Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / io / PContactPredictionFile.java

diff --git a/src/jalview/io/PContactPredictionFile.java b/src/jalview/io/PContactPredictionFile.java
index 92500c0..164d7cc 100644 (file)
--- a/src/jalview/io/PContactPredictionFile.java
+++ b/src/jalview/io/PContactPredictionFile.java
@@ -25,6 +25,7 @@ import jalview.datamodel.SequenceI;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -44,8 +45,10 @@ import java.util.Map;
  */
 public class PContactPredictionFile extends AlignFile
 {
-  public PContactPredictionFile(String inFile, DataSourceType fileSourceType)
-          throws IOException
+  protected static final String CONTACT_PREDICTION = "CONTACT_PREDICTION";
+
+  public PContactPredictionFile(String inFile,
+          DataSourceType fileSourceType) throws IOException
   {
     super(inFile, fileSourceType);
 
@@ -106,7 +109,30 @@ public class PContactPredictionFile extends AlignFile
 
         if (cm == null)
         {
-          cm = new ContactMatrix(true);
+          cm = new ContactMatrix(true)
+          {
+            @Override
+            public String getType()
+            {
+              return CONTACT_PREDICTION;
+            }
+
+            @Override
+            public int getHeight()
+            {
+              // TODO Auto-generated method stub
+              // return maximum contact height
+              return 0;
+            }
+
+            @Override
+            public int getWidth()
+            {
+              // TODO Auto-generated method stub
+              // return total number of residues with contacts
+              return 0;
+            }
+          };
           models.add(cm);
         }
 
@@ -118,13 +144,15 @@ public class PContactPredictionFile extends AlignFile
         } catch (Exception x)
         {
           error = true;
-          errormessage = "Couldn't process line: "
-                  + x.getLocalizedMessage() + "\n" + line;
+          errormessage = "Couldn't process line: " + x.getLocalizedMessage()
+                  + "\n" + line;
           return;
         }
         cm.addContact(left, right, (float) strength);
       }
     }
+    // TODO COMPLETE
+    throw (new Error("Not Implemented yet."));
   }
 
   @Override