X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=ca72942e48234b6ade1b7c31f492172c335b0909;hb=174230b4233d9ce80f94527768d2cd2f76da11ab;hp=a197dfdef19176a02297897ca068349fb7ebc6b1;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index a197dfd..ca72942 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,81 +1,236 @@
+/*
+ * 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.awt.*;
-
-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;}
+import java.util.Hashtable;
+/**
+ * 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;
-/*
-
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
-*/
+ // Feature group can be set from a features file
+ // as a group of features between STARTGROUP and ENDGROUP markers
+ public String featureGroup;
-}
+ public SequenceFeature()
+ {}
+
+ 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;
+ }
+
+}