From d9b79c023346253c10dc907d1e75f509823266c4 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 25 Nov 2015 15:13:40 +0000
Subject: [PATCH 1/1] JAL-1479 applet build debug

---
 src/jalview/bin/Cache.java              |    7 +++++++
 src/jalview/gui/StructureChooser.java   |    2 ++
 src/jalview/ws/sifts/SiftsClient.java   |   34 ++++++++++++++-----------------
 src/jalview/ws/sifts/SiftsSettings.java |   12 +++++++++++
 4 files changed, 36 insertions(+), 19 deletions(-)

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 67d359a..b492067 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -217,6 +217,10 @@ public class Cache
 
   public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
 
+  public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
+          .getProperty("user.home")
+          + File.separatorChar
+          + ".sifts_downloads" + File.separatorChar;
   /**
    * Initialises the Jalview Application Log
    */
@@ -399,6 +403,9 @@ public class Cache
     SiftsSettings
             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 
+    SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
+            "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+
     System.out
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 3df7e0c..c86a90f 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -786,6 +786,8 @@ public class StructureChooser extends GStructureChooser
           ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
           for (SequenceI seq : sequences)
           {
+            new jalview.ws.DBRefFetcher(new SequenceI[] { seq }, null,
+                    null, null, false).fetchDBRefs(true);
             seqsMap.add(new SequenceI[] { seq });
           }
           SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 4951d2f..32bb7b7 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -96,14 +96,6 @@ public class SiftsClient implements SiftsClientI
 
   private static final String SIFTS_FTP_BASE_URL = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
 
-  public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
-          .getProperty("user.home")
-          + File.separatorChar
-          + ".sifts_downloads" + File.separatorChar;
-
-  public static final String SIFTS_DOWNLOAD_DIR = jalview.bin.Cache
-          .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR);
-
   private final static String NEWLINE = System.lineSeparator();
 
   private String curSourceDBRef;
@@ -227,7 +219,8 @@ public class SiftsClient implements SiftsClientI
    */
   public static File getSiftsFile(String pdbId) throws SiftsException
   {
-    File siftsFile = new File(SIFTS_DOWNLOAD_DIR + pdbId.toLowerCase()
+    File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
+            + pdbId.toLowerCase()
             + ".xml.gz");
     if (siftsFile.exists())
     {
@@ -252,8 +245,10 @@ public class SiftsClient implements SiftsClientI
   {
     String siftFile = pdbId + ".xml.gz";
     String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
-    String downloadedSiftsFile = SIFTS_DOWNLOAD_DIR + siftFile;
-    File siftsDownloadDir = new File(SIFTS_DOWNLOAD_DIR);
+    String downloadedSiftsFile = SiftsSettings.getSiftDownloadDirectory()
+            + siftFile;
+    File siftsDownloadDir = new File(
+            SiftsSettings.getSiftDownloadDirectory());
     if (!siftsDownloadDir.exists())
     {
       siftsDownloadDir.mkdirs();
@@ -291,7 +286,8 @@ public class SiftsClient implements SiftsClientI
    */
   public static boolean deleteSiftsFileByPDBId(String pdbId)
   {
-    File siftsFile = new File(SIFTS_DOWNLOAD_DIR + pdbId.toLowerCase()
+    File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
+            + pdbId.toLowerCase()
             + ".xml.gz");
     if (siftsFile.exists())
     {
@@ -322,13 +318,13 @@ public class SiftsClient implements SiftsClientI
     else
     {
       DBRefEntry[] dbRefs = seq.getDBRefs();
-      if (dbRefs == null || dbRefs.length < 1)
-      {
-        final SequenceI[] seqs = new SequenceI[] { seq };
-        new jalview.ws.DBRefFetcher(seqs, null, null, null, false)
-                .fetchDBRefs(true);
-        dbRefs = seq.getDBRefs();
-      }
+      // if (dbRefs == null || dbRefs.length < 1)
+      // {
+      // // final SequenceI[] seqs = new SequenceI[] { seq };
+      // // new jalview.ws.DBRefFetcher(seqs, null, null, null, false)
+      // // .fetchDBRefs(true);
+      // dbRefs = seq.getDBRefs();
+      // }
 
       if (dbRefs == null || dbRefs.length < 1)
       {
diff --git a/src/jalview/ws/sifts/SiftsSettings.java b/src/jalview/ws/sifts/SiftsSettings.java
index c666e2c..5554658 100644
--- a/src/jalview/ws/sifts/SiftsSettings.java
+++ b/src/jalview/ws/sifts/SiftsSettings.java
@@ -4,6 +4,8 @@ public class SiftsSettings
 {
   private static boolean mapWithSifts = false;
 
+  private static String siftDownloadDirectory;
+
   public static boolean isMapWithSifts()
   {
     return mapWithSifts;
@@ -13,4 +15,14 @@ public class SiftsSettings
   {
     SiftsSettings.mapWithSifts = mapWithSifts;
   }
+
+  public static String getSiftDownloadDirectory()
+  {
+    return siftDownloadDirectory;
+  }
+
+  public static void setSiftDownloadDirectory(String siftDownloadDirectory)
+  {
+    SiftsSettings.siftDownloadDirectory = siftDownloadDirectory;
+  }
 }
-- 
1.7.10.2