X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=6a612a0602665d356b50b18cf8c150dd2905bf4a;hb=2dcd2b8cfb1b38575c8b2246d59ba1c1a2fb59cd;hp=2488f91141597f85f1b1ae23431babba671169cf;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 2488f91..6a612a0 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 .
+ * 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;
@@ -50,6 +52,7 @@ public class SequenceFetcher extends ASequenceFetcher
{
this(true);
}
+
public SequenceFetcher(boolean addDas)
{
addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);
@@ -58,13 +61,12 @@ public class SequenceFetcher extends ASequenceFetcher
addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);
addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);
- addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed
- // alignment is
- // 'default' for
- // PFAM
+ addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class);
+ // ensures Seed alignment is 'default' for PFAM
addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
- if (addDas) {
+ if (addDas)
+ {
registerDasSequenceSources();
}
}
@@ -165,13 +167,11 @@ public class SequenceFetcher extends ASequenceFetcher
{
nm = nm.substring(4);
}
- dassrc.add(new String[]
- { srcs[i], nm.toUpperCase() });
+ dassrc.add(new String[] { srcs[i], nm.toUpperCase() });
}
else
{
- nondas.add(new String[]
- { srcs[i], nm.toUpperCase() });
+ nondas.add(new String[] { srcs[i], nm.toUpperCase() });
}
}
}
@@ -222,13 +222,14 @@ public class SequenceFetcher extends ASequenceFetcher
+ "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
+ "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to and retrieve from it.\n"
+ "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
- boolean withDas=true;
- if (argv!=null && argv.length>0 && argv[0].toLowerCase().startsWith("-nodas"))
+ boolean withDas = true;
+ if (argv != null && argv.length > 0
+ && argv[0].toLowerCase().startsWith("-nodas"))
{
- withDas=false;
- String targs[] = new String[argv.length-1];
+ withDas = false;
+ String targs[] = new String[argv.length - 1];
System.arraycopy(argv, 1, targs, 0, targs.length);
- argv=targs;
+ argv = targs;
}
if (argv != null && argv.length > 0)
{
@@ -242,11 +243,13 @@ public class SequenceFetcher extends ASequenceFetcher
AlignmentI al = null;
try
{
- al = sp.getSequenceRecords(argv.length>1 ? argv[1] : sp.getTestQuery());
+ al = sp.getSequenceRecords(argv.length > 1 ? argv[1] : sp
+ .getTestQuery());
} catch (Exception e)
{
e.printStackTrace();
- System.err.println("Error when retrieving " + (argv.length>1 ? argv[1] : sp.getTestQuery())
+ System.err.println("Error when retrieving "
+ + (argv.length > 1 ? argv[1] : sp.getTestQuery())
+ " from " + argv[0] + "\nUsage: " + usage);
}
SequenceI[] prod = al.getSequencesArray();
@@ -278,7 +281,9 @@ public class SequenceFetcher extends ASequenceFetcher
String db = dbSources[dbsource];
// skip me
if (db.equals(DBRefSource.PDB))
+ {
continue;
+ }
for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
{
System.out.println("Source: " + sp.getDbName() + " (" + db
@@ -324,9 +329,8 @@ public class SequenceFetcher extends ASequenceFetcher
}
else
{
- noProds.addElement((dna ? new Object[]
- { al, al } : new Object[]
- { al }));
+ noProds.addElement((dna ? new Object[] { al, al }
+ : new Object[] { al }));
}
}
@@ -341,9 +345,13 @@ public class SequenceFetcher extends ASequenceFetcher
System.out.println("ERROR:No alignment retrieved.");
StringBuffer raw = sp.getRawRecords();
if (raw != null)
+ {
System.out.println(raw.toString());
+ }
else
+ {
System.out.println("ERROR:No Raw results.");
+ }
}
else
{
@@ -358,8 +366,7 @@ public class SequenceFetcher extends ASequenceFetcher
}
if (ds == null)
{
- ds = new Alignment(new SequenceI[]
- { sq });
+ ds = new Alignment(new SequenceI[] { sq });
}
else