X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=483c82177bf07915e3eba54dd845b5f65d3e681a;hb=aaace4c8c53d4bb08a5bad0ea18ccfedbef90cd9;hp=20a3633499bb6ad34b38881de60969c6162266c6;hpb=86bf99474fd78966716a9d82ff925e4ec7c0663b;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 20a3633..483c821 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,20 +1,19 @@
/*
- * 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 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 .
*/
package jalview.datamodel;
@@ -23,14 +22,16 @@ 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;
@@ -57,38 +58,39 @@ public class AlignmentAnnotation
/**
* Score associated with label and description.
*/
- public double score= Double.NaN;
+ public double score = Double.NaN;
+
/**
* flag indicating if annotation has a score.
*/
- public boolean hasScore=false;
+ 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;
@@ -98,6 +100,34 @@ public class AlignmentAnnotation
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)
{
@@ -117,14 +147,16 @@ public class AlignmentAnnotation
/**
* Creates a new AlignmentAnnotation object.
- *
- * @param label DOCUMENT ME!
- * @param description DOCUMENT ME!
- * @param annotations DOCUMENT ME!about:blank
-Loading...
+ *
+ * @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;
@@ -132,59 +164,78 @@ Loading...
this.description = description;
this.annotations = annotations;
- validateRangeAndDisplay();
+ validateRangeAndDisplay();
}
void areLabelsSecondaryStructure()
{
boolean nonSSLabel = false;
+ 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;
}
- if(annotations[i].displayCharacter==null)
+ if (annotations[i].displayCharacter == null)
+ {
continue;
-
-
- 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.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 != '-'
+ && 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;
}
}
+ }
- 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 = ' ';
}
@@ -193,22 +244,28 @@ Loading...
annotationId = this.hashCode() + "";
}
+
/**
* 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;
@@ -218,18 +275,17 @@ Loading...
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() {
+ private void validateRangeAndDisplay()
+ {
- if (annotations==null)
+ if (annotations == null)
{
- visible=false; // try to prevent renderer from displaying.
+ visible = false; // try to prevent renderer from displaying.
return; // this is a non-annotation row annotation - ie a sequence score.
}
@@ -248,9 +304,8 @@ Loading...
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;
}
@@ -265,6 +320,18 @@ Loading...
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;
@@ -285,8 +352,9 @@ Loading...
}
/**
- * 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)
@@ -299,6 +367,7 @@ Loading...
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;
@@ -311,39 +380,47 @@ Loading...
{
this.score = annotation.score;
}
- if (threshold!=null) {
+ 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= 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=spos && pos.intValue()<=epos)
+ if (pos.intValue() >= spos && pos.intValue() <= epos)
{
newmapping.put(pos, sequenceMapping.get(pos));
}
@@ -386,33 +477,37 @@ Loading...
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.lengthlength;
+ return annotations.length > length;
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String toString()
@@ -439,8 +534,8 @@ Loading...
buffer.append(", ");
}
-
- if (label.equals("Consensus"))
+ // TODO: remove disgusting hack for 'special' treatment of consensus line.
+ if (label.indexOf("Consensus") == 0)
{
buffer.append("\n");
@@ -469,22 +564,24 @@ Loading...
}
/**
- * 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)
+ sequenceRef = seqRef;
+ if (annotations == null)
{
return;
}
@@ -513,10 +610,10 @@ Loading...
public void adjustForAlignment()
{
- if (sequenceRef==null)
+ if (sequenceRef == null)
return;
- if (annotations==null)
+ if (annotations == null)
{
return;
}
@@ -525,7 +622,7 @@ Loading...
if (aSize == 0)
{
- //Its been deleted
+ // Its been deleted
return;
}
@@ -546,31 +643,45 @@ Loading...
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;
+ }
}