[jvm-packages] create dmatrix with specified missing value (#1272)

* create dmatrix with specified missing value

* update dmlc-core

* support for predict method in spark package

repartitioning

work around

* add more elements to work around training set empty partition issue

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/DMatrix.java

@@ -118,6 +118,19 @@ public class DMatrix {
     handle = out[0];
   }
 
+  /**
+   * create DMatrix from dense matrix
+   * @param data data values
+   * @param nrow number of rows
+   * @param ncol number of columns
+   * @param missing the specified value to represent the missing value
+   */
+  public DMatrix(float[] data, int nrow, int ncol, float missing) throws XGBoostError {
+    long[] out = new long[1];
+    JNIErrorHandle.checkCall(XGBoostJNI.XGDMatrixCreateFromMat(data, nrow, ncol, missing, out));
+    handle = out[0];
+  }
+
   /**
    * used for DMatrix slice
    */

jvm-packages/xgboost4j/src/main/scala/ml/dmlc/xgboost4j/scala/DMatrix.scala

@@ -67,6 +67,19 @@ class DMatrix private[scala](private[scala] val jDMatrix: JDMatrix) {
     this(new JDMatrix(data, nrow, ncol))
   }
 
+  /**
+   * create DMatrix from dense matrix
+   *
+   * @param data data values
+   * @param nrow number of rows
+   * @param ncol number of columns
+   * @param missing the specified value to represent the missing value
+   */
+  @throws(classOf[XGBoostError])
+  def this(data: Array[Float], nrow: Int, ncol: Int, missing: Float) {
+    this(new JDMatrix(data, nrow, ncol, missing))
+  }
+
   /**
    * set label of dmatrix
    *