label.SEQUENCE_ID_for_DB_ACCESSION1 = Please review your URL links in the 'Connections' tab of the Preferences window:
label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'.
label.do_not_display_again = Do not display this message again
+ exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name
+ exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one line
+ label.filter = Filter text:
+ action.customfilter = Custom only
+ action.showall = Show All
+ label.insert = Insert:
+ action.seq_id = $SEQUENCE_ID$
+ action.db_acc = $DB_ACCESSION$
+ label.primary = Double Click
+ label.inmenu = In Menu
+ label.id = ID
+ label.database = Database
+ label.urltooltip = Only one url, which must use a sequence id, can be selected for the 'On Click' option
+ label.edit_sequence_url_link = Edit sequence URL link
+ warn.name_cannot_be_duplicate = User-defined URL names must be unique and cannot be MIRIAM ids
+ label.invalid_name = Invalid Name !
label.output_seq_details = Output Sequence Details to list all database references
++<<<<<<< HEAD
+label.phyre2_model_prediction = 3D Protein Model prediction with Phyre2
+label.run_phyre2_prediction = Run Phyre2 Prediction
- status.obtaining_mapping_with_phyre2_template_alignment = Obtaining mapping with Phyre2 Template alignment
++status.obtaining_mapping_with_phyre2_template_alignment = Obtaining mapping with Phyre2 Template alignment
++=======
+ label.urllinks = Links
++>>>>>>> develop
--- /dev/null
+ package jalview.ext.rbvi.chimera;
+
+ import jalview.util.RangeComparator;
+
+ import java.util.ArrayList;
+ import java.util.Collections;
+ import java.util.Iterator;
+ import java.util.List;
+ import java.util.Map;
+ import java.util.TreeMap;
+
+ /**
+ * A class to model a Chimera atomspec pattern, for example
+ *
+ * <pre>
+ * #0:15.A,28.A,54.A,63.A,70-72.A,83-84.A,97-98.A|#1:2.A,6.A,11.A,13-14.A,70.A,82.A,96-97.A
+ * </pre>
+ *
+ * where
+ * <ul>
+ * <li>#0 is a model number</li>
+ * <li>15 or 70-72 is a residue number, or range of residue numbers</li>
+ * <li>.A is a chain identifier</li>
+ * <li>residue ranges are separated by comma</li>
+ * <li>atomspecs for distinct models are separated by | (or)</li>
+ * </ul>
+ *
+ * <pre>
+ * @see http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
+ * </pre>
+ */
+ public class AtomSpecModel
+ {
+ private Map<Integer, Map<String, List<int[]>>> atomSpec;
+
+ /**
+ * Constructor
+ */
+ public AtomSpecModel()
+ {
+ atomSpec = new TreeMap<Integer, Map<String, List<int[]>>>();
+ }
+
+ /**
+ * Adds one contiguous range to this atom spec
+ *
+ * @param model
+ * @param startPos
+ * @param endPos
+ * @param chain
+ */
+ public void addRange(int model, int startPos, int endPos, String chain)
+ {
+ /*
+ * Get/initialize map of data for the colour and model
+ */
+ Map<String, List<int[]>> modelData = atomSpec.get(model);
+ if (modelData == null)
+ {
+ atomSpec.put(model, modelData = new TreeMap<String, List<int[]>>());
+ }
+
+ /*
+ * Get/initialize map of data for colour, model and chain
+ */
+ List<int[]> chainData = modelData.get(chain);
+ if (chainData == null)
+ {
+ chainData = new ArrayList<int[]>();
+ modelData.put(chain, chainData);
+ }
+
+ /*
+ * Add the start/end positions
+ */
+ chainData.add(new int[] { startPos, endPos });
+ // TODO add intelligently, using a RangeList class
+ }
+
+ /**
+ * Returns the range(s) formatted as a Chimera atomspec
+ *
+ * @return
+ */
+ public String getAtomSpec()
+ {
+ StringBuilder sb = new StringBuilder(128);
+ boolean firstModel = true;
+ for (Integer model : atomSpec.keySet())
+ {
+ if (!firstModel)
+ {
+ sb.append("|");
+ }
+ firstModel = false;
+ sb.append("#").append(model).append(":");
+
+ boolean firstPositionForModel = true;
+ final Map<String, List<int[]>> modelData = atomSpec.get(model);
+
+ for (String chain : modelData.keySet())
+ {
- chain = chain.trim();
++ // chain = chain.trim();
+
+ List<int[]> rangeList = modelData.get(chain);
+
+ /*
+ * sort ranges into ascending start position order
+ */
+ Collections.sort(rangeList, new RangeComparator(true));
+
+ int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0];
+ int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1];
+
+ Iterator<int[]> iterator = rangeList.iterator();
+ while (iterator.hasNext())
+ {
+ int[] range = iterator.next();
+ if (range[0] <= end + 1)
+ {
+ /*
+ * range overlaps or is contiguous with the last one
+ * - so just extend the end position, and carry on
+ * (unless this is the last in the list)
+ */
+ end = Math.max(end, range[1]);
+ }
+ else
+ {
+ /*
+ * we have a break so append the last range
+ */
+ appendRange(sb, start, end, chain, firstPositionForModel);
+ firstPositionForModel = false;
+ start = range[0];
+ end = range[1];
+ }
+ }
+
+ /*
+ * and append the last range
+ */
+ if (!rangeList.isEmpty())
+ {
+ appendRange(sb, start, end, chain, firstPositionForModel);
+ firstPositionForModel = false;
+ }
+ }
+ }
+ return sb.toString();
+ }
+
+ /**
+ * @param sb
+ * @param start
+ * @param end
+ * @param chain
+ * @param firstPositionForModel
+ */
+ protected void appendRange(StringBuilder sb, int start, int end,
+ String chain, boolean firstPositionForModel)
+ {
+ if (!firstPositionForModel)
+ {
+ sb.append(",");
+ }
+ if (end == start)
+ {
+ sb.append(start);
+ }
+ else
+ {
+ sb.append(start).append("-").append(end);
+ }
+ if (chain.length() > 0)
+ {
+ sb.append(".").append(chain);
+ }
+ }
+ }
closeViewer(false);
}
});
- initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
+ initJmol(loadStatus); // pdbentry, seq, JBPCHECK!ˇ
+
}
- private void initMenus()
+ @Override
+ protected void initMenus()
{
- seqColour.setSelected(jmb.isColourBySequence());
- viewerColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
-
- seqColourBy = new ViewSelectionMenu(
- MessageManager.getString("label.colour_by"), this, _colourwith,
- new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- if (!seqColour.isSelected())
- {
- seqColour.doClick();
- }
- else
- {
- // update the jmol display now.
- seqColour_actionPerformed(null);
- }
- }
- });
- viewMenu.add(seqColourBy);
- final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu(
- MessageManager.getString("label.superpose_with"), this,
- _alignwith, handler = new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText(MessageManager
- .formatMessage(
- "label.align_structures_using_linked_alignment_views",
- new String[] { new Integer(_alignwith
- .size()).toString() }));
- }
- });
- handler.itemStateChanged(null);
- viewerActionMenu.add(alpanels);
- viewerActionMenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent e)
- {
- handler.itemStateChanged(null);
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- // TODO Auto-generated method stub
+ super.initMenus();
- }
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- // TODO Auto-generated method stub
+ viewerActionMenu.setText(MessageManager.getString("label.jmol"));
- }
- });
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_jmol"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_jmol_manage_structure_colours"));
}
IProgressIndicator progressBar = null;
}
@Override
+ protected String getViewerName()
+ {
+ return "Jmol";
+ }
++
++ @Override
+ protected AAStructureBindingModel getBindingModel()
+ {
+ return jmb;
+ }
-
}
}
@Override
- protected AAStructureBindingModel getBindingModel()
+ protected String getViewerName()
{
- return jmb;
+ return "Chimera";
+ }
+
+ /**
+ * Sends commands to align structures according to associated alignment(s).
+ *
+ * @return
+ */
+ @Override
+ protected String alignStructs_withAllAlignPanels()
+ {
+ String reply = super.alignStructs_withAllAlignPanels();
+ if (reply != null)
+ {
+ statusBar.setText("Superposition failed: " + reply);
+ }
+ return reply;
}
+
+ @Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return progressBar;
+ }
++
++ @Override
++ protected AAStructureBindingModel getBindingModel()
++ {
++ return jmb;
++ }
}
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.GraphLine;
import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
- import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureSelectionManager;
+ import jalview.util.ColorUtils;
+ import java.awt.Color;
import java.io.BufferedReader;
+import java.io.File;
import java.io.FileReader;
import java.io.InputStreamReader;
import java.io.StringReader;
return seqmappings;
}
+ public boolean isPhyre2Template(String structureFile)
+ {
+ if (structureFile == null || phyre2ModelTemplates == null
+ || phyre2ModelTemplates.isEmpty())
+ {
+ return false;
+ }
+ return phyre2ModelTemplates.get(structureFile) != null
+ && !phyre2ModelTemplates.get(structureFile).isEmpty();
+ }
+
+ public String getPhyre2FastaFileFor(String structureFile)
+ {
+ return phyre2ModelTemplates.get(structureFile);
+ }
+
+
+ public static StructureSelectionManager getStructureSelectionManager()
+ {
+ return instances.values().iterator().next();
+ }
+
++ public void addStructureMapping(StructureMapping smapping)
++ {
++ mappings.add(smapping);
++ }
++
}
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamReader;
-import MCview.Atom;
-import MCview.PDBChain;
-
-public class SiftsClient implements SiftsClientI
+public class SiftsClient extends StructureMappingClient implements
+ SiftsClientI
{
+ /*
+ * for use in mocking out file fetch for tests only
+ * - reset to null after testing!
+ */
+ private static File mockSiftsFile;
+
private Entry siftsEntry;
- private StructureFile pdb;
-
private String pdbId;
private String structId;
git://source.jalview.org / jalview.git / commitdiff