X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=5b8a3aec3c87a9976a86752afa805e3d03a38b13;hb=02e38bb826828ab2991584cf4b737c0138cb6c44;hp=d5b65052b6c92bf9287e1651c287b2603e099cc2;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index d5b6505..5b8a3ae 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,153 +1,164 @@
-/*
- * 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 .
- */
-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 DbSourceProxyImpl implements
- DbSourceProxy
-{
-
- public Pfam()
- {
- super();
- // all extensions of this PFAM source base class are DOMAINDB sources
- addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
- }
-
- /*
- * (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()
- */
- public String getDbVersion()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- /**
- *
- * @return PFAM URL stub for this DbSource
- */
- protected abstract String getPFAMURL();
-
- /*
- * (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(getPFAMURL()
- + 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(); }
- */
-}
+/*
+ * 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.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+
+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
+{
+
+ public Pfam()
+ {
+ super();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+ */
+ @Override
+ public String getAccessionSeparator()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+ */
+ @Override
+ 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[])
+ */
+ @Override
+ 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 FormatAdapter().readFile(getXFAMURL()
+ + queries.trim().toUpperCase(), DataSourceType.URL,
+ FileFormat.Stockholm);
+ for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
+ {
+ rcds.getSequenceAt(s).addDBRef(
+new DBRefEntry(DBRefSource.PFAM,
+ // getDbSource(),
+ getDbVersion(), queries.trim().toUpperCase()));
+ if (!getDbSource().equals(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)
+ */
+ @Override
+ public boolean isValidReference(String accession)
+ {
+ return accession.indexOf("PF") == 0;
+ }
+
+ /*
+ * public String getDbName() { return "PFAM"; // getDbSource(); }
+ */
+
+ @Override
+ public String getXfamSource()
+ {
+ return DBRefSource.PFAM;
+ }
+
+}