JAL-2349 JAL-2382 Contact prediction/CASP-RR importer

diff --git a/src/jalview/io/PContactPredictionFile.java b/src/jalview/io/PContactPredictionFile.java
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+++ b/src/jalview/io/PContactPredictionFile.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.datamodel.ContactMatrix;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * A file parser for contact prediction files.
+ * 
+ * An example file is the following
+ * 
+ * <pre>
+ * 
+ * </pre>
+ * 
+ * 
+ * @author jim procter
+ * 
+ */
+public class PContactPredictionFile extends AlignFile
+{
+  public PContactPredictionFile(String inFile, DataSourceType fileSourceType)
+          throws IOException
+  {
+    super(inFile, fileSourceType);
+
+  }
+
+  public PContactPredictionFile(FileParse source) throws IOException
+  {
+    super(source);
+  }
+
+  Integer fWidth;
+
+  List<ContactMatrix> models = new ArrayList<ContactMatrix>();
+
+  public List<ContactMatrix> getContactMatrices()
+  {
+    return models;
+  }
+
+  /*
+   * RaptorX pattern:
+   * for a contact prediction
+   * Target sequence
+   * alignment for target sequence
+   * contact matrix for sequence
+   * models generated that fit matrix
+   */
+
+  /*
+   * TODO: create annotation rows from contact matrices.
+   * (non-Javadoc)
+   * @see jalview.io.AlignFile#parse()
+   */
+  @Override
+  public void parse() throws IOException
+  {
+    String line;
+    /*
+     * stash any header lines if we've been given a CASP-RR file 
+     */
+    Map<String, String> header = new HashMap<String, String>();
+    ContactMatrix cm = null;
+
+    while ((line = nextLine()) != null)
+    {
+      int left, right;
+      double strength = Float.NaN;
+      String parts[] = line.split("\\s+");
+
+      // check for header tokens in parts[0]
+
+      // others - stash details
+      // MODEL - start a new matrix
+      // skip comments ?
+
+      if (parts.length == 3) // and all are integers
+      {
+
+        if (cm == null)
+        {
+          cm = new ContactMatrix(true);
+          models.add(cm);
+        }
+
+        try
+        {
+          left = Integer.parseInt(parts[0]);
+          right = Integer.parseInt(parts[1]);
+          strength = Double.parseDouble(parts[2]);
+        } catch (Exception x)
+        {
+          error = true;
+          errormessage = "Couldn't process line: "
+                  + x.getLocalizedMessage() + "\n" + line;
+          return;
+        }
+        cm.addContact(left, right, (float) strength);
+      }
+    }
+  }
+
+  @Override
+  public String print(SequenceI[] sqs, boolean jvsuffix)
+  {
+    // TODO Auto-generated method stub
+    return "Not valid.";
+  }
+}