From c4f290671231c0bf33aedceffde3354c24fc1dad Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 31 Oct 2014 16:14:27 +0000
Subject: [PATCH] JAL-674 JAL-961 pass row reference to handler to check
 calcId and any specific properties (e.g. originating PDB ID
 for the row data)

---
 src/MCview/PDBfile.java                              |   18 ++++++++++--------
 src/jalview/structure/StructureSelectionManager.java |    3 +--
 test/jalview/io/AnnotatedPDBFileInputTest.java       |    4 ++--
 3 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 11e7188..b22eb29 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -273,19 +273,19 @@ 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);
+ && (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,
@@ -308,7 +308,9 @@ public class PDBfile extends jalview.io.AlignFile
         {
           oldId = "";
         }
-        aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId);
+        aa.setCalcId(calcIdPrefix);
+        aa.setProperty("PDBID", id);
+        aa.setProperty("oldCalcId", oldId);
       }
     }
   }
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 9396be1..7a1b100 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -260,11 +260,10 @@ public class StructureSelectionManager
         {
           for (AlignmentAnnotation ala : ds.getAnnotation())
           {
-
             // false if any annotation present from this structure
             // JBPNote this fails for jmol/chimera view because the *file* is
             // passed, not the structure data ID -
-            if (MCview.PDBfile.isCalcIdForFile(ala.getCalcId(),
+            if (MCview.PDBfile.isCalcIdForFile(ala,
                     findIdForPDBFile(pdbFile)))
             {
               parseSecStr = false;
diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index 7e99409..7bef5db 100644
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -68,7 +68,7 @@ public class AnnotatedPDBFileInputTest
       {
 
         System.out.println("CalcId: " + aa.getCalcId());
-        assertTrue(MCview.PDBfile.isCalcIdForFile(aa.getCalcId(), pdbId));
+        assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
       }
     }
   }
@@ -160,7 +160,7 @@ public class AnnotatedPDBFileInputTest
                   && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
           {
             exists = true;
-            if (MCview.PDBfile.isCalcIdForFile(ana.getCalcId(),
+            if (MCview.PDBfile.isCalcIdForFile(ana,
                     pdbentry.getId()))
             {
               found = true;
-- 
1.7.10.2