/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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 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.
- *
- * 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
+ * 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
+ *
+ * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.datamodel;
+import jalview.analysis.Rna;
+
import java.util.Enumeration;
import java.util.Hashtable;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class AlignmentAnnotation
{
- /** If true, this annotations is calculated every edit,
- * eg consensus, quality or conservation graphs */
+ /**
+ * If true, this annotations is calculated every edit, eg consensus, quality
+ * or conservation graphs
+ */
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;
+
+ public String rnaStructure;
+
+ /**
+ * 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(String RNAannot)
+ {
+ _rnasecstr = Rna.GetBasePairs(RNAannot);
+ Rna.HelixMap(_rnasecstr);
+
+ setRNAStruc(RNAannot);
+
+ if (_rnasecstr != null && _rnasecstr.length > 0)
+ {
+ // show all the RNA secondary structure annotation symbols.
+ showAllColLabels = true;
+ scaleColLabel = true;
+ }
+ // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+ }
+
public java.util.Hashtable sequenceMapping;
/** DOCUMENT ME!! */
/** DOCUMENT ME!! */
public float graphMax;
+ /**
+ * Score associated with label and description.
+ */
+ public double score = Double.NaN;
+
+ /**
+ * flag indicating if annotation has a score.
+ */
+ public boolean hasScore = false;
+
public GraphLine threshold;
// Graphical hints and tips
- /** DOCUMENT ME!! */
+ /** Can this row be edited by the user ? */
public boolean editable = false;
- /** DOCUMENT ME!! */
+ /** Indicates if annotation has a graphical symbol track */
public boolean hasIcons; //
- /** DOCUMENT ME!! */
+ /** Indicates if annotation has a text character label */
public boolean hasText;
- /** DOCUMENT ME!! */
+ /** is the row visible */
public boolean visible = true;
public int graphGroup = -1;
- /** DOCUMENT ME!! */
+ /** Displayed height of row in pixels */
public int height = 0;
public int graph = 0;
public int graphHeight = 40;
- public boolean padGaps = true;
+ public boolean padGaps = false;
public static final int NO_GRAPH = 0;
public static final int LINE_GRAPH = 2;
+ public boolean belowAlignment = true;
+
+ public SequenceGroup groupRef = null;
+
+ /**
+ * display every column label, even if there is a row of identical labels
+ */
+ public boolean showAllColLabels = false;
+
+ /**
+ * scale the column label to fit within the alignment column.
+ */
+ public boolean scaleColLabel = false;
+
+ /**
+ * centre the column labels relative to the alignment column
+ */
+ public boolean centreColLabels = false;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Object#finalize()
+ */
+ protected void finalize() throws Throwable
+ {
+ sequenceRef = null;
+ groupRef = null;
+ super.finalize();
+ }
+
public static int getGraphValueFromString(String string)
{
if (string.equalsIgnoreCase("BAR_GRAPH"))
/**
* Creates a new AlignmentAnnotation object.
- *
- * @param label DOCUMENT ME!
- * @param description DOCUMENT ME!
- * @param annotations DOCUMENT ME!
+ *
+ * @param label
+ * short label shown under sequence labels
+ * @param description
+ * text displayed on mouseover
+ * @param annotations
+ * set of positional annotation elements
*/
public AlignmentAnnotation(String label, String description,
- Annotation[] annotations)
+ Annotation[] annotations)
{
// always editable?
editable = true;
this.description = description;
this.annotations = annotations;
- validateRangeAndDisplay();
+ validateRangeAndDisplay();
}
+ /**
+ * Checks if annotation labels represent secondary structures
+ *
+ */
void areLabelsSecondaryStructure()
{
boolean nonSSLabel = false;
+ boolean isrna = false;
+ StringBuffer rnastring = new StringBuffer();
+
+ char firstChar = 0;
for (int i = 0; i < annotations.length; i++)
{
if (annotations[i] == null)
{
- padGaps = false;
continue;
}
- if (annotations[i].secondaryStructure == 'H' ||
- annotations[i].secondaryStructure == 'E')
+ if (annotations[i].secondaryStructure == 'H'
+ || annotations[i].secondaryStructure == 'E')
+ {
+ hasIcons |= true;
+ }
+ else
+ // Check for RNA secondary structure
{
- hasIcons = true;
+ if (annotations[i].secondaryStructure == 'S')
+ {
+ hasIcons |= true;
+ isrna |= true;
+ }
}
- if (annotations[i].displayCharacter!=null)
+ // System.out.println("displaychar " + annotations[i].displayCharacter);
+
+ if (annotations[i].displayCharacter == null
+ || annotations[i].displayCharacter.length() == 0)
{
- if (annotations[i].displayCharacter.length() == 1
- && !annotations[i].displayCharacter.equals("H")
- && !annotations[i].displayCharacter.equals("E")
- && !annotations[i].displayCharacter.equals("-")
- && !annotations[i].displayCharacter.equals("."))
+ rnastring.append('.');
+ continue;
+ }
+ if (annotations[i].displayCharacter.length() == 1)
+ {
+ 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'
+ && firstChar != 'E'
+ && firstChar != 'S'
+ && firstChar != '-'
+ && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
{
- if (jalview.schemes.ResidueProperties.aaIndex
- [annotations[i].displayCharacter.charAt(0)] < 23)
+ 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)
- {
- hasText = true;
- }
- else
- padGaps = false;
+ if (annotations[i].displayCharacter.length() > 0)
+ {
+ hasText = true;
}
}
-
if (nonSSLabel)
{
hasIcons = false;
for (int j = 0; j < annotations.length; j++)
{
- if (annotations[j] != null && annotations[j].secondaryStructure != ' ')
+ if (annotations[j] != null
+ && annotations[j].secondaryStructure != ' ')
{
- annotations[j].displayCharacter
- = String.valueOf(annotations[j].secondaryStructure);
+ annotations[j].displayCharacter = String
+ .valueOf(annotations[j].secondaryStructure);
annotations[j].secondaryStructure = ' ';
}
}
}
+ else
+ {
+ if (isrna)
+ {
+ _updateRnaSecStr(rnastring.toString());
+ }
+ }
annotationId = this.hashCode() + "";
}
- /**
+
+ public void setRNAStruc(String string) {
+ rnaStructure=string;
+}
+
+ public String getRNAStruc(){
+ return rnaStructure;
+ }
+
+/**
* Creates a new AlignmentAnnotation object.
- *
- * @param label DOCUMENT ME!
- * @param description DOCUMENT ME!
- * @param annotations DOCUMENT ME!
- * @param min DOCUMENT ME!
- * @param max DOCUMENT ME!
- * @param winLength DOCUMENT ME!
+ *
+ * @param label
+ * DOCUMENT ME!
+ * @param description
+ * DOCUMENT ME!
+ * @param annotations
+ * DOCUMENT ME!
+ * @param min
+ * DOCUMENT ME!
+ * @param max
+ * DOCUMENT ME!
+ * @param winLength
+ * DOCUMENT ME!
*/
public AlignmentAnnotation(String label, String description,
- Annotation[] annotations, float min, float max,
- int graphType)
+ Annotation[] annotations, float min, float max, int graphType)
{
// graphs are not editable
- editable = graphType==0;
+ editable = graphType == 0;
this.label = label;
this.description = description;
graphMax = max;
validateRangeAndDisplay();
}
+
/**
- * checks graphMin and graphMax,
- * secondary structure symbols,
- * sets graphType appropriately,
- * sets null labels to the empty string
- * if appropriate.
+ * 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)
+ {
+ visible = false; // try to prevent renderer from displaying.
+ return; // this is a non-annotation row annotation - ie a sequence score.
+ }
+
int graphType = graph;
float min = graphMin;
float max = graphMax;
continue;
}
- if (drawValues && annotations[i].displayCharacter!=null && annotations[i].displayCharacter.length() > 1)
+ if (drawValues && annotations[i].displayCharacter != null
+ && annotations[i].displayCharacter.length() > 1)
{
drawValues = false;
}
min = annotations[i].value;
}
}
+ // ensure zero is origin for min/max ranges on only one side of zero
+ if (min > 0)
+ {
+ min = 0;
+ }
+ else
+ {
+ if (max < 0)
+ {
+ max = 0;
+ }
+ }
}
graphMin = min;
}
/**
- * Copy constructor
- * creates a new independent annotation row with the same associated sequenceRef
+ * Copy constructor creates a new independent annotation row with the same
+ * associated sequenceRef
+ *
* @param annotation
*/
public AlignmentAnnotation(AlignmentAnnotation annotation)
this.graph = annotation.graph;
this.graphHeight = annotation.graphHeight;
this.graphGroup = annotation.graphGroup;
+ this.groupRef = annotation.groupRef;
this.editable = annotation.editable;
this.autoCalculated = annotation.autoCalculated;
this.hasIcons = annotation.hasIcons;
this.height = annotation.height;
this.label = annotation.label;
this.padGaps = annotation.padGaps;
- if (threshold!=null) {
+ this.visible = annotation.visible;
+ if (this.hasScore = annotation.hasScore)
+ {
+ this.score = annotation.score;
+ }
+ if (annotation.threshold != null)
+ {
threshold = new GraphLine(annotation.threshold);
}
- if (annotation.annotations!=null) {
+ if (annotation.annotations != null)
+ {
Annotation[] ann = annotation.annotations;
this.annotations = new Annotation[ann.length];
- for (int i=0; i<ann.length; i++) {
+ for (int i = 0; i < ann.length; i++)
+ {
annotations[i] = new Annotation(ann[i]);
- };
- if (annotation.sequenceRef!=null) {
+ }
+ ;
+ if (annotation.sequenceRef != null)
+ {
this.sequenceRef = annotation.sequenceRef;
- if (annotation.sequenceMapping!=null)
+ if (annotation.sequenceMapping != null)
{
- Integer p=null;
+ Integer p = null;
sequenceMapping = new Hashtable();
- Enumeration pos=annotation.sequenceMapping.keys();
- while (pos.hasMoreElements()) {
+ Enumeration pos = annotation.sequenceMapping.keys();
+ while (pos.hasMoreElements())
+ {
// could optimise this!
p = (Integer) pos.nextElement();
Annotation a = (Annotation) annotation.sequenceMapping.get(p);
- if (a==null)
+ if (a == null)
{
continue;
}
- for (int i=0; i<ann.length; i++)
+ for (int i = 0; i < ann.length; i++)
{
- if (ann[i]==a)
- {
+ if (ann[i] == a)
+ {
sequenceMapping.put(p, annotations[i]);
}
}
}
- } else {
+ }
+ else
+ {
this.sequenceMapping = null;
}
}
/**
* clip the annotation to the columns given by startRes and endRes (inclusive)
* and prune any existing sequenceMapping to just those columns.
+ *
* @param startRes
* @param endRes
*/
public void restrict(int startRes, int endRes)
{
- Annotation[] temp = new Annotation[endRes-startRes+1];
- if (startRes<annotations.length)
+ if (annotations == null)
{
- System.arraycopy(annotations, startRes, temp, 0, Math.min(endRes, annotations.length-1)-startRes+1);
+ // non-positional
+ return;
+ }
+ if (startRes < 0)
+ startRes = 0;
+ if (startRes >= annotations.length)
+ startRes = annotations.length - 1;
+ if (endRes >= annotations.length)
+ endRes = annotations.length - 1;
+ if (annotations == null)
+ return;
+ Annotation[] temp = new Annotation[endRes - startRes + 1];
+ if (startRes < annotations.length)
+ {
+ System.arraycopy(annotations, startRes, temp, 0, endRes - startRes
+ + 1);
}
- if (sequenceRef!=null) {
+ if (sequenceRef != null)
+ {
// Clip the mapping, if it exists.
int spos = sequenceRef.findPosition(startRes);
int epos = sequenceRef.findPosition(endRes);
- if (sequenceMapping!=null)
+ if (sequenceMapping != null)
{
Hashtable newmapping = new Hashtable();
Enumeration e = sequenceMapping.keys();
while (e.hasMoreElements())
{
Integer pos = (Integer) e.nextElement();
- if (pos.intValue()>=spos && pos.intValue()<=epos)
+ if (pos.intValue() >= spos && pos.intValue() <= epos)
{
newmapping.put(pos, sequenceMapping.get(pos));
}
sequenceMapping = newmapping;
}
}
- annotations=temp;
+ annotations = temp;
}
+
/**
* set the annotation row to be at least length Annotations
- * @param length minimum number of columns required in the annotation row
+ *
+ * @param length
+ * minimum number of columns required in the annotation row
* @return false if the annotation row is greater than length
*/
- public boolean padAnnotation(int length) {
- if (annotations==null)
+ public boolean padAnnotation(int length)
+ {
+ if (annotations == null)
{
- annotations = new Annotation[length];
- return true;
+ return true; // annotation row is correct - null == not visible and
+ // undefined length
}
- if (annotations.length<length)
+ if (annotations.length < length)
{
Annotation[] na = new Annotation[length];
System.arraycopy(annotations, 0, na, 0, annotations.length);
annotations = na;
return true;
}
- return annotations.length>length;
-
+ return annotations.length > length;
+
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String toString()
buffer.append(", ");
}
-
- if (label.equals("Consensus"))
+ // TODO: remove disgusting hack for 'special' treatment of consensus line.
+ if (label.indexOf("Consensus") == 0)
{
buffer.append("\n");
}
/**
- * Attach the annotation to seqRef, starting from startRes position. If alreadyMapped is true then the indices of the annotation[] array are sequence positions rather than alignment column positions.
+ * Attach the annotation to seqRef, starting from startRes position. If
+ * alreadyMapped is true then the indices of the annotation[] array are
+ * sequence positions rather than alignment column positions.
+ *
* @param seqRef
* @param startRes
* @param alreadyMapped
*/
- public void createSequenceMapping(SequenceI seqRef,
- int startRes,
- boolean alreadyMapped)
+ public void createSequenceMapping(SequenceI seqRef, int startRes,
+ boolean alreadyMapped)
{
if (seqRef == null)
{
return;
}
-
+ sequenceRef = seqRef;
+ if (annotations == null)
+ {
+ return;
+ }
sequenceMapping = new java.util.Hashtable();
- sequenceRef = seqRef;
int seqPos;
for (int i = 0; i < annotations.length; i++)
public void adjustForAlignment()
{
- if (sequenceRef==null)
+ if (sequenceRef == null)
return;
+ if (annotations == null)
+ {
+ return;
+ }
+
int a = 0, aSize = sequenceRef.getLength();
if (aSize == 0)
{
- //Its been deleted
+ // Its been deleted
return;
}
annotations = temp;
}
+
/**
- * remove any null entries in annotation row and return the
- * number of non-null annotation elements.
+ * remove any null entries in annotation row and return the number of non-null
+ * annotation elements.
+ *
* @return
*/
- private int compactAnnotationArray() {
- int j=0;
- for (int i=0;i<annotations.length; i++) {
- if (annotations[i]!=null && j!=i) {
- annotations[j++] = annotations[i];
+ public int compactAnnotationArray()
+ {
+ int i = 0, iSize = annotations.length;
+ while (i < iSize)
+ {
+ if (annotations[i] == null)
+ {
+ if (i + 1 < iSize)
+ System.arraycopy(annotations, i + 1, annotations, i, iSize - i
+ - 1);
+ iSize--;
+ }
+ else
+ {
+ i++;
}
}
Annotation[] ann = annotations;
- annotations = new Annotation[j];
- System.arraycopy(ann, 0, annotations, 0, j);
+ annotations = new Annotation[i];
+ System.arraycopy(ann, 0, annotations, 0, i);
ann = null;
- return j;
+ return iSize;
}
/**
* Associate this annotion with the aligned residues of a particular sequence.
- * sequenceMapping will be updated in the following way:
- * null sequenceI - existing mapping will be discarded but annotations left in mapped positions.
- * valid sequenceI not equal to current sequenceRef: mapping is discarded and rebuilt assuming 1:1 correspondence
- * TODO: overload with parameter to specify correspondence between current and new sequenceRef
+ * sequenceMapping will be updated in the following way: null sequenceI -
+ * existing mapping will be discarded but annotations left in mapped
+ * positions. valid sequenceI not equal to current sequenceRef: mapping is
+ * discarded and rebuilt assuming 1:1 correspondence TODO: overload with
+ * parameter to specify correspondence between current and new sequenceRef
+ *
* @param sequenceI
*/
public void setSequenceRef(SequenceI sequenceI)
{
if (sequenceRef != null)
{
- if (sequenceRef != sequenceI && !sequenceRef.equals(sequenceI) && sequenceRef.getDatasetSequence()!=sequenceI.getDatasetSequence())
+ if (sequenceRef != sequenceI
+ && !sequenceRef.equals(sequenceI)
+ && sequenceRef.getDatasetSequence() != sequenceI
+ .getDatasetSequence())
{
// if sequenceRef isn't intersecting with sequenceI
// throw away old mapping and reconstruct.
sequenceRef = null;
}
}
+
+ /**
+ * @return the score
+ */
+ public double getScore()
+ {
+ return score;
+ }
+
+ /**
+ * @param score
+ * the score to set
+ */
+ public void setScore(double score)
+ {
+ hasScore = true;
+ this.score = score;
+ }
+
+ /**
+ *
+ * @return true if annotation has an associated score
+ */
+ public boolean hasScore()
+ {
+ return hasScore || !Double.isNaN(score);
+ }
+
+ /**
+ * Score only annotation
+ *
+ * @param label
+ * @param description
+ * @param score
+ */
+ public AlignmentAnnotation(String label, String description, double score)
+ {
+ this(label, description, null);
+ setScore(score);
+ }
+
+ /**
+ * copy constructor with edit based on the hidden columns marked in colSel
+ *
+ * @param alignmentAnnotation
+ * @param colSel
+ */
+ public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
+ ColumnSelection colSel)
+ {
+ this(alignmentAnnotation);
+ if (annotations == null)
+ {
+ return;
+ }
+ colSel.makeVisibleAnnotation(this);
+ }
+
+ public void setPadGaps(boolean padgaps, char gapchar)
+ {
+ this.padGaps = padgaps;
+ if (padgaps)
+ {
+ hasText = true;
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i] == null)
+ annotations[i] = new Annotation(String.valueOf(gapchar), null,
+ ' ', 0f);
+ else if (annotations[i].displayCharacter == null
+ || annotations[i].displayCharacter.equals(" "))
+ annotations[i].displayCharacter = String.valueOf(gapchar);
+ }
+ }
+ }
+
+ /**
+ * format description string for display
+ *
+ * @param seqname
+ * @return Get the annotation description string optionally prefixed by
+ * associated sequence name (if any)
+ */
+ public String getDescription(boolean seqname)
+ {
+ if (seqname && this.sequenceRef != null)
+ {
+ 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 sequenceRef.getName() + " : " + description;
+ }
+ return description;
+ }
}
git://source.jalview.org / jalview.git / blobdiff