/*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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 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.
*
- * 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 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;
/** 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 */
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.
*/
*/
public boolean centreColLabels = false;
-
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see java.lang.Object#finalize()
*/
protected void finalize() throws Throwable
{
+ sequenceRef = null;
groupRef = null;
super.finalize();
}
* 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)
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 != ' '
+ 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[firstChar] < 23) // TODO: parameterise to gap symbol number
+ if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
+ // parameterise
+ // to
+ // gap
+ // symbol
+ // number
{
nonSSLabel = true;
}
* 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)
}
}
// 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;
{
this.score = annotation.score;
}
- if (threshold != null)
+ if (annotation.threshold != null)
{
threshold = new GraphLine(annotation.threshold);
}
* 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)
if (annotations == null)
{
return true; // annotation row is correct - null == not visible and
- // undefined length
+ // undefined length
}
if (annotations.length < length)
{
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");
/**
* @param score
- * the score to set
+ * the score to set
*/
public void setScore(double score)
{
{
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