X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=094e060662c3f88331227235eab017b45c58c23b;hb=cfbeda226e2ac27f6d02572b1c9589a3e2f1c747;hp=702af732a8620e834056ced2021368895d8a9f69;hpb=1fe726c973fdbf14d6f09be74b5f06fe855d65ec;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 702af73..094e060 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,98 +1,267 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-package jalview.datamodel;
-
-public class SequenceFeature {
-    int begin;
-    int end;
-    String type;
-    String description;
-    String status;
-
-    public SequenceFeature() {
-    }
-
-    public SequenceFeature(String type, int start, int end, String description,
-        String status) {
-        this.type = type;
-        this.begin = start;
-        this.end = end;
-        this.description = description;
-        this.status = status;
-    }
-
-    public int getStart() {
-        return begin;
-    }
-
-    public int getEnd() {
-        return end;
-    }
-
-    public String getType() {
-        return type;
-    }
-
-    public String getDescription() {
-        return description;
-    }
-
-    public String getStatus() {
-        return status;
-    }
-
-    /*
-          <xs:enumeration value="active site" />
-    <xs:enumeration value="binding site" />
-    <xs:enumeration value="calcium-binding region" />
-    <xs:enumeration value="chain" />
-    <xs:enumeration value="cross-link" />
-    <xs:enumeration value="disulfide bond" />
-    <xs:enumeration value="DNA-binding region" />
-    <xs:enumeration value="domain" />
-    <xs:enumeration value="glycosylation site" />
-    <xs:enumeration value="helix" />
-    <xs:enumeration value="initiator methionine" />
-    <xs:enumeration value="lipid moiety-binding region" />
-    <xs:enumeration value="metal ion-binding site" />
-    <xs:enumeration value="modified residue" />
-    <xs:enumeration value="mutagenesis site" />
-    <xs:enumeration value="non-consecutive residues" />
-    <xs:enumeration value="non-terminal residue" />
-    <xs:enumeration value="nucleotide phosphate-binding region" />
-    <xs:enumeration value="peptide" />
-    <xs:enumeration value="propeptide" />
-    <xs:enumeration value="repeat" />
-    <xs:enumeration value="selenocysteine" />
-    <xs:enumeration value="sequence conflict" />
-    <xs:enumeration value="sequence variant" />
-    <xs:enumeration value="signal peptide" />
-    <xs:enumeration value="similar" />
-    <xs:enumeration value="site" />
-    <xs:enumeration value="splice variant" />
-    <xs:enumeration value="strand" />
-    <xs:enumeration value="thioether bond" />
-    <xs:enumeration value="thiolester bond" />
-    <xs:enumeration value="transit peptide" />
-    <xs:enumeration value="transmembrane region" />
-    <xs:enumeration value="turn" />
-    <xs:enumeration value="unsure residue" />
-    <xs:enumeration value="zinc finger region" />
-    */
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceFeature
+{
+    public int begin;
+    public int end;
+    public float score;
+    public String type;
+    public String description;
+    public Hashtable otherDetails;
+    public java.util.Vector links;
+
+    // Feature group can be set from a features file
+    // as a group of features between STARTGROUP and ENDGROUP markers
+    public String featureGroup;
+
+    public SequenceFeature()
+    {}
+    /**
+     * Constructs a duplicate feature. 
+     * Note: Uses clone on the otherDetails so only shallow copies are made 
+     * of additional properties and method will silently fail if unclonable 
+     * objects are found in the hash.
+     * @param cpy
+     */
+    public SequenceFeature(SequenceFeature cpy) {
+        if (cpy!=null) {
+            begin = cpy.begin;
+            end = cpy.end;
+            score = cpy.score;
+            type = new String(cpy.type);
+            description = new String(cpy.description);
+            featureGroup = new String(cpy.featureGroup);
+            if (cpy.otherDetails!=null) {
+                try {
+                    otherDetails = (Hashtable) cpy.otherDetails.clone();
+                } catch (Exception e) {
+                    // Uncloneable objects in the otherDetails - don't complain
+                }
+            }
+            if (cpy.links!=null && cpy.links.size()>0) {
+                links=new Vector();
+                for (int i=0,iSize=cpy.links.size(); i<iSize; i++) {
+                    links.setElementAt(cpy.links.elementAt(i), i);
+                }
+            }
+        }
+    }
+    public SequenceFeature(String type,
+                           String desc,
+                           String status,
+                           int begin, int end,
+                           String featureGroup)
+    {
+      this.type = type;
+      this.description = desc;
+      setValue("status", status);
+      this.begin = begin;
+      this.end = end;
+      this.featureGroup = featureGroup;
+    }
+
+    public SequenceFeature(String type,
+                           String desc,
+                           int begin, int end,
+                           float score,
+                           String featureGroup)
+    {
+      this.type = type;
+      this.description = desc;
+      this.begin = begin;
+      this.end = end;
+      this.score = score;
+      this.featureGroup = featureGroup;
+    }
+
+    public boolean equals(SequenceFeature sf)
+    {
+      if (begin != sf.begin
+          || end != sf.end
+          || score != sf.score)
+        return false;
+
+      if(!(type+description+featureGroup).equals
+         (sf.type+sf.description+sf.featureGroup))
+        return false;
+
+      return true;
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getBegin()
+    {
+        return begin;
+    }
+
+    public void setBegin(int start)
+    {
+      this.begin = start;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEnd()
+    {
+        return end;
+    }
+
+    public void setEnd(int end)
+    {
+      this.end = end;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getType()
+    {
+        return type;
+    }
+
+    public void setType(String type)
+    {
+      this.type = type;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getDescription()
+    {
+        return description;
+    }
+
+    public void setDescription(String desc)
+    {
+      description = desc;
+    }
+
+    public String getFeatureGroup()
+    {
+      return featureGroup;
+    }
+
+    public void setFeatureGroup(String featureGroup)
+    {
+      this.featureGroup = featureGroup;
+    }
+
+    public void addLink(String labelLink)
+    {
+      if(links==null)
+        links = new java.util.Vector();
+
+      links.insertElementAt(labelLink,0);
+    }
+
+    public float getScore()
+    {
+      return score;
+    }
+
+    public void setScore(float value)
+    {
+      score = value;
+    }
+
+    /**
+     * Used for getting values which are not in the
+     * basic set. eg STRAND, FRAME for GFF file
+     * @param key String
+     */
+    public Object getValue(String key)
+    {
+      if(otherDetails==null)
+        return null;
+      else
+        return otherDetails.get(key);
+    }
+
+    /**
+     * Used for setting values which are not in the
+     * basic set. eg STRAND, FRAME for GFF file
+     * @param key   eg STRAND
+     * @param value eg +
+     */
+    public void setValue(String key, Object value)
+    {
+      if(value!=null)
+      {
+        if (otherDetails == null)
+          otherDetails = new Hashtable();
+
+        otherDetails.put(key, value);
+      }
+    }
+
+
+    /*
+     * The following methods are added to maintain
+     * the castor Uniprot mapping file for the moment.
+     */
+    public void setStatus(String status)
+    {
+      setValue("status", status);
+    }
+
+    public String getStatus()
+    {
+      if (otherDetails != null)
+        return otherDetails.get("status").toString();
+      else
+        return null;
+    }
+
+    public void setPosition(int pos)
+    {
+      begin = pos;
+      end = pos;
+    }
+
+    public int getPosition()
+    {
+      return begin;
+    }
+
+}