Das client files

[jalview.git] / src / org / biojava / dasobert / dasregistry / DasCoordinateSystem.java

diff --git a/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java b/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
new file mode 100755 (executable)
index 0000000..31caaf5
--- /dev/null
+++ b/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
@@ -0,0 +1,159 @@
+/*
+ *                    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 15.04.2004
+ * @author Andreas Prlic
+ *
+ */
+package org.biojava.dasobert.dasregistry;
+
+
+/** a Bean to be returned via SOAP. It takes care of the DAS -  coordinate Systems 
+ * @author Andreas Prlic
+ */
+public class DasCoordinateSystem {
+
+    String name;
+    String category;
+    String organism_name;
+    int ncbi_tax_id ;
+    String uniqueId ;
+    String version;
+    String testCode;
+    
+    public DasCoordinateSystem () {
+        uniqueId = "";
+        name = "";
+        category ="";
+        organism_name = "";
+        ncbi_tax_id = 0;
+        version = "";
+        testCode = "";
+    }
+
+    public boolean equals(DasCoordinateSystem other){
+        boolean match = true;
+        System.out.println("comparing " + this.toString() + " to " + other.toString());
+        // URI has piority 
+        if ( (! uniqueId.equals("")) && ( uniqueId.equals( other.getUniqueId())))
+            return true;
+        
+        if ( ncbi_tax_id != other.getNCBITaxId()) {
+            System.out.println("mismatch in ncbi tax id " + ncbi_tax_id + " != " + other.getNCBITaxId());
+            match = false;
+        }
+        if ( ! version.equals(other.getVersion() )){
+            System.out.println("mismatch in version");
+            match = false;
+        }
+        if ( ! category.equals(other.getCategory())  ) {
+            System.out.println("mismatch in category");
+            match = false;
+        }
+        if ( ! name.equals(other.getName())) {
+            System.out.println("mismatch in name");   
+            match = false;
+        }
+        System.out.println(" match: " + match);
+        
+        return match;
+    }
+    
+    public Object clone() {
+        DasCoordinateSystem d = new DasCoordinateSystem();
+        d.setTestCode(testCode);
+        d.setCategory(category);
+        d.setName(name);
+        d.setNCBITaxId(ncbi_tax_id);
+        d.setUniqueId(getUniqueId());
+        d.setOrganismName(getOrganismName());
+        d.setVersion(getVersion());
+        return d;
+    }
+    
+    public String getTestCode() {
+        return testCode;
+    }
+
+
+
+    public void setTestCode(String testCode) {
+        if ( testCode == null)
+            testCode = "";
+        this.testCode = testCode;
+    }
+
+
+
+    public void setUniqueId(String id) { uniqueId = id ;   }
+    public String getUniqueId() { return uniqueId;         }
+
+    public void setName(String n) { name = n; }
+    public String getName() { return name; }
+    
+    public void setCategory(String c) { category = c;}
+    public String getCategory() { return category;}
+
+    public void setOrganismName(String t) { organism_name  =t;} 
+    public String getOrganismName() { return organism_name;}
+
+    public void setNCBITaxId(int id) { ncbi_tax_id = id;}
+    public int getNCBITaxId(){ return ncbi_tax_id ;}
+    
+    
+    
+
+    public String getVersion() {
+        return version;
+    }
+
+    public void setVersion(String version) {
+        if ( version == null)
+            version = "";
+        this.version = version;
+    }
+
+    public String toString() {
+        String nam = name;
+        if ( ! version.equals(""))
+            nam += "_" + version;
+        
+       if ( organism_name.equals("") ) 
+           return nam+","+category ;
+       else 
+           return nam+","+category+"," + organism_name ;
+    }
+
+    public static DasCoordinateSystem fromString(String rawString) {
+       String[] spl = rawString.split(",");
+       DasCoordinateSystem dcs = new DasCoordinateSystem();
+       if ( spl.length == 2 ) {
+           dcs.setName(spl[0]);           
+           dcs.setCategory(spl[1]);
+       } 
+       if ( spl.length == 3 ) {
+           dcs.setName(spl[0]);
+           dcs.setCategory(spl[1]);
+           dcs.setOrganismName(spl[2]);
+       }
+       return dcs;
+    }
+
+
+}