*/
package jalview.ws.uimodel;
+/**
+ * configures annotation worker style web service clients
+ *
+ * @author jprocter
+ *
+ */
public class AlignAnalysisUIText
{
return isPr;
}
+ /**
+ * @return true if service can accept sequences with gaps
+ */
public boolean isAA()
{
return isAA;
private boolean isAA;
+ private boolean filterSymbols;
+
+
+ private boolean needsAlignedSeqs;
+
+ private int min_valid_seqs;
+
+
public AlignAnalysisUIText(String serviceType, Class<?> client,
String calcId, boolean acceptNucl, boolean acceptProt,
- boolean acceptGaps, String toggle, String toggleTooltip,
+ boolean acceptGaps, boolean alignedSeq,
+ boolean filterNonStandardSymbols, int minSeq, String toggle,
+ String toggleTooltip,
String settings, String settingsTooltip)
{
this.serviceType = serviceType;
isNa = acceptNucl;
isPr = acceptProt;
isAA = acceptGaps;
+ this.needsAlignedSeqs = alignedSeq;
+ this.filterSymbols = filterNonStandardSymbols;
this.client = client;
this.AAconToggle = toggle;
this.AAconToggleTooltip = toggleTooltip;
this.AAeditSettings = settings;
this.AAeditSettingsTooltip = settingsTooltip;
+ this.min_valid_seqs = minSeq;
+ }
+
+ /**
+ *
+ * @return true if non-standard nucleotides and amino acids should be replaced
+ * or omitted
+ *
+ */
+ public boolean isFilterSymbols()
+ {
+ return filterSymbols;
+ }
+
+ /**
+ *
+ * @return true if service needs sequences all the same length (ie padded with
+ * gaps if necessary)
+ */
+ public boolean isNeedsAlignedSeqs()
+ {
+ return needsAlignedSeqs;
}
public Class getClient()
AAeditSettingsTooltip = aAeditSettingsTooltip;
}
+ public int getMinimumSequences()
+ {
+ return min_valid_seqs;
+ }
+
}