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 7e37277..a99f172 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -272,11 +272,30 @@ public class PDBfile extends jalview.io.AlignFile
     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("JalviewPDB:" + pdbFile
-            + ":JalviewPDB:"));
+    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)
@@ -308,6 +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)
@@ -336,6 +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)