X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fsifts%2FSiftsClient.java;h=00da2fce7e89e622f7deaa258422dbdcfcff3fed;hb=26a8bcef19885071a20e238d06c514404ecbc573;hp=106a66effa2e9fedcb2d30c26e065d577ef3a165;hpb=4ff572f7cf17f5ca9c23f82bbe41005af8af55cc;p=jalview.git

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 106a66e..00da2fc 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;
@@ -185,12 +177,11 @@ public class SiftsClient implements SiftsClientI
    */
   private Entry parseSIFTs(File siftFile) throws SiftsException
   {
-    try
+    try (InputStream in = new FileInputStream(siftFile);
+            GZIPInputStream gzis = new GZIPInputStream(in);)
     {
       System.out.println("File : " + siftFile.getAbsolutePath());
       JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.sifts");
-      InputStream in = new FileInputStream(siftFile);
-      GZIPInputStream gzis = new GZIPInputStream(in);
       XMLStreamReader streamReader = XMLInputFactory.newInstance()
               .createXMLStreamReader(gzis);
       Unmarshaller um = jc.createUnmarshaller();
@@ -228,7 +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())
     {
@@ -253,8 +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();
@@ -292,7 +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())
     {
@@ -325,14 +320,6 @@ public class SiftsClient implements SiftsClientI
       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)
-      {
         throw new SiftsException("Could not get source DB Ref");
       }