import jalview.analysis.AlignSeq;
import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import vamsas.objects.simple.JpredResult;
vamsas.objects.simple.Msfalignment msa;
- java.util.Hashtable SequenceInfo = null;
+ Object SequenceInfo = null;
int msaIndex = 0; // the position of the original sequence in the array of
{
sqs[i] = al.getSequenceAt(i);
}
- if (!SeqsetUtils.deuniquify(SequenceInfo, sqs))
+ if (!SeqsetUtils.deuniquify((Map<String, SequenceInfo>)SequenceInfo, sqs))
{
throw (new Exception(MessageManager.getString(
"exception.couldnt_recover_sequence_properties_for_alignment")));
}
if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
- al.getSequenceAt(FirstSeq), SequenceInfo))
+ al.getSequenceAt(FirstSeq), (SequenceInfo)SequenceInfo))
{
throw (new Exception(MessageManager.getString(
"exception.couldnt_recover_sequence_props_for_jnet_query")));
}
}
- public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
+ public JPredJob(Object SequenceInfo, SequenceI seq, int[] delMap)
{
super();
this.predMap = delMap;
}
}
- public JPredJob(Hashtable SequenceInfo, SequenceI[] msf, int[] delMap)
+ public JPredJob(Object SequenceInfo, SequenceI[] msf, int[] delMap)
{
this(SequenceInfo, msf[0], delMap);
if (sequence != null)
}
JPredThread(WebserviceInfo wsinfo, String altitle,
- ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,
+ ext.vamsas.Jpred server, String wsurl, SequenceInfo SequenceInfo,
SequenceI seq, int[] delMap, AlignmentView alview,
AlignFrame alframe)
{
}
JPredThread(WebserviceInfo wsinfo, String altitle,
- ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf,
- int[] delMap, AlignmentView alview, AlignFrame alframe,
- String wsurl)
+ ext.vamsas.Jpred server, Map<String, SequenceInfo> SequenceInfo,
+ SequenceI[] msf, int[] delMap, AlignmentView alview,
+ AlignFrame alframe, String wsurl)
{
this(wsinfo, altitle, server, wsurl, alview, alframe);
JPredJob job = new JPredJob(SequenceInfo, msf, delMap);