import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
if (links != null && links.size() > 0)
{
- Menu linkMenu = new Menu(MessageManager.getString("action.link"));
- for (int i = 0; i < links.size(); i++)
- {
- String link = links.elementAt(i);
- UrlLink urlLink = new UrlLink(link);
- if (!urlLink.isValid())
- {
- System.err.println(urlLink.getInvalidMessage());
- continue;
- }
- final String target = urlLink.getTarget(); // link.substring(0,
- // link.indexOf("|"));
- final String label = urlLink.getLabel();
- if (seq != null && urlLink.isDynamic())
- {
-
- // collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
- seq.getDBRefs(), new String[] { target });
- // collect id string too
- String id = seq.getName();
- String descr = seq.getDescription();
- if (descr != null && descr.length() < 1)
- {
- descr = null;
- }
- if (dbr != null)
- {
- for (int r = 0; r < dbr.length; r++)
- {
- if (id != null && dbr[r].getAccessionId().equals(id))
- {
- // suppress duplicate link creation for the bare sequence ID
- // string with this link
- id = null;
- }
- // create Bare ID link for this RUL
- String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
- true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
- }
- }
- }
- }
- if (id != null)
- {
- // create Bare ID link for this RUL
- String[] urls = urlLink.makeUrls(id, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- // addshowLink(linkMenu, target, url_pref + id + url_suff);
- }
- // Now construct URLs from description but only try to do it for regex
- // URL links
- if (descr != null && urlLink.getRegexReplace() != null)
- {
- // create link for this URL from description only if regex matches
- String[] urls = urlLink.makeUrls(descr, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
- }
- else
- {
- addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
- }
- /*
- * final String url;
- *
- * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
- * string and any matching database reference accessions String url_pref
- * = link.substring(link.indexOf("|") + 1,
- * link.indexOf("$SEQUENCE_ID$"));
- *
- * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
- * // collect matching db-refs DBRefEntry[] dbr =
- * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
- * String[]{target}); // collect id string too String id =
- * seq.getName(); if (id.indexOf("|") > -1) { id =
- * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
- * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
- * suppress duplicate link creation for the bare sequence ID string with
- * this link id = null; } addshowLink(linkMenu,
- * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
- * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
- * create Bare ID link for this RUL addshowLink(linkMenu, target,
- * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
- * link.substring(link.lastIndexOf("|")+1)); }
- */
- }
- if (linkMenu.getItemCount() > 0)
- {
- if (seq != null)
- {
- seqMenu.add(linkMenu);
- }
- else
- {
- add(linkMenu);
- }
- }
+ addFeatureLinks(seq, links);
}
+
// TODO: add group link menu entry here
if (seq != null)
{
}
/**
+ * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
+ *
+ * @param seq
+ * @param links
+ */
+ void addFeatureLinks(final SequenceI seq, List<String> links)
+ {
+ Menu linkMenu = new Menu(MessageManager.getString("action.link"));
+ Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+
+ for (String link : links)
+ {
+ UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(link);
+ } catch (Exception foo)
+ {
+ System.err.println("Exception for URLLink '" + link + "': "
+ + foo.getMessage());
+ continue;
+ }
+
+ if (!urlLink.isValid())
+ {
+ System.err.println(urlLink.getInvalidMessage());
+ continue;
+ }
+
+ urlLink.createLinksFromSeq(seq, linkset);
+ }
+
+ addshowLinks(linkMenu, linkset.values());
+
+ // disable link menu if there are no valid entries
+ if (linkMenu.getItemCount() > 0)
+ {
+ linkMenu.setEnabled(true);
+ }
+ else
+ {
+ linkMenu.setEnabled(false);
+ }
+
+ if (seq != null)
+ {
+ seqMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+
+ }
+
+ private void addshowLinks(Menu linkMenu, Collection<List<String>> linkset)
+ {
+ for (List<String> linkstrset : linkset)
+ {
+ // split linkstr into label and url
+ addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
+ }
+ }
+
+ /**
* Build menus for annotation types that may be shown or hidden, and for
* 'reference annotations' that may be added to the alignment.
*/
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
- StringBuffer contents = new StringBuffer();
+ StringBuilder contents = new StringBuilder(128);
for (SequenceI seq : sequences)
{
contents.append(MessageManager.formatMessage(
seq,
true,
true,
- false,
(ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
.getMinMax() : null);
contents.append("</p>");
void addPDB()
{
- if (seq.getAllPDBEntries() != null)
+ Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
+ if (pdbs != null&& !pdbs.isEmpty())
{
- PDBEntry entry = seq.getAllPDBEntries().firstElement();
+ PDBEntry entry = pdbs.firstElement();
if (ap.av.applet.jmolAvailable)
{
if (conservationMenuItem.getState())
{
-
- sg.cs.setConservation(Conservation.calculateConservation("Group", 3,
- sg.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
- .getAlignment().getWidth(), false, ap.av
- .getConsPercGaps(), false));
+ sg.cs.setConservation(Conservation.calculateConservation("Group", sg
+ .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
+ .getAlignment().getWidth(), false, ap.av.getConsPercGaps(),
+ false));
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}
import java.util.Map;
import java.util.Vector;
- import javajs.awt.Dimension;
-
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolSelectionListener;
Vector<String> atomsPicked = new Vector<String>();
- public Vector<String> chainNames;
+ private List<String> chainNames;
Hashtable<String, String> chainFile;
public Viewer viewer;
public JalviewJmolBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
String protocol)
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
+ super(ssm, pdbentry, sequenceIs, protocol);
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
* "jalviewJmol", ap.av.applet .getDocumentBase(),
fileLoadingError = null;
String[] oldmodels = modelFileNames;
modelFileNames = null;
- chainNames = new Vector<String>();
+ chainNames = new ArrayList<String>();
chainFile = new Hashtable<String, String>();
boolean notifyLoaded = false;
String[] modelfilenames = getPdbFile();
for (int pe = 0; pe < getPdbCount(); pe++)
{
boolean matches = false;
+ addSequence(pe, getSequence()[pe]);
if (fileName == null)
{
if (false)
String chid = new String(pdb.getId() + ":"
+ pdb.getChains().elementAt(i).id);
chainFile.put(chid, fileName);
- chainNames.addElement(chid);
+ chainNames.add(chid);
}
notifyLoaded = true;
}
setLoadingFromArchive(false);
}
+ @Override
+ public List<String> getChainNames()
+ {
+ return chainNames;
+ }
+
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
notifyAtomPicked(iatom, strMeasure, null);
}
@Override
- public Dimension resizeInnerPanel(String data)
+ public int[] resizeInnerPanel(String data)
{
// Jalview doesn't honour resize panel requests
return null;
git://source.jalview.org / jalview.git / commitdiff