public static int getImageMinWidth2(Context context) {
if (mScreenWidth <= 0) {
mScreenWidth =
DensityUtil.getImageWeidth(context, 1.0F) - DensityUtil.getDisplayMetrics(context, 40F);
mScreenWidth = mScreenWidth / 4;
}
return mScreenWidth;
}
static void calculateEigenvector(String file, String chr, int binsize) throws IOException {
if (!file.endsWith("hic")) {
System.err.println("Only 'hic' files are supported");
System.exit(-1);
}
// Load the expected density function, if it exists.
Map<Integer, DensityFunction> zoomToDensityMap = null;
String densityFile = file + ".densities";
if (FileUtils.resourceExists(densityFile)) {
InputStream is = null;
try {
is = ParsingUtils.openInputStream(densityFile);
zoomToDensityMap = DensityUtil.readDensities(is);
} finally {
if (is != null) is.close();
}
} else {
System.err.println("Densities file doesn't exist");
System.exit(-1);
}
SeekableStream ss = IGVSeekableStreamFactory.getStreamFor(file);
Dataset dataset = (new DatasetReader(ss)).read();
Chromosome[] tmp = dataset.getChromosomes();
Map<String, Chromosome> chromosomeMap = new HashMap<String, Chromosome>();
for (Chromosome c : tmp) {
chromosomeMap.put(c.getName(), c);
}
if (!chromosomeMap.containsKey(chr)) {
System.err.println("Unknown chromosome: " + chr);
System.exit(-1);
}
int zoomIdx = 0;
boolean found = false;
for (; zoomIdx < HiCGlobals.zoomBinSizes.length; zoomIdx++) {
if (HiCGlobals.zoomBinSizes[zoomIdx] == binsize) {
found = true;
break;
}
}
if (!found) {
System.err.println("Unknown bin size: " + binsize);
System.exit(-1);
}
Matrix matrix = dataset.getMatrix(chromosomeMap.get(chr), chromosomeMap.get(chr));
MatrixZoomData zd = matrix.getObservedMatrix(zoomIdx);
final DensityFunction df = zoomToDensityMap.get(zd.getZoom());
double[] eigenvector = zd.computeEigenvector(df, 0);
for (double ev : eigenvector) System.out.print(ev + " ");
System.out.println();
}
/**
* 获取圆角位图的方法
*
* @param bitmap 需要转化成圆角的位图
* @param pixels 圆角的度数，数值越大，圆角越大
* @return 处理后的圆角位图
*/
public static Bitmap toRoundCorner(Context context, Bitmap bitmap, int pixels) {
Bitmap newbmp =
ThumbnailUtils.extractThumbnail(
bitmap,
DensityUtil.dip2px(context, 60),
DensityUtil.dip2px(context, 60),
ThumbnailUtils.OPTIONS_RECYCLE_INPUT);
Bitmap output = Bitmap.createBitmap(newbmp.getWidth(), newbmp.getHeight(), Config.ARGB_8888);
Canvas canvas = new Canvas(output);
final int color = 0xff424242;
final Paint paint = new Paint();
final Rect rect = new Rect(0, 0, newbmp.getWidth(), newbmp.getWidth());
final RectF rectF = new RectF(rect);
final float roundPx = pixels;
paint.setAntiAlias(true);
canvas.drawARGB(0, 0, 0, 0);
paint.setColor(color);
canvas.drawRoundRect(rectF, roundPx, roundPx, paint);
paint.setXfermode(new PorterDuffXfermode(Mode.SRC_IN));
canvas.drawBitmap(newbmp, rect, rect, paint);
newbmp.recycle();
return output;
}
private void initView() {
drawerLayout = (DrawerLayout) findViewById(R.id.drawer_layout);
RelativeLayout menu = (RelativeLayout) findViewById(R.id.menu);
int width =
getResources().getDisplayMetrics().widthPixels - DensityUtil.dip2px(mContext, 56 - 8);
DrawerLayout.LayoutParams params =
(android.support.v4.widget.DrawerLayout.LayoutParams) menu.getLayoutParams();
params.width = width;
menu.setLayoutParams(params);
drawerLayout.setDrawerListener(
new DrawerLayout.DrawerListener() {
@Override
public void onDrawerSlide(View view, float v) {}
@Override
public void onDrawerOpened(View view) {
closePopView();
updateLockStatus();
}
@Override
public void onDrawerClosed(View view) {}
@Override
public void onDrawerStateChanged(int i) {}
});
tv_lock_status = (TextView) findViewById(R.id.tv_lock_status);
drawer_logo = (ImageView) findViewById(R.id.drawer_logo);
actionView = (ActionView) findViewById(R.id.btn_more);
tv_tab_box = (TextView) findViewById(R.id.tab_box);
tv_tab_lock = (TextView) findViewById(R.id.tab_lock);
// tab_thumb
tab_thumb = findViewById(R.id.tab_thumb);
RelativeLayout.LayoutParams thumbLp = (RelativeLayout.LayoutParams) tab_thumb.getLayoutParams();
thumbLp.width = 0;
tab_thumb.requestLayout();
// vp_main
vp_main = (ViewPager) findViewById(R.id.vp_main);
mainAdapter = new MainPagerAdapter(mContext);
vp_main.setAdapter(mainAdapter);
vp_main.setOnPageChangeListener(new PagerListener());
// pop
popView = findViewById(R.id.layout_pop);
pop_background = findViewById(R.id.pop_background);
pop_background.setOnClickListener(
new View.OnClickListener() {
@Override
public void onClick(View v) {
closePopView();
}
});
pop_background.setVisibility(View.INVISIBLE);
// image info
btn_menu = (ImageView) findViewById(R.id.btn_menu);
// txt
txt_drawer_version_num = (TextView) findViewById(R.id.txt_drawer_version_num);
txt_drawer_info_reply = (TextView) findViewById(R.id.txt_drawer_info_reply);
}
static void dumpMatrix(String file, String chr1, String chr2, int binsize, String type)
throws IOException {
if (!file.endsWith("hic")) {
System.err.println("Only 'hic' files are supported");
System.exit(-1);
}
// Load the expected density function, if it exists.
Map<Integer, DensityFunction> zoomToDensityMap = null;
if (type.equals("oe") || type.equals("pearson")) {
String densityFile = file + ".densities";
if (FileUtils.resourceExists(densityFile)) {
InputStream is = null;
try {
is = ParsingUtils.openInputStream(densityFile);
zoomToDensityMap = DensityUtil.readDensities(is);
} finally {
if (is != null) is.close();
}
} else {
System.err.println("Densities file doesn't exist, cannot calculate O/E or Pearson's");
System.exit(-1);
}
}
SeekableStream ss = IGVSeekableStreamFactory.getStreamFor(file);
Dataset dataset = (new DatasetReader(ss)).read();
Chromosome[] tmp = dataset.getChromosomes();
Map<String, Chromosome> chromosomeMap = new HashMap<String, Chromosome>();
for (Chromosome c : tmp) {
chromosomeMap.put(c.getName(), c);
}
if (!chromosomeMap.containsKey(chr1)) {
System.err.println("Unknown chromosome: " + chr1);
System.exit(-1);
} else if (!chromosomeMap.containsKey(chr2)) {
System.err.println("Unknown chromosome: " + chr2);
System.exit(-1);
}
if (type.equals("oe") || type.equals("pearson")) {
if (!chr1.equals(chr2)) {
System.err.println("Chromosome " + chr1 + " not equal to Chromosome " + chr2);
System.err.println("Currently only intrachromosomal O/E and Pearson's are supported.");
System.exit(-1);
}
}
int zoomIdx = 0;
boolean found = false;
for (; zoomIdx < HiCGlobals.zoomBinSizes.length; zoomIdx++) {
if (HiCGlobals.zoomBinSizes[zoomIdx] == binsize) {
found = true;
break;
}
}
if (!found) {
System.err.println("Unknown bin size: " + binsize);
}
Matrix matrix = dataset.getMatrix(chromosomeMap.get(chr1), chromosomeMap.get(chr2));
MatrixZoomData zd = matrix.getObservedMatrix(zoomIdx);
if (type.equals("oe") || type.equals("pearson")) {
final DensityFunction df = zoomToDensityMap.get(zd.getZoom());
if (df == null) {
System.err.println("Densities not calculated to this resolution.");
System.exit(-1);
}
zd.dumpOE(df, type.equals("oe"));
} else zd.dump();
}