From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 25 Jul 2024 14:04:34 +0000 (+0100)
Subject: JAL-4386 TODOs re standardising and more efficient linking of PDB ID and provider... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=066b2ddcb06a5c4ff0a6f34999c19f9fc37801af;p=jalview.git

JAL-4386 TODOs re standardising and more efficient linking of PDB ID and provider to annotation row
---

diff --git a/.settings/org.eclipse.buildship.core.prefs b/.settings/org.eclipse.buildship.core.prefs
index e479558..a07cb48 100644
--- a/.settings/org.eclipse.buildship.core.prefs
+++ b/.settings/org.eclipse.buildship.core.prefs
@@ -1,13 +1,13 @@
 arguments=
 auto.sync=false
 build.scans.enabled=false
-connection.gradle.distribution=GRADLE_DISTRIBUTION(WRAPPER)
+connection.gradle.distribution=GRADLE_DISTRIBUTION(VERSION(7.6.4))
 connection.project.dir=
 eclipse.preferences.version=1
 gradle.user.home=
 java.home=
 jvm.arguments=
 offline.mode=false
-override.workspace.settings=false
+override.workspace.settings=true
 show.console.view=false
 show.executions.view=false
diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 40cf903..d78bcdc 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -3045,15 +3045,18 @@ public class AlignmentUtils
         Vector<PDBEntry> pdbEntries = aa.sequenceRef.getDatasetSequence()
                 .getAllPDBEntries();
 
+        // TODO: this is an incredibly fragile mechanism
         for (PDBEntry entry : pdbEntries)
         {
 
           String entryProvider = entry.getProvider();
           if (entryProvider == null)
           {
+            // No provider - so this is either an old Jalview project, or not retrieved from recognised source
             entryProvider = "PDB";
           }
 
+          // Should (re)use a standard mechanism for extracting the PDB ID as it is written 1QWXTUV:CHAIN 
           // Trim the string from first occurrence of colon
           String entryID = entry.getId();
           int index = entryID.indexOf(':');
@@ -3067,6 +3070,7 @@ public class AlignmentUtils
 
           }
 
+          // TODO: shouldn't need to extract from description what the originating ID is for this annotation!
           if (entryProvider == "PDB" && aa.description.toLowerCase()
                   .contains("secondary structure for "
                           + entryID.toLowerCase()))