X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=3e516a621b58bc6421027ef62559ccef480f154f;hb=968c3bcde941e502fcf7d497343600f4f58f6c9a;hp=014a8a5996fc84d69fa5119d9fdcec1ef6f55b6d;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 014a8a5..3e516a6 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -32,6 +32,7 @@ import jalview.fts.api.FTSRestClientI; import jalview.fts.core.FTSRestRequest; import jalview.fts.core.FTSRestResponse; import jalview.fts.service.pdb.PDBFTSRestClient; +import jalview.io.DataSourceType; import jalview.jbgui.GStructureChooser; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; @@ -52,7 +53,6 @@ import java.util.Vector; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JLabel; -import javax.swing.JOptionPane; import javax.swing.table.AbstractTableModel; /** @@ -65,6 +65,8 @@ import javax.swing.table.AbstractTableModel; public class StructureChooser extends GStructureChooser implements IProgressIndicator { + private static int MAX_QLENGTH = 7820; + private SequenceI selectedSequence; private SequenceI[] selectedSequences; @@ -81,6 +83,8 @@ public class StructureChooser extends GStructureChooser implements private boolean isValidPBDEntry; + private boolean cachedPDBExists; + public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq, AlignmentPanel ap) { @@ -102,7 +106,7 @@ public class StructureChooser extends GStructureChooser implements } // ensure a filter option is in force for search - populateFilterComboBox(true); + populateFilterComboBox(true, cachedPDBExists); Thread discoverPDBStructuresThread = new Thread(new Runnable() { @Override @@ -118,7 +122,7 @@ public class StructureChooser extends GStructureChooser implements startTime); fetchStructuresMetaData(); // revise filter options if no results were found - populateFilterComboBox(isStructuresDiscovered()); + populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists); updateProgressIndicator(null, startTime); mainFrame.setVisible(true); updateCurrentView(); @@ -212,9 +216,9 @@ public class StructureChooser extends GStructureChooser implements { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog(this, errorMsg.toString(), + JvOptionPane.showMessageDialog(this, errorMsg.toString(), MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } } @@ -237,7 +241,7 @@ public class StructureChooser extends GStructureChooser implements } } } - + cachedPDBExists = !entries.isEmpty(); PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries); tbl_local_pdb.setModel(tableModelx); } @@ -257,7 +261,8 @@ public class StructureChooser extends GStructureChooser implements StringBuilder queryBuilder = new StringBuilder(); Set seqRefs = new LinkedHashSet(); - if (seq.getAllPDBEntries() != null) + if (seq.getAllPDBEntries() != null + && queryBuilder.length() < MAX_QLENGTH) { for (PDBEntry entry : seq.getAllPDBEntries()) { @@ -266,7 +271,6 @@ public class StructureChooser extends GStructureChooser implements queryBuilder.append("pdb_id:") .append(entry.getId().toLowerCase()).append(" OR "); isPDBRefsFound = true; - // seqRefs.add(entry.getId()); } } } @@ -275,7 +279,8 @@ public class StructureChooser extends GStructureChooser implements { for (DBRefEntry dbRef : seq.getDBRefs()) { - if (isValidSeqName(getDBRefId(dbRef))) + if (isValidSeqName(getDBRefId(dbRef)) + && queryBuilder.length() < MAX_QLENGTH) { if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT)) { @@ -479,11 +484,11 @@ public class StructureChooser extends GStructureChooser implements { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog( + JvOptionPane.showMessageDialog( null, errorMsg.toString(), MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } @@ -524,7 +529,8 @@ public class StructureChooser extends GStructureChooser implements * Populates the filter combo-box options dynamically depending on discovered * structures */ - protected void populateFilterComboBox(boolean haveData) + protected void populateFilterComboBox(boolean haveData, + boolean cachedPDBExists) { /* * temporarily suspend the change listener behaviour @@ -535,22 +541,28 @@ public class StructureChooser extends GStructureChooser implements if (haveData) { cmb_filterOption.addItem(new FilterOption("Best Quality", - "overall_quality", VIEWS_FILTER)); + "overall_quality", VIEWS_FILTER, false)); cmb_filterOption.addItem(new FilterOption("Best Resolution", - "resolution", VIEWS_FILTER)); + "resolution", VIEWS_FILTER, false)); cmb_filterOption.addItem(new FilterOption("Most Protein Chain", - "number_of_protein_chains", VIEWS_FILTER)); + "number_of_protein_chains", VIEWS_FILTER, false)); cmb_filterOption.addItem(new FilterOption("Most Bound Molecules", - "number_of_bound_molecules", VIEWS_FILTER)); + "number_of_bound_molecules", VIEWS_FILTER, false)); cmb_filterOption.addItem(new FilterOption("Most Polymer Residues", - "number_of_polymer_residues", VIEWS_FILTER)); + "number_of_polymer_residues", VIEWS_FILTER, true)); } cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-", - VIEWS_ENTER_ID)); + VIEWS_ENTER_ID, false)); cmb_filterOption.addItem(new FilterOption("From File", "-", - VIEWS_FROM_FILE)); - cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-", - VIEWS_LOCAL_PDB)); + VIEWS_FROM_FILE, false)); + + if (cachedPDBExists) + { + FilterOption cachedOption = new FilterOption("Cached PDB Entries", + "-", VIEWS_LOCAL_PDB, false); + cmb_filterOption.addItem(cachedOption); + cmb_filterOption.setSelectedItem(cachedOption); + } cmb_filterOption.addItemListener(this); } @@ -743,7 +755,7 @@ public class StructureChooser extends GStructureChooser implements int[] selectedRows = getResultTable().getSelectedRows(); PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; int count = 0; - ArrayList selectedSeqsToView = new ArrayList(); + List selectedSeqsToView = new ArrayList(); for (int row : selectedRows) { String pdbIdStr = getResultTable().getValueAt(row, @@ -779,7 +791,7 @@ public class StructureChooser extends GStructureChooser implements .getModelIndex(); int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") .getModelIndex(); - ArrayList selectedSeqsToView = new ArrayList(); + List selectedSeqsToView = new ArrayList(); for (int row : selectedRows) { PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row, @@ -823,19 +835,19 @@ public class StructureChooser extends GStructureChooser implements PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry }; launchStructureViewer(ssm, pdbEntriesToView, ap, new SequenceI[] { selectedSequence }); - } - else if (currentView == VIEWS_FROM_FILE) - { - SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel - .getCmb_assSeq().getSelectedItem()).getSequence(); - if (userSelectedSeq != null) - { - selectedSequence = userSelectedSeq; - } - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - jalview.io.AppletFormatAdapter.FILE, - selectedSequence, true, Desktop.instance); + } + else if (currentView == VIEWS_FROM_FILE) + { + SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel + .getCmb_assSeq().getSelectedItem()).getSequence(); + if (userSelectedSeq != null) + { + selectedSequence = userSelectedSeq; + } + PDBEntry fileEntry = new AssociatePdbFileWithSeq() + .associatePdbWithSeq(selectedPdbFileName, + DataSourceType.FILE, + selectedSequence, true, Desktop.instance); launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new SequenceI[] { selectedSequence });