import jalview.analysis.Rna;
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!
*
public boolean autoCalculated = false;
public String annotationId;
-
+
public SequenceI sequenceRef;
/** DOCUMENT ME!! */
/** DOCUMENT ME!! */
public Annotation[] annotations;
+
+
/**
* 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
*/
private void _updateRnaSecStr(CharSequence RNAannot)
{
- try {
- _rnasecstr = Rna.GetBasePairs(RNAannot);
- invalidrnastruc=-1;
- }
- catch (WUSSParseException px)
+ try
+ {
+ _rnasecstr = Rna.GetBasePairs(RNAannot);
+ invalidrnastruc = -1;
+ } catch (WUSSParseException px)
{
- invalidrnastruc=px.getProblemPos();
+ 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!! */
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 == '1'
+ || annotations[i].secondaryStructure == 'F'
+ || annotations[i].secondaryStructure == 'G'
+ || annotations[i].secondaryStructure == '2'
+ || 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;
firstChar != ' '
&& firstChar != 'H'
&& firstChar != 'E'
+ && firstChar != '('
+ && firstChar != '['
+ && firstChar != '>'
+ && firstChar != '{'
+ && firstChar != 'A'
+ && firstChar != 'B'
+ && firstChar != 'C'
+ && firstChar != 'D'
+ && firstChar != '1'
+ && firstChar != 'F'
+ && firstChar != 'G'
+ && firstChar != '2'
+ && 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)
{
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<mx;i++)
+ char[] string = new char[max - offset];
+ int mx = annotations.length;
+
+ for (int i = offset; i < mx; i++)
{
String dc;
- string[i]=(annotations[i]==null || (dc=annotations[i].displayCharacter.trim()).length()<1 )? '.' : dc.charAt(0);
+ string[i] = (annotations[i] == null || (dc = annotations[i].displayCharacter
+ .trim()).length() < 1) ? '.' : dc.charAt(0);
}
return new String(string);
}
};
-
- private long _lastrnaannot=-1;
- public String getRNAStruc(){
+
+ private long _lastrnaannot = -1;
+
+ public String getRNAStruc()
+ {
if (isrna)
{
String rnastruc = new AnnotCharSequence().toString();
- if (_lastrnaannot!=rnastruc.hashCode())
+ if (_lastrnaannot != rnastruc.hashCode())
{
// ensure rna structure contacts are up to date
- _lastrnaannot=rnastruc.hashCode();
+ _lastrnaannot = rnastruc.hashCode();
_updateRnaSecStr(rnastruc);
}
return rnastruc;
return null;
}
-/**
+ /**
* Creates a new AlignmentAnnotation object.
*
* @param label
float min = graphMin;
float max = graphMax;
boolean drawValues = true;
-
+ _linecolour=null;
if (min == max)
{
min = 999999999;
{
min = annotations[i].value;
}
+ if (_linecolour == null && annotations[i].colour != null)
+ {
+ _linecolour = annotations[i].colour;
+ }
}
// ensure zero is origin for min/max ranges on only one side of zero
if (min > 0)
{
if (annotations[i] != null)
{
- annotations[i].displayCharacter = "";
+ annotations[i].displayCharacter = "X";
}
}
}
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.calcId = annotation.calcId;
if (this.hasScore = annotation.hasScore)
{
this.score = annotation.score;
}
}
}
+ // TODO: check if we need to do this: JAL-952
+ // if (this.isrna=annotation.isrna)
+ {
+ // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
+ }
validateRangeAndDisplay(); // construct hashcodes, etc.
}
{
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);
{
if (seqname && this.sequenceRef != null)
{
- int i=description.toLowerCase().indexOf("<html>");
- if (i>-1)
+ int i = description.toLowerCase().indexOf("<html>");
+ if (i > -1)
{
// move the html tag to before the sequence reference.
- return "<html>"+sequenceRef.getName()+" : "+description.substring(i+6);
+ return "<html>" + sequenceRef.getName() + " : "
+ + description.substring(i + 6);
}
return sequenceRef.getName() + " : " + description;
}
public boolean isValidStruc()
{
- return invalidrnastruc==-1;
+ return invalidrnastruc == -1;
}
+
public long getInvalidStrucPos()
{
return invalidrnastruc;
}
-
+
+ /**
+ * machine readable ID string indicating what generated this annotation
+ */
+ 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;
+ }
+
+ public void setCalcId(String calcId)
+ {
+ this.calcId = calcId;
+ }
}
git://source.jalview.org / jalview.git / blobdiff