add restriction on the values of (x,y),if the value of x is less than…

… -width or the value of y is less than -height,the windows will be hidden.

src/main/java/org/broad/igv/prefs/IGVPreferences.java

@@ -568,6 +568,13 @@ public File getLastGenomeImportDirectory() {
     public void setApplicationFrameBounds(Rectangle bounds) {
 
         if (bounds.width > 0 && bounds.height > 0) {
+            // check the values of MaxX(x+width) and MaxY(y+width)
+            if(bounds.getMaxY()<300) {
+                bounds.setLocation(bounds.x,0);
+            }
+            if(bounds.getMaxX()<300) {
+                bounds.setLocation(0,bounds.y);
+            }
             StringBuffer buffer = new StringBuffer();
             buffer.append(bounds.x);
             buffer.append(",");

src/main/java/org/broad/igv/ui/IGV.java

@@ -247,7 +247,9 @@ public void windowGainedFocus(WindowEvent windowEvent) {
         Rectangle applicationBounds = preferences.getApplicationFrameBounds();
 
         if (applicationBounds == null || applicationBounds.getMaxX() > screenBounds.getWidth() ||
+                applicationBounds.getMaxX() < 300 ||
                 applicationBounds.getMaxY() > screenBounds.getHeight() ||
+                applicationBounds.getMaxY() < 300 ||
                 applicationBounds.width == 0 || applicationBounds.height == 0) {
             int width = Math.min(1150, (int) screenBounds.getWidth());
             int height = Math.min(800, (int) screenBounds.getHeight());