Resolved diffs from 2.8.3

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 3a54cc1..5c86ce2 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -27,6 +27,7 @@ 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;
@@ -38,13 +39,15 @@ import java.awt.event.ItemEvent;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.Hashtable;
 import java.util.LinkedHashSet;
 import java.util.List;
-import java.util.Vector;
 
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JLabel;
+import javax.swing.table.DefaultTableModel;
+
 
 /**
  * Provides the behaviors for the Structure chooser Panel
@@ -73,6 +76,8 @@ public class StructureChooser extends GStructureChooser
 
   private boolean isValidPBDEntry;
 
+  private static Hashtable<String, PDBEntry> cachedEntryMap;
+
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
   {
@@ -96,6 +101,7 @@ public class StructureChooser extends GStructureChooser
         long startTime = System.currentTimeMillis();
         String msg = MessageManager.getString("status.fetching_db_refs");
         updateProgressIndicator(msg, startTime);
+        loadLocalCachedPDBEntries();
         fetchStructuresMetaData();
         populateFilterComboBox();
         updateProgressIndicator(null, startTime);
@@ -168,6 +174,33 @@ public class StructureChooser extends GStructureChooser
             + " Found (" + totalTime + ")");
   }
 
+  public void loadLocalCachedPDBEntries()
+  {
+    DefaultTableModel tableModel = new DefaultTableModel();
+    tableModel.addColumn("Sequence");
+    tableModel.addColumn("PDB Id");
+    tableModel.addColumn("Type");
+    tableModel.addColumn("File");
+    cachedEntryMap = new Hashtable<String, PDBEntry>();
+    for (SequenceI seq : selectedSequences)
+    {
+      if (seq.getDatasetSequence() != null
+              && seq.getDatasetSequence().getPDBId() != null)
+      {
+        for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
+        {
+          String[] pdbEntryRowData = new String[]
+          { seq.getDisplayId(false), pdbEntry.getId(), pdbEntry.getType(),
+              pdbEntry.getFile() };
+          tableModel.addRow(pdbEntryRowData);
+          cachedEntryMap.put(seq.getDisplayId(false) + pdbEntry.getId(),
+                  pdbEntry);
+        }
+      }
+    }
+    tbl_local_pdb.setModel(tableModel);
+  }
+
   /**
    * Update the DBRef entry for a given sequence with values retrieved from
    * PDBResponseSummary
@@ -196,7 +229,7 @@ public class StructureChooser extends GStructureChooser
    *          the sequences to build a query for
    * @return the built query string
    */
-  @SuppressWarnings("unchecked")
+
   public static String buildQuery(SequenceI seq)
   {
     String query = seq.getName();
@@ -205,7 +238,7 @@ public class StructureChooser extends GStructureChooser
 
     if (seq.getPDBId() != null)
     {
-      for (PDBEntry entry : (Vector<PDBEntry>) seq.getPDBId())
+      for (PDBEntry entry : seq.getPDBId())
       {
         queryBuilder.append("text:").append(entry.getId()).append(" OR ");
       }
@@ -353,6 +386,8 @@ public class StructureChooser extends GStructureChooser
             VIEWS_ENTER_ID));
     cmb_filterOption.addItem(new FilterOption("From File", "-",
             VIEWS_FROM_FILE));
+    cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
+            VIEWS_LOCAL_PDB));
   }
 
   /**
@@ -373,7 +408,8 @@ public class StructureChooser extends GStructureChooser
       chk_invertFilter.setVisible(true);
       filterResultSet(selectedFilterOpt.getValue());
     }
-    else
+    else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
+            || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
     {
       idInputAssSeqPanel.loadCmbAssSeq();
       fileChooserAssSeqPanel.loadCmbAssSeq();
@@ -398,6 +434,13 @@ public class StructureChooser extends GStructureChooser
         btn_view.setEnabled(true);
       }
     }
+    else if (currentView == VIEWS_LOCAL_PDB)
+    {
+      if (tbl_local_pdb.getSelectedRows().length > 0)
+      {
+        btn_view.setEnabled(true);
+      }
+    }
     else if (currentView == VIEWS_ENTER_ID)
     {
       validateAssociationEnterPdb();
@@ -513,35 +556,78 @@ public class StructureChooser extends GStructureChooser
         pdbEntry.setType("PDB");
         pdbEntriesToView[count++] = pdbEntry;
       }
-      new StructureViewer(ap.getStructureSelectionManager())
-              .viewStructures(ap, pdbEntriesToView,
-                      ap.av.collateForPDB(pdbEntriesToView));
+
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              pdbEntriesToView, ap, selectedSequences);
+    }
+    else if(currentView == VIEWS_LOCAL_PDB){
+      int[] selectedRows = tbl_local_pdb.getSelectedRows();
+      PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+      int count = 0;
+      for (int row : selectedRows)
+      {
+         String entryKey = tbl_local_pdb.getValueAt(row, 0).toString() + tbl_local_pdb.getValueAt(row, 1).toString();
+        pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
+      }
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              pdbEntriesToView, ap, selectedSequences);
     }
     else if (currentView == VIEWS_ENTER_ID)
     {
-      selectedSequence = ((AssociateSeqOptions) idInputAssSeqPanel
+      SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
               .getCmb_assSeq().getSelectedItem()).getSequence();
+      if (userSelectedSeq != null)
+      {
+        selectedSequence = userSelectedSeq;
+      }
       PDBEntry pdbEntry = new PDBEntry();
       pdbEntry.setId(txt_search.getText());
       pdbEntry.setType("PDB");
       selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
       PDBEntry[] pdbEntriesToView = new PDBEntry[]
       { pdbEntry };
-      new StructureViewer(ap.getStructureSelectionManager())
-              .viewStructures(ap, pdbEntriesToView,
-                      ap.av.collateForPDB(pdbEntriesToView));
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              pdbEntriesToView, ap, new SequenceI[]
+              { selectedSequence });
     }
     else if (currentView == VIEWS_FROM_FILE)
     {
-      selectedSequence = ((AssociateSeqOptions) fileChooserAssSeqPanel
+      SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
               .getCmb_assSeq().getSelectedItem()).getSequence();
-      new AssociatePdbFileWithSeq().associatePdbWithSeq(
+      if (userSelectedSeq != null)
+      {
+        selectedSequence = userSelectedSeq;
+      }
+      PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+              .associatePdbWithSeq(
               selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
               selectedSequence, true, Desktop.instance);
+
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              new PDBEntry[]
+              { fileEntry }, ap, new SequenceI[]
+              { selectedSequence });
     }
     mainFrame.dispose();
   }
 
+  private void launchStructureViewer(StructureSelectionManager ssm,
+          PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
+          SequenceI[] selectedSequences)
+  {
+    StructureViewer sViewer = new StructureViewer(ssm);
+    if (pdbEntriesToView.length > 1)
+    {
+      sViewer.viewStructures(alignPanel, pdbEntriesToView,
+              alignPanel.av.collateForPDB(pdbEntriesToView));
+    }
+    else
+    {
+      sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null,
+              alignPanel);
+    }
+  }
+
   /**
    * Populates the combo-box used in associating manually fetched structures to
    * a unique sequence when more than one sequence selection is made.