import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
+import jalview.ws.EnfinEnvision2OneWay;
/**
* DOCUMENT ME!
*/
groupURLLinks = new Vector();
- groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
- groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
+ //groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
+ //groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
}
fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
- conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
- quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
- identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
-
conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
showUnconserved.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+ showNpTooltip.setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
for (int i = 0; i < 13; i++)
{
autoCalculateConsCheck.setSelected(Cache.getDefault(
"AUTO_CALC_CONSENSUS", true));
+ showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",false));
+ showGroupConservation.setSelected(Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
+ showConsensHistogram.setSelected(Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",true));
+ showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",false));
+
padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
/***************************************************************************
usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
questionnaire.setSelected(Cache.getProperty("NOQUESTIONNAIRES")==null); // note antisense here
versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default is true
-
+ annotations_actionPerformed(null); // update the display of the annotation settings
try
{
jbInit();
Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
.toString(idItalics.isSelected()));
Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",Boolean.toString(showGroupConsensus.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",Boolean.toString(showGroupConservation.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",Boolean.toString(showConsensHistogram.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",Boolean.toString(showConsensLogo.isSelected()));
Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
.toString(smoothFont.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", Boolean.toString(showNpTooltip.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", Boolean.toString(showDbRefTooltip.isSelected()));
Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
.toString(wrap.isSelected()));
conservation.setEnabled(annotations.isSelected());
quality.setEnabled(annotations.isSelected());
identity.setEnabled(annotations.isSelected());
+ showGroupConsensus.setEnabled(annotations.isSelected());
+ showGroupConservation.setEnabled(annotations.isSelected());
+ showConsensHistogram.setEnabled(annotations.isSelected() && (identity.isSelected() || showGroupConsensus.isSelected()));
+ showConsensLogo.setEnabled(annotations.isSelected() && (identity.isSelected() || showGroupConsensus.isSelected()));
}
public void newLink_actionPerformed(ActionEvent e)
private void jbInit() throws Exception
{
}
+
+ public static Collection getGroupURLLinks()
+ {
+ return groupURLLinks;
+ }
}