X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=d5e4cbca905aa6dd956d54156abbf90215e1709c;hb=a5741a64054ad42d0c950ba655bf7fdfda5bfd15;hp=2e3b37ab56bc29b704a629cf60a22b4d5cb97583;hpb=3bc2fbe640abb0d8941aead117c9624dd16773a3;p=jalview.git diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 2e3b37a..d5e4cbc 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -22,6 +22,19 @@ package jalview.gui; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GStructureChooser; +import jalview.jbgui.PDBDocFieldPreferences; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; +import jalview.ws.dbsources.PDBRestClient; +import jalview.ws.dbsources.PDBRestClient.PDBDocField; +import jalview.ws.uimodel.PDBRestRequest; +import jalview.ws.uimodel.PDBRestResponse; +import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; + import java.awt.event.ItemEvent; import java.util.ArrayList; import java.util.Collection; @@ -36,19 +49,6 @@ import javax.swing.JLabel; import javax.swing.JOptionPane; import javax.swing.table.DefaultTableModel; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.jbgui.GStructureChooser; -import jalview.jbgui.PDBDocFieldPreferences; -import jalview.structure.StructureSelectionManager; -import jalview.util.MessageManager; -import jalview.ws.dbsources.PDBRestClient; -import jalview.ws.dbsources.PDBRestClient.PDBDocField; -import jalview.ws.uimodel.PDBRestRequest; -import jalview.ws.uimodel.PDBRestResponse; -import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; - /** * Provides the behaviors for the Structure chooser Panel @@ -153,7 +153,7 @@ public class StructureChooser extends GStructureChooser pdbRequest.setFieldToSearchBy("(text:"); pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); - pdbRequest.setAssociatedSequence(seq.getName()); + pdbRequest.setAssociatedSequence(seq); pdbRestCleint = new PDBRestClient(); PDBRestResponse resultList; try @@ -161,6 +161,7 @@ public class StructureChooser extends GStructureChooser resultList = pdbRestCleint.executeRequest(pdbRequest); } catch (Exception e) { + e.printStackTrace(); errors.add(e.getMessage()); continue; } @@ -193,7 +194,7 @@ public class StructureChooser extends GStructureChooser if (errors.size() > 0) { StringBuilder errorMsg = new StringBuilder(); - // "Operation was unsucessful due to the following: \n"); + // "Operation was unsuccessful due to the following: \n"); for (String error : errors) { errorMsg.append(error).append("\n"); @@ -206,8 +207,15 @@ public class StructureChooser extends GStructureChooser public void loadLocalCachedPDBEntries() { - DefaultTableModel tableModel = new DefaultTableModel(); - tableModel.addColumn("Sequence"); + DefaultTableModel tableModel = new DefaultTableModel() + { + @Override + public boolean isCellEditable(int row, int column) + { + return false; + } + }; + tableModel.addColumn("Ref Sequence"); tableModel.addColumn("PDB Id"); tableModel.addColumn("Chain"); tableModel.addColumn("Type"); @@ -223,8 +231,8 @@ public class StructureChooser extends GStructureChooser String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry .getChainCode(); - String[] pdbEntryRowData = new String[] - { seq.getDisplayId(false), pdbEntry.getId(), + Object[] pdbEntryRowData = new Object[] + { seq, pdbEntry.getId(), chain, pdbEntry.getType(), pdbEntry.getFile() }; @@ -293,7 +301,10 @@ public class StructureChooser extends GStructureChooser { for (PDBEntry entry : seq.getPDBId()) { - seqRefs.add(entry.getId()); + if (isValidSeqName(entry.getId())) + { + seqRefs.add(entry.getId()); + } } } @@ -302,7 +313,10 @@ public class StructureChooser extends GStructureChooser int count = 0; for (DBRefEntry dbRef : seq.getDBRef()) { - seqRefs.add(getDBRefId(dbRef)); + if (isValidSeqName(getDBRefId(dbRef))) + { + seqRefs.add(getDBRefId(dbRef)); + } ++count; if (count > 10) { @@ -330,14 +344,20 @@ public class StructureChooser extends GStructureChooser */ public static boolean isValidSeqName(String seqName) { - String ignoreList = "pdb,uniprot"; + // System.out.println("seqName : " + seqName); + String ignoreList = "pdb,uniprot,swiss-prot"; if (seqName.length() < 3) { return false; } + if (seqName.contains(":")) + { + return false; + } + seqName = seqName.toLowerCase(); for (String ignoredEntry : ignoreList.split(",")) { - if (seqName.equalsIgnoreCase(ignoredEntry)) + if (seqName.contains(ignoredEntry)) { return false; } @@ -380,7 +400,7 @@ public class StructureChooser extends GStructureChooser !chk_invertFilter.isSelected()); pdbRequest.setSearchTerm(buildQuery(seq) + ")"); pdbRequest.setWantedFields(wantedFields); - pdbRequest.setAssociatedSequence(seq.getName()); + pdbRequest.setAssociatedSequence(seq); pdbRestCleint = new PDBRestClient(); PDBRestResponse resultList; try @@ -388,6 +408,7 @@ public class StructureChooser extends GStructureChooser resultList = pdbRestCleint.executeRequest(pdbRequest); } catch (Exception e) { + e.printStackTrace(); errors.add(e.getMessage()); continue; } @@ -663,16 +684,21 @@ public class StructureChooser extends GStructureChooser String currentView = selectedFilterOpt.getView(); if (currentView == VIEWS_FILTER) { - int pdbIdCol = PDBRestClient.getPDBIdColumIndex( - lastPdbRequest.getWantedFields(), true); + int pdbIdColIndex = tbl_summary.getColumn( + PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex(); + int refSeqColIndex = tbl_summary.getColumn("Ref Sequence") + .getModelIndex(); int[] selectedRows = tbl_summary.getSelectedRows(); PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; int count = 0; + ArrayList selectedSeqsToView = new ArrayList(); for (int summaryRow : selectedRows) { - String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol) + String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdColIndex) .toString(); - + SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt( + summaryRow, refSeqColIndex); + selectedSeqsToView.add(selectedSeq); PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase()); if (pdbEntry == null) { @@ -682,21 +708,34 @@ public class StructureChooser extends GStructureChooser } pdbEntriesToView[count++] = pdbEntry; } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); launchStructureViewer(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, selectedSequences); + pdbEntriesToView, ap, selectedSeqs); } else if(currentView == VIEWS_LOCAL_PDB){ int[] selectedRows = tbl_local_pdb.getSelectedRows(); PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length]; int count = 0; + int pdbIdColIndex = tbl_local_pdb.getColumn( + PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex(); + int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence") + .getModelIndex(); + ArrayList selectedSeqsToView = new ArrayList(); for (int row : selectedRows) { - String entryKey = tbl_local_pdb.getValueAt(row, 1).toString() + String entryKey = tbl_local_pdb.getValueAt(row, pdbIdColIndex) + .toString() .toLowerCase(); pdbEntriesToView[count++] = cachedEntryMap.get(entryKey); + SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row, + refSeqColIndex); + selectedSeqsToView.add(selectedSeq); } + SequenceI[] selectedSeqs = selectedSeqsToView + .toArray(new SequenceI[selectedSeqsToView.size()]); launchStructureViewer(ap.getStructureSelectionManager(), - pdbEntriesToView, ap, selectedSequences); + pdbEntriesToView, ap, selectedSeqs); } else if (currentView == VIEWS_ENTER_ID) { @@ -751,8 +790,18 @@ public class StructureChooser extends GStructureChooser StructureViewer sViewer = new StructureViewer(ssm); if (pdbEntriesToView.length > 1) { - sViewer.viewStructures(pdbEntriesToView, alignPanel.av.collateForPDB(pdbEntriesToView), + ArrayList seqsMap = new ArrayList(); + for (SequenceI seq : sequences) + { + seqsMap.add(new SequenceI[] + { seq }); + } + SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]); + sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel); + // sViewer.viewStructures(pdbEntriesToView, + // alignPanel.av.collateForPDB(pdbEntriesToView), + // alignPanel); } else { @@ -820,7 +869,7 @@ public class StructureChooser extends GStructureChooser pdbRequest.setFieldToSearchBy("(pdb_id:"); pdbRequest.setWantedFields(wantedFields); pdbRequest.setSearchTerm(txt_search.getText() + ")"); - pdbRequest.setAssociatedSequence(selectedSequence.getName()); + pdbRequest.setAssociatedSequence(selectedSequence); pdbRestCleint = new PDBRestClient(); PDBRestResponse resultList; try