refactor abstract sequence fetching and DBSource machinery to their own package

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 3e046c2..f355d1f 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -11,8 +11,8 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.DBRefEntry;\r
 import jalview.datamodel.Sequence;\r
 import jalview.datamodel.SequenceI;\r
-import jalview.ws.ASequenceFetcher;\r
 import jalview.ws.SequenceFetcher;\r
+import jalview.ws.seqfetcher.ASequenceFetcher;\r
 \r
 /**\r
  * Functions for cross-referencing sequence databases. user must first specify\r

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index e6fc385..5243111 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -8,6 +8,8 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;\r
 import jalview.datamodel.DBRefSource;\r
 import jalview.datamodel.SequenceI;\r
+import jalview.ws.seqfetcher.ASequenceFetcher;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
 \r
 /**\r
  * prototype of abstract sequence retrieval interface\r
@@ -35,7 +37,7 @@ public class SequenceFetcher extends ASequenceFetcher
     FETCHABLEDBS.put(DBRefSource.PDB, new jalview.ws.dbsources.Pdb());\r
     FETCHABLEDBS.put(DBRefSource.PFAM, new jalview.ws.dbsources.Pfam());\r
   };\r
-\r
+  \r
   public static void main(String[] argv)\r
   {\r
     AlignmentI ds = null;\r

diff --git a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
index c91904d..ec5d234 100644 (file)
--- 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;\r
 \r
 import jalview.datamodel.AlignmentI;\r
-import jalview.ws.DbSourceProxyImpl;\r
+import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
 \r
 public abstract class EbiFileRetrievedProxy extends DbSourceProxyImpl\r
 {\r

diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 9912c9c..d448830 100644 (file)
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -6,7 +6,7 @@ import com.stevesoft.pat.Regex;
 \r
 import jalview.datamodel.AlignmentI;\r
 import jalview.datamodel.DBRefSource;\r
-import jalview.ws.DbSourceProxy;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
 \r
 public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy\r
 {\r

diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 57818a0..6b7756e 100644 (file)
--- 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;\r
 import jalview.datamodel.SequenceI;\r
 import jalview.datamodel.xdb.embl.EmblEntry;\r
-import jalview.ws.DbSourceProxy;\r
-import jalview.ws.DbSourceProxyImpl;\r
 import jalview.ws.EBIFetchClient;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
 \r
 /**\r
  * @author JimP\r

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 07df2c4..8da1525 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -21,9 +21,9 @@ import com.stevesoft.pat.Regex;
 \r
 import jalview.datamodel.AlignmentI;\r
 import jalview.io.FileParse;\r
-import jalview.ws.DbSourceProxy;\r
-import jalview.ws.DbSourceProxyImpl;\r
 import jalview.ws.EBIFetchClient;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
 \r
 /**\r
  * @author JimP\r

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index d1f5ea2..4d9c93d 100644 (file)
--- 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;\r
 \r
 import jalview.datamodel.AlignmentI;\r
-import jalview.ws.DbSourceProxy;\r
-import jalview.ws.DbSourceProxyImpl;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
 /**\r
  * TODO: later PFAM is a complex datasource - it currently returns a seed alignment, but could optionally return a full alignment.\r
  * TODO: later PFAM is a complex datasource - it could return a tree in addition to an alignment\r

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index aa324dc..8dc000e 100644 (file)
--- 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;\r
 import jalview.io.IdentifyFile;\r
 import jalview.ws.DBRefFetcher;\r
-import jalview.ws.DbSourceProxy;\r
-import jalview.ws.DbSourceProxyImpl;\r
 import jalview.ws.EBIFetchClient;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
 \r
 /**\r
  * @author JimP\r

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 (file)
--- a/src/jalview/ws/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -1,4 +1,4 @@
-package jalview.ws;\r
+package jalview.ws.seqfetcher;\r
 \r
 import jalview.datamodel.AlignmentI;\r
 import jalview.datamodel.SequenceI;\r

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 (file)
--- a/src/jalview/ws/DbSourceProxy.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java
@@ -1,4 +1,4 @@
-package jalview.ws;\r
+package jalview.ws.seqfetcher;\r
 \r
 import jalview.datamodel.AlignmentI;\r
 \r

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 (file)
--- a/src/jalview/ws/DbSourceProxyImpl.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
@@ -1,4 +1,4 @@
-package jalview.ws;\r
+package jalview.ws.seqfetcher;\r
 \r
 import jalview.datamodel.Alignment;\r
 import jalview.datamodel.DBRefSource;\r