// individual references to each sequence in each family alignment that's\r
// retrieved.\r
startQuery();\r
- AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()\r
+ AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()\r
+ queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,\r
"STH");\r
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)\r
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 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 <http://www.gnu.org/licenses/>.
+ */
+package jalview.ws.dbsources;
+
+import com.stevesoft.pat.Regex;
+
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+/**
+ * Contains methods for fetching sequences from Rfam database
+ *
+ * @author Lauren Michelle Lui
+ */
+abstract public class Rfam extends Xfam implements DbSourceProxy
+{
+
+ public Rfam()
+ {
+ super();
+ // all extensions of this RFAM source base class are DOMAINDB sources
+ addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for
+ * consistency with Pfam class
+ */
+ public String getAccessionSeparator()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for
+ */
+ public Regex getAccessionValidator()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * Left here for consistency with Pfam class
+ *
+ * @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 : RFAM is an
+ * 'alignment' source - means proxy is higher level than a sequence source.
+ * return jalview.datamodel.DBRefSource.RFAM; }
+ */
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbVersion()
+ */
+ @Override
+ public String getDbVersion()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**Returns base URL for selected Rfam alignment type
+ *
+ * @return RFAM URL stub for this DbSource
+ */
+ @Override
+ protected abstract String getXFAMURL();
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+ */
+ public boolean isValidReference(String accession)
+ {
+ return accession.indexOf("RF") == 0;
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.ws.dbsources.Xfam#getXfamSource()
+ */
+ public String getXfamSource()
+ {
+ return jalview.datamodel.DBRefSource.RFAM;
+ }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 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 <http://www.gnu.org/licenses/>.
+ */
+
+package jalview.ws.dbsources;
+
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+/**
+ * Flyweight class specifying retrieval of Full family alignments from RFAM
+ *
+ * @author Lauren Michelle Lui
+ *
+ */
+public class RfamFull extends Rfam implements DbSourceProxy
+{
+ public RfamFull()
+ {
+ super();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.dbsources.Rfam#getXFAMURL()
+ */
+ protected String getXFAMURL()
+ {
+ return "http://rfam.sanger.ac.uk/family/alignment/download/format?alnType=full&nseLabels=0&format=stockholm&acc=";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
+ */
+ public String getDbName()
+ {
+ return "RFAM (Full)";
+ }
+
+ public String getDbSource()
+ {
+ return getDbName(); // so we have unique DbSource string.
+ }
+
+ public String getTestQuery()
+ {
+ // Can be retrieved from http://rfam.janelia.org/cgi-bin/getdesc?acc=RF00014
+ // or
+ // http://rfam.sanger.ac.uk/family/alignment/download/format?alnType=full&nseLabels=0&format=stockholm&acc=RF00014
+ return "RF00014";
+ }
+
+ public String getDbVersion()
+ {
+ return null;
+ }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 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 <http://www.gnu.org/licenses/>.
+ */
+package jalview.ws.dbsources;
+
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+/**
+ * Flyweight class specifying retrieval of Seed family alignments from RFAM
+ *
+ * @author Lauren Michelle Lui
+ *
+ */
+public class RfamSeed extends Rfam implements DbSourceProxy
+{
+ public RfamSeed()
+ {
+ super();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.dbsources.Rfam#getRFAMURL()
+ */
+ protected String getXFAMURL()
+ {
+ return "http://rfam.sanger.ac.uk/family/alignment/download/format?alnType=seed&nseLabels=0&format=stockholm&acc=";
+ // Janelia Farms url
+ // "http://rfam.janelia.org/cgi-bin/getalignment?type=seed&fmt=stockholm&acc=";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
+ */
+ public String getDbName()
+ {
+ return "RFAM (Seed)";
+ }
+
+ public String getDbSource()
+ {
+ return getDbName(); // so we have unique DbSource string.
+ }
+
+ public String getTestQuery()
+ {
+ return "RF00014";
+ } // http://rfam.janelia.org/cgi-bin/getdesc?acc=RF00014
+
+ public String getDbVersion()
+ {
+ return null;
+ }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 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 <http://www.gnu.org/licenses/>.
+ */
+package jalview.ws.dbsources;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
+/**
+ * Acts as a superclass for the Rfam and Pfam classes
+ *
+ * @author Lauren Michelle Lui
+ *
+ */
+public abstract class Xfam extends DbSourceProxyImpl
+{
+
+ public Xfam()
+ {
+ super();
+ }
+
+ protected abstract String getXFAMURL();
+
+ public abstract String getDbVersion();
+
+ abstract String getXfamSource();
+
+ 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(getXfamSource(),
+ // getDbSource(),
+ getDbVersion(), queries.trim().toUpperCase()));
+ if (!getDbSource().equals(getXfamSource()))
+ { // add the specific ref too
+ rcds.getSequenceAt(s).addDBRef(
+ new DBRefEntry(getDbSource(), getDbVersion(), queries
+ .trim().toUpperCase()));
+ }
+ }
+ stopQuery();
+ return rcds;
+ }
+
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / commitdiff