JAL-1541 BioJs MSA Viewer export option implementation

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 19e13e7..a99f172 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -20,16 +20,21 @@
  */
 package MCview;
 
-import java.io.*;
-import java.util.*;
-import java.util.List;
-import java.awt.*;
-
 import jalview.analysis.AlignSeq;
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
+
 public class PDBfile extends jalview.io.AlignFile
 {
   public Vector chains;
@@ -215,7 +220,6 @@ public class PDBfile extends jalview.io.AlignFile
         {
           for (int ai = 0; ai < chainannot.length; ai++)
           {
-
             chainannot[ai].visible = VisibleChainAnnotation;
             annotations.addElement(chainannot[ai]);
           }
@@ -224,6 +228,7 @@ public class PDBfile extends jalview.io.AlignFile
       if (processSecondaryStructure)
       {
       if (rna.size() > 0)
+      {
         try
         {
           processPdbFileWithAnnotate3d(rna);
@@ -234,8 +239,10 @@ public class PDBfile extends jalview.io.AlignFile
           x.printStackTrace();
 
         }
+      }
       ;
       if (prot.size() > 0)
+      {
         try
         {
           processPdbFileWithJmol(prot);
@@ -247,6 +254,7 @@ public class PDBfile extends jalview.io.AlignFile
 
         }
       }
+      }
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
@@ -261,8 +269,48 @@ public class PDBfile extends jalview.io.AlignFile
         System.err.println(line);
       }
     }
+    markCalcIds();
   }
 
+  private static String calcIdPrefix = "JalviewPDB:";
+
+  public static boolean isCalcIdHandled(String calcId)
+  {
+    return calcId != null
+            && (calcId.startsWith(calcIdPrefix) && calcId.indexOf(
+                    calcIdPrefix,
+            calcIdPrefix.length() + 1) > -1);
+  }
+  public static boolean isCalcIdForFile(String calcId, String pdbFile)
+  {
+    return (calcId != null && calcId.startsWith(calcIdPrefix + pdbFile
+            + ":" + calcIdPrefix));
+  }
+
+  public static String relocateCalcId(String calcId,
+          Hashtable<String, String> alreadyLoadedPDB) throws Exception
+  {
+    int s = calcIdPrefix.length(), end = calcId.indexOf(calcIdPrefix, s);
+    String between = calcId.substring(s, end - 1);
+    return calcIdPrefix + alreadyLoadedPDB.get(between) + ":"
+            + calcId.substring(end);
+  }
+
+  private void markCalcIds()
+  {
+    for (SequenceI sq : seqs)
+    {
+      for (AlignmentAnnotation aa : sq.getAnnotation())
+      {
+        String oldId = aa.getCalcId();
+        if (oldId == null)
+        {
+          oldId = "";
+        }
+        aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId);
+      }
+    }
+  }
   private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
           throws Exception
   {
@@ -279,6 +327,17 @@ public class PDBfile extends jalview.io.AlignFile
                 {}).invoke(jmf));
         cl.getMethod("addAnnotations", new Class[]
         { Alignment.class }).invoke(jmf, al);
+        for (SequenceI sq : al.getSequences())
+        {
+          if (sq.getDatasetSequence() != null)
+          {
+            sq.getDatasetSequence().getPDBId().clear();
+          }
+          else
+          {
+            sq.getPDBId().clear();
+          }
+        }
         AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
       }
     } catch (ClassNotFoundException q)
@@ -307,6 +366,17 @@ public class PDBfile extends jalview.io.AlignFile
                 new Class[]
                 { FileParse.class }).invoke(annotate3d, new Object[]
         { new FileParse(getDataName(), type) }));
+        for (SequenceI sq : al.getSequences())
+        {
+          if (sq.getDatasetSequence() != null)
+          {
+            sq.getDatasetSequence().getPDBId().clear();
+          }
+          else
+          {
+            sq.getPDBId().clear();
+          }
+        }
         AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
       }
     } catch (ClassNotFoundException x)
@@ -382,7 +452,7 @@ public class PDBfile extends jalview.io.AlignFile
     for (int i = 0; i < chains.size(); i++)
     {
       ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
-              1.0f / (float) i, .4f, 1.0f));
+              1.0f / i, .4f, 1.0f));
     }
   }