X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=e39c0b781610b56f3e2be9fdaac1f516e76c3935;hb=0e2054d29bc49351f000d478659dc3c4371b251c;hp=ddb420a1aff6a9553a91aa7f0c9ac80e893f7008;hpb=520cc5fe77f3f625c9a58cb6b8b83bbca68084b6;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index ddb420a..e39c0b7 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,26 +1,34 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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!
*
@@ -47,6 +55,54 @@ public class AlignmentAnnotation
/** DOCUMENT ME!! */
public Annotation[] annotations;
+
+
+
+ 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;
+
+ /**
+ * Updates the _rnasecstr field Determines the positions that base pair and
+ * the positions of helices based on secondary structure from a Stockholm file
+ *
+ * @param RNAannot
+ */
+ private void _updateRnaSecStr(CharSequence RNAannot)
+ {
+ 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)
+ {
+ return;
+ }
+ Rna.HelixMap(_rnasecstr);
+ // setRNAStruc(RNAannot);
+
+ if (_rnasecstr != null && _rnasecstr.length > 0)
+ {
+ // show all the RNA secondary structure annotation symbols.
+ isrna = true;
+ showAllColLabels = true;
+ scaleColLabel = true;
+ }
+ // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+ }
public java.util.Hashtable sequenceMapping;
@@ -76,7 +132,7 @@ public class AlignmentAnnotation
/** Indicates if annotation has a graphical symbol track */
public boolean hasIcons; //
- /** Indicates if annotation has a text character label */
+ /** Indicates if annotation has a text character label */
public boolean hasText;
/** is the row visible */
@@ -101,13 +157,13 @@ public class AlignmentAnnotation
public boolean belowAlignment = true;
- public SequenceGroup groupRef =null ;
+ public SequenceGroup groupRef = null;
/**
* display every column label, even if there is a row of identical labels
*/
- public boolean showAllColLabels=false;
-
+ public boolean showAllColLabels = false;
+
/**
* scale the column label to fit within the alignment column.
*/
@@ -118,8 +174,11 @@ public class AlignmentAnnotation
*/
public boolean centreColLabels = false;
-
- /* (non-Javadoc)
+ private boolean isrna;
+
+ /*
+ * (non-Javadoc)
+ *
* @see java.lang.Object#finalize()
*/
protected void finalize() throws Throwable
@@ -144,16 +203,20 @@ 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.
*
* @param label
- * short label shown under sequence labels
+ * short label shown under sequence labels
* @param description
- * text displayed on mouseover
+ * text displayed on mouseover
* @param annotations
- * set of positional annotation elements
+ * set of positional annotation elements
*/
public AlignmentAnnotation(String label, String description,
Annotation[] annotations)
@@ -167,9 +230,16 @@ public class AlignmentAnnotation
validateRangeAndDisplay();
}
+ /**
+ * Checks if annotation labels represent secondary structures
+ *
+ */
void areLabelsSecondaryStructure()
{
boolean nonSSLabel = false;
+ isrna = false;
+ StringBuffer rnastring = new StringBuffer();
+
char firstChar = 0;
for (int i = 0; i < annotations.length; i++)
{
@@ -182,9 +252,52 @@ public class AlignmentAnnotation
{
hasIcons |= true;
}
+ else
+ // Check for RNA secondary structure
+ {
+ //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;
+ }
+ }
+
+ // System.out.println("displaychar " + annotations[i].displayCharacter);
- if (annotations[i].displayCharacter == null)
+ if (annotations[i].displayCharacter == null
+ || annotations[i].displayCharacter.length() == 0)
{
+ rnastring.append('.');
continue;
}
if (annotations[i].displayCharacter.length() == 1)
@@ -192,25 +305,67 @@ public class AlignmentAnnotation
firstChar = annotations[i].displayCharacter.charAt(0);
// check to see if it looks like a sequence or is secondary structure
// labelling.
- if (annotations[i].secondaryStructure!=' ' && !hasIcons &&
- // Uncomment to only catch case where displayCharacter==secondary
- // Structure
- // to correctly redisplay SS annotation imported from Stockholm,
- // exported to JalviewXML and read back in again.
- // &&
- // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
- firstChar != ' '
- && firstChar != 'H'
+ if (annotations[i].secondaryStructure != ' '
+ && !hasIcons
+ &&
+ // Uncomment to only catch case where
+ // displayCharacter==secondary
+ // Structure
+ // to correctly redisplay SS annotation imported from Stockholm,
+ // exported to JalviewXML and read back in again.
+ // &&
+ // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
+ firstChar != ' '
+ && firstChar != '$'
+ && firstChar != 'ยต' // 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)
{
- if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO: parameterise to gap symbol number
+ if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
+ // parameterise
+ // to
+ // gap
+ // symbol
+ // number
{
nonSSLabel = true;
}
}
}
+ else
+ {
+ rnastring.append(annotations[i].displayCharacter.charAt(1));
+ }
if (annotations[i].displayCharacter.length() > 0)
{
@@ -233,25 +388,111 @@ public class AlignmentAnnotation
}
}
+ else
+ {
+ if (isrna)
+ {
+ _updateRnaSecStr(new AnnotCharSequence());
+ }
+ }
annotationId = this.hashCode() + "";
}
/**
+ * flyweight access to positions in the alignment annotation row for RNA
+ * processing
+ *
+ * @author jimp
+ *
+ */
+ private class AnnotCharSequence implements CharSequence
+ {
+ int offset = 0;
+
+ int max = 0;
+
+ public AnnotCharSequence()
+ {
+ this(0, annotations.length);
+ }
+
+ 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);
+ }
+
+ @Override
+ public int length()
+ {
+ 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);
+ }
+
+ public String toString()
+ {
+ 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);
+ }
+ return new String(string);
+ }
+ };
+
+ private long _lastrnaannot = -1;
+
+ public String getRNAStruc()
+ {
+ if (isrna)
+ {
+ String rnastruc = new AnnotCharSequence().toString();
+ if (_lastrnaannot != rnastruc.hashCode())
+ {
+ // ensure rna structure contacts are up to date
+ _lastrnaannot = rnastruc.hashCode();
+ _updateRnaSecStr(rnastruc);
+ }
+ return rnastruc;
+ }
+ return null;
+ }
+
+ /**
* Creates a new AlignmentAnnotation object.
*
* @param label
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param description
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param annotations
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param min
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param max
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param winLength
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public AlignmentAnnotation(String label, String description,
Annotation[] annotations, float min, float max, int graphType)
@@ -272,7 +513,7 @@ public class AlignmentAnnotation
* checks graphMin and graphMax, secondary structure symbols, sets graphType
* appropriately, sets null labels to the empty string if appropriate.
*/
- private void validateRangeAndDisplay()
+ public void validateRangeAndDisplay()
{
if (annotations == null)
@@ -285,7 +526,7 @@ public class AlignmentAnnotation
float min = graphMin;
float max = graphMax;
boolean drawValues = true;
-
+ _linecolour = null;
if (min == max)
{
min = 999999999;
@@ -311,16 +552,23 @@ public class AlignmentAnnotation
{
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 (min > 0)
+ {
min = 0;
- } else {
- if (max<0)
+ }
+ else
+ {
+ if (max < 0)
{
max = 0;
}
- }
+ }
}
graphMin = min;
@@ -334,7 +582,7 @@ public class AlignmentAnnotation
{
if (annotations[i] != null)
{
- annotations[i].displayCharacter = "";
+ annotations[i].displayCharacter = "X";
}
}
}
@@ -365,11 +613,15 @@ 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.calcId = annotation.calcId;
if (this.hasScore = annotation.hasScore)
{
this.score = annotation.score;
}
- if (threshold != null)
+ if (annotation.threshold != null)
{
threshold = new GraphLine(annotation.threshold);
}
@@ -379,7 +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)
@@ -414,6 +673,11 @@ public class AlignmentAnnotation
}
}
}
+ // TODO: check if we need to do this: JAL-952
+ // if (this.isrna=annotation.isrna)
+ {
+ // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
+ }
validateRangeAndDisplay(); // construct hashcodes, etc.
}
@@ -473,7 +737,7 @@ public class AlignmentAnnotation
* set the annotation row to be at least length Annotations
*
* @param length
- * minimum number of columns required in the annotation row
+ * minimum number of columns required in the annotation row
* @return false if the annotation row is greater than length
*/
public boolean padAnnotation(int length)
@@ -481,7 +745,7 @@ public class AlignmentAnnotation
if (annotations == null)
{
return true; // annotation row is correct - null == not visible and
- // undefined length
+ // undefined length
}
if (annotations.length < length)
{
@@ -524,7 +788,7 @@ public class AlignmentAnnotation
buffer.append(", ");
}
// TODO: remove disgusting hack for 'special' treatment of consensus line.
- if (label.indexOf("Consensus")==0)
+ if (label.indexOf("Consensus") == 0)
{
buffer.append("\n");
@@ -726,7 +990,7 @@ public class AlignmentAnnotation
/**
* @param score
- * the score to set
+ * the score to set
*/
public void setScore(double score)
{
@@ -783,7 +1047,7 @@ 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);
@@ -802,8 +1066,46 @@ public class AlignmentAnnotation
{
if (seqname && this.sequenceRef != null)
{
+ 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;
}
return description;
}
+
+ public boolean isValidStruc()
+ {
+ 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;
+ }
}