JAL-674 hang on to sequences created by secondary parsiing process to manage transfer...

[jalview.git] / src / MCview / PDBChain.java

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 823e02c..5dd38a4 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,32 +1,40 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.
+ * 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/>.
+ * 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 MCview;
 
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
 
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
 public class PDBChain
 {
   /**
@@ -46,7 +54,16 @@ public class PDBChain
 
   public int offset;
 
-  public Sequence sequence;
+  /**
+   * sequence is the sequence extracted by the chain parsing code
+   */
+  public SequenceI sequence;
+
+  /**
+   * shadow is the sequence created by any other parsing processes (e.g. Jmol,
+   * RNAview)
+   */
+  public SequenceI shadow = null;
 
   public boolean isNa = false;
 
@@ -73,6 +90,8 @@ public class PDBChain
    */
   protected String newline = System.getProperty("line.separator");
 
+  public Mapping shadowMap;
+
   public void setNewlineString(String nl)
   {
     newline = nl;
@@ -185,7 +204,9 @@ public class PDBChain
                 + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
                         : ":" + tx.getStatus()));
         if (tx.begin != 0 && tx.end != 0)
+        {
           sq.addSequenceFeature(tx);
+        }
       }
     }
     return features;
@@ -273,7 +294,7 @@ public class PDBChain
       // remains the same as the first atom's resNumber (res)
       while ((resNumber == res) && (i < atoms.size()))
       {
-        resAtoms.addElement((Atom) atoms.elementAt(i));
+        resAtoms.addElement(atoms.elementAt(i));
         i++;
 
         if (i < atoms.size())
@@ -362,7 +383,9 @@ public class PDBChain
     {
       annots[i] = (Annotation) resAnnotation.elementAt(i);
       if (annots[i].value > max)
+      {
         max = annots[i].value;
+      }
       resAnnotation.setElementAt(null, i);
     }
     AlignmentAnnotation tfactorann = new AlignmentAnnotation(
@@ -482,11 +505,51 @@ public class PDBChain
   public void transferResidueAnnotation(StructureMapping mapping)
   {
     SequenceI sq = mapping.getSequence();
+    SequenceI dsq = sq;
     if (sq != null)
     {
-      if (sequence != null && sequence.getAnnotation() != null)
+      while (dsq.getDatasetSequence() != null)
+      {
+        dsq = dsq.getDatasetSequence();
+      }
+      // any annotation will be transferred onto the dataset sequence
+
+      if (shadow != null && shadow.getAnnotation() != null)
       {
 
+        for (AlignmentAnnotation ana : shadow.getAnnotation())
+        {
+          List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
+                  ana.getCalcId(), ana.label);
+          if (transfer == null || transfer.size() == 0)
+          {
+            ana.liftOver(sequence, shadowMap);
+            mapping.transfer(ana);
+          }
+          else
+          {
+            continue;
+          }
+        }
+      }
+      else
+      {
+      if (sequence != null && sequence.getAnnotation() != null)
+      {
+        for (AlignmentAnnotation ana : sequence.getAnnotation())
+        {
+          List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
+                  ana.getCalcId(), ana.label);
+          if (transfer == null || transfer.size() == 0)
+          {
+            mapping.transfer(ana);
+          }
+          else
+          {
+            continue;
+          }
+        }
+      }
       }
       float min = -1, max = 0;
       Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
@@ -494,7 +557,7 @@ public class PDBChain
       {
         int prn = mapping.getPDBResNum(k + 1);
 
-        an[k] = new Annotation((float) prn);
+        an[k] = new Annotation(prn);
         if (min == -1)
         {
           min = k;
@@ -514,7 +577,8 @@ public class PDBChain
       }
       sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
               "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
-              an, (float) min, (float) max, AlignmentAnnotation.LINE_GRAPH));
+              an, min, max, AlignmentAnnotation.LINE_GRAPH));
+
     }
   }
 }