X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureMapping.java;h=d2dcb34108b6565ba24c3574b4946b68e6487db2;hb=1f491c8c9e66b3accb8bb9eae78c7d9caa63c1ac;hp=06e6bc3507f528ac69d7430b6552bd81f773a78d;hpb=6905363d02254a557f93f66a2b69d85aa0b23696;p=jalview.git

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 06e6bc3..d2dcb34 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -1,100 +1,101 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.structure;
-
-import jalview.datamodel.*;
-
-public class StructureMapping
-{
-  String mappingDetails;
-  SequenceI sequence;
-  String pdbfile;
-  String pdbid;
-  String pdbchain;
-
-  //Mapping index 0 is resNum, index 1 is atomNo
-  int[][] mapping;
-
-  public StructureMapping(SequenceI seq,
-                          String pdbfile,
-                          String pdbid,
-                          String chain,
-                          int[][] mapping,
-                          String mappingDetails)
-  {
-    sequence = seq;
-    this.pdbfile = pdbfile;
-    this.pdbid = pdbid;
-    this.pdbchain = chain;
-    this.mapping = mapping;
-    this.mappingDetails = mappingDetails;
-  }
-
-  public SequenceI getSequence()
-  {
-    return sequence;
-  }
-
-  public String getChain()
-  {
-    return pdbchain;
-  }
-
-  public String getPdbId()
-  {
-    return pdbid;
-  }
-
-  public int getAtomNum(int seqpos)
-  {
-    if (mapping.length > seqpos)
-    {
-      return mapping[seqpos][1];
-    }
-    else
-    {
-      return 0;
-    }
-  }
-
-  public int getPDBResNum(int seqpos)
-  {
-    if (mapping.length > seqpos)
-    {
-      return mapping[seqpos][0];
-    }
-    else
-    {
-      return 0;
-    }
-  }
-
-  public int getSeqPos(int pdbResNum)
-  {
-    for (int i = 0; i < mapping.length; i++)
-    {
-      if (mapping[i][0] == pdbResNum)
-      {
-        return i;
-      }
-    }
-    return -1;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.structure;
+
+import jalview.datamodel.*;
+
+public class StructureMapping
+{
+  String mappingDetails;
+
+  SequenceI sequence;
+
+  String pdbfile;
+
+  String pdbid;
+
+  String pdbchain;
+
+  // Mapping index 0 is resNum, index 1 is atomNo
+  int[][] mapping;
+
+  public StructureMapping(SequenceI seq, String pdbfile, String pdbid,
+          String chain, int[][] mapping, String mappingDetails)
+  {
+    sequence = seq;
+    this.pdbfile = pdbfile;
+    this.pdbid = pdbid;
+    this.pdbchain = chain;
+    this.mapping = mapping;
+    this.mappingDetails = mappingDetails;
+  }
+
+  public SequenceI getSequence()
+  {
+    return sequence;
+  }
+
+  public String getChain()
+  {
+    return pdbchain;
+  }
+
+  public String getPdbId()
+  {
+    return pdbid;
+  }
+
+  public int getAtomNum(int seqpos)
+  {
+    if (mapping.length > seqpos)
+    {
+      return mapping[seqpos][1];
+    }
+    else
+    {
+      return 0;
+    }
+  }
+
+  public int getPDBResNum(int seqpos)
+  {
+    if (mapping.length > seqpos)
+    {
+      return mapping[seqpos][0];
+    }
+    else
+    {
+      return 0;
+    }
+  }
+
+  public int getSeqPos(int pdbResNum)
+  {
+    for (int i = 0; i < mapping.length; i++)
+    {
+      if (mapping[i][0] == pdbResNum)
+      {
+        return i;
+      }
+    }
+    return -1;
+  }
+}