From: Charles Ofoegbu Date: Wed, 4 Mar 2015 20:49:30 +0000 (+0000) Subject: JAL-1668 First version JAL-1668 X-Git-Tag: Jalview_2_9~71^2~11 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7d76e402efd4e04e179bc9bb264551bc2d3df936;p=jalview.git JAL-1668 First version JAL-1668 --- diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 7c2a41a..2e37ee4 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1193,3 +1193,6 @@ label.display_name = Display Label label.description = Description label.include_description= Include Description action.back = Back +label.hide_insertions = Hide Insertions +label.mark_as_representative = Mark as representative +label.open_jabaws_web_page = Open JABAWS web page \ No newline at end of file diff --git a/src/jalview/gui/EBIFetchPanel.java b/src/jalview/gui/EBIFetchPanel.java deleted file mode 100644 index 7fe9f2e..0000000 --- a/src/jalview/gui/EBIFetchPanel.java +++ /dev/null @@ -1,121 +0,0 @@ -package jalview.gui; - -import jalview.jbgui.GEBIFetchPanel; -import jalview.ws.dbsources.PDBRestClient; -import jalview.ws.uimodel.PDBSearchOptionListModel; -import jalview.ws.uimodel.PDBSearchResultPojo; -import jalview.ws.uimodel.PDBSummaryListModel; - -import javax.swing.DefaultListModel; -import javax.swing.SwingUtilities; - -@SuppressWarnings("serial") -public class EBIFetchPanel extends GEBIFetchPanel -{ - private SequenceFetcher seqFetcher; - - public EBIFetchPanel() - { - } - - public EBIFetchPanel(SequenceFetcher seqFetcher) - { - this(); - this.seqFetcher = seqFetcher; - } - - public static void main(String[] args) - { - SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - new EBIFetchPanel(); - } - }); - } - - @Override - public void searchStringAction() - { - - jListSearchResult.setModel(new DefaultListModel()); - mainFrame.setTitle("PDB Sequence Fetcher"); - if (search.getText().trim().length() > 0) - { - long startTime = System.currentTimeMillis(); - - PDBSearchResultPojo resultList = new PDBRestClient().searchResult( - ((PDBSearchOptionListModel) searchFeild.getSelectedItem()).getCode(), - search.getText()); - if (resultList.getSearchSummary() != null) - { - jListSearchResult.setModel(resultList.getSearchSummary()); - } - long endTime = System.currentTimeMillis(); - mainFrame.setTitle("PDB Sequence Fetcher - " - + resultList.getItemFound() + " results (" - + (endTime - startTime) + " milli secs)"); - } - - } - - @Override - public void okActionPerformed() - { - processPDBResponseData(); - } - - - @Override - public void backActionPerformed() - { - System.out.println("back! pressed!"); - } - - @Override - public void cancelActionPerformed() - { - mainFrame.dispose(); - } - - private void processPDBResponseData() - { - mainFrame.dispose(); - StringBuilder selectedIds = new StringBuilder(); - for (PDBSummaryListModel dataSelected : jListSearchResult - .getSelectedValuesList()) - { - selectedIds.append(";").append(dataSelected.getPdbId()); - } - String ids = selectedIds.deleteCharAt(0).toString(); - seqFetcher.textArea.setText(ids); - Thread worker = new Thread(seqFetcher); - - // Thread worker = new Thread(this); - worker.start(); - } - - // @Override - // public void run() - // { - // for (PDBSummaryListModel sum : jListSearchResult - // .getSelectedValuesList()) - // { - // System.out.println("you selected ------------> " + sum.getPdbId()); - // } - // seqFetcher.guiWindow.setProgressBar(MessageManager - // .getString("status.processing"), Thread.currentThread() - // .hashCode()); - // try - // { - // Thread.sleep(1000 * 2); - // } catch (InterruptedException e) - // { - // e.printStackTrace(); - // } - // seqFetcher.guiWindow.setProgressBar(null, Thread.currentThread() - // .hashCode()); - // } - -} diff --git a/src/jalview/gui/PDBFetchPanel.java b/src/jalview/gui/PDBFetchPanel.java new file mode 100644 index 0000000..c7e5362 --- /dev/null +++ b/src/jalview/gui/PDBFetchPanel.java @@ -0,0 +1,243 @@ +package jalview.gui; + +import jalview.jbgui.GPDBFetchPanel; +import jalview.ws.dbsources.PDBRestClient; +import jalview.ws.uimodel.PDBSearchRequest; +import jalview.ws.uimodel.PDBSearchResponse; +import jalview.ws.uimodel.PDBSummaryListModel; +import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField; + +import java.util.ArrayList; +import java.util.List; + +import javax.swing.DefaultListModel; +import javax.swing.SwingUtilities; + +@SuppressWarnings("serial") +public class PDBFetchPanel extends GPDBFetchPanel +{ + private SequenceFetcher seqFetcher; + + public enum FieldType + { + INT, STRING, BOOLEAN; + } + + public PDBFetchPanel() + { + } + + public PDBFetchPanel(SequenceFetcher seqFetcher) + { + this(); + this.seqFetcher = seqFetcher; + } + + public static void main(String[] args) + { + SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + new PDBFetchPanel(); + } + }); + } + + @Override + public void searchStringAction() + { + boolean allowEmptySequence = false; + jListSearchResult.setModel(new DefaultListModel()); + mainFrame.setTitle("PDB Sequence Fetcher"); + if (search.getText().trim().length() > 0) + { + long startTime = System.currentTimeMillis(); + PDBRestClient pdbRestCleint = new PDBRestClient(); + String searchTarget = ((PDBSearchOptionList) searchTargetOptions + .getSelectedItem()).getCode(); + + PDBSearchRequest request = new PDBSearchRequest(); + request.setAllowEmptySeq(allowEmptySequence); + request.setResponseSize(100); + request.setSearchTarget(searchTarget + ":"); + request.setSearchTerm(search.getText()); + List wantedFields = new ArrayList(); + wantedFields.add(PDBDocField.MOLECULE_TYPE); + wantedFields.add(PDBDocField.PDB_ID); + wantedFields.add(PDBDocField.GENUS); + wantedFields.add(PDBDocField.GENE_NAME); + wantedFields.add(PDBDocField.TITLE); + request.setWantedFields(wantedFields); + + PDBSearchResponse resultList = pdbRestCleint.executeRequest(request); + + if (resultList.getSearchSummary() != null) + { + jListSearchResult.setModel(PDBSearchResponse + .getListModel(resultList.getSearchSummary())); + } + long endTime = System.currentTimeMillis(); + mainFrame.setTitle("PDB Sequence Fetcher - " + + resultList.getItemsFound() + " results (" + + (endTime - startTime) + " milli secs)"); + } + + } + + @Override + public void okActionPerformed() + { + processPDBResponseData(); + } + + + @Override + public void backActionPerformed() + { + System.out.println("back! pressed!"); + } + + @Override + public void cancelActionPerformed() + { + mainFrame.dispose(); + } + + private void processPDBResponseData() + { + mainFrame.dispose(); + StringBuilder selectedIds = new StringBuilder(); + for (PDBSummaryListModel dataSelected : jListSearchResult + .getSelectedValuesList()) + { + selectedIds.append(";").append(dataSelected.getPdbId()); + } + String ids = selectedIds.deleteCharAt(0).toString(); + seqFetcher.textArea.setText(ids); + Thread worker = new Thread(seqFetcher); + worker.start(); + } + + @SuppressWarnings("unchecked") + public void populateSearchOptionCombo() + + { + List searchOptions = new ArrayList(); + searchOptions.add(new PDBSearchOptionList("PDB ID", "pdb_id", + FieldType.STRING)); + searchOptions.add(new PDBSearchOptionList("PFAM Name", "pfam_name", + FieldType.STRING)); + searchOptions.add(new PDBSearchOptionList("ALL", "text", + FieldType.STRING)); + searchOptions.add(new PDBSearchOptionList("Molecule Type", + "molecule_type", FieldType.STRING)); + searchOptions.add(new PDBSearchOptionList("Title", "title", + FieldType.STRING)); + searchOptions.add(new PDBSearchOptionList("Molecule Name", + "molecule_name", FieldType.STRING)); + searchOptions.add(new PDBSearchOptionList("Tax ID", "tax_id", + FieldType.STRING)); + searchOptions.add(new PDBSearchOptionList("UniProt Accession", + "uniprot_accession", FieldType.STRING)); + searchOptions.add(new PDBSearchOptionList("Gene Name", "gene_name", + FieldType.STRING)); + searchOptions.add(new PDBSearchOptionList("Genus", "genus", + FieldType.STRING)); + + java.util.Collections.sort(searchOptions); + + for (PDBSearchOptionList pdbSO : searchOptions) + { + searchTargetOptions.addItem(pdbSO); + } + } + + @SuppressWarnings("rawtypes") + public class PDBSearchOptionList implements Comparable + { + private String name; + + private String code; + + private boolean showInSummary; + + private boolean searchFilter; + + private FieldType type; + + public PDBSearchOptionList(String name, String code, FieldType type) + { + this.name = name; + this.code = code; + this.type = type; + } + + public String getName() + { + return name; + } + + public void setName(String name) + { + this.name = name; + } + + public String getCode() + { + return code; + } + + public void setCode(String code) + { + this.code = code; + } + + public boolean isShowInSummary() + { + return showInSummary; + } + + public void setShowInSummary(boolean showInSummary) + { + this.showInSummary = showInSummary; + } + + public boolean isSearchFilter() + { + return searchFilter; + } + + public void setSearchFilter(boolean searchFilter) + { + this.searchFilter = searchFilter; + } + + public FieldType getFieldType() + { + return type; + } + + public void setFieldType(FieldType type) + { + this.type = type; + } + + public String toString() + { + return name; + } + + public PDBSearchOptionList() + { + + } + + @Override + public int compareTo(Object o) + { + return this.name.compareTo(((PDBSearchOptionList) o).getName()); + } + + } +} diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 1137990..72313be 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -212,7 +212,7 @@ public class PopupMenu extends JPopupMenu JMenu jMenu1 = new JMenu(); - JMenu structureMenu = new JMenu(); + JMenuItem structureMenu = new JMenuItem(); JMenu viewStructureMenu = new JMenu(); @@ -639,50 +639,50 @@ public class PopupMenu extends JPopupMenu new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray( new PDBEntry[reppdb.size()]); final JMenuItem gpdbview, rpdbview; - if (pdbe.size() == 1) - { - structureMenu.add(gpdbview = new JMenuItem(MessageManager - .formatMessage("label.view_structure_for", new String[] - { sqass.getDisplayId(false) }))); - } - else - { - structureMenu.add(gpdbview = new JMenuItem(MessageManager - .formatMessage("label.view_all_structures", new String[] - { new Integer(pdbe.size()).toString() }))); - } - gpdbview.setToolTipText(MessageManager - .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment")); - gpdbview.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - new StructureViewer(ap.getStructureSelectionManager()) - .viewStructures(ap, pe, ap.av.collateForPDB(pe)); - } - }); - if (reppdb.size() > 1 && reppdb.size() < pdbe.size()) - { - structureMenu.add(rpdbview = new JMenuItem(MessageManager - .formatMessage( - "label.view_all_representative_structures", - new String[] - { new Integer(reppdb.size()).toString() }))); - rpdbview.setToolTipText(MessageManager - .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment")); - rpdbview.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - new StructureViewer(ap.getStructureSelectionManager()) - .viewStructures(ap, pr, ap.av.collateForPDB(pr)); - } - }); - } + // if (pdbe.size() == 1) + // { + // structureMenu.add(gpdbview = new JMenuItem(MessageManager + // .formatMessage("label.view_structure_for", new String[] + // { sqass.getDisplayId(false) }))); + // } + // else + // { + // structureMenu.add(gpdbview = new JMenuItem(MessageManager + // .formatMessage("label.view_all_structures", new String[] + // { new Integer(pdbe.size()).toString() }))); + // } + // gpdbview.setToolTipText(MessageManager + // .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment")); + // gpdbview.addActionListener(new ActionListener() + // { + // + // @Override + // public void actionPerformed(ActionEvent e) + // { + // new StructureViewer(ap.getStructureSelectionManager()) + // .viewStructures(ap, pe, ap.av.collateForPDB(pe)); + // } + // }); + // if (reppdb.size() > 1 && reppdb.size() < pdbe.size()) + // { + // structureMenu.add(rpdbview = new JMenuItem(MessageManager + // .formatMessage( + // "label.view_all_representative_structures", + // new String[] + // { new Integer(reppdb.size()).toString() }))); + // rpdbview.setToolTipText(MessageManager + // .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment")); + // rpdbview.addActionListener(new ActionListener() + // { + // + // @Override + // public void actionPerformed(ActionEvent e) + // { + // new StructureViewer(ap.getStructureSelectionManager()) + // .viewStructures(ap, pr, ap.av.collateForPDB(pr)); + // } + // }); + // } } } else @@ -1502,7 +1502,17 @@ public class PopupMenu extends JPopupMenu } }); jMenu1.setText(MessageManager.getString("label.group")); - structureMenu.setText(MessageManager.getString("label.structure")); + // structureMenu.setText(MessageManager.getString("label.structure")); + structureMenu.setText(MessageManager.getString("label.view_structure")); + structureMenu.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + new StructureChooser(ap, sequence); + } + }); + viewStructureMenu.setText(MessageManager .getString("label.view_structure")); // colStructureMenu.setText("Colour By Structure"); @@ -1640,8 +1650,8 @@ public class PopupMenu extends JPopupMenu jMenu1.add(showColourText); jMenu1.add(outline); jMenu1.add(displayNonconserved); - structureMenu.add(pdbMenu); - structureMenu.add(viewStructureMenu); + // structureMenu.add(pdbMenu); + // structureMenu.add(viewStructureMenu); // structureMenu.add(colStructureMenu); noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 2f4ace3..56b4b87 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -390,7 +390,7 @@ public class SequenceFetcher extends JPanel implements Runnable private void pdbSourceAction() { databaseButt.setText(database.getSelectedItem()); - new EBIFetchPanel(this); + new PDBFetchPanel(this); frame.dispose(); } diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java new file mode 100644 index 0000000..07e36ec --- /dev/null +++ b/src/jalview/gui/StructureChooser.java @@ -0,0 +1,273 @@ +package jalview.gui; + +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GStructureChooser; +import jalview.util.MessageManager; +import jalview.ws.dbsources.PDBRestClient; +import jalview.ws.uimodel.PDBSearchRequest; +import jalview.ws.uimodel.PDBSearchResponse; +import jalview.ws.uimodel.PDBSummaryListModel; +import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField; + +import java.util.ArrayList; +import java.util.Collection; +import java.util.HashSet; +import java.util.List; + +import javax.swing.JOptionPane; +import javax.swing.SwingUtilities; + +@SuppressWarnings("serial") +public class StructureChooser extends GStructureChooser +{ + + + private SequenceI sequence; + + + public StructureChooser(AlignmentPanel ap, final SequenceI sequence) + { + this.ap = ap; + this.sequence = sequence; + fetchStructures(); + } + + @Override + public void ok_ActionPerformed() + { + jListFoundStructures.setSelectedValue("op1x", true); + } + + public void pdbFromFile_actionPerformed() + { + jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle(MessageManager.formatMessage( + "label.select_pdb_file_for", new String[] + { sequence.getDisplayId(false) })); + chooser.setToolTipText(MessageManager.formatMessage( + "label.load_pdb_file_associate_with_sequence", new String[] + { sequence.getDisplayId(false) })); + + int value = chooser.showOpenDialog(null); + + if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, + jalview.io.AppletFormatAdapter.FILE, sequence, true, + Desktop.instance); + } + + } + + public void discoverPDB_actionPerformed() + { + + final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] + { sequence } + : ap.av.getSequenceSelection()); + Thread discpdb = new Thread(new Runnable() + { + @Override + public void run() + { + + new jalview.ws.DBRefFetcher(sequences, ap.alignFrame) + .fetchDBRefs(false); + } + + }); + discpdb.start(); + } + + // rpdbview.addActionListener(new ActionListener() + // { + // + // @Override + // public void actionPerformed(ActionEvent e) + // { + // new StructureViewer(ap.getStructureSelectionManager()) + // .viewStructures(ap, pr, ap.av.collateForPDB(pr)); + // } + // }); + + public void enterPDB_actionPerformed() + { + String id = JOptionPane.showInternalInputDialog(Desktop.desktop, + MessageManager.getString("label.enter_pdb_id"), + MessageManager.getString("label.enter_pdb_id"), + JOptionPane.QUESTION_MESSAGE); + if (id != null && id.length() > 0) + { + PDBEntry entry = new PDBEntry(); + entry.setId(id.toUpperCase()); + sequence.getDatasetSequence().addPDBId(entry); + } + } + + public static void main(String[] args) + { + SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + new StructureChooser(null, null); + } + }); + } + + @SuppressWarnings("unchecked") + protected void populateFilterOptions() + { + filterOptions.addItem(new FilterOptions("- Filter Criteria -", "", + VIEWS_AUTO)); + filterOptions.addItem(new FilterOptions("All", "all", VIEWS_AUTO)); + filterOptions + .addItem(new FilterOptions("Best Coverage", "", VIEWS_AUTO)); + filterOptions.addItem(new FilterOptions("Best Resolution", "", + VIEWS_AUTO)); + filterOptions + .addItem(new FilterOptions("Best Quality", "", VIEWS_AUTO)); + filterOptions.addItem(new FilterOptions("Enter PDB Id", "", VIEWS_ID)); + filterOptions.addItem(new FilterOptions("From File", "", VIEWS_FILE)); + } + + protected void updateCurrentView() + { + String currentView = ((FilterOptions) filterOptions.getSelectedItem()) + .getView(); + switchableViewsLayout.show(switchableViewsPanel, currentView); + } + + private void fetchStructures() + { + long startTime = System.currentTimeMillis(); + final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] + { sequence } + : ap.av.getSequenceSelection()); + int foundStructures = 0; + PDBSearchRequest request = new PDBSearchRequest(); + request.setAllowEmptySeq(false); + request.setResponseSize(500); + request.setSearchTarget("(text:"); + List wantedFields = new ArrayList(); + wantedFields.add(PDBDocField.MOLECULE_TYPE); + wantedFields.add(PDBDocField.PDB_ID); + wantedFields.add(PDBDocField.GENUS); + wantedFields.add(PDBDocField.GENE_NAME); + wantedFields.add(PDBDocField.TITLE); + request.setWantedFields(wantedFields); + + Collection searchSummaries = new HashSet(); + // searchSummaries. + for (SequenceI seq : sequences) + { + // System.out.println("Selected : " + seq.getName()); + request.setSearchTerm(buildQuery(seq) + ")"); + + PDBRestClient pdbRestCleint = new PDBRestClient(); + + PDBSearchResponse resultList = pdbRestCleint + .executeRequest(request); + if (resultList.getSearchSummary() != null + && !resultList.getSearchSummary().isEmpty()) + { + searchSummaries.addAll(resultList.getSearchSummary()); + } + } + + foundStructures = searchSummaries.size(); + if (searchSummaries != null) + { + jListFoundStructures.setModel(PDBSearchResponse + .getListModel(searchSummaries)); + } + + String totalTime = (System.currentTimeMillis() - startTime) + + " milli secs"; + mainFrame.setTitle("Structure Chooser - " + foundStructures + + " Found (" + totalTime + ")"); + } + + private String buildQuery(SequenceI seq) + { + String query = seq.getName(); + StringBuilder queryBuilder = new StringBuilder(); + int count = 0; + if (seq.getDBRef() != null && seq.getDBRef().length != 0) + { + for (DBRefEntry dbRef : seq.getDBRef()) + { + System.out.println("dbref : " + dbRef.getAccessionId()); + queryBuilder.append("text:").append(dbRef.getAccessionId()) + .append(" OR "); + ++count; + if (count > 10) + { + break; + } + } + // int beginIndex = queryBuilder. firstIndexOf("text"); + int endIndex = queryBuilder.lastIndexOf(" OR "); + query = queryBuilder.toString().substring(5, endIndex); + } + System.out.println("------------> " + query); + return query; + } + + public class FilterOptions + { + private String name; + + private String value; + + private String view; + + public FilterOptions(String name, String value, String view) + { + this.name = name; + this.value = value; + this.view = view; + } + + public String getName() + { + return name; + } + + public void setName(String name) + { + this.name = name; + } + + public String getValue() + { + return value; + } + + public void setValue(String value) + { + this.value = value; + } + + public String getView() + { + return view; + } + + public void setView(String view) + { + this.view = view; + } + + public String toString() + { + return this.name; + } + } +} diff --git a/src/jalview/jbgui/GEBIFetchPanel.java b/src/jalview/jbgui/GPDBFetchPanel.java similarity index 89% rename from src/jalview/jbgui/GEBIFetchPanel.java rename to src/jalview/jbgui/GPDBFetchPanel.java index e00830b..18c33cd 100644 --- a/src/jalview/jbgui/GEBIFetchPanel.java +++ b/src/jalview/jbgui/GPDBFetchPanel.java @@ -1,8 +1,8 @@ package jalview.jbgui; import jalview.gui.Desktop; +import jalview.gui.PDBFetchPanel.PDBSearchOptionList; import jalview.util.MessageManager; -import jalview.ws.uimodel.PDBSearchOptionListModel; import jalview.ws.uimodel.PDBSummaryListModel; import java.awt.BorderLayout; @@ -23,13 +23,13 @@ import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; @SuppressWarnings("serial") -public abstract class GEBIFetchPanel extends JPanel +public abstract class GPDBFetchPanel extends JPanel { protected String frameTitle = "PDB Sequence Fetcher"; protected JInternalFrame mainFrame = new JInternalFrame(frameTitle); - protected JComboBox searchFeild = new JComboBox(); + protected JComboBox searchTargetOptions = new JComboBox(); protected JButton ok = new JButton(); @@ -54,7 +54,7 @@ public abstract class GEBIFetchPanel extends JPanel - public GEBIFetchPanel() + public GPDBFetchPanel() { try { @@ -109,8 +109,8 @@ public abstract class GEBIFetchPanel extends JPanel .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); resultPanel.add(searchResultScroller); - searchFeild.setFont(new java.awt.Font("Verdana", 0, 12)); - searchFeild.addActionListener(new ActionListener() + searchTargetOptions.setFont(new java.awt.Font("Verdana", 0, 12)); + searchTargetOptions.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -119,7 +119,7 @@ public abstract class GEBIFetchPanel extends JPanel } }); - PDBSearchOptionListModel.populateCombo(searchFeild); + populateSearchOptionCombo(); search.setFont(new java.awt.Font("Verdana", 0, 12)); search.getDocument().addDocumentListener(new DocumentListener() @@ -143,7 +143,7 @@ public abstract class GEBIFetchPanel extends JPanel } }); - inputPanel.add(searchFeild); + inputPanel.add(searchTargetOptions); inputPanel.add(search); @@ -165,4 +165,6 @@ public abstract class GEBIFetchPanel extends JPanel public abstract void cancelActionPerformed(); + protected abstract void populateSearchOptionCombo(); + } diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java new file mode 100644 index 0000000..69b1fe6 --- /dev/null +++ b/src/jalview/jbgui/GStructureChooser.java @@ -0,0 +1,172 @@ +package jalview.jbgui; + +import jalview.gui.AlignmentPanel; +import jalview.gui.Desktop; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.CardLayout; +import java.awt.Dimension; +import java.awt.FlowLayout; +import java.awt.event.ActionEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; + +import javax.swing.JButton; +import javax.swing.JCheckBox; +import javax.swing.JComboBox; +import javax.swing.JFrame; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JList; +import javax.swing.JPanel; +import javax.swing.JScrollPane; +import javax.swing.JTextField; +import javax.swing.ListSelectionModel; + +@SuppressWarnings("serial") +public abstract class GStructureChooser extends JPanel implements + ItemListener +{ + protected String frameTitle = "Structure Chooser"; + + protected JInternalFrame mainFrame = new JInternalFrame(frameTitle); + + + + protected JComboBox filterOptions = new JComboBox(); + + protected AlignmentPanel ap; + + protected JLabel resultLabel = new JLabel("View : "); + + protected JButton ok = new JButton(); + + protected JButton cancel = new JButton(); + + protected JButton selectFile = new JButton(); + + protected JTextField search = new JTextField(16); + + protected JPanel actionPanel = new JPanel(); + + protected JPanel filterPanel = new JPanel(); + + protected JPanel idInputPanel = new JPanel(); + + protected JPanel fileChooserPanel = new JPanel(); + + protected JPanel switchableViewsPanel = new JPanel(new CardLayout()); + + protected CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel + .getLayout()); + + protected BorderLayout mainLayout = new BorderLayout(); + + protected BorderLayout idInputPanelLayout = new BorderLayout(); + + protected BorderLayout fileChooserPanelLayout = new BorderLayout(); + + protected JCheckBox rememberSettings = new JCheckBox("Don't ask me again"); + + + protected static final String VIEWS_AUTO = "auto_view"; + + protected static final String VIEWS_FILE = "file_view"; + + protected static final String VIEWS_ID = "id_view"; + + protected JList jListFoundStructures = new JList(); + + protected JScrollPane foundStructuresScroller = new JScrollPane( + jListFoundStructures); + + public GStructureChooser() + { + try + { + jbInit(); + mainFrame.invalidate(); + mainFrame.pack(); + } catch (Exception e) + { + e.printStackTrace(); + } + } + + private void jbInit() throws Exception + { + + ok.setFont(new java.awt.Font("Verdana", 0, 12)); + ok.setText(MessageManager.getString("action.ok")); + ok.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ok_ActionPerformed(); + } + }); + cancel.setFont(new java.awt.Font("Verdana", 0, 12)); + cancel.setText(MessageManager.getString("action.cancel")); + cancel.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + mainFrame.dispose(); + } + }); + + jListFoundStructures + .setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); + jListFoundStructures.setLayoutOrientation(JList.VERTICAL); + jListFoundStructures.setVisibleRowCount(-1); + foundStructuresScroller.setPreferredSize(new Dimension(500, 300)); + foundStructuresScroller + .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER); + + actionPanel.add(rememberSettings); + actionPanel.add(ok); + actionPanel.add(cancel); + + filterOptions.addItemListener(this); + + filterPanel.add(resultLabel); + filterPanel.add(filterOptions); + + idInputPanel.setLayout(new FlowLayout()); + idInputPanel.add(search); + + + selectFile.setText(" Select File "); + fileChooserPanel.setLayout(new FlowLayout()); + fileChooserPanel.add(selectFile); + + switchableViewsPanel.add(fileChooserPanel, VIEWS_FILE); + switchableViewsPanel.add(idInputPanel, VIEWS_ID); + switchableViewsPanel.add(foundStructuresScroller, VIEWS_AUTO); + + + this.setLayout(mainLayout); + this.add(filterPanel, java.awt.BorderLayout.NORTH); + this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER); + this.add(actionPanel, java.awt.BorderLayout.SOUTH); + populateFilterOptions(); + updateCurrentView(); + mainFrame.setVisible(true); + mainFrame.setContentPane(this); + mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); + Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400); + } + + @Override + public void itemStateChanged(ItemEvent e) + { + updateCurrentView(); + } + + protected abstract void updateCurrentView(); + + protected abstract void ok_ActionPerformed(); + + protected abstract void populateFilterOptions(); +} diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java index 0c41d61..bdc507f 100644 --- a/src/jalview/ws/dbsources/PDBRestClient.java +++ b/src/jalview/ws/dbsources/PDBRestClient.java @@ -1,11 +1,14 @@ package jalview.ws.dbsources; -import jalview.ws.uimodel.PDBSearchResultPojo; +import jalview.ws.uimodel.PDBSearchRequest; +import jalview.ws.uimodel.PDBSearchResponse; import jalview.ws.uimodel.PDBSummaryListModel; +import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField; +import java.util.ArrayList; import java.util.Iterator; +import java.util.List; -import javax.swing.DefaultListModel; import javax.ws.rs.core.MediaType; import org.json.simple.JSONArray; @@ -24,23 +27,44 @@ public class PDBRestClient { private String pdbSearchEndpoint = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?"; - public static void main(String[] args) { - new PDBRestClient().searchResult("pfam_name", "Lipoc*"); + PDBSearchRequest request = new PDBSearchRequest(); + request.setAllowEmptySeq(false); + request.setResponseSize(100); + request.setSearchTarget("pfam_name"); + request.setSearchTerm("Lipoc*"); + List wantedFields = new ArrayList(); + wantedFields.add(PDBDocField.MOLECULE_TYPE); + wantedFields.add(PDBDocField.PDB_ID); + wantedFields.add(PDBDocField.GENUS); + wantedFields.add(PDBDocField.GENE_NAME); + wantedFields.add(PDBDocField.TITLE); + request.setWantedFields(wantedFields); + new PDBRestClient().executeRequest(request); } - private String executeRestSearch(String qParam, - String searchTerm) + public PDBSearchResponse executeRequest(PDBSearchRequest request) { ClientConfig clientConfig = new DefaultClientConfig(); clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING, Boolean.TRUE); Client client = Client.create(clientConfig); + + String query = request.getSearchTarget() + + request.getSearchTerm() + + ((request.isAllowEmptySeq()) ? "" + : " AND molecule_sequence:['' TO *]"); + + String wantedFields = getFieldsAsCommaDelimitedString(request + .getWantedFields()); + + String responseSize = (request.getResponseSize() == 0) ? "200" : String + .valueOf(request.getResponseSize()); WebResource webResource = client.resource(pdbSearchEndpoint) - .queryParam("wt", "json") -.queryParam("rows", "100") - .queryParam("q", qParam + ":" + searchTerm); + .queryParam("wt", "json").queryParam("fl", wantedFields) + .queryParam("rows", responseSize) + .queryParam("q", query); ClientResponse clientResponse = webResource.accept( MediaType.APPLICATION_JSON).get(ClientResponse.class); @@ -50,20 +74,20 @@ public class PDBRestClient throw new RuntimeException("Failed : HTTP error code : " + clientResponse.getStatus()); } - return responseString; + // System.out.println("--------------> " + responseString); + return parseResponse(responseString, request.getWantedFields()); } - public PDBSearchResultPojo searchResult(String qParam, - String searchTerm) + private PDBSearchResponse parseResponse(String jsonResponse, + List wantedFields) { - String jsonResponseString = executeRestSearch(qParam, searchTerm); - PDBSearchResultPojo searchResult = new PDBSearchResultPojo(); - DefaultListModel result = null; + PDBSearchResponse searchResult = new PDBSearchResponse(); + List result = null; try { JSONParser jsonParser = new JSONParser(); JSONObject jsonObj = (JSONObject) jsonParser - .parse(jsonResponseString); +.parse(jsonResponse); JSONObject pdbResponse = (JSONObject) jsonObj.get("response"); String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get( @@ -72,18 +96,18 @@ public class PDBRestClient .valueOf(pdbResponse.get("numFound").toString()); if (numFound > 0) { - result = new DefaultListModel(); + result = new ArrayList(); JSONArray docs = (JSONArray) pdbResponse.get("docs"); for (Iterator docIter = docs.iterator(); docIter .hasNext();) { JSONObject doc = docIter.next(); - if (doc.get("molecule_sequence") != null) - { - result.addElement(new PDBSummaryListModel(doc)); - } + // if (doc.get("molecule_sequence") != null) + // { + result.add(new PDBSummaryListModel(doc, wantedFields)); + // } } - searchResult.setItemFound(numFound); + searchResult.setItemsFound(numFound); searchResult.setResponseTime(queryTime); searchResult.setSearchSummary(result); } @@ -95,4 +119,21 @@ public class PDBRestClient return searchResult; } + private String getFieldsAsCommaDelimitedString(List fields) + { + String result = ""; + if (fields != null && !fields.isEmpty()) + { + StringBuilder returnedFields = new StringBuilder(); + for (PDBDocField field : fields) + { + returnedFields.append(",").append(field.getCode()); + } + returnedFields.deleteCharAt(0); + result = returnedFields.toString(); + } + return result; + } + + } diff --git a/src/jalview/ws/uimodel/PDBSearchOptionListModel.java b/src/jalview/ws/uimodel/PDBSearchOptionListModel.java deleted file mode 100644 index 093f038..0000000 --- a/src/jalview/ws/uimodel/PDBSearchOptionListModel.java +++ /dev/null @@ -1,133 +0,0 @@ -package jalview.ws.uimodel; - -import java.util.ArrayList; -import java.util.List; - -import javax.swing.DefaultListModel; -import javax.swing.JComboBox; - -@SuppressWarnings( -{ "unchecked", "serial", "rawtypes" }) -public class PDBSearchOptionListModel extends DefaultListModel implements Comparable -{ - private String name; - - private String code; - - private boolean showInSummary; - - private boolean searchFilter; - - private FieldType type; - - public enum FieldType - { - INT, STRING, BOOLEAN; - }; - - public PDBSearchOptionListModel(String name, String code, FieldType type) - { - this.name = name; - this.code = code; - this.type = type; - } - - public String getName() - { - return name; - } - - public void setName(String name) - { - this.name = name; - } - - public String getCode() - { - return code; - } - - public void setCode(String code) - { - this.code = code; - } - - public boolean isShowInSummary() - { - return showInSummary; - } - - public void setShowInSummary(boolean showInSummary) - { - this.showInSummary = showInSummary; - } - - public boolean isSearchFilter() - { - return searchFilter; - } - - public void setSearchFilter(boolean searchFilter) - { - this.searchFilter = searchFilter; - } - - public FieldType getFieldType() - { - return type; - } - - public void setFieldType(FieldType type) - { - this.type = type; - } - - public String toString() - { - return name; - } - - public PDBSearchOptionListModel() - { - - } - - public static void populateCombo(JComboBox searchItems) - { - List searchOptions = new ArrayList(); - searchOptions.add(new PDBSearchOptionListModel("PDB ID", "pdb_id", - PDBSearchOptionListModel.FieldType.STRING)); - searchOptions.add(new PDBSearchOptionListModel("PFAM Name", "pfam_name", - PDBSearchOptionListModel.FieldType.STRING)); - searchOptions.add(new PDBSearchOptionListModel("ALL", "text", - PDBSearchOptionListModel.FieldType.STRING)); - searchOptions.add(new PDBSearchOptionListModel("Molecule Type", "molecule_type", - PDBSearchOptionListModel.FieldType.STRING)); - searchOptions.add(new PDBSearchOptionListModel("Title", "title", - PDBSearchOptionListModel.FieldType.STRING)); - searchOptions.add(new PDBSearchOptionListModel("Molecule Name", "molecule_name", - PDBSearchOptionListModel.FieldType.STRING)); - searchOptions.add(new PDBSearchOptionListModel("Tax ID", "tax_id", - PDBSearchOptionListModel.FieldType.STRING)); - searchOptions.add(new PDBSearchOptionListModel("UniProt Accession", - "uniprot_accession", PDBSearchOptionListModel.FieldType.STRING)); - searchOptions.add(new PDBSearchOptionListModel("Gene Name", "gene_name", - PDBSearchOptionListModel.FieldType.STRING)); - searchOptions.add(new PDBSearchOptionListModel("Genus", "genus", - PDBSearchOptionListModel.FieldType.STRING)); - - java.util.Collections.sort(searchOptions); - - for (PDBSearchOptionListModel pdbSO : searchOptions) - { - searchItems.addItem(pdbSO); - } - } - - @Override - public int compareTo(Object o) - { - return this.name.compareTo(((PDBSearchOptionListModel) o).getName()); - } - -} diff --git a/src/jalview/ws/uimodel/PDBSearchRequest.java b/src/jalview/ws/uimodel/PDBSearchRequest.java new file mode 100644 index 0000000..bb24cf5 --- /dev/null +++ b/src/jalview/ws/uimodel/PDBSearchRequest.java @@ -0,0 +1,69 @@ +package jalview.ws.uimodel; + +import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField; + +import java.util.ArrayList; +import java.util.List; + +public class PDBSearchRequest +{ + private String searchTarget; + + private String searchTerm; + + private boolean allowEmptySeq; + + private int responseSize; + + private List wantedFields = new ArrayList(); + + public String getSearchTarget() + { + return searchTarget; + } + + public void setSearchTarget(String searchTarget) + { + this.searchTarget = searchTarget; + } + + public String getSearchTerm() + { + return searchTerm; + } + + public void setSearchTerm(String searchTerm) + { + this.searchTerm = searchTerm; + } + + public boolean isAllowEmptySeq() + { + return allowEmptySeq; + } + + public void setAllowEmptySeq(boolean allowEmptySeq) + { + this.allowEmptySeq = allowEmptySeq; + } + + public int getResponseSize() + { + return responseSize; + } + + public void setResponseSize(int responseSize) + { + this.responseSize = responseSize; + } + + public List getWantedFields() + { + return wantedFields; + } + + public void setWantedFields(List wantedFields) + { + this.wantedFields = wantedFields; + } +} diff --git a/src/jalview/ws/uimodel/PDBSearchResponse.java b/src/jalview/ws/uimodel/PDBSearchResponse.java new file mode 100644 index 0000000..9f44102 --- /dev/null +++ b/src/jalview/ws/uimodel/PDBSearchResponse.java @@ -0,0 +1,56 @@ +package jalview.ws.uimodel; + +import java.util.Collection; + +import javax.swing.DefaultListModel; + +public class PDBSearchResponse +{ + private int itemsFound; + + private String responseTime; + + private Collection searchSummary; + + public int getItemsFound() + { + return itemsFound; + } + + public void setItemsFound(int itemFound) + { + this.itemsFound = itemFound; + } + + public String getResponseTime() + { + return responseTime; + } + + public void setResponseTime(String responseTime) + { + this.responseTime = responseTime; + } + + public Collection getSearchSummary() + { + return searchSummary; + } + + public void setSearchSummary(Collection searchSummary) + { + this.searchSummary = searchSummary; + } + + public static DefaultListModel getListModel( + Collection summariesList) + { + DefaultListModel defaultListModel = new DefaultListModel(); + for (PDBSummaryListModel summaryList : summariesList) + { + defaultListModel.addElement(summaryList); + } + return defaultListModel; + } +} + diff --git a/src/jalview/ws/uimodel/PDBSearchResultPojo.java b/src/jalview/ws/uimodel/PDBSearchResultPojo.java deleted file mode 100644 index aef7820..0000000 --- a/src/jalview/ws/uimodel/PDBSearchResultPojo.java +++ /dev/null @@ -1,43 +0,0 @@ -package jalview.ws.uimodel; - -import javax.swing.DefaultListModel; - -public class PDBSearchResultPojo -{ - private int itemFound; - - private String responseTime; - - private DefaultListModel searchSummary; - - public int getItemFound() - { - return itemFound; - } - - public void setItemFound(int itemFound) - { - this.itemFound = itemFound; - } - - public String getResponseTime() - { - return responseTime; - } - - public void setResponseTime(String responseTime) - { - this.responseTime = responseTime; - } - - public DefaultListModel getSearchSummary() - { - return searchSummary; - } - - public void setSearchSummary( - DefaultListModel searchSummary) - { - this.searchSummary = searchSummary; - } -} diff --git a/src/jalview/ws/uimodel/PDBSummaryListModel.java b/src/jalview/ws/uimodel/PDBSummaryListModel.java index 37c0855..3a68e05 100644 --- a/src/jalview/ws/uimodel/PDBSummaryListModel.java +++ b/src/jalview/ws/uimodel/PDBSummaryListModel.java @@ -1,5 +1,7 @@ package jalview.ws.uimodel; +import java.util.List; + import javax.swing.DefaultListModel; import org.json.simple.JSONObject; @@ -13,64 +15,53 @@ public class PDBSummaryListModel extends DefaultListModel private String summary; - private JSONObject rawJson; - private int width = 480; - public PDBSummaryListModel(JSONObject doc) + public PDBSummaryListModel(JSONObject doc, List diplayFields) { - this.rawJson = doc; - StringBuilder summary = new StringBuilder(); - if (doc.get("molecule_type") != null) + StringBuilder summaryBuilder = new StringBuilder(); + + for (PDBDocField field : diplayFields) { - String moleculeType = doc.get("molecule_type").toString(); - if (moleculeType.equalsIgnoreCase("protein")) - { - summary.append(""); - } - if (moleculeType.equalsIgnoreCase("dna")) + if (field.equals(PDBDocField.MOLECULE_TYPE) + && doc.get("molecule_type") != null) { - summary.append(""); - } - if (moleculeType.equalsIgnoreCase("rna")) - { - summary.append(""); - } - if (moleculeType.equalsIgnoreCase("sugar")) + String moleculeType = doc.get("molecule_type").toString(); + if (moleculeType.equalsIgnoreCase("protein")) + { + summaryBuilder.append(""); + } + if (moleculeType.equalsIgnoreCase("dna")) + { + summaryBuilder.append(""); + } + if (moleculeType.equalsIgnoreCase("rna")) + { + summaryBuilder.append(""); + } + if (moleculeType.equalsIgnoreCase("sugar")) + { + summaryBuilder.append(""); + } + }else if (doc.get(field.getCode()) != null) { - summary.append(""); + summaryBuilder.append(field.getName()).append(": ") + .append(doc.get(field.getCode())).append(" | "); } } - this.pdbId = doc.get("pdb_id").toString(); - summary.append("PDB ID: ").append(pdbId); + int endIndex = summaryBuilder.lastIndexOf(" | "); + String fSummary = summaryBuilder.toString().substring(0, endIndex); + this.summary = fSummary.trim(); - - if (doc.get("molecule_name") != null) - { - summary.append(" | Molecule Name: ").append(doc.get("molecule_name")); - } - if (doc.get("gene_name") != null) - { - summary.append(" | Gene Name: ").append(doc.get("gene_name")); - } - if (doc.get("genus") != null) - { - summary.append(" | Genus: ").append(doc.get("genus")); - } - if (doc.get("title") != null) - { - summary.append(" | Title: ").append(doc.get("title")); - } - this.summary = summary.toString(); } public String getPdbId() @@ -93,15 +84,6 @@ public class PDBSummaryListModel extends DefaultListModel this.summary = summary; } - public JSONObject getRawJson() - { - return rawJson; - } - - public void setRawJson(JSONObject rawJson) - { - this.rawJson = rawJson; - } public String toString() { @@ -112,4 +94,51 @@ public class PDBSummaryListModel extends DefaultListModel html.append(""); return html.toString(); } + + + public enum PDBDocField + { + PDB_ID("PDB Id", "pdb_id"), TITLE("Title", "title"), MOLECULE_NAME( + "Molecule", "molecule_name"), MOLECULE_TYPE("Molecule Type", + "molecule_type"), MOLECULE_SEQUENCE("Sequence", + "molecule_sequence"), UNIPROT_FEATURES("Uniprot Features", + "uniprot_features"), PFAM_ACCESSION("PFAM Accession", + "pfam_accession"), INTERPRO_ACCESSION("InterPro Accession", + "interpro_accession"), UNIPROT_ACCESSION("UniProt Accession", + "uniprot_accession"), R_FACTOR("R Factor", "r_factor"), RESOLUTION( + "Resolution", "resolution"), DATA_QUALITY("Data Quality", + "data_quality"), OVERALL_QUALITY("Overall Quality", + "overall_quality"), POLYMER_COUNT("Polymer Count", + "number_of_polymers"), PROTEIN_CHAIN_COUNT( + "Protein Chain Count", "number_of_protein_chains"), BOUND_MOLECULE_COUNT( + "Bound Molecule Count", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT( + "Polymer Residue Count", "number_of_polymer_residues"), UNIPROT_COVERAGE( + "UniProt Coverage", "uniprot_coverage"), GENUS("GENUS", "genus"), GENE_NAME( + "Gene Name", "gene_name"); + + private String name; + + private String code; + + PDBDocField(String name, String code) + { + this.name = name; + this.code = code; + } + + public String getName() + { + return name; + } + + public String getCode() + { + return code; + } + + public String toString() + { + return name; + } + } }