPerformed(ActionEvent e) {
                        highlightTextAreaSelection(textArea);
                    }
                });
                textArea.addMouseListener(new MouseAdapter() {    
                    @Override
                    public void mousePressed(MouseEvent e) {
                        super.mousePressed(e);
                        if (e.getButton() == MouseEvent.BUTTON3) {
                            highlightTextAreaSelection(textArea);
                        }
                    }
                });
                JPanel panel = new JPanel(new BorderLayout());
                panel.add(textArea);
                panel.add(b, BorderLayout.SOUTH);
                JFrame f = new JFrame();
                f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
                f.setContentPane(panel);
                f.pack();
                f.setVisible(true);
            }
        });
    }

    private static void highlightTextAreaSelection(JTextArea textArea) {
        String highlightedText = textArea.getSelectedText();
        if (highlightedText != null) {
            try {
                int index = textArea.getText().indexOf(highlightedText, textArea.getSelectionStart());
                textArea.getHighlighter().addHighlight(index, index + highlightedText.length(),
                        new DefaultHighlighter.DefaultHighlightPainter(Color.ORANGE));
            } catch (BadLocationException ex) {
            }
        }
    }
}

JTextArea or JTextPane Set Highlighted Text Color

If you mean the "normal" highlight color (when you drag your mouse over the text), this can simply be achieved by

textArea.setSelectionColor(Color.LIGHT_GRAY);

(or whatever color you want it to have.)

If you want to programmatically highlight a character sequence in your text area:

String searchedWord = "word";
int pos1 = textArea.getText().indexOf(searchedWord);
int pos2 = pos1 + searchedWord.length();
try {
    textArea.getHighlighter().addHighlight(pos1, pos2,
            new DefaultHighlighter.DefaultHighlightPainter(Color.LIGHT_GRAY));
} catch (BadLocationException e) {
    e.printStackTrace();
}

(The same works for a JTextPane too)

Different text color in a JTextArea

Not with a JTextArea. You can, however, use a JTextPane which allows for attributes to be applied to text. If you want examples, take a look at the Text Component Tutorial.