X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=4c6e2a56a24ba992a70ba1c81d82bd69ebc50302;hb=1889827c44c51f6353fe8619e5d44b421158af23;hp=0a8e08794387aaaaeda626ba917c1147ebe07eab;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 0a8e087..4c6e2a5 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,28 +1,36 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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.
+ * 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
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+
import jalview.analysis.WUSSParseException;
+import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
* DOCUMENT ME!
*
@@ -49,7 +57,10 @@ public class AlignmentAnnotation
/** DOCUMENT ME!! */
public Annotation[] annotations;
+
+
+ public ArrayList bps=null;
/**
* RNA secondary structure contact positions
*/
@@ -68,13 +79,15 @@ public class AlignmentAnnotation
*/
private void _updateRnaSecStr(CharSequence RNAannot)
{
- try
- {
- _rnasecstr = Rna.GetBasePairs(RNAannot);
- invalidrnastruc = -1;
- } catch (WUSSParseException px)
+ try {
+ _rnasecstr = Rna.GetBasePairs(RNAannot);
+ bps = Rna.GetModeleBP(RNAannot);
+ invalidrnastruc=-1;
+ }
+ catch (WUSSParseException px)
{
- invalidrnastruc = px.getProblemPos();
+ // DEBUG System.out.println(px);
+ invalidrnastruc=px.getProblemPos();
}
if (invalidrnastruc > -1)
{
@@ -192,7 +205,11 @@ public class AlignmentAnnotation
return NO_GRAPH;
}
}
-
+ // JBPNote: what does this do ?
+ public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
+ {
+ bps = Rna.GetModeleBP(RNAannot);
+ }
/**
* Creates a new AlignmentAnnotation object.
*
@@ -240,7 +257,37 @@ public class AlignmentAnnotation
else
// Check for RNA secondary structure
{
- if (annotations[i].secondaryStructure == 'S')
+ //System.out.println(annotations[i].secondaryStructure);
+ if (annotations[i].secondaryStructure == '('
+ || annotations[i].secondaryStructure == '['
+ || annotations[i].secondaryStructure == '<'
+ || annotations[i].secondaryStructure == '{'
+ || annotations[i].secondaryStructure == 'A'
+ || annotations[i].secondaryStructure == 'B'
+ || annotations[i].secondaryStructure == 'C'
+ || annotations[i].secondaryStructure == 'D'
+ || annotations[i].secondaryStructure == 'E'
+ || annotations[i].secondaryStructure == 'F'
+ || annotations[i].secondaryStructure == 'G'
+ || annotations[i].secondaryStructure == 'H'
+ || annotations[i].secondaryStructure == 'I'
+ || annotations[i].secondaryStructure == 'J'
+ || annotations[i].secondaryStructure == 'K'
+ || annotations[i].secondaryStructure == 'L'
+ || annotations[i].secondaryStructure == 'M'
+ || annotations[i].secondaryStructure == 'N'
+ || annotations[i].secondaryStructure == 'O'
+ || annotations[i].secondaryStructure == 'P'
+ || annotations[i].secondaryStructure == 'Q'
+ || annotations[i].secondaryStructure == 'R'
+ || annotations[i].secondaryStructure == 'S'
+ || annotations[i].secondaryStructure == 'T'
+ || annotations[i].secondaryStructure == 'U'
+ || annotations[i].secondaryStructure == 'V'
+ || annotations[i].secondaryStructure == 'W'
+ || annotations[i].secondaryStructure == 'X'
+ || annotations[i].secondaryStructure == 'Y'
+ || annotations[i].secondaryStructure == 'Z')
{
hasIcons |= true;
isrna |= true;
@@ -271,9 +318,38 @@ public class AlignmentAnnotation
// &&
// annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
firstChar != ' '
- && firstChar != 'H'
+ && firstChar != '$'
+ && firstChar != '�' // JBPNote should explicitly express as unicode number to avoid source code translation problems
+ && firstChar != '('
+ && firstChar != '['
+ && firstChar != '>'
+ && firstChar != '{'
+ && firstChar != 'A'
+ && firstChar != 'B'
+ && firstChar != 'C'
+ && firstChar != 'D'
&& firstChar != 'E'
+ && firstChar != 'F'
+ && firstChar != 'G'
+ && firstChar != 'H'
+ && firstChar != 'I'
+ && firstChar != 'J'
+ && firstChar != 'K'
+ && firstChar != 'L'
+ && firstChar != 'M'
+ && firstChar != 'N'
+ && firstChar != 'O'
+ && firstChar != 'P'
+ && firstChar != 'Q'
+ && firstChar != 'R'
&& firstChar != 'S'
+ && firstChar != 'T'
+ && firstChar != 'U'
+ && firstChar != 'V'
+ && firstChar != 'W'
+ && firstChar != 'X'
+ && firstChar != 'Y'
+ && firstChar != 'Z'
&& firstChar != '-'
&& firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
{
@@ -508,7 +584,7 @@ public class AlignmentAnnotation
{
if (annotations[i] != null)
{
- annotations[i].displayCharacter = "";
+ annotations[i].displayCharacter = "X";
}
}
}
@@ -973,7 +1049,7 @@ public class AlignmentAnnotation
{
if (annotations[i] == null)
annotations[i] = new Annotation(String.valueOf(gapchar), null,
- ' ', 0f);
+ ' ', 0f,null);
else if (annotations[i].displayCharacter == null
|| annotations[i].displayCharacter.equals(" "))
annotations[i].displayCharacter = String.valueOf(gapchar);
@@ -1034,5 +1110,4 @@ public class AlignmentAnnotation
{
this.calcId = calcId;
}
-
}