/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview 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 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview 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
import java.util.Enumeration;
import java.util.Vector;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
*
* Implements the SequenceI interface for a char[] based sequence object.
String vamsasId;
DBRefEntry[] dbrefs;
+
+ RNA rna;
/**
* This annotation is displayed below the alignment but the positions are tied
* to the residues of this sequence
*/
Vector annotation;
-
+
/**
- * The index of the sequence in a MSA
+ * The index of the sequence in a MSA
*/
int index = -1;
- /** array of seuqence features - may not be null for a valid sequence object */
+ /** array of sequence features - may not be null for a valid sequence object */
public SequenceFeature[] sequenceFeatures;
/**
void checkValidRange()
{
- // Note: JAL-774 : http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
+ // Note: JAL-774 :
+ // http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
{
int endRes = 0;
for (int j = 0; j < sequence.length; j++)
endRes += start - 1;
}
- if (end<endRes) {
+ if (end < endRes)
+ {
end = endRes;
}
}
return this.description;
}
- /**
- * Return the alignment position for a sequence position
- *
- * @param pos
- * lying from start to end
+ /*
+ * (non-Javadoc)
*
- * @return aligned position of residue pos
+ * @see jalview.datamodel.SequenceI#findIndex(int)
*/
public int findIndex(int pos)
{
{
tmp = new char[i];
System.arraycopy(sequence, 0, tmp, 0, i);
+ j=sequence.length;
}
else
{
System.arraycopy(sequence, j, tmp, i, sequence.length - j);
}
boolean createNewDs = false;
+ // TODO: take a look at the new dataset creation validation method below -
+ // this could become time comsuming for large sequences - consider making it
+ // more efficient
for (int s = i; s < j; s++)
{
if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
}
/**
- * @return The index (zero-based) on this sequence in the MSA.
- * It returns {@code -1} if this information is not available.
+ * @return The index (zero-based) on this sequence in the MSA. It returns
+ * {@code -1} if this information is not available.
*/
- public int getIndex() { return index; }
-
+ public int getIndex()
+ {
+ return index;
+ }
+
/**
- * Defines the position of this sequence in the MSA.
- * Use the value {@code -1} if this information is undefined.
+ * Defines the position of this sequence in the MSA. Use the value {@code -1}
+ * if this information is undefined.
*
- * @param The position for this sequence. This value is zero-based (zero for this first sequence)
+ * @param The
+ * position for this sequence. This value is zero-based (zero for
+ * this first sequence)
*/
- public void setIndex(int value) { index = value; }
+ public void setIndex(int value)
+ {
+ index = value;
+ }
+
+ public void setRNA(RNA r){rna=r;}
+
+ public RNA getRNA() { return rna; }
+
}