X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=23b7fcf1ca9392937e2dba73f57d11cba22b2f48;hb=d9f0a24d9662a0b530fd79b51108dd074d03d6e0;hp=1b69989952864235bfd1b4cdd3d6378393268014;hpb=39a640a77b531e7b4801eebf6c43502cc9821180;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 1b69989..23b7fcf 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -69,6 +69,8 @@ import javax.swing.table.AbstractTableModel; public class StructureChooser extends GStructureChooser implements IProgressIndicator { + private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE"; + private static int MAX_QLENGTH = 7820; private SequenceI selectedSequence; @@ -81,7 +83,7 @@ public class StructureChooser extends GStructureChooser private FTSRestRequest lastPdbRequest; - private FTSRestClientI pdbRestCleint; + private FTSRestClientI pdbRestClient; private String selectedPdbFileName; @@ -89,6 +91,8 @@ public class StructureChooser extends GStructureChooser private boolean cachedPDBExists; + private static StructureViewer lastTargetedView = null; + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -102,14 +106,14 @@ public class StructureChooser extends GStructureChooser /** * Initializes parameters used by the Structure Chooser Panel */ - public void init() + protected void init() { if (!Jalview.isHeadlessMode()) { progressBar = new ProgressBar(this.statusPanel, this.statusBar); } - chk_superpose.setSelected(Cache.getDefault("AUTOSUPERIMPOSE", true)); + chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true)); // ensure a filter option is in force for search populateFilterComboBox(true, cachedPDBExists); @@ -137,18 +141,21 @@ public class StructureChooser extends GStructureChooser discoverPDBStructuresThread.start(); } + /** + * Builds a drop-down choice list of existing structure viewers to which new + * structures may be added. If this list is empty then it, and the 'Add' + * button, are hidden. + */ private void discoverStructureViews() { if (Desktop.instance != null) { targetView.removeAllItems(); - targetView.addItem( - new StructureViewer(ap.getStructureSelectionManager())); if (lastTargetedView != null && !lastTargetedView.isVisible()) { lastTargetedView = null; } - int linkedViewsAt = 1; + int linkedViewsAt = 0; for (StructureViewerBase view : Desktop.instance .getStructureViewers(null, null)) { @@ -166,18 +173,27 @@ public class StructureChooser extends GStructureChooser targetView.addItem(viewHandler); } } - targetView.setVisible(targetView.getItemCount() > 1); - // finally, restore last targeted view by default. - if (lastTargetedView != null) + /* + * show option to Add to viewer if at least 1 viewer found + */ + targetView.setVisible(false); + if (targetView.getItemCount() > 0) { - targetView.setSelectedItem(lastTargetedView); + targetView.setVisible(true); + if (lastTargetedView != null) + { + targetView.setSelectedItem(lastTargetedView); + } + else + { + targetView.setSelectedIndex(0); + } } + btn_add.setVisible(targetView.isVisible()); } } - private static StructureViewer lastTargetedView = null; - /** * Updates the progress indicator with the specified message * @@ -186,7 +202,7 @@ public class StructureChooser extends GStructureChooser * @param id * unique handle for this indicator */ - public void updateProgressIndicator(String message, long id) + protected void updateProgressIndicator(String message, long id) { if (progressIndicator != null) { @@ -198,10 +214,10 @@ public class StructureChooser extends GStructureChooser * Retrieve meta-data for all the structure(s) for a given sequence(s) in a * selection group */ - public void fetchStructuresMetaData() + void fetchStructuresMetaData() { long startTime = System.currentTimeMillis(); - pdbRestCleint = PDBFTSRestClient.getInstance(); + pdbRestClient = PDBFTSRestClient.getInstance(); Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); @@ -223,7 +239,7 @@ public class StructureChooser extends GStructureChooser FTSRestResponse resultList; try { - resultList = pdbRestCleint.executeRequest(pdbRequest); + resultList = pdbRestClient.executeRequest(pdbRequest); } catch (Exception e) { e.printStackTrace(); @@ -269,7 +285,7 @@ public class StructureChooser extends GStructureChooser } } - public void loadLocalCachedPDBEntries() + protected void loadLocalCachedPDBEntries() { ArrayList entries = new ArrayList<>(); for (SequenceI seq : selectedSequences) @@ -300,7 +316,7 @@ public class StructureChooser extends GStructureChooser * @return the built query string */ - public static String buildQuery(SequenceI seq) + static String buildQuery(SequenceI seq) { boolean isPDBRefsFound = false; boolean isUniProtRefsFound = false; @@ -321,10 +337,12 @@ public class StructureChooser extends GStructureChooser } } - if (seq.getDBRefs() != null && seq.getDBRefs().length != 0) + List refs = seq.getDBRefs(); + if (refs != null && refs.size() != 0) { - for (DBRefEntry dbRef : seq.getDBRefs()) + for (int ib = 0, nb = refs.size(); ib < nb; ib++) { + DBRefEntry dbRef = refs.get(ib); if (isValidSeqName(getDBRefId(dbRef)) && queryBuilder.length() < MAX_QLENGTH) { @@ -402,7 +420,7 @@ public class StructureChooser extends GStructureChooser * @param seqName * @return */ - public static boolean isValidSeqName(String seqName) + static boolean isValidSeqName(String seqName) { // System.out.println("seqName : " + seqName); String ignoreList = "pdb,uniprot,swiss-prot"; @@ -425,7 +443,7 @@ public class StructureChooser extends GStructureChooser return true; } - public static String getDBRefId(DBRefEntry dbRef) + static String getDBRefId(DBRefEntry dbRef) { String ref = dbRef.getAccessionId().replaceAll("GO:", ""); return ref; @@ -437,7 +455,7 @@ public class StructureChooser extends GStructureChooser * @param fieldToFilterBy * the field to filter by */ - public void filterResultSet(final String fieldToFilterBy) + void filterResultSet(final String fieldToFilterBy) { Thread filterThread = new Thread(new Runnable() { @@ -445,7 +463,7 @@ public class StructureChooser extends GStructureChooser public void run() { long startTime = System.currentTimeMillis(); - pdbRestCleint = PDBFTSRestClient.getInstance(); + pdbRestClient = PDBFTSRestClient.getInstance(); lbl_loading.setVisible(true); Collection wantedFields = pdbDocFieldPrefs .getStructureSummaryFields(); @@ -481,7 +499,7 @@ public class StructureChooser extends GStructureChooser FTSRestResponse resultList; try { - resultList = pdbRestCleint.executeRequest(pdbRequest); + resultList = pdbRestClient.executeRequest(pdbRequest); } catch (Exception e) { e.printStackTrace(); @@ -547,8 +565,10 @@ public class StructureChooser extends GStructureChooser * Handles action event for btn_pdbFromFile */ @Override - public void pdbFromFile_actionPerformed() + protected void pdbFromFile_actionPerformed() { + // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and StructureChooser + // works jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); @@ -648,28 +668,37 @@ public class StructureChooser extends GStructureChooser } /** - * Validates user selection and activates the view button if all parameters - * are correct + * Validates user selection and enables the 'Add' and 'New View' buttons if + * all parameters are correct (the Add button will only be visible if there is + * at least one existing structure viewer open). This basically means at least + * one structure selected and no error messages. + *

+ * The 'Superpose Structures' option is enabled if either more than one + * structure is selected, or the 'Add' to existing view option is enabled, and + * disabled if the only option is to open a new view of a single structure. */ @Override - public void validateSelections() + protected void validateSelections() { FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption .getSelectedItem()); - btn_view.setEnabled(false); + btn_add.setEnabled(false); String currentView = selectedFilterOpt.getView(); + int selectedCount = 0; if (currentView == VIEWS_FILTER) { - if (getResultTable().getSelectedRows().length > 0) + selectedCount = getResultTable().getSelectedRows().length; + if (selectedCount > 0) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); } } else if (currentView == VIEWS_LOCAL_PDB) { - if (tbl_local_pdb.getSelectedRows().length > 0) + selectedCount = tbl_local_pdb.getSelectedRows().length; + if (selectedCount > 0) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); } } else if (currentView == VIEWS_ENTER_ID) @@ -680,12 +709,21 @@ public class StructureChooser extends GStructureChooser { validateAssociationFromFile(); } + + btn_newView.setEnabled(btn_add.isEnabled()); + + /* + * enable 'Superpose' option if more than one structure is selected, + * or there are view(s) available to add structure(s) to + */ + chk_superpose + .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0); } /** * Validates inputs from the Manual PDB entry panel */ - public void validateAssociationEnterPdb() + protected void validateAssociationEnterPdb() { AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel .getCmb_assSeq().getSelectedItem(); @@ -711,7 +749,7 @@ public class StructureChooser extends GStructureChooser txt_search.setEnabled(true); if (isValidPBDEntry) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); lbl_pdbManualFetchStatus.setToolTipText(""); lbl_pdbManualFetchStatus.setIcon(goodImage); } @@ -726,7 +764,7 @@ public class StructureChooser extends GStructureChooser /** * Validates inputs for the manual PDB file selection options */ - public void validateAssociationFromFile() + protected void validateAssociationFromFile() { AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel .getCmb_assSeq().getSelectedItem(); @@ -737,7 +775,7 @@ public class StructureChooser extends GStructureChooser btn_pdbFromFile.setEnabled(true); if (selectedPdbFileName != null && selectedPdbFileName.length() > 0) { - btn_view.setEnabled(true); + btn_add.setEnabled(true); lbl_fromFileStatus.setIcon(goodImage); } } @@ -749,7 +787,7 @@ public class StructureChooser extends GStructureChooser } @Override - public void cmbAssSeqStateChanged() + protected void cmbAssSeqStateChanged() { validateSelections(); } @@ -813,11 +851,22 @@ public class StructureChooser extends GStructureChooser } return found; } + + /** + * Handles the 'New View' action + */ + @Override + protected void newView_ActionPerformed() + { + targetView.setSelectedItem(null); + showStructures(false); + } + /** - * Handles action event for btn_ok + * Handles the 'Add to existing viewer' action */ @Override - public void ok_ActionPerformed() + protected void add_ActionPerformed() { showStructures(false); } @@ -1003,24 +1052,29 @@ public class StructureChooser extends GStructureChooser } /** + * Answers a structure viewer (new or existing) configured to superimpose + * added structures or not according to the user's choice + * * @param ssm - * @return targetted structure view (new or existing) configured according to - * superpose checkbox + * @return */ - public StructureViewer getTargetedStructureViewer( + StructureViewer getTargetedStructureViewer( StructureSelectionManager ssm) { - Object _sv = targetView.getSelectedItem(); - StructureViewer sv; - if (_sv == null) - { - sv = new StructureViewer(ssm); - } else { - sv = (StructureViewer) _sv; - } - sv.setSuperpose(chk_superpose.isSelected()); - return sv; + Object sv = targetView.getSelectedItem(); + + return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv; } + + /** + * Adds PDB structures to a new or existing structure viewer + * + * @param ssm + * @param pdbEntriesToView + * @param alignPanel + * @param sequences + * @return + */ private StructureViewer launchStructureViewer( StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView, @@ -1029,8 +1083,15 @@ public class StructureChooser extends GStructureChooser long progressId = sequences.hashCode(); setProgressBar(MessageManager .getString("status.launching_3d_structure_viewer"), progressId); - final StructureViewer sViewer = getTargetedStructureViewer(ssm); - sViewer.setSuperpose(chk_superpose.isSelected()); + final StructureViewer theViewer = getTargetedStructureViewer(ssm); + boolean superimpose = chk_superpose.isSelected(); + theViewer.setSuperpose(superimpose); + + /* + * remember user's choice of superimpose or not + */ + Cache.setProperty(AUTOSUPERIMPOSE, + Boolean.valueOf(superimpose).toString()); setProgressBar(null, progressId); if (SiftsSettings.isMapWithSifts()) @@ -1057,7 +1118,7 @@ public class StructureChooser extends GStructureChooser } } } - if (seq.getPrimaryDBRefs().size() == 0) + if (seq.getPrimaryDBRefs().isEmpty()) { seqsWithoutSourceDBRef.add(seq); continue; @@ -1069,13 +1130,8 @@ public class StructureChooser extends GStructureChooser setProgressBar(MessageManager.formatMessage( "status.fetching_dbrefs_for_sequences_without_valid_refs", y), progressId); - SequenceI[] seqWithoutSrcDBRef = new SequenceI[y]; - int x = 0; - for (SequenceI fSeq : seqsWithoutSourceDBRef) - { - seqWithoutSrcDBRef[x++] = fSeq; - } - + SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef + .toArray(new SequenceI[y]); DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef); dbRefFetcher.fetchDBRefs(true); @@ -1087,19 +1143,19 @@ public class StructureChooser extends GStructureChooser setProgressBar(MessageManager.getString( "status.fetching_3d_structures_for_selected_entries"), progressId); - sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); + theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel); } else { setProgressBar(MessageManager.formatMessage( "status.fetching_3d_structures_for", pdbEntriesToView[0].getId()),progressId); - sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); + theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } setProgressBar(null, progressId); // remember the last viewer we used... - lastTargetedView = sViewer; - return sViewer; + lastTargetedView = theViewer; + return theViewer; } /** @@ -1107,7 +1163,7 @@ public class StructureChooser extends GStructureChooser * a unique sequence when more than one sequence selection is made. */ @Override - public void populateCmbAssociateSeqOptions( + protected void populateCmbAssociateSeqOptions( JComboBox cmb_assSeq, JLabel lbl_associateSeq) { @@ -1132,30 +1188,32 @@ public class StructureChooser extends GStructureChooser } } - public boolean isStructuresDiscovered() + protected boolean isStructuresDiscovered() { return discoveredStructuresSet != null && !discoveredStructuresSet.isEmpty(); } - public Collection getDiscoveredStructuresSet() - { - return discoveredStructuresSet; - } + protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes this. + // Doing a search for "1" or "1c" is valuable? + // Those work but are enormously slow. @Override protected void txt_search_ActionPerformed() { + String text = txt_search.getText().trim(); + if (text.length() >= PDB_ID_MIN) new Thread() { - @Override + + @Override public void run() { errorWarning.setLength(0); isValidPBDEntry = false; - if (txt_search.getText().length() > 0) + if (text.length() > 0) { - String searchTerm = txt_search.getText().toLowerCase(); + String searchTerm = text.toLowerCase(); searchTerm = searchTerm.split(":")[0]; // System.out.println(">>>>> search term : " + searchTerm); List wantedFields = new ArrayList<>(); @@ -1166,12 +1224,12 @@ public class StructureChooser extends GStructureChooser pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(searchTerm + ")"); pdbRequest.setAssociatedSequence(selectedSequence); - pdbRestCleint = PDBFTSRestClient.getInstance(); - wantedFields.add(pdbRestCleint.getPrimaryKeyColumn()); + pdbRestClient = PDBFTSRestClient.getInstance(); + wantedFields.add(pdbRestClient.getPrimaryKeyColumn()); FTSRestResponse resultList; try { - resultList = pdbRestCleint.executeRequest(pdbRequest); + resultList = pdbRestClient.executeRequest(pdbRequest); } catch (Exception e) { errorWarning.append(e.getMessage()); @@ -1192,7 +1250,7 @@ public class StructureChooser extends GStructureChooser } @Override - public void tabRefresh() + protected void tabRefresh() { if (selectedSequences != null) {