From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 28 Jun 2015 16:11:41 +0000 (+0100)
Subject: JAL-1705 concrete classes for different ENSEMBL sequence retrieval modes
X-Git-Tag: Release_2_10_0~296^2~90^2~15
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9eec40eae88ae4330adc4d6ae38c513742b9e853;p=jalview.git

JAL-1705 concrete classes for different ENSEMBL sequence retrieval modes
---

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
new file mode 100644
index 0000000..4fc80ca
--- /dev/null
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -0,0 +1,25 @@
+package jalview.ext.ensembl;
+
+import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
+
+public class EnsemblCdna extends EnsemblSeqProxy
+{
+
+  public EnsemblCdna() throws Exception
+  {
+    super();
+  }
+
+  @Override
+  public String getDbName()
+  {
+    return "ENSEMBL (CDNA)";
+  }
+
+  @Override
+  protected EnsemblSeqType getSourceEnsemblType()
+  {
+    return EnsemblSeqType.CDNA;
+  }
+
+}
diff --git a/src/jalview/ext/ensembl/EnsemblCds.java b/src/jalview/ext/ensembl/EnsemblCds.java
new file mode 100644
index 0000000..1f63e05
--- /dev/null
+++ b/src/jalview/ext/ensembl/EnsemblCds.java
@@ -0,0 +1,25 @@
+package jalview.ext.ensembl;
+
+import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
+
+public class EnsemblCds extends EnsemblSeqProxy
+{
+
+  public EnsemblCds() throws Exception
+  {
+    super();
+  }
+
+  @Override
+  public String getDbName()
+  {
+    return "ENSEMBL (CDS)";
+  }
+
+  @Override
+  protected EnsemblSeqType getSourceEnsemblType()
+  {
+    return EnsemblSeqType.CDS;
+  }
+
+}
diff --git a/src/jalview/ext/ensembl/EnsemblGenome.java b/src/jalview/ext/ensembl/EnsemblGenome.java
new file mode 100644
index 0000000..37e8e2b
--- /dev/null
+++ b/src/jalview/ext/ensembl/EnsemblGenome.java
@@ -0,0 +1,25 @@
+package jalview.ext.ensembl;
+
+import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
+
+public class EnsemblGenome extends EnsemblSeqProxy
+{
+
+  public EnsemblGenome() throws Exception
+  {
+    super();
+  }
+
+  @Override
+  public String getDbName()
+  {
+    return "ENSEMBL (Genome)";
+  }
+
+  @Override
+  protected EnsemblSeqType getSourceEnsemblType()
+  {
+    return EnsemblSeqType.GENOMIC;
+  }
+
+}
diff --git a/src/jalview/ext/ensembl/EnsemblProtein.java b/src/jalview/ext/ensembl/EnsemblProtein.java
new file mode 100644
index 0000000..db8d9d5
--- /dev/null
+++ b/src/jalview/ext/ensembl/EnsemblProtein.java
@@ -0,0 +1,25 @@
+package jalview.ext.ensembl;
+
+import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
+
+public class EnsemblProtein extends EnsemblSeqProxy
+{
+
+  public EnsemblProtein() throws Exception
+  {
+    super();
+  }
+
+  @Override
+  public String getDbName()
+  {
+    return "ENSEMBL (Protein)";
+  }
+
+  @Override
+  protected EnsemblSeqType getSourceEnsemblType()
+  {
+    return EnsemblSeqType.PROTEIN;
+  }
+
+}
diff --git a/src/jalview/ext/ensembl/EnsemblTranscript.java b/src/jalview/ext/ensembl/EnsemblTranscript.java
new file mode 100644
index 0000000..68ed310
--- /dev/null
+++ b/src/jalview/ext/ensembl/EnsemblTranscript.java
@@ -0,0 +1,25 @@
+package jalview.ext.ensembl;
+
+import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
+
+public class EnsemblTranscript extends EnsemblSeqProxy
+{
+
+  public EnsemblTranscript() throws Exception
+  {
+    super();
+  }
+
+  @Override
+  public String getDbName()
+  {
+    return "ENSEMBL (Protein)";
+  }
+
+  @Override
+  protected EnsemblSeqType getSourceEnsemblType()
+  {
+    return EnsemblSeqType.PROTEIN;
+  }
+
+}