join predicates together

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15942 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/alignment/SAMRecordFlagConjunctionPredicate.java

+/* SAMRecordFlagConjunctionPredicate
+ *
+ * This file is part of Artemis
+ * 
+ * Copyright (C) 2011  Genome Research Limited
+ * 
+ * This program 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 2
+ * 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 General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ **/
+
+package uk.ac.sanger.artemis.components.alignment;
+
+import net.sf.samtools.SAMRecord;
+
+/**
+ *  Test the SAMRecord flag.
+ **/
+public class SAMRecordFlagConjunctionPredicate implements SAMRecordPredicate
+{
+  private SAMRecordPredicate p1;
+  private SAMRecordPredicate p2;
+  private int type;  // AND or OR
+  private boolean is1 = true;
+  private boolean is2 = true;
+  private static int AND = 0;
+  
+  public SAMRecordFlagConjunctionPredicate(SAMRecordPredicate p1, SAMRecordPredicate p2, int type, boolean is1, boolean is2)
+  {
+    this.p1 = p1;
+    this.p2 = p2;
+    this.type = type;
+    this.is1 = is1;
+    this.is2 = is2;
+  }
+  
+  public boolean testPredicate(SAMRecord samRecord)
+  {
+    if(type == AND)
+    {
+      if(!is1 && !is2)
+      {
+        if(!p1.testPredicate(samRecord) && !p2.testPredicate(samRecord))
+          return true;
+      }
+      else if(!is1)
+      {
+        if(!p1.testPredicate(samRecord) && p2.testPredicate(samRecord))
+          return true;
+      }
+      else if(!is2)
+      {
+        if(p1.testPredicate(samRecord) && !p2.testPredicate(samRecord))
+          return true;
+      }
+      else if(is1 && is2)
+      {
+        if(p1.testPredicate(samRecord) && p2.testPredicate(samRecord))
+          return true;
+      }
+    }
+    else
+    {
+      if(!is1 && !is2)
+      {
+        if(!p1.testPredicate(samRecord) || !p2.testPredicate(samRecord))
+          return true;
+      }
+      else if(!is1)
+      {
+        if(!p1.testPredicate(samRecord) || p2.testPredicate(samRecord))
+          return true;
+      }
+      else if(!is2)
+      {
+        if(p1.testPredicate(samRecord) || !p2.testPredicate(samRecord))
+          return true;
+      }
+      else if(is1 && is2)
+      {
+        if(p1.testPredicate(samRecord) || p2.testPredicate(samRecord))
+          return true;
+      }
+    }
+    return false;
+  }
+  
+}
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