From 6b406c397d41a0f2d84b75f13e7ab478932bf57d Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
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