/**
* Write out the current jalview desktop state as a Jalview XML stream.
- *
+ *
* Note: the vamsas objects referred to here are primitive versions of the
* VAMSAS project schema elements - they are not the same and most likely never
* will be :)
- *
+ *
* @author $author$
* @version $Revision: 1.134 $
*/
{
/**
* create/return unique hash string for sq
- *
+ *
* @param sq
* @return new or existing unique string for sq
*/
/**
* Writes a jalview project archive to the given Jar output stream.
- *
+ *
* @param jout
*/
public void SaveState(JarOutputStream jout)
/**
* create a JalviewModel from an algnment view and marshall it to a
* JarOutputStream
- *
+ *
* @param ap
* panel to create jalview model for
* @param fileName
}
JSeq jseq;
- Set<String> calcIdSet=new HashSet<String>();
+ Set<String> calcIdSet = new HashSet<String>();
// SAVE SEQUENCES
String id = "";
// Construct new annotation from model.
AnnotationElement[] ae = an[i].getAnnotationElement();
jalview.datamodel.Annotation[] anot = null;
- java.awt.Color firstColour=null;
+ java.awt.Color firstColour = null;
int anpos;
if (!an[i].getScoreOnly())
{
// {
// anot[ae[aa].getPosition()].displayCharacter = "";
// }
- anot[anpos].colour = new java.awt.Color(
- ae[aa].getColour());
- if (firstColour==null)
+ anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
+ if (firstColour == null)
{
- firstColour=anot[anpos].colour;
+ firstColour = anot[anpos].colour;
}
}
}
an[i].getGraphType());
jaa.graphGroup = an[i].getGraphGroup();
- jaa._linecolour=firstColour;
+ jaa._linecolour = firstColour;
if (an[i].getThresholdLine() != null)
{
jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
{
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
an[i].getDescription(), anot);
- jaa._linecolour=firstColour;
+ jaa._linecolour = firstColour;
}
// register new annotation
if (an[i].getId() != null)
if (view.hasNormaliseSequenceLogo())
{
af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
- }
+ }
if (view.hasShowDbRefTooltip())
{
af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
/**
* TODO remove this method
- *
+ *
* @param view
* @return AlignFrame bound to sequenceSetId from view, if one exists. private
* AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
/**
* Check if the Jalview view contained in object should be skipped or not.
- *
+ *
* @param object
* @return true if view's sequenceSetId is a key in skipList
*/
}
/**
- *
+ *
* @param vamsasSeq
* sequence definition to create/merge dataset sequence for
* @param ds
/**
* make a new dataset ID for this jalview dataset alignment
- *
+ *
* @param dataset
* @return
*/
/*
* (non-Javadoc)
- *
+ *
* @see java.lang.Object#finalize()
*/
@Override
* finalize and clearSeqRefs will not clear the tables when the Jalview2XML
* object goes out of scope. - also populates the datasetIds hashtable with
* alignment objects containing dataset sequences
- *
+ *
* @param vobj2jv
* Map from ID strings to jalview datamodel
* @param jv2vobj
* Map from jalview datamodel to ID strings
- *
- *
+ *
+ *
*/
public void setObjectMappingTables(Hashtable vobj2jv,
IdentityHashMap jv2vobj)
* set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
* objects created from the project archive. If string is null (default for
* construction) then suffix will be set automatically.
- *
+ *
* @param string
*/
public void setUniqueSetSuffix(String string)
/**
* uses skipList2 as the skipList for skipping views on sequence sets
* associated with keys in the skipList
- *
+ *
* @param skipList2
*/
public void setSkipList(Hashtable skipList2)