package jalview.ws.jws1;
import jalview.analysis.AlignSeq;
+import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
*
* @return null or { Alignment(+features and annotation), NewickFile)}
*/
- public Object[] getAlignment(Alignment dataset,
- Map<String, Object> featureColours)
+ public Object[] getAlignment(AlignmentI dataset,
+ Map<String, FeatureColourI> featureColours)
{
if (result != null && result.isFinished())
if (inFile != null && inFile.length() > 0)
{
new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,
- jalview.io.AppletFormatAdapter.PASTE);
+ jalview.io.DataSourceType.PASTE);
}
} catch (Exception e)
{
if (inFile != null && inFile.length() > 0)
{
jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(
- inFile, jalview.io.AppletFormatAdapter.PASTE);
+ inFile, jalview.io.DataSourceType.PASTE);
ff.parse(al, featureColours, false);
}
} catch (Exception e)
if (inFile != null && inFile.length() > 0)
{
nf = new jalview.io.NewickFile(inFile,
- jalview.io.AppletFormatAdapter.PASTE);
+ jalview.io.DataSourceType.PASTE);
if (!nf.isValid())
{
nf.close();
String alTitle; // name which will be used to form new alignment window.
- Alignment dataset; // dataset to which the new alignment will be
+ AlignmentI dataset; // dataset to which the new alignment will be
// associated.
SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
String wsname, String title, AlignmentView _msa, String db,
- Alignment seqset)
+ AlignmentI seqset)
{
this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db);
OutputHeader = wsInfo.getProgressText();
// NewickFile nf[] = new NewickFile[jobs.length];
for (int j = 0; j < jobs.length; j++)
{
- Map<String, Object> featureColours = new HashMap<String, Object>();
+ Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
Alignment al = null;
NewickFile nf = null;
if (jobs[j].hasResults())
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
if (nf != null)
{
- af.ShowNewickTree(nf, MessageManager.formatMessage(
+ af.showNewickTree(nf, MessageManager.formatMessage(
"label.tree_from", new String[] { this.alTitle }));
}
// initialise with same renderer settings as in parent alignframe.