1 files changed, 172 insertions, 0 deletions
diff --git a/src/de/lmu/ifi/dbs/elki/persistent/OnDiskUpperTriangleMatrix.java b/src/de/lmu/ifi/dbs/elki/persistent/OnDiskUpperTriangleMatrix.java
new file mode 100644
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+++ b/src/de/lmu/ifi/dbs/elki/persistent/OnDiskUpperTriangleMatrix.java
@@ -0,0 +1,172 @@
+package de.lmu.ifi.dbs.elki.persistent;
+/*
+This file is part of ELKI:
+Environment for Developing KDD-Applications Supported by Index-Structures
+
+Copyright (C) 2011
+Ludwig-Maximilians-Universität München
+Lehr- und Forschungseinheit für Datenbanksysteme
+ELKI Development Team
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU Affero General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Affero General Public License for more details.
+
+You should have received a copy of the GNU Affero General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+
+/**
+ * Class representing an upper triangle matrix backed by an on-disk array of
+ * O((n+1)*n/2) size
+ * 
+ * @apiviz.composedOf OnDiskArray
+ * 
+ * @author Erich Schubert
+ */
+public class OnDiskUpperTriangleMatrix {
+  /**
+   * Serial number, also used for generating a magic
+   */
+  private static final long serialVersionUID = -4489942156357634702L;
+
+  /**
+   * Size of this class' header
+   */
+  private static final int TRIANGLE_HEADER_SIZE = 4;
+
+  /**
+   * Size of the matrix
+   */
+  private int matrixsize;
+
+  /**
+   * Data storage
+   */
+  private OnDiskArray array;
+
+  /**
+   * Constructor to access an existing array.
+   * 
+   * @param filename File name
+   * @param magicseed Magic number
+   * @param extraheadersize Size of extra header data
+   * @param recordsize Record size
+   * @param writable flag to open writable
+   * @throws IOException on IO errors
+   */
+  public OnDiskUpperTriangleMatrix(File filename, int magicseed, int extraheadersize, int recordsize, boolean writable) throws IOException {
+    array = new OnDiskArray(filename, OnDiskArray.mixMagic((int) serialVersionUID, magicseed), extraheadersize + TRIANGLE_HEADER_SIZE, recordsize, writable);
+    ByteBuffer header = array.getExtraHeader();
+    this.matrixsize = header.getInt();
+    if(arraysize(matrixsize) != array.getNumRecords()) {
+      throw new IOException("Matrix file size doesn't match specified dimensions: " + matrixsize + "->" + arraysize(matrixsize) + " vs. " + array.getNumRecords());
+    }
+  }
+
+  /**
+   * Constructor to access a new array.
+   * 
+   * @param filename File name
+   * @param magicseed Magic number
+   * @param extraheadersize Size of extra header data
+   * @param recordsize Record size
+   * @param matrixsize Size of matrix to store
+   * @throws IOException on IO errors
+   */
+  public OnDiskUpperTriangleMatrix(File filename, int magicseed, int extraheadersize, int recordsize, int matrixsize) throws IOException {
+    if(matrixsize >= 0xFFFF) {
+      throw new RuntimeException("Matrix size is too big and will overflow the integer datatype.");
+    }
+    this.matrixsize = matrixsize;
+    array = new OnDiskArray(filename, OnDiskArray.mixMagic((int) serialVersionUID, magicseed), extraheadersize + TRIANGLE_HEADER_SIZE, recordsize, arraysize(matrixsize));
+    ByteBuffer header = array.getExtraHeader();
+    header.putInt(this.matrixsize);
+  }
+
+  /**
+   * Resize the matrix to cover newsize x newsize.
+   * 
+   * @param newsize New matrix size.
+   * @throws IOException on IO errors
+   */
+  public synchronized void resizeMatrix(int newsize) throws IOException {
+    if(newsize >= 0xFFFF) {
+      throw new RuntimeException("Matrix size is too big and will overflow the integer datatype.");
+    }
+    if(!array.isWritable()) {
+      throw new IOException("Can't resize a read-only array.");
+    }
+    array.resizeFile(arraysize(newsize));
+    this.matrixsize = newsize;
+    ByteBuffer header = array.getExtraHeader();
+    header.putInt(this.matrixsize);
+  }
+
+  /**
+   * Compute the size of the needed backing array from the matrix dimensions.
+   * 
+   * @param matrixsize size of the matrix
+   * @return size of the array
+   */
+  private static int arraysize(int matrixsize) {
+    return matrixsize * (matrixsize + 1) / 2;
+  }
+
+  /**
+   * Compute the offset within the file.
+   * 
+   * @param x First coordinate
+   * @param y Second coordinate
+   * @return Linear offset
+   */
+  private int computeOffset(int x, int y) {
+    if(y > x) {
+      return computeOffset(y, x);
+    }
+    return (x * (x + 1)) / 2 + y;
+  }
+
+  /**
+   * Get a record buffer
+   * 
+   * @param x First coordinate
+   * @param y Second coordinate
+   * @return Byte buffer for the record
+   * @throws IOException on IO errors
+   */
+  public synchronized ByteBuffer getRecordBuffer(int x, int y) throws IOException {
+    if(x >= matrixsize || y >= matrixsize) {
+      throw new ArrayIndexOutOfBoundsException();
+    }
+    return array.getRecordBuffer(computeOffset(x, y));
+  }
+  
+  /**
+   * Close the matrix file.
+   * 
+   * @throws IOException on IO errors
+   */
+  public synchronized void close() throws IOException {
+    array.close();
+  }
+
+  /**
+   * Query the size of the matrix.
+   * 
+   * @return size of the matrix
+   */
+  public int getMatrixSize() {
+    return matrixsize;
+  }
+}