X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=e6aa47246536da0f8e6a6e950c08df3ff2264a5e;hb=e838644df5d5a10a16cf0ad7fb23d24dd7d2729a;hp=4a0a55d8ad3dc05aa09c47cdec6b8f5e20cc30bd;hpb=6c96743ff6c65895e4b96523d0e3d05f6dc3cb01;p=jalview.git diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java index 4a0a55d..e6aa472 100755 --- a/src/jalview/util/DBRefUtils.java +++ b/src/jalview/util/DBRefUtils.java @@ -26,6 +26,7 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import java.util.ArrayList; +import java.util.Arrays; import java.util.HashMap; import java.util.HashSet; import java.util.List; @@ -300,7 +301,8 @@ public class DBRefUtils @Override public boolean matches(DBRefEntry refa, DBRefEntry refb) { - if (refa.getSource() != null && refb.getSource() != null + if (refa.getSource() != null + && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource()).equals( DBRefUtils.getCanonicalName(refa.getSource()))) { @@ -332,7 +334,8 @@ public class DBRefUtils @Override public boolean matches(DBRefEntry refa, DBRefEntry refb) { - if (refa.getSource() != null && refb.getSource() != null + if (refa.getSource() != null + && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource()).equals( DBRefUtils.getCanonicalName(refa.getSource()))) { @@ -369,7 +372,8 @@ public class DBRefUtils @Override public boolean matches(DBRefEntry refa, DBRefEntry refb) { - if (refa.getSource() != null && refb.getSource() != null + if (refa.getSource() != null + && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource()).equals( DBRefUtils.getCanonicalName(refa.getSource()))) { @@ -409,7 +413,8 @@ public class DBRefUtils @Override public boolean matches(DBRefEntry refa, DBRefEntry refb) { - if (refa.getSource() != null && refb.getSource() != null + if (refa.getSource() != null + && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource()).equals( DBRefUtils.getCanonicalName(refa.getSource()))) { @@ -605,4 +610,127 @@ public class DBRefUtils return matches; } + /** + * promote direct database references to primary for nucleotide or protein + * sequences if they have an appropriate primary ref + *
Seq Type | + *Primary DB | + *Direct which will be promoted | + *
---|---|---|
peptides | + *Ensembl | + *Uniprot | + *
peptides | + *Ensembl | + *Uniprot | + *
dna | + *Ensembl | + *ENA | + *