X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;h=e75a3329c176d6e727074bd98dc055b632e58ec3;hb=0233fbee0ff0d7fad302aa2da743c51fd64be101;hp=86458e6f545740b621853019a94b1e92026b704c;hpb=09ee1649c4427f534331aa2017a890529f0932f5;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index 86458e6..e75a332 100755
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,10 +1,21 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1)
+ * Copyright (C) 2009 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.schemabinding.version2;
 
   //---------------------------------/
@@ -147,6 +158,53 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_textColThreshold;
 
     /**
+     * Field _showUnconserved.
+     */
+    private boolean _showUnconserved;
+
+    /**
+     * keeps track of state for field: _showUnconserved
+     */
+    private boolean _has_showUnconserved;
+
+    /**
+     * Field _ignoreGapsinConsensus.
+     */
+    private boolean _ignoreGapsinConsensus = true;
+
+    /**
+     * keeps track of state for field: _ignoreGapsinConsensus
+     */
+    private boolean _has_ignoreGapsinConsensus;
+
+    /**
+     * Field _showConsensusHistogram.
+     */
+    private boolean _showConsensusHistogram = true;
+
+    /**
+     * keeps track of state for field: _showConsensusHistogram
+     */
+    private boolean _has_showConsensusHistogram;
+
+    /**
+     * Field _showSequenceLogo.
+     */
+    private boolean _showSequenceLogo = false;
+
+    /**
+     * keeps track of state for field: _showSequenceLogo
+     */
+    private boolean _has_showSequenceLogo;
+
+    /**
+     * Optional sequence group ID (only needs to be unique for this
+     * alignment)
+     *  
+     */
+    private java.lang.String _id;
+
+    /**
      * Field _seqList.
      */
     private java.util.Vector _seqList;
@@ -174,9 +232,9 @@ public class JGroup implements java.io.Serializable {
      * given is outside the bounds of the collection
      */
     public void addSeq(
-            final int vSeq)
+            final java.lang.String vSeq)
     throws java.lang.IndexOutOfBoundsException {
-        this._seqList.addElement(new java.lang.Integer(vSeq));
+        this._seqList.addElement(vSeq);
     }
 
     /**
@@ -189,9 +247,9 @@ public class JGroup implements java.io.Serializable {
      */
     public void addSeq(
             final int index,
-            final int vSeq)
+            final java.lang.String vSeq)
     throws java.lang.IndexOutOfBoundsException {
-        this._seqList.add(index, new java.lang.Integer(vSeq));
+        this._seqList.add(index, vSeq);
     }
 
     /**
@@ -231,6 +289,13 @@ public class JGroup implements java.io.Serializable {
 
     /**
      */
+    public void deleteIgnoreGapsinConsensus(
+    ) {
+        this._has_ignoreGapsinConsensus= false;
+    }
+
+    /**
+     */
     public void deleteOutlineColour(
     ) {
         this._has_outlineColour= false;
@@ -245,6 +310,27 @@ public class JGroup implements java.io.Serializable {
 
     /**
      */
+    public void deleteShowConsensusHistogram(
+    ) {
+        this._has_showConsensusHistogram= false;
+    }
+
+    /**
+     */
+    public void deleteShowSequenceLogo(
+    ) {
+        this._has_showSequenceLogo= false;
+    }
+
+    /**
+     */
+    public void deleteShowUnconserved(
+    ) {
+        this._has_showUnconserved= false;
+    }
+
+    /**
+     */
     public void deleteStart(
     ) {
         this._has_start= false;
@@ -274,7 +360,7 @@ public class JGroup implements java.io.Serializable {
     /**
      * Method enumerateSeq.
      * 
-     * @return an Enumeration over all int elements
+     * @return an Enumeration over all java.lang.String elements
      */
     public java.util.Enumeration enumerateSeq(
     ) {
@@ -342,6 +428,29 @@ public class JGroup implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'id'. The field 'id' has the
+     * following description: Optional sequence group ID (only
+     * needs to be unique for this alignment)
+     *  
+     * 
+     * @return the value of field 'Id'.
+     */
+    public java.lang.String getId(
+    ) {
+        return this._id;
+    }
+
+    /**
+     * Returns the value of field 'ignoreGapsinConsensus'.
+     * 
+     * @return the value of field 'IgnoreGapsinConsensus'.
+     */
+    public boolean getIgnoreGapsinConsensus(
+    ) {
+        return this._ignoreGapsinConsensus;
+    }
+
+    /**
      * Returns the value of field 'name'.
      * 
      * @return the value of field 'Name'.
@@ -377,9 +486,9 @@ public class JGroup implements java.io.Serializable {
      * @param index
      * @throws java.lang.IndexOutOfBoundsException if the index
      * given is outside the bounds of the collection
-     * @return the value of the int at the given index
+     * @return the value of the java.lang.String at the given index
      */
-    public int getSeq(
+    public java.lang.String getSeq(
             final int index)
     throws java.lang.IndexOutOfBoundsException {
         // check bounds for index
@@ -387,24 +496,22 @@ public class JGroup implements java.io.Serializable {
             throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
         }
         
-        return ((java.lang.Integer) _seqList.get(index)).intValue();
+        return (java.lang.String) _seqList.get(index);
     }
 
     /**
      * Method getSeq.Returns the contents of the collection in an
-     * Array.  
+     * Array.  <p>Note:  Just in case the collection contents are
+     * changing in another thread, we pass a 0-length Array of the
+     * correct type into the API call.  This way we <i>know</i>
+     * that the Array returned is of exactly the correct length.
      * 
      * @return this collection as an Array
      */
-    public int[] getSeq(
+    public java.lang.String[] getSeq(
     ) {
-        int size = this._seqList.size();
-        int[] array = new int[size];
-        java.util.Iterator iter = _seqList.iterator();
-        for (int index = 0; index < size; index++) {
-            array[index] = ((java.lang.Integer) iter.next()).intValue();
-        }
-        return array;
+        java.lang.String[] array = new java.lang.String[0];
+        return (java.lang.String[]) this._seqList.toArray(array);
     }
 
     /**
@@ -418,6 +525,36 @@ public class JGroup implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'showConsensusHistogram'.
+     * 
+     * @return the value of field 'ShowConsensusHistogram'.
+     */
+    public boolean getShowConsensusHistogram(
+    ) {
+        return this._showConsensusHistogram;
+    }
+
+    /**
+     * Returns the value of field 'showSequenceLogo'.
+     * 
+     * @return the value of field 'ShowSequenceLogo'.
+     */
+    public boolean getShowSequenceLogo(
+    ) {
+        return this._showSequenceLogo;
+    }
+
+    /**
+     * Returns the value of field 'showUnconserved'.
+     * 
+     * @return the value of field 'ShowUnconserved'.
+     */
+    public boolean getShowUnconserved(
+    ) {
+        return this._showUnconserved;
+    }
+
+    /**
      * Returns the value of field 'start'.
      * 
      * @return the value of field 'Start'.
@@ -508,6 +645,17 @@ public class JGroup implements java.io.Serializable {
     }
 
     /**
+     * Method hasIgnoreGapsinConsensus.
+     * 
+     * @return true if at least one IgnoreGapsinConsensus has been
+     * added
+     */
+    public boolean hasIgnoreGapsinConsensus(
+    ) {
+        return this._has_ignoreGapsinConsensus;
+    }
+
+    /**
      * Method hasOutlineColour.
      * 
      * @return true if at least one OutlineColour has been added
@@ -528,6 +676,37 @@ public class JGroup implements java.io.Serializable {
     }
 
     /**
+     * Method hasShowConsensusHistogram.
+     * 
+     * @return true if at least one ShowConsensusHistogram has been
+     * added
+     */
+    public boolean hasShowConsensusHistogram(
+    ) {
+        return this._has_showConsensusHistogram;
+    }
+
+    /**
+     * Method hasShowSequenceLogo.
+     * 
+     * @return true if at least one ShowSequenceLogo has been added
+     */
+    public boolean hasShowSequenceLogo(
+    ) {
+        return this._has_showSequenceLogo;
+    }
+
+    /**
+     * Method hasShowUnconserved.
+     * 
+     * @return true if at least one ShowUnconserved has been added
+     */
+    public boolean hasShowUnconserved(
+    ) {
+        return this._has_showUnconserved;
+    }
+
+    /**
      * Method hasStart.
      * 
      * @return true if at least one Start has been added
@@ -598,6 +777,46 @@ public class JGroup implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'ignoreGapsinConsensus'.
+     * 
+     * @return the value of field 'IgnoreGapsinConsensus'.
+     */
+    public boolean isIgnoreGapsinConsensus(
+    ) {
+        return this._ignoreGapsinConsensus;
+    }
+
+    /**
+     * Returns the value of field 'showConsensusHistogram'.
+     * 
+     * @return the value of field 'ShowConsensusHistogram'.
+     */
+    public boolean isShowConsensusHistogram(
+    ) {
+        return this._showConsensusHistogram;
+    }
+
+    /**
+     * Returns the value of field 'showSequenceLogo'.
+     * 
+     * @return the value of field 'ShowSequenceLogo'.
+     */
+    public boolean isShowSequenceLogo(
+    ) {
+        return this._showSequenceLogo;
+    }
+
+    /**
+     * Returns the value of field 'showUnconserved'.
+     * 
+     * @return the value of field 'ShowUnconserved'.
+     */
+    public boolean isShowUnconserved(
+    ) {
+        return this._showUnconserved;
+    }
+
+    /**
      * Method isValid.
      * 
      * @return true if this object is valid according to the schema
@@ -658,8 +877,8 @@ public class JGroup implements java.io.Serializable {
      * @return true if the object was removed from the collection.
      */
     public boolean removeSeq(
-            final int vSeq) {
-        boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
+            final java.lang.String vSeq) {
+        boolean removed = _seqList.remove(vSeq);
         return removed;
     }
 
@@ -669,10 +888,10 @@ public class JGroup implements java.io.Serializable {
      * @param index
      * @return the element removed from the collection
      */
-    public int removeSeqAt(
+    public java.lang.String removeSeqAt(
             final int index) {
         java.lang.Object obj = this._seqList.remove(index);
-        return ((java.lang.Integer) obj).intValue();
+        return (java.lang.String) obj;
     }
 
     /**
@@ -741,6 +960,31 @@ public class JGroup implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'id'. The field 'id' has the
+     * following description: Optional sequence group ID (only
+     * needs to be unique for this alignment)
+     *  
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(
+            final java.lang.String id) {
+        this._id = id;
+    }
+
+    /**
+     * Sets the value of field 'ignoreGapsinConsensus'.
+     * 
+     * @param ignoreGapsinConsensus the value of field
+     * 'ignoreGapsinConsensus'.
+     */
+    public void setIgnoreGapsinConsensus(
+            final boolean ignoreGapsinConsensus) {
+        this._ignoreGapsinConsensus = ignoreGapsinConsensus;
+        this._has_ignoreGapsinConsensus = true;
+    }
+
+    /**
      * Sets the value of field 'name'.
      * 
      * @param name the value of field 'name'.
@@ -782,14 +1026,14 @@ public class JGroup implements java.io.Serializable {
      */
     public void setSeq(
             final int index,
-            final int vSeq)
+            final java.lang.String vSeq)
     throws java.lang.IndexOutOfBoundsException {
         // check bounds for index
         if (index < 0 || index >= this._seqList.size()) {
             throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
         }
         
-        this._seqList.set(index, new java.lang.Integer(vSeq));
+        this._seqList.set(index, vSeq);
     }
 
     /**
@@ -798,16 +1042,50 @@ public class JGroup implements java.io.Serializable {
      * @param vSeqArray
      */
     public void setSeq(
-            final int[] vSeqArray) {
+            final java.lang.String[] vSeqArray) {
         //-- copy array
         _seqList.clear();
         
         for (int i = 0; i < vSeqArray.length; i++) {
-                this._seqList.add(new java.lang.Integer(vSeqArray[i]));
+                this._seqList.add(vSeqArray[i]);
         }
     }
 
     /**
+     * Sets the value of field 'showConsensusHistogram'.
+     * 
+     * @param showConsensusHistogram the value of field
+     * 'showConsensusHistogram'.
+     */
+    public void setShowConsensusHistogram(
+            final boolean showConsensusHistogram) {
+        this._showConsensusHistogram = showConsensusHistogram;
+        this._has_showConsensusHistogram = true;
+    }
+
+    /**
+     * Sets the value of field 'showSequenceLogo'.
+     * 
+     * @param showSequenceLogo the value of field 'showSequenceLogo'
+     */
+    public void setShowSequenceLogo(
+            final boolean showSequenceLogo) {
+        this._showSequenceLogo = showSequenceLogo;
+        this._has_showSequenceLogo = true;
+    }
+
+    /**
+     * Sets the value of field 'showUnconserved'.
+     * 
+     * @param showUnconserved the value of field 'showUnconserved'.
+     */
+    public void setShowUnconserved(
+            final boolean showUnconserved) {
+        this._showUnconserved = showUnconserved;
+        this._has_showUnconserved = true;
+    }
+
+    /**
      * Sets the value of field 'start'.
      * 
      * @param start the value of field 'start'.