private static String defaultFTSFrameTitle = MessageManager
.getString("label.uniprot_sequence_fetcher");
- private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+ private static Map<String, Integer> tempUserPrefs = new HashMap<>();
private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
- public UniprotFTSPanel(SequenceFetcher seqFetcher)
+ public UniprotFTSPanel(SequenceFetcher fetcher)
{
super();
pageLimit = UniProtFTSRestClient.getInstance()
.getDefaultResponsePageSize();
- this.seqFetcher = seqFetcher;
- this.progressIndicator = (seqFetcher == null) ? null
- : seqFetcher.getProgressIndicator();
+ this.seqFetcher = fetcher;
+ this.progressIndicator = (fetcher == null) ? null
+ : fetcher.getProgressIndicator();
}
@Override
request.setSearchTerm(searchTerm);
request.setOffSet(offSet);
request.setWantedFields(wantedFields);
- FTSRestClientI uniProtRestCleint = UniProtFTSRestClient
+ FTSRestClientI uniProtRestClient = UniProtFTSRestClient
.getInstance();
FTSRestResponse resultList;
try
{
- resultList = uniProtRestCleint.executeRequest(request);
+ resultList = uniProtRestClient.executeRequest(request);
} catch (Exception e)
{
- e.printStackTrace();
setErrorMessage(e.getMessage());
checkForErrors();
+ setSearchInProgress(false);
return;
}
{
disableActionButtons();
StringBuilder selectedIds = new StringBuilder();
- HashSet<String> selectedIdsSet = new HashSet<String>();
+ HashSet<String> selectedIdsSet = new HashSet<>();
int primaryKeyColIndex = 0;
try
{
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class CigarArrayTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = "Functional")
+ public void testConstructor()
+ {
+ SequenceI seq1 = new Sequence("sq1",
+ "ASFDDABACBACBACBACBACBACBABCABCBACBABCAB");
+ Sequence seq2 = new Sequence("sq2",
+ "TTTTTTACBCBABCABCABCABCBACBACBABCABCABCBA");
+
+ // construct alignment
+ AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+
+ // hide columns
+ HiddenColumns hc = new HiddenColumns();
+ hc.hideColumns(3, 6);
+ hc.hideColumns(16, 20);
+
+ // select group
+ SequenceGroup sg1 = new SequenceGroup();
+ sg1.addSequence(seq1, false);
+ sg1.setStartRes(2);
+ sg1.setEndRes(23);
+
+ // Cigar array meanings:
+ // M = match
+ // D = deletion
+ // I = insertion
+ // number preceding M/D/I is the number of residues which
+ // match/are deleted/are inserted
+ // In the CigarArray constructor only matches or deletions are created, as
+ // we are comparing a sequence to its own subsequence (the group) + hidden
+ // columns.
+
+ // no hidden columns case
+ CigarArray cig = new CigarArray(al, null, sg1);
+ String result = cig.getCigarstring();
+ assertEquals(result, "22M");
+
+ cig = new CigarArray(al, hc, sg1);
+ result = cig.getCigarstring();
+ assertEquals(result, "1M4D9M5D3M");
+
+ // group starts at hidden cols
+ sg1.setStartRes(3);
+ cig = new CigarArray(al, hc, sg1);
+ result = cig.getCigarstring();
+ assertEquals(result, "4D9M5D3M");
+
+ // group starts at last but 1 hidden col
+ sg1.setStartRes(5);
+ cig = new CigarArray(al, hc, sg1);
+ result = cig.getCigarstring();
+ assertEquals(result, "2D9M5D3M");
+
+ // group starts at last hidden col
+ sg1.setStartRes(6);
+ cig = new CigarArray(al, hc, sg1);
+ result = cig.getCigarstring();
+ assertEquals(result, "1D9M5D3M");
+
+ // group starts just after hidden region
+ sg1.setStartRes(7);
+ cig = new CigarArray(al, hc, sg1);
+ result = cig.getCigarstring();
+ assertEquals(result, "9M5D3M");
+
+ // group ends just before start of hidden region
+ sg1.setStartRes(5);
+ sg1.setEndRes(15);
+ cig = new CigarArray(al, hc, sg1);
+ result = cig.getCigarstring();
+ assertEquals(result, "2D9M");
+
+ // group ends at start of hidden region
+ sg1.setEndRes(16);
+ cig = new CigarArray(al, hc, sg1);
+ result = cig.getCigarstring();
+ assertEquals(result, "2D9M1D");
+
+ // group ends 1 after start of hidden region
+ sg1.setEndRes(17);
+ cig = new CigarArray(al, hc, sg1);
+ result = cig.getCigarstring();
+ assertEquals(result, "2D9M2D");
+
+ // group ends at end of hidden region
+ sg1.setEndRes(20);
+ cig = new CigarArray(al, hc, sg1);
+ result = cig.getCigarstring();
+ assertEquals(result, "2D9M5D");
+
+ // group ends just after end of hidden region
+ sg1.setEndRes(21);
+ cig = new CigarArray(al, hc, sg1);
+ result = cig.getCigarstring();
+ assertEquals(result, "2D9M5D1M");
+
+ // group ends 2 after end of hidden region
+ sg1.setEndRes(22);
+ cig = new CigarArray(al, hc, sg1);
+ result = cig.getCigarstring();
+ assertEquals(result, "2D9M5D2M");
+ }
+}
git://source.jalview.org / jalview.git / commitdiff