X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=0fcf43dc0ca1ff782c1482d516ac8c055c67bd08;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=1196d05c02f0f93a5625077639dc702026f252d2;hpb=c5677e9860106a821a3e6e0429b20ede7b9a732a;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 1196d05..0fcf43d 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,23 +1,26 @@
/*
- * 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 2.8.2)
+ * 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.
- *
+ *
* 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 .
+ * 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;
@@ -41,7 +44,7 @@ public class AlignmentAnnotation
public boolean autoCalculated = false;
public String annotationId;
-
+
public SequenceI sequenceRef;
/** DOCUMENT ME!! */
@@ -55,14 +58,17 @@ public class AlignmentAnnotation
+ public ArrayList bps=null;
/**
* RNA secondary structure contact positions
*/
public SequenceFeature[] _rnasecstr = null;
+
/**
* position of annotation resulting in invalid WUSS parsing or -1
*/
- private long invalidrnastruc=-1;
+ private long invalidrnastruc = -1;
+
/**
* Updates the _rnasecstr field Determines the positions that base pair and
* the positions of helices based on secondary structure from a Stockholm file
@@ -73,28 +79,31 @@ public class AlignmentAnnotation
{
try {
_rnasecstr = Rna.GetBasePairs(RNAannot);
+ bps = Rna.GetModeleBP(RNAannot);
invalidrnastruc=-1;
}
catch (WUSSParseException px)
{
+ // DEBUG System.out.println(px);
invalidrnastruc=px.getProblemPos();
}
- if (invalidrnastruc>-1)
+ if (invalidrnastruc > -1)
{
return;
}
Rna.HelixMap(_rnasecstr);
// setRNAStruc(RNAannot);
-
+
if (_rnasecstr != null && _rnasecstr.length > 0)
{
// show all the RNA secondary structure annotation symbols.
- isrna=true;
+ isrna = true;
showAllColLabels = true;
scaleColLabel = true;
}
// System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
}
+
public java.util.Hashtable sequenceMapping;
/** DOCUMENT ME!! */
@@ -194,7 +203,11 @@ 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.
*
@@ -242,8 +255,37 @@ public class AlignmentAnnotation
else
// Check for RNA secondary structure
{
- if (annotations[i].secondaryStructure == 'S'
- || annotations[i].secondaryStructure == 'C')
+ //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;
@@ -274,9 +316,38 @@ 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)
{
@@ -327,65 +398,79 @@ public class AlignmentAnnotation
annotationId = this.hashCode() + "";
}
+
/**
- * flyweight access to positions in the alignment annotation row for RNA processing
+ * flyweight access to positions in the alignment annotation row for RNA
+ * processing
+ *
* @author jimp
- *
+ *
*/
- private class AnnotCharSequence implements CharSequence
+ private class AnnotCharSequence implements CharSequence
{
- int offset=0;
- int max=0;
-
- public AnnotCharSequence() {
- this(0,annotations.length);
+ int offset = 0;
+
+ int max = 0;
+
+ public AnnotCharSequence()
+ {
+ this(0, annotations.length);
}
- public AnnotCharSequence(int start, int end) {
- offset=start;
- max=end;
+
+ public AnnotCharSequence(int start, int end)
+ {
+ offset = start;
+ max = end;
}
+
@Override
public CharSequence subSequence(int start, int end)
{
- return new AnnotCharSequence(offset+start, offset+end);
+ return new AnnotCharSequence(offset + start, offset + end);
}
-
+
@Override
public int length()
{
- return max-offset;
+ return max - offset;
}
-
+
@Override
public char charAt(int index)
{
String dc;
- return ((index+offset<0) || (index+offset)>=max || annotations[index+offset]==null || (dc=annotations[index+offset].displayCharacter.trim()).length()<1)
- ? '.' : dc.charAt(0);
+ return ((index + offset < 0) || (index + offset) >= max
+ || annotations[index + offset] == null || (dc = annotations[index
+ + offset].displayCharacter.trim()).length() < 1) ? '.' : dc
+ .charAt(0);
}
+
public String toString()
{
- char[] string=new char[max-offset];
- int mx=annotations.length;
-
- for (int i=offset;i 0)
@@ -493,7 +582,7 @@ public class AlignmentAnnotation
{
if (annotations[i] != null)
{
- annotations[i].displayCharacter = "";
+ annotations[i].displayCharacter = "X";
}
}
}
@@ -524,9 +613,9 @@ public class AlignmentAnnotation
this.label = annotation.label;
this.padGaps = annotation.padGaps;
this.visible = annotation.visible;
- this.centreColLabels=annotation.centreColLabels;
- this.scaleColLabel=annotation.scaleColLabel;
- this.showAllColLabels=annotation.showAllColLabels;
+ this.centreColLabels = annotation.centreColLabels;
+ this.scaleColLabel = annotation.scaleColLabel;
+ this.showAllColLabels = annotation.showAllColLabels;
this.calcId = annotation.calcId;
if (this.hasScore = annotation.hasScore)
{
@@ -542,7 +631,14 @@ public class AlignmentAnnotation
this.annotations = new Annotation[ann.length];
for (int i = 0; i < ann.length; i++)
{
- annotations[i] = new Annotation(ann[i]);
+ if (ann[i] != null)
+ {
+ annotations[i] = new Annotation(ann[i]);
+ if (_linecolour != null)
+ {
+ _linecolour = annotations[i].colour;
+ }
+ }
}
;
if (annotation.sequenceRef != null)
@@ -578,7 +674,7 @@ public class AlignmentAnnotation
}
}
// TODO: check if we need to do this: JAL-952
- //if (this.isrna=annotation.isrna)
+ // if (this.isrna=annotation.isrna)
{
// _rnasecstr=new SequenceFeature[annotation._rnasecstr];
}
@@ -970,11 +1066,12 @@ public class AlignmentAnnotation
{
if (seqname && this.sequenceRef != null)
{
- int i=description.toLowerCase().indexOf("");
- if (i>-1)
+ int i = description.toLowerCase().indexOf("");
+ if (i > -1)
{
// move the html tag to before the sequence reference.
- return ""+sequenceRef.getName()+" : "+description.substring(i+6);
+ return "" + sequenceRef.getName() + " : "
+ + description.substring(i + 6);
}
return sequenceRef.getName() + " : " + description;
}
@@ -983,8 +1080,9 @@ public class AlignmentAnnotation
public boolean isValidStruc()
{
- return invalidrnastruc==-1;
+ return invalidrnastruc == -1;
}
+
public long getInvalidStrucPos()
{
return invalidrnastruc;
@@ -993,7 +1091,14 @@ public class AlignmentAnnotation
/**
* machine readable ID string indicating what generated this annotation
*/
- protected String calcId="";
+ protected String calcId = "";
+
+ /**
+ * base colour for line graphs. If null, will be set automatically by
+ * searching the alignment annotation
+ */
+ public java.awt.Color _linecolour;
+
public String getCalcId()
{
return calcId;
@@ -1003,7 +1108,4 @@ public class AlignmentAnnotation
{
this.calcId = calcId;
}
-
-
-
}