JAL-1620 version bump and release notes

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 11e7188..cb36989 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -47,32 +47,38 @@ public class PDBfile extends jalview.io.AlignFile
    */
   boolean VisibleChainAnnotation = false;
 
-  boolean processSecondaryStructure=true;
-  
+  boolean processSecondaryStructure = true;
+
+  boolean externalSecondaryStructure = false;
 
   public PDBfile(boolean visibleChainAnnotation,
-          boolean processSecondaryStructure)
+          boolean processSecondaryStructure, boolean externalSecStr)
   {
     super();
     VisibleChainAnnotation = visibleChainAnnotation;
     this.processSecondaryStructure = processSecondaryStructure;
+    this.externalSecondaryStructure = externalSecStr;
   }
 
   public PDBfile(boolean visibleChainAnnotation,
-          boolean processSecondaryStructure, String file, String protocol) throws IOException
+          boolean processSecondaryStructure, boolean externalSecStr,
+          String file, String protocol) throws IOException
   {
     super(false, file, protocol);
     VisibleChainAnnotation = visibleChainAnnotation;
     this.processSecondaryStructure = processSecondaryStructure;
+    this.externalSecondaryStructure = externalSecStr;
     doParse();
   }
 
   public PDBfile(boolean visibleChainAnnotation,
-          boolean processSecondaryStructure, FileParse source) throws IOException
+          boolean processSecondaryStructure, boolean externalSecStr,
+          FileParse source) throws IOException
   {
     super(false, source);
     VisibleChainAnnotation = visibleChainAnnotation;
     this.processSecondaryStructure = processSecondaryStructure;
+    this.externalSecondaryStructure = externalSecStr;
     doParse();
   }
 
@@ -189,8 +195,7 @@ public class PDBfile extends jalview.io.AlignFile
         entry.setProperty(new Hashtable());
         if (chains.elementAt(i).id != null)
         {
-          entry.getProperty().put("CHAIN",
-                  chains.elementAt(i).id);
+          entry.getProperty().put("CHAIN", chains.elementAt(i).id);
         }
         if (inFile != null)
         {
@@ -217,7 +222,7 @@ public class PDBfile extends jalview.io.AlignFile
 
         AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
 
-        if (chainannot != null)
+        if (chainannot != null && VisibleChainAnnotation)
         {
           for (int ai = 0; ai < chainannot.length; ai++)
           {
@@ -228,34 +233,34 @@ public class PDBfile extends jalview.io.AlignFile
       }
       if (processSecondaryStructure)
       {
-      if (rna.size() > 0)
-      {
-        try
-        {
-          processPdbFileWithAnnotate3d(rna);
-        } catch (Exception x)
+        if (externalSecondaryStructure && rna.size() > 0)
         {
-          System.err
-                  .println("Exceptions when dealing with RNA in pdb file");
-          x.printStackTrace();
+          try
+          {
+            processPdbFileWithAnnotate3d(rna);
+          } catch (Exception x)
+          {
+            System.err
+                    .println("Exceptions when dealing with RNA in pdb file");
+            x.printStackTrace();
 
+          }
         }
-      }
-      ;
-      if (prot.size() > 0)
-      {
-        try
-        {
-          processPdbFileWithJmol(prot);
-        } catch (Exception x)
+        ;
+        if (prot.size() > 0)
         {
-          System.err
-                  .println("Exceptions from Jmol when processing data in pdb file");
-          x.printStackTrace();
+          try
+          {
+            processPdbFileWithJmol(prot);
+          } catch (Exception x)
+          {
+            System.err
+                    .println("Exceptions from Jmol when processing data in pdb file");
+            x.printStackTrace();
 
+          }
         }
       }
-      }
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
@@ -273,19 +278,19 @@ public class PDBfile extends jalview.io.AlignFile
     markCalcIds();
   }
 
-  private static String calcIdPrefix = "JalviewPDB:";
+  private static String calcIdPrefix = "JalviewPDB";
 
   public static boolean isCalcIdHandled(String calcId)
   {
-    return calcId != null
-            && (calcId.startsWith(calcIdPrefix) && calcId.indexOf(
-                    calcIdPrefix,
-            calcIdPrefix.length() + 1) > -1);
+    return calcId != null && (calcIdPrefix.equals(calcId));
   }
-  public static boolean isCalcIdForFile(String calcId, String pdbFile)
+
+  public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+          String pdbFile)
   {
-    return (calcId != null && calcId.startsWith(calcIdPrefix + pdbFile
-            + ":" + calcIdPrefix));
+    return alan.getCalcId() != null
+            && calcIdPrefix.equals(alan.getCalcId())
+            && pdbFile.equals(alan.getProperty("PDBID"));
   }
 
   public static String relocateCalcId(String calcId,
@@ -301,17 +306,23 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (SequenceI sq : seqs)
     {
-      for (AlignmentAnnotation aa : sq.getAnnotation())
+      if (sq.getAnnotation() != null)
       {
-        String oldId = aa.getCalcId();
-        if (oldId == null)
+        for (AlignmentAnnotation aa : sq.getAnnotation())
         {
-          oldId = "";
+          String oldId = aa.getCalcId();
+          if (oldId == null)
+          {
+            oldId = "";
+          }
+          aa.setCalcId(calcIdPrefix);
+          aa.setProperty("PDBID", id);
+          aa.setProperty("oldCalcId", oldId);
         }
-        aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId);
       }
     }
   }
+
   private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
           throws Exception
   {
@@ -350,8 +361,8 @@ public class PDBfile extends jalview.io.AlignFile
           AlignmentI al, String pep, boolean b)
   {
     List<List<? extends Object>> replaced = AlignSeq
-            .replaceMatchingSeqsWith(seqs,
-            annotations, prot, al, AlignSeq.PEP, false);
+            .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
+                    false);
     for (PDBChain ch : chains)
     {
       int p = 0;
@@ -369,8 +380,7 @@ public class PDBfile extends jalview.io.AlignFile
         p = -p - 1;
         // set shadow entry for chains
         ch.shadow = (SequenceI) replaced.get(1).get(p);
-        ch.shadowMap = ((AlignSeq) replaced.get(2)
-.get(p))
+        ch.shadowMap = ((AlignSeq) replaced.get(2).get(p))
                 .getMappingFromS1(false);
       }
     }
@@ -443,7 +453,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      chains.elementAt(i).makeResidueList();
+      chains.elementAt(i).makeResidueList(VisibleChainAnnotation);
     }
   }
 
@@ -488,8 +498,8 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      chains.elementAt(i).setChainColours(Color.getHSBColor(
-              1.0f / i, .4f, 1.0f));
+      chains.elementAt(i).setChainColours(
+              Color.getHSBColor(1.0f / i, .4f, 1.0f));
     }
   }