removed all dasobert code and begun to replace with Jdas calls.

[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
deleted file mode 100755 (executable)
index 8936a16..0000000
--- a/src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
+++ /dev/null
@@ -1,233 +0,0 @@
-/*
- *                    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 int hashCode()
-  {
-    int h = 7;
-
-    h = 31 * h + (null == name ? 0 : name.hashCode());
-    h = 31 * h + (null == category ? 0 : category.hashCode());
-
-    return h;
-  }
-
-  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;
-  }
-
-}