From: tcofoegbu Date: Mon, 20 Mar 2017 15:14:27 +0000 (+0000) Subject: Merge JAL-2136_phyre2_integration to develop X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bcd6cac49e4d2b1f91917753da0d119eb79055d1;p=jalview.git Merge JAL-2136_phyre2_integration to develop --- bcd6cac49e4d2b1f91917753da0d119eb79055d1 diff --cc resources/lang/Messages.properties index ae913ae,d6d3034..6e1bd40 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@@ -1274,7 -1278,21 +1278,27 @@@ label.SEQUENCE_ID_no_longer_used = $SEQ label.SEQUENCE_ID_for_DB_ACCESSION1 = Please review your URL links in the 'Connections' tab of the Preferences window: label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$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 diff --cc src/jalview/ext/rbvi/chimera/AtomSpecModel.java index 0000000,d62cc3c..7632b65 mode 000000,100644..100644 --- a/src/jalview/ext/rbvi/chimera/AtomSpecModel.java +++ b/src/jalview/ext/rbvi/chimera/AtomSpecModel.java @@@ -1,0 -1,180 +1,180 @@@ + 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 + * + * 
+  * #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
+  *
+ * + * where + * + * + * 
+  * @see http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
+  *
+ */ + public class AtomSpecModel + { + private Map>> atomSpec; + + /** + * Constructor + */ + public AtomSpecModel() + { + atomSpec = new TreeMap>>(); + } + + /** + * 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> modelData = atomSpec.get(model); + if (modelData == null) + { + atomSpec.put(model, modelData = new TreeMap>()); + } + + /* + * Get/initialize map of data for colour, model and chain + */ + List chainData = modelData.get(chain); + if (chainData == null) + { + chainData = new ArrayList(); + 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> modelData = atomSpec.get(model); + + for (String chain : modelData.keySet()) + { - chain = chain.trim(); ++ // chain = chain.trim(); + + List 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 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); + } + } + } diff --cc src/jalview/gui/AppJmol.java index bdd8c4b,5d23f49..9c4dd9d --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@@ -163,85 -138,20 +138,21 @@@ public class AppJmol extends StructureV 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(); - } - if (_alignwith == null) - { - _alignwith = new Vector(); - } - - 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; @@@ -1142,9 -747,8 +753,14 @@@ } @Override + protected String getViewerName() + { + return "Jmol"; + } ++ ++ @Override + protected AAStructureBindingModel getBindingModel() + { + return jmb; + } - } diff --cc src/jalview/gui/ChimeraViewFrame.java index d9ba9c5,fe4a000..b4a57a2 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@@ -1140,14 -852,24 +853,36 @@@ public class ChimeraViewFrame extends S } @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; ++ } } diff --cc src/jalview/io/AnnotationFile.java index 01f6e6f,9a4071d..b72184b --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@@ -28,18 -28,14 +28,19 @@@ import jalview.datamodel.Annotation 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; diff --cc src/jalview/structure/StructureSelectionManager.java index 5ff2da4,3ab642f..991ba82 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@@ -1400,26 -1369,4 +1415,31 @@@ public class StructureSelectionManage 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); ++ } ++ } diff --cc src/jalview/ws/sifts/SiftsClient.java index 716a047,ea65125..1328260 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@@ -70,11 -69,21 +70,17 @@@ import javax.xml.bind.Unmarshaller 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;