Das client files

[jalview.git] / src / org / biojava / dasobert / das / AlignmentParameters.java

diff --git a/src/org/biojava/dasobert/das/AlignmentParameters.java b/src/org/biojava/dasobert/das/AlignmentParameters.java
new file mode 100755 (executable)
index 0000000..faf6924
--- /dev/null
+++ b/src/org/biojava/dasobert/das/AlignmentParameters.java
@@ -0,0 +1,154 @@
+/*
+ *                  BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ * 
+ * Created on Dec 10, 2005
+ *
+ */
+package org.biojava.dasobert.das;
+
+import org.biojava.dasobert.dasregistry.Das1Source;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+
+/** a class that stores the arguments that can be sent to the AlignmentThread class
+ * 
+ * @author Andreas Prlic
+ *
+ */
+public class AlignmentParameters {
+
+    String query;
+    String subject;
+    String queryPDBChainId;
+    String subjectPDBChainId;
+    
+    
+    DasCoordinateSystem queryCoordinateSystem;
+    DasCoordinateSystem subjectCoordinateSystem;
+    Das1Source[] dasSources;
+    
+    
+    public static String DEFAULT_PDBCOORDSYS     = "PDBresnum,Protein Structure";
+    public static String DEFAULT_UNIPROTCOORDSYS = "UniProt,Protein Sequence";
+    public static String DEFAULT_ENSPCOORDSYS    = "Ensembl,Protein Sequence";
+    
+    
+    public AlignmentParameters() {
+        super();
+        dasSources = new SpiceDasSource[0];
+
+    }
+
+    public DasCoordinateSystem getDefaultPDBCoordSys(){
+        return DasCoordinateSystem.fromString(DEFAULT_PDBCOORDSYS);
+    }
+    public DasCoordinateSystem getDefaultUniProtCoordSys(){
+        return DasCoordinateSystem.fromString(DEFAULT_UNIPROTCOORDSYS);
+    }
+    public DasCoordinateSystem getDefaultEnspCoordSys(){
+        return DasCoordinateSystem.fromString(DEFAULT_ENSPCOORDSYS);
+    }
+    
+
+    public Das1Source[] getDasSources() {
+        return dasSources;
+    }
+
+
+
+    public void setDasSources(SpiceDasSource[] dasSources) {
+        this.dasSources = dasSources;
+    }
+
+
+
+    public String getQuery() {
+        return query;
+    }
+
+
+
+    public void setQuery(String query) {
+        this.query = query;
+    }
+
+
+
+    public DasCoordinateSystem getQueryCoordinateSystem() {
+        return queryCoordinateSystem;
+    }
+
+
+
+    public void setQueryCoordinateSystem(DasCoordinateSystem queryCoordinateSystem) {
+        this.queryCoordinateSystem = queryCoordinateSystem;
+    }
+
+
+
+    public String getQueryPDBChainId() {
+        return queryPDBChainId;
+    }
+
+
+
+    public void setQueryPDBChainId(String queryPDBChainId) {
+        this.queryPDBChainId = queryPDBChainId;
+    }
+
+
+
+    public String getSubject() {
+        return subject;
+    }
+
+
+
+    public void setSubject(String subject) {
+        this.subject = subject;
+    }
+
+
+
+    public DasCoordinateSystem getSubjectCoordinateSystem() {
+        return subjectCoordinateSystem;
+    }
+
+
+
+    public void setSubjectCoordinateSystem(
+            DasCoordinateSystem subjectCoordinateSystem) {
+        this.subjectCoordinateSystem = subjectCoordinateSystem;
+    }
+
+
+
+    public String getSubjectPDBChainId() {
+        return subjectPDBChainId;
+    }
+
+
+
+    public void setSubjectPDBChainId(String subjectPDBChainId) {
+        this.subjectPDBChainId = subjectPDBChainId;
+    }
+    
+    
+    
+
+}