Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / src / jalview / ws / dbsources / EmblFlatfileSource.java

diff --git a/src/jalview/ws/dbsources/EmblFlatfileSource.java b/src/jalview/ws/dbsources/EmblFlatfileSource.java
new file mode 100644 (file)
index 0000000..6694a52
--- /dev/null
+++ b/src/jalview/ws/dbsources/EmblFlatfileSource.java
@@ -0,0 +1,126 @@
+package jalview.ws.dbsources;
+
+import java.util.Locale;
+
+import java.io.File;
+import java.io.IOException;
+
+import com.stevesoft.pat.Regex;
+
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.EmblFlatFile;
+import jalview.io.FileParse;
+import jalview.ws.ebi.EBIFetchClient;
+
+/**
+ * A class that does partial parsing of an EMBL flatfile.
+ * 
+ * @author gmcarstairs
+ *
+ */
+public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
+{
+  private static final Regex ACCESSION_REGEX = null;
+
+  @Override
+  public String getDbVersion()
+  {
+    return "0";
+  }
+
+  @Override
+  public String getAccessionSeparator()
+  {
+    return null;
+  }
+
+  @Override
+  public Regex getAccessionValidator()
+  {
+    if (ACCESSION_REGEX == null)
+    {
+      ACCESSION_REGEX = Platform.newRegex("^[A-Z]+[0-9]+");
+    }
+    return ACCESSION_REGEX;
+  }
+
+  @Override
+  public boolean isValidReference(String accession)
+  {
+    if (accession == null || accession.length() < 2)
+    {
+      return false;
+    }
+    return getAccessionValidator().search(accession);
+  }
+
+  @Override
+  public AlignmentI getSequenceRecords(String queries) throws Exception
+  {
+    return null;
+  }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
+
+  protected AlignmentI getEmblSequenceRecords(String dbName, String query)
+          throws Exception
+  {
+    startQuery();
+    EBIFetchClient dbFetch = new EBIFetchClient();
+    File reply;
+    try
+    {
+      reply = dbFetch.fetchDataAsFile(
+              dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null, "gz");
+    } catch (Exception e)
+    {
+      stopQuery();
+      throw new Exception(
+              String.format("EBI EMBL retrieval failed for %s:%s",
+                      dbName.toLowerCase(Locale.ROOT), query.trim()),
+              e);
+    }
+    return getEmblSequenceRecords(dbName, query, reply);
+  }
+
+  private AlignmentI getEmblSequenceRecords(String dbName, String query,
+          File reply) throws IOException
+  {
+    AlignmentI al = null;
+
+    if (reply != null && reply.exists())
+    {
+      file = reply.getAbsolutePath();
+      FileParse fp = new FileParse(file, DataSourceType.FILE);
+      EmblFlatFile emblParser = new EmblFlatFile(fp, getDbSource());
+      SequenceI[] seqs = emblParser.getSeqsAsArray();
+      if (seqs.length > 0)
+      {
+        al = new Alignment(seqs);
+      }
+
+      if (al == null)
+      {
+        Cache.log.error(
+                "No record found for '" + dbName + ":" + query + "'");
+      }
+    }
+
+    stopQuery();
+    return al;
+  }
+
+  @Override
+  public boolean isDnaCoding()
+  {
+    return true;
+  }
+}