+ return hasResults;
+ }
+
+ /**
+ * @return the alignment
+ */
+ public AlignmentI getAlignment()
+ {
+ return alignment;
+ }
+
+ /**
+ * @param alignment
+ * the alignment to set
+ */
+ public void setAlignment(AlignmentI alignment)
+ {
+ this.alignment = alignment;
+ }
+
+ /**
+ * @return the caseSensitive
+ */
+ public boolean isCaseSensitive()
+ {
+ return caseSensitive;
+ }
+
+ /**
+ * @param caseSensitive
+ * the caseSensitive to set
+ */
+ public void setCaseSensitive(boolean caseSensitive)
+ {
+ this.caseSensitive = caseSensitive;
+ }
+
+ /**
+ * @return the findAll
+ */
+ public boolean isFindAll()
+ {
+ return findAll;
+ }
+
+ /**
+ * @param findAll
+ * the findAll to set
+ */
+ public void setFindAll(boolean findAll)
+ {
+ this.findAll = findAll;
+ }
+
+ /**
+ * @return the selection
+ */
+ public jalview.datamodel.SequenceGroup getSelection()
+ {
+ return selection;
+ }
+
+ /**
+ * @param selection
+ * the selection to set
+ */
+ public void setSelection(jalview.datamodel.SequenceGroup selection)
+ {
+ this.selection = selection;
+ }
+
+ /**
+ * Returns the (possibly empty) list of matching sequences (when search
+ * includes searching sequence names)
+ *
+ * @return
+ */
+ public Vector<SequenceI> getIdMatch()
+ {
+ return idMatch;
+ }
+
+ /**
+ * @return the regex
+ */
+ public com.stevesoft.pat.Regex getRegex()
+ {
+ return regex;
+ }
+
+ /**
+ * @return the searchResults
+ */
+ public SearchResultsI getSearchResults()
+ {
+ return searchResults;
+ }
+
+ /**
+ * @return the resIndex
+ */
+ public int getResIndex()
+ {
+ return resIndex;
+ }
+
+ /**
+ * @param resIndex
+ * the resIndex to set
+ */
+ public void setResIndex(int resIndex)
+ {
+ this.resIndex = resIndex;
+ }
+
+ /**
+ * @return the seqIndex
+ */
+ public int getSeqIndex()
+ {
+ return seqIndex;
+ }
+
+ /**
+ * @param seqIndex
+ * the seqIndex to set
+ */
+ public void setSeqIndex(int seqIndex)
+ {
+ this.seqIndex = seqIndex;
+ }
+
+ public boolean isIncludeDescription()
+ {
+ return includeDescription;
+ }
+
+ public void setIncludeDescription(boolean includeDescription)
+ {
+ this.includeDescription = includeDescription;
+ }