From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 15 Nov 2024 11:42:31 +0000 (+0000)
Subject: JAL-3914 tidy up convenience methods for get/set PDBEntry metadata
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9d9daa8ff97976f3b2bb6dacb17717cbc189f21e;p=jalview.git

JAL-3914 tidy up convenience methods for get/set PDBEntry metadata
---

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index b77ee85..8d19518 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -4086,7 +4086,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       if (needtoadd)
       {
-        pdbentry.setProperty("protocol", protocol);
+        pdbentry.setProtocol(protocol);
         toaddpdb.addPDBId(pdbentry);
         alignPanel.getStructureSelectionManager()
                 .registerPDBEntry(pdbentry);
diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index cca9aff..8172569 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -293,7 +293,7 @@ public class AppletJmol extends EmbmenuFrame implements
         closeViewer();
       }
     });
-    pdbentry.setProperty("protocol", protocol);
+    pdbentry.setProtocol(protocol);
     if (pdbentry.getFile() != null)
 
     {
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 9246744..6385210 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -24,6 +24,7 @@ import java.util.Collections;
 import java.util.Enumeration;
 import java.util.Hashtable;
 
+import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.structure.StructureImportSettings.TFType;
 import jalview.util.CaseInsensitiveString;
@@ -563,7 +564,6 @@ public class PDBEntry
 
   private static final String PROVIDERCATEGORY = "PROVIDERCATEGORY";
 
-  private static final String TEMPFACTYPE = "TEMPFACTYPE";
 
   private static final String MODELCONFIDENCE = "MODELCONFIDENCE";
 
@@ -571,6 +571,10 @@ public class PDBEntry
 
   private static final String MODELCONFVER = "MODELCONFVER";
 
+  // Pre 2.11.4 properties - case preserved
+  private static final String TEMPFACTYPE = "TFType";
+  private static final String PAEFILE = "PAEFile";
+  private final static String PROTOCOL="protocol";
   
   /**
    * Permanent URI for retrieving the original structure data
@@ -739,5 +743,30 @@ public class PDBEntry
   {
     return (Double) getProperty(MODELCONFIDENCE);
   }
+  
+  public void setPAEFile(String paeFilename)
+  {
+    setProperty(PAEFILE,paeFilename);
+  }
+  public String getPAEFile()
+  {
+    return (String) getProperty(PAEFILE);
+  }
+  public boolean hasPAEFile()
+  {
+    return _hasProperty(PAEFILE);
+  }
 
-}
+  public void setProtocol(DataSourceType protocol)
+  {
+    setProperty(PROTOCOL, protocol.name());
+  }
+  public boolean hasProtocol()
+  {
+    return _hasProperty(PROTOCOL);
+  }
+  public DataSourceType getProtocol()
+  {
+    return DataSourceType.valueOf((String) getProperty(PROTOCOL));
+  }
+}
\ No newline at end of file
diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index b2689be..0a57cf1 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -58,6 +58,7 @@ public class AssociatePdbFileWithSeq
           String paeFilename, boolean doXferSettings)
   {
     PDBEntry entry = new PDBEntry();
+    
     StructureFile pdbfile = StructureSelectionManager
             .getStructureSelectionManager(ssmp)
             .setMapping(false, new SequenceI[]
@@ -102,9 +103,9 @@ public class AssociatePdbFileWithSeq
               .registerPDBEntry(entry);
     }
     if (tft != null)
-      entry.setProperty("TFType", tft.name());
+      entry.setTempFacType(tft);
     if (paeFilename != null)
-      entry.setProperty("PAEFile", paeFilename);
+      entry.setPAEFile(paeFilename);
     return entry;
   }
 }