From 6b406c397d41a0f2d84b75f13e7ab478932bf57d Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 16 Nov 2007 11:28:41 +0000 Subject: [PATCH] refactor abstract sequence fetching and DBSource machinery to their own package --- src/jalview/analysis/CrossRef.java | 2 +- src/jalview/ws/SequenceFetcher.java | 4 +++- src/jalview/ws/dbsources/EbiFileRetrievedProxy.java | 2 +- src/jalview/ws/dbsources/EmblCdsSouce.java | 2 +- src/jalview/ws/dbsources/EmblSource.java | 4 ++-- src/jalview/ws/dbsources/Pdb.java | 4 ++-- src/jalview/ws/dbsources/Pfam.java | 4 ++-- src/jalview/ws/dbsources/Uniprot.java | 4 ++-- src/jalview/ws/{ => seqfetcher}/ASequenceFetcher.java | 2 +- src/jalview/ws/{ => seqfetcher}/DbSourceProxy.java | 2 +- src/jalview/ws/{ => seqfetcher}/DbSourceProxyImpl.java | 2 +- 11 files changed, 17 insertions(+), 15 deletions(-) rename src/jalview/ws/{ => seqfetcher}/ASequenceFetcher.java (96%) rename src/jalview/ws/{ => seqfetcher}/DbSourceProxy.java (95%) rename src/jalview/ws/{ => seqfetcher}/DbSourceProxyImpl.java (94%) diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java index 3e046c2..f355d1f 100644 --- a/src/jalview/analysis/CrossRef.java +++ b/src/jalview/analysis/CrossRef.java @@ -11,8 +11,8 @@ import jalview.datamodel.DBRefSource; import jalview.datamodel.DBRefEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; -import jalview.ws.ASequenceFetcher; import jalview.ws.SequenceFetcher; +import jalview.ws.seqfetcher.ASequenceFetcher; /** * Functions for cross-referencing sequence databases. user must first specify diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java index e6fc385..5243111 100644 --- a/src/jalview/ws/SequenceFetcher.java +++ b/src/jalview/ws/SequenceFetcher.java @@ -8,6 +8,8 @@ import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceI; +import jalview.ws.seqfetcher.ASequenceFetcher; +import jalview.ws.seqfetcher.DbSourceProxy; /** * prototype of abstract sequence retrieval interface @@ -35,7 +37,7 @@ public class SequenceFetcher extends ASequenceFetcher FETCHABLEDBS.put(DBRefSource.PDB, new jalview.ws.dbsources.Pdb()); FETCHABLEDBS.put(DBRefSource.PFAM, new jalview.ws.dbsources.Pfam()); }; - + public static void main(String[] argv) { AlignmentI ds = null; diff --git a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java index c91904d..ec5d234 100644 --- a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java +++ b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java @@ -7,7 +7,7 @@ import java.io.FileReader; import com.stevesoft.pat.Regex; import jalview.datamodel.AlignmentI; -import jalview.ws.DbSourceProxyImpl; +import jalview.ws.seqfetcher.DbSourceProxyImpl; public abstract class EbiFileRetrievedProxy extends DbSourceProxyImpl { diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java index 9912c9c..d448830 100644 --- a/src/jalview/ws/dbsources/EmblCdsSouce.java +++ b/src/jalview/ws/dbsources/EmblCdsSouce.java @@ -6,7 +6,7 @@ import com.stevesoft.pat.Regex; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefSource; -import jalview.ws.DbSourceProxy; +import jalview.ws.seqfetcher.DbSourceProxy; public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy { diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java index 57818a0..6b7756e 100644 --- a/src/jalview/ws/dbsources/EmblSource.java +++ b/src/jalview/ws/dbsources/EmblSource.java @@ -15,9 +15,9 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceI; import jalview.datamodel.xdb.embl.EmblEntry; -import jalview.ws.DbSourceProxy; -import jalview.ws.DbSourceProxyImpl; import jalview.ws.EBIFetchClient; +import jalview.ws.seqfetcher.DbSourceProxy; +import jalview.ws.seqfetcher.DbSourceProxyImpl; /** * @author JimP diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java index 07df2c4..8da1525 100644 --- a/src/jalview/ws/dbsources/Pdb.java +++ b/src/jalview/ws/dbsources/Pdb.java @@ -21,9 +21,9 @@ import com.stevesoft.pat.Regex; import jalview.datamodel.AlignmentI; import jalview.io.FileParse; -import jalview.ws.DbSourceProxy; -import jalview.ws.DbSourceProxyImpl; import jalview.ws.EBIFetchClient; +import jalview.ws.seqfetcher.DbSourceProxy; +import jalview.ws.seqfetcher.DbSourceProxyImpl; /** * @author JimP diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java index d1f5ea2..4d9c93d 100644 --- a/src/jalview/ws/dbsources/Pfam.java +++ b/src/jalview/ws/dbsources/Pfam.java @@ -8,8 +8,8 @@ import java.util.Hashtable; import com.stevesoft.pat.Regex; import jalview.datamodel.AlignmentI; -import jalview.ws.DbSourceProxy; -import jalview.ws.DbSourceProxyImpl; +import jalview.ws.seqfetcher.DbSourceProxy; +import jalview.ws.seqfetcher.DbSourceProxyImpl; /** * TODO: later PFAM is a complex datasource - it currently returns a seed alignment, but could optionally return a full alignment. * TODO: later PFAM is a complex datasource - it could return a tree in addition to an alignment diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java index aa324dc..8dc000e 100644 --- a/src/jalview/ws/dbsources/Uniprot.java +++ b/src/jalview/ws/dbsources/Uniprot.java @@ -22,9 +22,9 @@ import jalview.datamodel.UniprotEntry; import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; import jalview.ws.DBRefFetcher; -import jalview.ws.DbSourceProxy; -import jalview.ws.DbSourceProxyImpl; import jalview.ws.EBIFetchClient; +import jalview.ws.seqfetcher.DbSourceProxy; +import jalview.ws.seqfetcher.DbSourceProxyImpl; /** * @author JimP diff --git a/src/jalview/ws/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java similarity index 96% rename from src/jalview/ws/ASequenceFetcher.java rename to src/jalview/ws/seqfetcher/ASequenceFetcher.java index 9605ad0..7b455bf 100644 --- a/src/jalview/ws/ASequenceFetcher.java +++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java @@ -1,4 +1,4 @@ -package jalview.ws; +package jalview.ws.seqfetcher; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; diff --git a/src/jalview/ws/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java similarity index 95% rename from src/jalview/ws/DbSourceProxy.java rename to src/jalview/ws/seqfetcher/DbSourceProxy.java index 8db6116..5459ae9 100644 --- a/src/jalview/ws/DbSourceProxy.java +++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java @@ -1,4 +1,4 @@ -package jalview.ws; +package jalview.ws.seqfetcher; import jalview.datamodel.AlignmentI; diff --git a/src/jalview/ws/DbSourceProxyImpl.java b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java similarity index 94% rename from src/jalview/ws/DbSourceProxyImpl.java rename to src/jalview/ws/seqfetcher/DbSourceProxyImpl.java index 17040d4..21272be 100644 --- a/src/jalview/ws/DbSourceProxyImpl.java +++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java @@ -1,4 +1,4 @@ -package jalview.ws; +package jalview.ws.seqfetcher; import jalview.datamodel.Alignment; import jalview.datamodel.DBRefSource; -- 1.7.10.2