X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=456236a02efd63d3b5954230320e0aa5f646ab77;hb=1724567f3dfc3b4637aac7bdeb6633628e6a8335;hp=d9a2ec0c802ff6b261fd1d72cdfa5a4715f8e689;hpb=2026a420963f094072607c0495b6369ba96e60c0;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index d9a2ec0..456236a 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,161 +1,135 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
- */
-package jalview.ws.dbsources;
-
-import java.util.Hashtable;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.FastaFile;
-import jalview.io.StockholmFile;
-import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
-
-/**
- * TODO: later PFAM is a complex datasource - it could return a tree in addition
- * to an alignment TODO: create interface to pass alignment properties and tree
- * back to sequence fetcher
- *
- * @author JimP
- *
- */
-abstract public class Pfam extends Xfam implements
- DbSourceProxy
-{
-
- public Pfam()
- {
- super();
- // all extensions of this PFAM source base class are DOMAINDB sources
- addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
- addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
- */
- public String getAccessionSeparator()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getAccessionValidator()
- */
- public Regex getAccessionValidator()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
- * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
- * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
- * 'alignment' source - means proxy is higher level than a sequence source.
- * return jalview.datamodel.DBRefSource.PFAM; }
- */
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
- * getDbSourceProperties() {
- *
- * return null; }
- */
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getDbVersion()
- */
- @Override
-public String getDbVersion()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- /**Returns base URL for selected Pfam alignment type
- *
- * @return PFAM URL stub for this DbSource
- */
- @Override
-protected abstract String getXFAMURL();
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
- */
- public AlignmentI getSequenceRecords(String queries) throws Exception
- {
- // TODO: this is not a perfect implementation. We need to be able to add
- // individual references to each sequence in each family alignment that's
- // retrieved.
- startQuery();
- AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
- + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
- "STH");
- for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
- {
- rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
- // getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
- if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
- { // add the specific ref too
- rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(getDbSource(), getDbVersion(), queries
- .trim().toUpperCase()));
- }
- }
- stopQuery();
- return rcds;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
- */
- public boolean isValidReference(String accession)
- {
- return accession.indexOf("PF") == 0;
- }
-
- /*
- * public String getDbName() { return "PFAM"; // getDbSource(); }
- */
-
-
- public String getXfamSource() { return jalview.datamodel.DBRefSource.PFAM; }
-
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefSource;
+import jalview.util.Platform;
+
+import com.stevesoft.pat.Regex;
+
+/**
+ * TODO: later PFAM is a complex datasource - it could return a tree in addition
+ * to an alignment TODO: create interface to pass alignment properties and tree
+ * back to sequence fetcher
+ *
+ * @author JimP
+ *
+ */
+abstract public class Pfam extends Xfam
+{
+ /*
+ * append to URLs to retrieve as a gzipped file
+ */
+ protected static final String GZIPPED = "/gzipped";
+
+ static final String PFAM_BASEURL_KEY = "PFAM_BASEURL";
+
+ private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org";
+ static {
+ Platform.addJ2SDirectDatabaseCall(DEFAULT_PFAM_BASEURL);
+ }
+
+ public Pfam()
+ {
+ super();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+ */
+ @Override
+ public String getAccessionSeparator()
+ {
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+ */
+ @Override
+ public Regex getAccessionValidator()
+ {
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
+ * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
+ * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
+ * 'alignment' source - means proxy is higher level than a sequence source.
+ * return jalview.datamodel.DBRefSource.PFAM; }
+ */
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
+ * getDbSourceProperties() {
+ *
+ * return null; }
+ */
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbVersion()
+ */
+ @Override
+ public String getDbVersion()
+ {
+ return null;
+ }
+
+ @Override
+ protected String getURLPrefix()
+ {
+ return Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+ */
+ @Override
+ public boolean isValidReference(String accession)
+ {
+ return accession.indexOf("PF") == 0;
+ }
+
+ /*
+ * public String getDbName() { return "PFAM"; // getDbSource(); }
+ */
+
+ @Override
+ public String getXfamSource()
+ {
+ return DBRefSource.PFAM;
+ }
+
+}