X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=543958e8bd1bf7bfb5ce134976a587c5c9160fcb;hb=refs%2Fheads%2Ffeatures%2FJAL-2465_No-mapping_Jmol-structures-loaded-via-url;hp=2577e71df4e41c9ac5c32bad3e6b81e0458def6d;hpb=701b986332c4b74ab922c33654a90af0622ae7b6;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 2577e71..543958e 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,86 +1,221 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
- * 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 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
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class AlignmentAnnotation
{
- /** If true, this annotations is calculated every edit,
- * eg consensus, quality or conservation graphs */
+ private static final String ANNOTATION_ID_PREFIX = "ann";
+
+ /*
+ * Identifers for different types of profile data
+ */
+ public static final int SEQUENCE_PROFILE = 0;
+
+ public static final int STRUCTURE_PROFILE = 1;
+
+ public static final int CDNA_PROFILE = 2;
+
+ private static long counter = 0;
+
+ /**
+ * If true, this annotations is calculated every edit, eg consensus, quality
+ * or conservation graphs
+ */
public boolean autoCalculated = false;
+ /**
+ * unique ID for this annotation, used to match up the same annotation row
+ * shown in multiple views and alignments
+ */
public String annotationId;
+ /**
+ * the sequence this annotation is associated with (or null)
+ */
public SequenceI sequenceRef;
- /** DOCUMENT ME!! */
+ /** label shown in dropdown menus and in the annotation label area */
public String label;
- /** DOCUMENT ME!! */
+ /** longer description text shown as a tooltip */
public String description;
- /** DOCUMENT ME!! */
+ /** Array of annotations placed in the current coordinate system */
public Annotation[] annotations;
- public java.util.Hashtable sequenceMapping;
+ public List bps = null;
+
+ /**
+ * RNA secondary structure contact positions
+ */
+ public SequenceFeature[] _rnasecstr = null;
+
+ /**
+ * position of annotation resulting in invalid WUSS parsing or -1. -2 means
+ * there was no RNA structure in this annotation
+ */
+ private long invalidrnastruc = -2;
+
+ /**
+ * 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
+ {
+ bps = Rna.getModeleBP(RNAannot);
+ _rnasecstr = Rna.getBasePairs(bps);
+ invalidrnastruc = -1;
+ } catch (WUSSParseException px)
+ {
+ // DEBUG System.out.println(px);
+ invalidrnastruc = px.getProblemPos();
+ }
+ if (invalidrnastruc > -1)
+ {
+ return;
+ }
+ Rna.HelixMap(_rnasecstr);
+ // setRNAStruc(RNAannot);
- /** DOCUMENT ME!! */
+ if (_rnasecstr != null && _rnasecstr.length > 0)
+ {
+ // show all the RNA secondary structure annotation symbols.
+ isrna = true;
+ showAllColLabels = true;
+ scaleColLabel = true;
+ _markRnaHelices();
+ }
+ // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+
+ }
+
+ private void _markRnaHelices()
+ {
+ int mxval = 0;
+ // Figure out number of helices
+ // Length of rnasecstr is the number of pairs of positions that base pair
+ // with each other in the secondary structure
+ for (int x = 0; x < _rnasecstr.length; x++)
+ {
+
+ /*
+ * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+ * this.annotation._rnasecstr[x].getBegin());
+ */
+ // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+ int val = 0;
+ try
+ {
+ val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
+ if (mxval < val)
+ {
+ mxval = val;
+ }
+ } catch (NumberFormatException q)
+ {
+ }
+ ;
+
+ annotations[_rnasecstr[x].getBegin()].value = val;
+ annotations[_rnasecstr[x].getEnd()].value = val;
+
+ // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
+ // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
+ }
+ setScore(mxval);
+ }
+
+ /**
+ * map of positions in the associated annotation
+ */
+ private Map sequenceMapping;
+
+ /**
+ * lower range for quantitative data
+ */
public float graphMin;
- /** DOCUMENT ME!! */
+ /**
+ * Upper range for quantitative data
+ */
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;
@@ -88,6 +223,40 @@ public class AlignmentAnnotation
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;
+
+ private boolean isrna;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Object#finalize()
+ */
+ @Override
+ protected void finalize() throws Throwable
+ {
+ sequenceRef = null;
+ groupRef = null;
+ super.finalize();
+ }
+
public static int getGraphValueFromString(String string)
{
if (string.equalsIgnoreCase("BAR_GRAPH"))
@@ -104,97 +273,310 @@ public class AlignmentAnnotation
}
}
+ // JBPNote: what does this do ?
+ public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
+ {
+ bps = Rna.getModeleBP(RNAannot);
+ }
+
/**
* 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)
{
+ setAnnotationId();
// always editable?
editable = true;
this.label = label;
this.description = description;
this.annotations = annotations;
- validateRangeAndDisplay();
+ 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++)
{
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;
+ hasIcons |= true;
}
+ else
+ // Check for RNA secondary structure
+ {
+ // System.out.println(annotations[i].secondaryStructure);
+ // TODO: 2.8.2 should this ss symbol validation check be a function in
+ // RNA/ResidueProperties ?
+ 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.length() == 1
- && !annotations[i].displayCharacter.equals("H")
- && !annotations[i].displayCharacter.equals("E")
- && !annotations[i].displayCharacter.equals("-")
- && !annotations[i].displayCharacter.equals("."))
+ if (annotations[i].displayCharacter == null
+ || annotations[i].displayCharacter.length() == 0)
+ {
+ rnastring.append('.');
+ continue;
+ }
+ if (annotations[i].displayCharacter.length() == 1)
{
- if (jalview.schemes.ResidueProperties.aaIndex
- [annotations[i].displayCharacter.charAt(0)] < 23)
+ 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 != '$'
+ && firstChar != 0xCE
+ && 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)
{
- nonSSLabel = true;
+ 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 (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(new AnnotCharSequence());
+ }
+ }
+ }
+
+ /**
+ * 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);
+ }
+
+ 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)
+ {
+ return ((index + offset < 0) || (index + offset) >= max
+ || annotations[index + offset] == null
+ || (annotations[index + offset].secondaryStructure <= ' ') ? ' '
+ : annotations[index + offset].displayCharacter == null
+ || annotations[index + offset].displayCharacter
+ .length() == 0 ? annotations[index + offset].secondaryStructure
+ : annotations[index + offset].displayCharacter
+ .charAt(0));
+ }
+
+ @Override
+ public String toString()
+ {
+ char[] string = new char[max - offset];
+ int mx = annotations.length;
+
+ for (int i = offset; i < mx; i++)
+ {
+ string[i] = (annotations[i] == null || (annotations[i].secondaryStructure <= 32)) ? ' '
+ : (annotations[i].displayCharacter == null
+ || annotations[i].displayCharacter.length() == 0 ? annotations[i].secondaryStructure
+ : annotations[i].displayCharacter.charAt(0));
+ }
+ return new String(string);
+ }
+ };
+
+ private long _lastrnaannot = -1;
- annotationId = this.hashCode() + "";
+ 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!
- * @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)
{
+ setAnnotationId();
// graphs are not editable
- editable = graphType==0;
+ editable = graphType == 0;
this.label = label;
this.description = description;
@@ -204,19 +586,26 @@ public class AlignmentAnnotation
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.
+ invalidrnastruc = -1;
+ return; // this is a non-annotation row annotation - ie a sequence score.
+ }
+
int graphType = graph;
float min = graphMin;
float max = graphMax;
boolean drawValues = true;
-
+ _linecolour = null;
if (min == max)
{
min = 999999999;
@@ -227,7 +616,8 @@ public class AlignmentAnnotation
continue;
}
- if (drawValues && annotations[i].displayCharacter.length() > 1)
+ if (drawValues && annotations[i].displayCharacter != null
+ && annotations[i].displayCharacter.length() > 1)
{
drawValues = false;
}
@@ -241,6 +631,22 @@ 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)
+ {
+ min = 0;
+ }
+ else
+ {
+ if (max < 0)
+ {
+ max = 0;
+ }
}
}
@@ -262,65 +668,210 @@ public class AlignmentAnnotation
}
/**
- * 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)
{
+ setAnnotationId();
this.label = new String(annotation.label);
if (annotation.description != null)
+ {
this.description = new String(annotation.description);
+ }
this.graphMin = annotation.graphMin;
this.graphMax = annotation.graphMax;
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.hasText = annotation.hasText;
this.height = annotation.height;
this.label = annotation.label;
- if (threshold!=null) {
+ 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 (annotation.properties != null)
+ {
+ properties = new HashMap();
+ for (Map.Entry val : annotation.properties.entrySet())
+ {
+ properties.put(val.getKey(), val.getValue());
+ }
+ }
+ if (this.hasScore = annotation.hasScore)
+ {
+ this.score = annotation.score;
+ }
+ if (annotation.threshold != null)
+ {
threshold = new GraphLine(annotation.threshold);
}
- if (annotation.annotations!=null) {
- Vector anvec = new Vector();
- Annotation[] ann = annotation.annotations;
+ Annotation[] ann = annotation.annotations;
+ if (annotation.annotations != null)
+ {
this.annotations = new Annotation[ann.length];
- for (int i=0; i();
+ Iterator pos = annotation.sequenceMapping.keySet()
+ .iterator();
+ while (pos.hasNext())
+ {
+ // could optimise this!
+ p = pos.next();
+ Annotation a = annotation.sequenceMapping.get(p);
+ if (a == null)
+ {
+ continue;
+ }
+ if (ann != null)
+ {
+ for (int i = 0; i < ann.length; i++)
+ {
+ if (ann[i] == a)
+ {
+ sequenceMapping.put(p, annotations[i]);
+ }
+ }
}
- anvec.removeAllElements();
- } else {
- this.sequenceMapping = null;
}
}
+ else
+ {
+ this.sequenceMapping = null;
+ }
+ }
+ // TODO: check if we need to do this: JAL-952
+ // if (this.isrna=annotation.isrna)
+ {
+ // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
}
validateRangeAndDisplay(); // construct hashcodes, etc.
}
/**
+ * 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)
+ {
+ if (annotations == null)
+ {
+ // 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)
+ {
+ // Clip the mapping, if it exists.
+ int spos = sequenceRef.findPosition(startRes);
+ int epos = sequenceRef.findPosition(endRes);
+ if (sequenceMapping != null)
+ {
+ Map newmapping = new HashMap();
+ Iterator e = sequenceMapping.keySet().iterator();
+ while (e.hasNext())
+ {
+ Integer pos = e.next();
+ if (pos.intValue() >= spos && pos.intValue() <= epos)
+ {
+ newmapping.put(pos, sequenceMapping.get(pos));
+ }
+ }
+ sequenceMapping.clear();
+ sequenceMapping = newmapping;
+ }
+ }
+ annotations = temp;
+ }
+
+ /**
+ * set the annotation row to be at least length Annotations
+ *
+ * @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)
+ {
+ return true; // annotation row is correct - null == not visible and
+ // undefined 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;
+
+ }
+
+ /**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public String toString()
{
- StringBuffer buffer = new StringBuffer();
+ if (annotations == null)
+ {
+ return "";
+ }
+ StringBuilder buffer = new StringBuilder(256);
for (int i = 0; i < annotations.length; i++)
{
@@ -342,8 +893,8 @@ public class AlignmentAnnotation
buffer.append(", ");
}
-
- if (label.equals("Consensus"))
+ // TODO: remove disgusting hack for 'special' treatment of consensus line.
+ if (label.indexOf("Consensus") == 0)
{
buffer.append("\n");
@@ -372,24 +923,29 @@ public class AlignmentAnnotation
}
/**
- * 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;
}
-
- sequenceMapping = new java.util.Hashtable();
-
sequenceRef = seqRef;
+ if (annotations == null)
+ {
+ return;
+ }
+ sequenceMapping = new HashMap();
+
int seqPos;
for (int i = 0; i < annotations.length; i++)
@@ -411,90 +967,540 @@ public class AlignmentAnnotation
}
+ /**
+ * When positional annotation and a sequence reference is present, clears and
+ * resizes the annotations array to the current alignment width, and adds
+ * annotation according to aligned positions of the sequenceRef given by
+ * sequenceMapping.
+ */
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;
}
int position;
Annotation[] temp = new Annotation[aSize];
Integer index;
-
- for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+ if (sequenceMapping != null)
{
- index = new Integer(a);
- if (sequenceMapping.containsKey(index))
+ for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
{
- position = sequenceRef.findIndex(a) - 1;
+ index = new Integer(a);
+ Annotation annot = sequenceMapping.get(index);
+ if (annot != null)
+ {
+ position = sequenceRef.findIndex(a) - 1;
- temp[position] = (Annotation) sequenceMapping.get(index);
+ temp[position] = annot;
+ }
}
}
-
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");
+ 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 = "";
+
+ /**
+ * properties associated with the calcId
+ */
+ protected Map properties = new HashMap();
+
+ /**
+ * 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;
+ }
+
+ public boolean isRNA()
+ {
+ return isrna;
+ }
+
+ /**
+ * transfer annotation to the given sequence using the given mapping from the
+ * current positions or an existing sequence mapping
+ *
+ * @param sq
+ * @param sp2sq
+ * map involving sq as To or From
+ */
+ public void liftOver(SequenceI sq, Mapping sp2sq)
+ {
+ if (sp2sq.getMappedWidth() != sp2sq.getWidth())
+ {
+ // TODO: employ getWord/MappedWord to transfer annotation between cDNA and
+ // Protein reference frames
+ throw new Error(
+ "liftOver currently not implemented for transfer of annotation between different types of seqeunce");
+ }
+ boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
+ .getTo() == sq.getDatasetSequence()) : false;
+
+ // TODO build a better annotation element map and get rid of annotations[]
+ Map mapForsq = new HashMap();
+ if (sequenceMapping != null)
+ {
+ if (sp2sq != null)
+ {
+ for (Entry ie : sequenceMapping.entrySet())
+ {
+ Integer mpos = Integer.valueOf(mapIsTo ? sp2sq
+ .getMappedPosition(ie.getKey()) : sp2sq.getPosition(ie
+ .getKey()));
+ if (mpos >= sq.getStart() && mpos <= sq.getEnd())
+ {
+ mapForsq.put(mpos, ie.getValue());
+ }
+ }
+ sequenceMapping = mapForsq;
+ sequenceRef = sq;
+ adjustForAlignment();
+ }
+ else
+ {
+ // trim positions
+ }
+ }
+ }
+
+ /**
+ * like liftOver but more general.
+ *
+ * Takes an array of int pairs that will be used to update the internal
+ * sequenceMapping and so shuffle the annotated positions
+ *
+ * @param newref
+ * - new sequence reference for the annotation row - if null,
+ * sequenceRef is left unchanged
+ * @param mapping
+ * array of ints containing corresponding positions
+ * @param from
+ * - column for current coordinate system (-1 for index+1)
+ * @param to
+ * - column for destination coordinate system (-1 for index+1)
+ * @param idxoffset
+ * - offset added to index when referencing either coordinate system
+ * @note no checks are made as to whether from and/or to are sensible
+ * @note caller should add the remapped annotation to newref if they have not
+ * already
+ */
+ public void remap(SequenceI newref, HashMap mapping,
+ int from, int to, int idxoffset)
+ {
+ if (mapping != null)
+ {
+ Map old = sequenceMapping;
+ Map remap = new HashMap();
+ int index = -1;
+ for (int mp[] : mapping.values())
+ {
+ if (index++ < 0)
+ {
+ continue;
+ }
+ Annotation ann = null;
+ if (from == -1)
+ {
+ ann = sequenceMapping.get(Integer.valueOf(idxoffset + index));
+ }
+ else
+ {
+ if (mp != null && mp.length > from)
+ {
+ ann = sequenceMapping.get(Integer.valueOf(mp[from]));
+ }
+ }
+ if (ann != null)
+ {
+ if (to == -1)
+ {
+ remap.put(Integer.valueOf(idxoffset + index), ann);
+ }
+ else
+ {
+ if (to > -1 && to < mp.length)
+ {
+ remap.put(Integer.valueOf(mp[to]), ann);
+ }
+ }
+ }
+ }
+ sequenceMapping = remap;
+ old.clear();
+ if (newref != null)
+ {
+ sequenceRef = newref;
+ }
+ adjustForAlignment();
+ }
+ }
+
+ public String getProperty(String property)
+ {
+ if (properties == null)
+ {
+ return null;
+ }
+ return properties.get(property);
+ }
+
+ public void setProperty(String property, String value)
+ {
+ if (properties == null)
+ {
+ properties = new HashMap();
+ }
+ properties.put(property, value);
+ }
+
+ public boolean hasProperties()
+ {
+ return properties != null && properties.size() > 0;
+ }
+
+ public Collection getProperties()
+ {
+ if (properties == null)
+ {
+ return Collections.emptyList();
+ }
+ return properties.keySet();
+ }
+
+ /**
+ * Returns the Annotation for the given sequence position (base 1) if any,
+ * else null
+ *
+ * @param position
+ * @return
+ */
+ public Annotation getAnnotationForPosition(int position)
+ {
+ return sequenceMapping == null ? null : sequenceMapping.get(position);
+
+ }
+
+ /**
+ * Set the id to "ann" followed by a counter that increments so as to be
+ * unique for the lifetime of the JVM
+ */
+ protected final void setAnnotationId()
+ {
+ this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId());
+ }
+
+ /**
+ * Returns the match for the last unmatched opening RNA helix pair symbol
+ * preceding the given column, or '(' if nothing found to match.
+ *
+ * @param column
+ * @return
+ */
+ public String getDefaultRnaHelixSymbol(int column)
+ {
+ String result = "(";
+ if (annotations == null)
+ {
+ return result;
+ }
+
+ /*
+ * for each preceding column, if it contains an open bracket,
+ * count whether it is still unmatched at column, if so return its pair
+ * (likely faster than the fancy alternative using stacks)
+ */
+ for (int col = column - 1; col >= 0; col--)
+ {
+ Annotation annotation = annotations[col];
+ if (annotation == null)
+ {
+ continue;
+ }
+ String displayed = annotation.displayCharacter;
+ if (displayed == null || displayed.length() != 1)
+ {
+ continue;
+ }
+ char symbol = displayed.charAt(0);
+ if (!Rna.isOpeningParenthesis(symbol))
+ {
+ continue;
+ }
+
+ /*
+ * found an opening bracket symbol
+ * count (closing-opening) symbols of this type that follow it,
+ * up to and excluding the target column; if the count is less
+ * than 1, the opening bracket is unmatched, so return its match
+ */
+ String closer = String.valueOf(Rna
+ .getMatchingClosingParenthesis(symbol));
+ String opener = String.valueOf(symbol);
+ int count = 0;
+ for (int j = col + 1; j < column; j++)
+ {
+ if (annotations[j] != null)
+ {
+ String s = annotations[j].displayCharacter;
+ if (closer.equals(s))
+ {
+ count++;
+ }
+ else if (opener.equals(s))
+ {
+ count--;
+ }
+ }
+ }
+ if (count < 1)
+ {
+ return closer;
+ }
+ }
+ return result;
+ }
+
+ protected static synchronized long nextId()
+ {
+ return counter++;
+ }
+
+ /**
+ *
+ * @return true for rows that have a range of values in their annotation set
+ */
+ public boolean isQuantitative()
+ {
+ return graphMin < graphMax;
+ }
}