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package jalview.urls; |
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import static jalview.util.UrlConstants.DB_ACCESSION; |
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import static jalview.util.UrlConstants.DELIM; |
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import static jalview.util.UrlConstants.SEP; |
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import static jalview.util.UrlConstants.SEQUENCE_ID; |
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import jalview.util.MessageManager; |
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import jalview.util.UrlConstants; |
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import jalview.util.UrlLink; |
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import java.util.ArrayList; |
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import java.util.HashMap; |
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import java.util.Iterator; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Map.Entry; |
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import java.util.StringTokenizer; |
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@author |
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@version |
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| 0% |
Uncovered Elements: 158 (158) |
Complexity: 43 |
Complexity Density: 0.43 |
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public class CustomUrlProvider extends UrlProviderImpl |
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{ |
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private static final String SRS_LABEL = "SRS"; |
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private HashMap<String, UrlLink> selectedUrls; |
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private HashMap<String, UrlLink> nonselectedUrls; |
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@param |
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@param |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
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public CustomUrlProvider(String inMenuUrlList, String storedUrlList)... |
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{ |
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try |
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{ |
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selectedUrls = parseUrlStrings(inMenuUrlList); |
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nonselectedUrls = parseUrlStrings(storedUrlList); |
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} catch (Exception ex) |
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{ |
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System.out |
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.println(ex.getMessage() + "\nError parsing sequence links"); |
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} |
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} |
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@param |
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@param |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
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public CustomUrlProvider(Map<String, String> inMenuUrlList,... |
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Map<String, String> storedUrlList) |
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{ |
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try |
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{ |
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selectedUrls = parseUrlList(inMenuUrlList); |
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nonselectedUrls = parseUrlList(storedUrlList); |
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} catch (Exception ex) |
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{ |
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System.out |
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.println(ex.getMessage() + "\nError parsing sequence links"); |
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} |
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} |
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| 0% |
Uncovered Elements: 23 (23) |
Complexity: 7 |
Complexity Density: 0.47 |
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private HashMap<String, UrlLink> parseUrlStrings(String urlStrings)... |
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{ |
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HashMap<String, UrlLink> urls = new HashMap<>(); |
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StringTokenizer st = new StringTokenizer(urlStrings, SEP); |
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while (st.hasMoreElements()) |
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{ |
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String name = st.nextToken().trim(); |
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if (!isMiriamId(name)) |
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{ |
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String url = st.nextToken(); |
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int rxstart = url.indexOf(DELIM + DB_ACCESSION + DELIM); |
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if (rxstart == -1) |
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{ |
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rxstart = url.indexOf(DELIM + SEQUENCE_ID + DELIM); |
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} |
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while (rxstart == -1 && url.indexOf("/=" + DELIM) == -1 |
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&& st.hasMoreTokens()) |
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{ |
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url = url + SEP + st.nextToken(); |
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} |
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url = url.trim(); |
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urls.put(name, new UrlLink(name, url, name)); |
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} |
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} |
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upgradeOldLinks(urls); |
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return urls; |
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} |
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| 0% |
Uncovered Elements: 13 (13) |
Complexity: 3 |
Complexity Density: 0.33 |
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private HashMap<String, UrlLink> parseUrlList(Map<String, String> urlList)... |
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{ |
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HashMap<String, UrlLink> urls = new HashMap<>(); |
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if (urlList == null) |
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{ |
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return urls; |
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} |
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Iterator<Map.Entry<String, String>> it = urlList.entrySet().iterator(); |
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while (it.hasNext()) |
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{ |
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Map.Entry<String, String> pair = it.next(); |
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urls.put(pair.getKey(), |
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new UrlLink(pair.getKey(), pair.getValue(), pair.getKey())); |
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} |
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upgradeOldLinks(urls); |
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return urls; |
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} |
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| 0% |
Uncovered Elements: 17 (17) |
Complexity: 4 |
Complexity Density: 0.36 |
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private void upgradeOldLinks(HashMap<String, UrlLink> urls)... |
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{ |
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boolean upgrade = false; |
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if (urls.containsKey(SRS_LABEL)) |
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{ |
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urls.remove(SRS_LABEL); |
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upgrade = true; |
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} |
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if (urls.containsKey(UrlConstants.DEFAULT_LABEL)) |
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{ |
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urls.remove(UrlConstants.DEFAULT_LABEL); |
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upgrade = true; |
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} |
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if (upgrade) |
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{ |
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UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING); |
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link.setLabel(UrlConstants.DEFAULT_LABEL); |
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urls.put(UrlConstants.DEFAULT_LABEL, link); |
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} |
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} |
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| 0% |
Uncovered Elements: 8 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
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@Override... |
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public List<String> getLinksForMenu() |
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{ |
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List<String> links = new ArrayList<>(); |
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Iterator<Map.Entry<String, UrlLink>> it = selectedUrls.entrySet() |
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.iterator(); |
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while (it.hasNext()) |
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{ |
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Map.Entry<String, UrlLink> pair = it.next(); |
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links.add(pair.getValue().toString()); |
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} |
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return links; |
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} |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
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0 |
@Override... |
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public List<UrlLinkDisplay> getLinksForTable() |
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{ |
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ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<>(); |
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displayLinks = getLinksForTable(selectedUrls, true); |
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displayLinks.addAll(getLinksForTable(nonselectedUrls, false)); |
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return displayLinks; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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private ArrayList<UrlLinkDisplay> getLinksForTable(... |
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HashMap<String, UrlLink> urlList, boolean selected) |
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{ |
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return super.getLinksForTable(urlList, null, selected); |
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} |
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| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.5 |
|
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0 |
@Override... |
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public boolean setPrimaryUrl(String id) |
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{ |
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if (selectedUrls.containsKey(id)) |
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{ |
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primaryUrl = id; |
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} |
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else if (nonselectedUrls.containsKey(id)) |
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{ |
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primaryUrl = id; |
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} |
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else |
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{ |
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primaryUrl = null; |
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} |
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return (primaryUrl != null); |
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} |
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| 0% |
Uncovered Elements: 16 (16) |
Complexity: 3 |
Complexity Density: 0.25 |
|
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0 |
@Override... |
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public String writeUrlsAsString(boolean selected) |
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{ |
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StringBuffer links = new StringBuffer(); |
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HashMap<String, UrlLink> urls; |
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if (selected) |
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{ |
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urls = selectedUrls; |
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} |
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else |
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{ |
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urls = nonselectedUrls; |
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} |
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if (urls.size() > 0) |
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{ |
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for (Entry<String, UrlLink> entry : urls.entrySet()) |
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{ |
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links.append(entry.getValue().toString()); |
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links.append(SEP); |
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} |
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links.setLength(links.length() - 1); |
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} |
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else |
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{ |
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urls.clear(); |
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} |
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return links.toString(); |
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} |
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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
267 |
0 |
@Override... |
268 |
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public String getPrimaryUrl(String seqid) |
269 |
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{ |
270 |
0 |
String result = super.getPrimaryUrl(seqid, selectedUrls); |
271 |
0 |
if (result == null) |
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{ |
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result = super.getPrimaryUrl(seqid, nonselectedUrls); |
274 |
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} |
275 |
0 |
return result; |
276 |
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} |
277 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
278 |
0 |
@Override... |
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public String getPrimaryUrlId() |
280 |
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{ |
281 |
0 |
return primaryUrl; |
282 |
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} |
283 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
284 |
0 |
@Override... |
285 |
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public String getPrimaryTarget(String seqid) |
286 |
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{ |
287 |
0 |
return selectedUrls.get(primaryUrl).getTarget(); |
288 |
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} |
289 |
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| 0% |
Uncovered Elements: 25 (25) |
Complexity: 7 |
Complexity Density: 0.47 |
|
290 |
0 |
@Override... |
291 |
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public void setUrlData(List<UrlLinkDisplay> links) |
292 |
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{ |
293 |
0 |
HashMap<String, UrlLink> unselurls = new HashMap<>(); |
294 |
0 |
HashMap<String, UrlLink> selurls = new HashMap<>(); |
295 |
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|
296 |
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Iterator<UrlLinkDisplay> it = links.iterator(); |
297 |
0 |
while (it.hasNext()) |
298 |
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{ |
299 |
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UrlLinkDisplay link = it.next(); |
300 |
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|
301 |
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302 |
0 |
if (!isMiriamId(link.getId())) |
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{ |
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|
305 |
0 |
if (unselurls.containsKey(link.getId()) |
306 |
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|| selurls.containsKey(link.getId())) |
307 |
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{ |
308 |
0 |
throw new IllegalArgumentException(MessageManager.formatMessage( |
309 |
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"exception.url_cannot_have_duplicate_id", link.getId())); |
310 |
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} |
311 |
0 |
if (link.getIsSelected()) |
312 |
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{ |
313 |
0 |
selurls.put(link.getId(), new UrlLink(link.getDescription(), |
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link.getUrl(), link.getDescription())); |
315 |
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} |
316 |
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else |
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{ |
318 |
0 |
unselurls.put(link.getId(), new UrlLink(link.getDescription(), |
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link.getUrl(), link.getDescription())); |
320 |
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} |
321 |
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|
322 |
0 |
if (link.getIsPrimary()) |
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{ |
324 |
0 |
setPrimaryUrl(link.getId()); |
325 |
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} |
326 |
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} |
327 |
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|
328 |
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} |
329 |
0 |
nonselectedUrls = unselurls; |
330 |
0 |
selectedUrls = selurls; |
331 |
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} |
332 |
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| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
333 |
0 |
@Override... |
334 |
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public String choosePrimaryUrl() |
335 |
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{ |
336 |
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|
337 |
0 |
if ((!nonselectedUrls.containsKey(UrlConstants.DEFAULT_LABEL)) |
338 |
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&& (!selectedUrls.containsKey(UrlConstants.DEFAULT_LABEL))) |
339 |
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{ |
340 |
0 |
UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING); |
341 |
0 |
link.setLabel(UrlConstants.DEFAULT_LABEL); |
342 |
0 |
selectedUrls.put(UrlConstants.DEFAULT_LABEL, link); |
343 |
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} |
344 |
0 |
primaryUrl = UrlConstants.DEFAULT_LABEL; |
345 |
0 |
return UrlConstants.DEFAULT_LABEL; |
346 |
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} |
347 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
348 |
0 |
@Override... |
349 |
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public boolean contains(String id) |
350 |
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{ |
351 |
0 |
return (selectedUrls.containsKey(id) |
352 |
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|| nonselectedUrls.containsKey(id)); |
353 |
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} |
354 |
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} |