- ArrayList<String> aresultq = new ArrayList<String>();
- ArrayList<AlignmentI> aresult = new ArrayList<AlignmentI>();
- DbSourceProxy proxy = database.getSelectedSources().get(0);
- Enumeration en = new StringTokenizer(textArea.getText(), ";");
- boolean isAliSource = false;
- try
- {
- guiWindow.setProgressBar(
- "Fetching Sequences from " + proxy.getDbName(), Thread
- .currentThread().hashCode());
- isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
- if (proxy.getAccessionSeparator() == null)
+ // indicate if successive sources should be merged into one alignment.
+ boolean addToLast = false;
+ ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
+ ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
+ Iterator<DbSourceProxy> proxies = database.getSelectedSources()
+ .iterator();
+ String[] qries;
+ List<String> nextfetch = Arrays.asList(qries = textArea.getText()
+ .split(";"));
+ Iterator<String> en = Arrays.asList(new String[0]).iterator();
+ int nqueries = qries.length;
+ while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
+ {
+ if (!en.hasNext() && nextfetch.size() > 0)
+ {
+ en = nextfetch.iterator();
+ nqueries = nextfetch.size();
+ // save the remaining queries in the original array
+ qries = nextfetch.toArray(new String[nqueries]);
+ nextfetch = new ArrayList<String>();
+ }
+
+ DbSourceProxy proxy = proxies.next();
+ boolean isAliSource = false;
+ try