following several tutorials and examples I came up with the next algorithm to set the camera focus on a specific spot, the problem is that the camera completely ignores the spot and performs a normal overall focus instead of the rect area which I have specified. Is there anything else that I am missing in the algorithm? This has been tested on several phones all with Android 4.0 and above, so the focus area API is supported on these devices. Note, the app I am writing works in landscape mode only.
@Override
public boolean onTouchEvent(final MotionEvent event)
{
    if (event.getAction() == MotionEvent.ACTION_UP)
    {
        float x = event.getX();
        float y = event.getY();
        float touchMajor = event.getTouchMajor();
        float touchMinor = event.getTouchMinor();
        Rect touchRect = new Rect((int)(x - touchMajor / 2), (int)(y - touchMinor / 2), (int)(x + touchMajor / 2), (int)(y + touchMinor / 2));
        this.submitFocusAreaRect(touchRect);
    }
}
private void submitFocusAreaRect(final Rect touchRect)
{
    Camera.Parameters cameraParameters = camera.getParameters();
    if (cameraParameters.getMaxNumFocusAreas() == 0)
    {
        return;
    }
    // Convert from View's width and height to +/- 1000
    Rect focusArea = new Rect();
    focusArea.set(touchRect.left * 2000 / cameraSurfaceView.getWidth() - 1000, 
                      touchRect.top * 2000 / cameraSurfaceView.getHeight() - 1000,
                      touchRect.right * 2000 / cameraSurfaceView.getWidth() - 1000,
                      touchRect.bottom * 2000 / cameraSurfaceView.getHeight() - 1000);
    // Submit focus area to camera
    ArrayList<Camera.Area> focusAreas = new ArrayList<Camera.Area>();
    focusAreas.add(new Camera.Area(focusArea, 1000));
    cameraParameters.setFocusMode(Camera.Parameters.FOCUS_MODE_AUTO);
    cameraParameters.setFocusAreas(focusAreas);
    camera.setParameters(cameraParameters);
    // Start the autofocus operation
    camera.autoFocus(this);
}
Open the Camera app, then tap the Settings icon at the top left corner. Step 2. Tap the switch next to Tracking auto-focus to turn it off. If your camera still won't focus, resetting the camera to its default settings may also be a solution.
before cameraParameters.setFocusAreas(focusAreas);, you should add this:
cameraParameters.setFocusMode(Camera.Parameters.FOCUS_MODE_AUTO);
this is not my code, but you can try it. All credits go to the guy/s that made the example here Touch to select focus and metering area
Also I contributed to there code with a small line because when I was clicking the second time on the Surface View the app was crushing. So plese be free to use the class ("AndroidCamera") bellow:
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.Executors;
import java.util.concurrent.ScheduledExecutorService;
import java.util.concurrent.TimeUnit;
import android.app.Activity;
import android.content.ContentValues;
import android.content.Context;
import android.content.pm.ActivityInfo;
import android.graphics.Canvas;
import android.graphics.Color;
import android.graphics.Paint;
import android.graphics.PixelFormat;
import android.graphics.Rect;
import android.hardware.Camera;
import android.hardware.Camera.AutoFocusCallback;
import android.hardware.Camera.Face;
import android.hardware.Camera.FaceDetectionListener;
import android.hardware.Camera.Parameters;
import android.hardware.Camera.PictureCallback;
import android.hardware.Camera.ShutterCallback;
import android.net.Uri;
import android.os.Bundle;
import android.provider.MediaStore.Images.Media;
import android.view.LayoutInflater;
import android.view.SurfaceHolder;
import android.view.View;
import android.view.ViewGroup.LayoutParams;
import android.widget.Button;
import android.widget.TextView;
public class AndroidCamera extends Activity implements SurfaceHolder.Callback{
    Camera camera;
    CameraSurfaceView cameraSurfaceView;
    SurfaceHolder surfaceHolder;
    boolean previewing = false;
    LayoutInflater controlInflater = null;
    Button buttonTakePicture;
    TextView prompt;
    DrawingView drawingView;
    Face[] detectedFaces;
    final int RESULT_SAVEIMAGE = 0;
    private ScheduledExecutorService myScheduledExecutorService;
    /** Called when the activity is first created. */
    @Override
    public void onCreate(Bundle savedInstanceState) {
        super.onCreate(savedInstanceState);
        setContentView(R.layout.main);
        setRequestedOrientation(ActivityInfo.SCREEN_ORIENTATION_LANDSCAPE);
        getWindow().setFormat(PixelFormat.UNKNOWN);
        cameraSurfaceView = (CameraSurfaceView)findViewById(R.id.camerapreview);
        surfaceHolder = cameraSurfaceView.getHolder();
        surfaceHolder.addCallback(this);
        surfaceHolder.setType(SurfaceHolder.SURFACE_TYPE_PUSH_BUFFERS);
        drawingView = new DrawingView(this);
        LayoutParams layoutParamsDrawing
                = new LayoutParams(LayoutParams.FILL_PARENT,
                LayoutParams.FILL_PARENT);
        this.addContentView(drawingView, layoutParamsDrawing);
        controlInflater = LayoutInflater.from(getBaseContext());
        View viewControl = controlInflater.inflate(R.layout.control, null);
        LayoutParams layoutParamsControl
                = new LayoutParams(LayoutParams.FILL_PARENT,
                LayoutParams.FILL_PARENT);
        this.addContentView(viewControl, layoutParamsControl);
        buttonTakePicture = (Button)findViewById(R.id.takepicture);
        buttonTakePicture.setOnClickListener(new Button.OnClickListener(){
            @Override
            public void onClick(View arg0) {
                // TODO Auto-generated method stub
                camera.takePicture(myShutterCallback,
                        myPictureCallback_RAW, myPictureCallback_JPG);
            }});
        /*
        LinearLayout layoutBackground = (LinearLayout)findViewById(R.id.background);
        layoutBackground.setOnClickListener(new LinearLayout.OnClickListener(){
   @Override
   public void onClick(View arg0) {
    // TODO Auto-generated method stub
    buttonTakePicture.setEnabled(false);
    camera.autoFocus(myAutoFocusCallback);
   }});
  */
        prompt = (TextView)findViewById(R.id.prompt);
    }
    public void touchFocus(final Rect tfocusRect){
        buttonTakePicture.setEnabled(false);
        camera.stopFaceDetection();
        //Convert from View's width and height to +/- 1000
        final Rect targetFocusRect = new Rect(
                tfocusRect.left * 2000/drawingView.getWidth() - 1000,
                tfocusRect.top * 2000/drawingView.getHeight() - 1000,
                tfocusRect.right * 2000/drawingView.getWidth() - 1000,
                tfocusRect.bottom * 2000/drawingView.getHeight() - 1000);
        final List<Camera.Area> focusList = new ArrayList<Camera.Area>();
        Camera.Area focusArea = new Camera.Area(targetFocusRect, 1000);
        focusList.add(focusArea);
        Parameters para = camera.getParameters();
        para.setFocusAreas(focusList);
        para.setMeteringAreas(focusList);
        camera.setParameters(para);
        camera.autoFocus(myAutoFocusCallback);
        drawingView.setHaveTouch(true, tfocusRect);
        drawingView.invalidate();
        camera.startFaceDetection();
    }
    FaceDetectionListener faceDetectionListener
            = new FaceDetectionListener(){
        @Override
        public void onFaceDetection(Face[] faces, Camera tcamera) {
            if (faces.length == 0){
                //prompt.setText(" No Face Detected! ");
                drawingView.setHaveFace(false);
            }else{
                //prompt.setText(String.valueOf(faces.length) + " Face Detected :) ");
                drawingView.setHaveFace(true);
                detectedFaces = faces;
                //Set the FocusAreas using the first detected face
                List<Camera.Area> focusList = new ArrayList<Camera.Area>();
                Camera.Area firstFace = new Camera.Area(faces[0].rect, 1000);
                focusList.add(firstFace);
                Parameters para = camera.getParameters();
                if(para.getMaxNumFocusAreas()>0){
                    para.setFocusAreas(focusList);
                }
                if(para.getMaxNumMeteringAreas()>0){
                    para.setMeteringAreas(focusList);
                }
                camera.setParameters(para);
                buttonTakePicture.setEnabled(false);
                //Stop further Face Detection
                camera.stopFaceDetection();
                buttonTakePicture.setEnabled(false);
    /*
     * Allways throw java.lang.RuntimeException: autoFocus failed
     * if I call autoFocus(myAutoFocusCallback) here!
     *
     camera.autoFocus(myAutoFocusCallback);
    */
                //Delay call autoFocus(myAutoFocusCallback)
                myScheduledExecutorService = Executors.newScheduledThreadPool(1);
                myScheduledExecutorService.schedule(new Runnable(){
                    public void run() {
                        camera.autoFocus(myAutoFocusCallback);
                    }
                }, 500, TimeUnit.MILLISECONDS);
            }
            drawingView.invalidate();
        }};
    AutoFocusCallback myAutoFocusCallback = new AutoFocusCallback(){
        @Override
        public void onAutoFocus(boolean arg0, Camera arg1) {
            // TODO Auto-generated method stub
            if (arg0){
                buttonTakePicture.setEnabled(true);
                camera.cancelAutoFocus();
            }
            float focusDistances[] = new float[3];
            arg1.getParameters().getFocusDistances(focusDistances);
            prompt.setText("Optimal Focus Distance(meters): "
                    + focusDistances[Camera.Parameters.FOCUS_DISTANCE_OPTIMAL_INDEX]);
        }};
    ShutterCallback myShutterCallback = new ShutterCallback(){
        @Override
        public void onShutter() {
            // TODO Auto-generated method stub
        }};
    PictureCallback myPictureCallback_RAW = new PictureCallback(){
        @Override
        public void onPictureTaken(byte[] arg0, Camera arg1) {
            // TODO Auto-generated method stub
        }};
    PictureCallback myPictureCallback_JPG = new PictureCallback(){
        @Override
        public void onPictureTaken(byte[] arg0, Camera arg1) {
            // TODO Auto-generated method stub
   /*Bitmap bitmapPicture
    = BitmapFactory.decodeByteArray(arg0, 0, arg0.length); */
            Uri uriTarget = getContentResolver().insert(Media.EXTERNAL_CONTENT_URI, new ContentValues());
            OutputStream imageFileOS;
            try {
                imageFileOS = getContentResolver().openOutputStream(uriTarget);
                imageFileOS.write(arg0);
                imageFileOS.flush();
                imageFileOS.close();
                prompt.setText("Image saved: " + uriTarget.toString());
            } catch (FileNotFoundException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            } catch (IOException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
            camera.startPreview();
            camera.startFaceDetection();
        }};
    @Override
    public void surfaceChanged(SurfaceHolder holder, int format, int width,
                               int height) {
        // TODO Auto-generated method stub
        if(previewing){
            camera.stopFaceDetection();
            camera.stopPreview();
            previewing = false;
        }
        if (camera != null){
            try {
                camera.setPreviewDisplay(surfaceHolder);
                camera.startPreview();
                prompt.setText(String.valueOf(
                        "Max Face: " + camera.getParameters().getMaxNumDetectedFaces()));
                camera.startFaceDetection();
                previewing = true;
            } catch (IOException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
        }
    }
    @Override
    public void surfaceCreated(SurfaceHolder holder) {
        // TODO Auto-generated method stub
        camera = Camera.open();
        camera.setFaceDetectionListener(faceDetectionListener);
    }
    @Override
    public void surfaceDestroyed(SurfaceHolder holder) {
        // TODO Auto-generated method stub
        camera.stopFaceDetection();
        camera.stopPreview();
        camera.release();
        camera = null;
        previewing = false;
    }
    private class DrawingView extends View{
        boolean haveFace;
        Paint drawingPaint;
        boolean haveTouch;
        Rect touchArea;
        public DrawingView(Context context) {
            super(context);
            haveFace = false;
            drawingPaint = new Paint();
            drawingPaint.setColor(Color.GREEN);
            drawingPaint.setStyle(Paint.Style.STROKE);
            drawingPaint.setStrokeWidth(2);
            haveTouch = false;
        }
        public void setHaveFace(boolean h){
            haveFace = h;
        }
        public void setHaveTouch(boolean t, Rect tArea){
            haveTouch = t;
            touchArea = tArea;
        }
        @Override
        protected void onDraw(Canvas canvas) {
            // TODO Auto-generated method stub
            if(haveFace){
                // Camera driver coordinates range from (-1000, -1000) to (1000, 1000).
                // UI coordinates range from (0, 0) to (width, height).
                int vWidth = getWidth();
                int vHeight = getHeight();
                for(int i=0; i<detectedFaces.length; i++){
                    if(i == 0){
                        drawingPaint.setColor(Color.GREEN);
                    }else{
                        drawingPaint.setColor(Color.RED);
                    }
                    int l = detectedFaces[i].rect.left;
                    int t = detectedFaces[i].rect.top;
                    int r = detectedFaces[i].rect.right;
                    int b = detectedFaces[i].rect.bottom;
                    int left = (l+1000) * vWidth/2000;
                    int top  = (t+1000) * vHeight/2000;
                    int right = (r+1000) * vWidth/2000;
                    int bottom = (b+1000) * vHeight/2000;
                    canvas.drawRect(
                            left, top, right, bottom,
                            drawingPaint);
                }
            }else{
                canvas.drawColor(Color.TRANSPARENT);
            }
            if(haveTouch){
                drawingPaint.setColor(Color.BLUE);
                canvas.drawRect(
                        touchArea.left, touchArea.top, touchArea.right, touchArea.bottom,
                        drawingPaint);
            }
        }
    }
}
All I did was to add camera.startFaceDetection(); after drawingView.invalidate();
P.S. On that site is a link for downloading the entire project!
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